race/history/evolution notes

Miscellaneous links

2012-01-05T22:31:00.000Z

Larger monkey groups lose fights because they contain more deserters

In the Battle of Rorke’s Drift, 150 or so British troops defended a mission station against thousands of Zulu warriors. At the Battle of Thermopylae, around 7,000 Greeks successfully held back a Persian army of hundreds of thousands for seven days. Human history has many examples of a small force defeating or holding their own against a much larger one.Among animals too, the underdogs often become the victors. One such example exists in the rainforests of Panama. There, capuchin monkeys live in large groups, each with its own territory. The monkeys often invade each other’s land. Numbers provide an obvious advantage in such conflicts, but small groups can often successfully defend their territory against big ones. Unlike human underdogs, they don’t win because of superior tactics or weapons. They win because their rivals are full of deserters.

Whole genome sequences of a male and female supercentenarian, ages greater than 114 years

We show that: (1) the sequence variant spectrum of these two individuals’ DNA sequences is largely comparable to existing non-supercentenarian genomes; (2) the two individuals do not appear to carry most of the well-established human longevity enabling variants already reported in the literature; (3) they have a comparable number of known disease-associated variants relative to most human genomes sequenced to-date;

Comparison of measures of marker informativeness for ancestry and admixture mapping.

BACKGROUND: Admixture mapping is a powerful gene mapping approach for an admixed population formed from ancestral populations with different allele frequencies. The power of this method relies on the ability of ancestry informative markers (AIMs) to infer ancestry along the chromosomes of admixed individuals. In this study, more than one million SNPs from HapMap databases have been interrogated in an admixed populations using various measures of ancestry informativeness: Fisher Information Content (FIC), Shannon Information Content (SIC), F statistics (FST), Informativeness for Assignment Measure (In), and the Absolute Allele Frequency Differences (delta). The objectives are to compare these measures of informativeness to select SNP markers for ancestry inference, and to determine the accuracy of AIM panels selected by each measure in estimating the contributions of the ancestors to the admixed population.RESULTS: FST and In had the highest Spearman correlation and the best agreement as measured by Kappa statistics based on deciles. Although the different measures of marker informativeness performed comparably well, analyses based on the top 1 to 10% ranked informative markers of simulated data showed that In was better in estimating ancestry for an admixed population.CONCLUSIONS: Although millions of SNPs have been identified, only a small subset needs to be genotyped in order to accurately predict ancestry with a minimal error rate in a cost-effective manner. In this article, we compared various methods for selecting ancestry informative SNPs using simulations as well as SNP genotype data from samples of admixed populations and showed that the In measure estimates ancestry proportion (in an admixed population) with lower bias and mean square error.

Fluid insight moderates the relationship between psychoticism and crystallized intelligence

To elucidate potential relationships between personality and intelligence it is necessary to move beyond the ad hoc reporting of correlation coefficients and focus instead on testing deductions from well established theories. To this end the present paper references Eysenck’s (1995) theoretical work linking the dimension of psychoticism to both psychosis and creative genius. Drawing on this theory it was argued that the relationship between psychoticism and crystallized ability will be conditional on the level of fluid intelligence. Participants (N = 100) completed the Eysenck Personality Questionnaire-Revised (EPQ-R) and the Kaufman Brief Intelligence Test (K-BIT). Moderated multiple regression revealed a significant interaction effect. Crystallized ability (K-BIT vocabulary) was negatively related to psychoticism at low levels of fluid ability (K-BIT matrices) and positively related to psychoticism at high levels of fluid ability. These findings highlight the potential importance of psychoticism within GfGc investment theory.

MH/CHAOS: The CIA’s Campaign against the Radical New Left and the Black Panthers

Operation MHCHAOS was the code name for a secret domestic spying program conducted by the Central Intelligence Agency in the late 1960s and early 1970s charged with unmasking any foreign influences on left wing protestors. CIA counterintelligence officer Frank Rafalko was a part of that operation. When The New York Times revealed MHCHAOS in 1974 and Congress investigated, MHCHAOS took its place in the pantheon of intelligence abuses. However, in his new book Rafalko says that the operation was justified and that the CIA was the logical agency to conduct it. Listen as he defends his perspective with dramatic intelligence collected on the New Left and black radicals. This event took place on 26 October 2011.

India paper

2011-12-09T11:12:00.001Z

The paper, Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia, is free.

Summing up, our results confirm both ancestry and temporal complexity shaping the still on-going process of genetic structuring of South Asian populations. This intricacy cannot be readily explained by the putative recent influx of Indo-Aryans alone but suggests multiple gene flows to the South Asian gene pool, both from the west and east, over a much longer time span.

Dienekes: "I haven't read the paper fully yet (it's open access), but the abstract seems to agree with what I've written both here and over at the Dodecad blog, about South Asians being primarily a West Asian/South Asian variable mix." In fact, the authors note in the body of the paper:

Another example of an heuristic interpretation appears when we look at the two blue ancestry components (Figure 2B) that explain most of the genetic diversity observed in West Eurasian populations (at K = 8), we see that only the k4 dark blue component is present in India and northern Pakistani populations, whereas, in contrast, the k3 light blue component dominates in southern Pakistan and Iran. This patterning suggests additional complexity of gene flow between geographically adjacent populations because it would be difficult to explain the western ancestry component in Indian populations by simple and recent admixture from the Middle East.

Moreover:

Both PC2 and k5 light green at K = 8 extend from South Asia to Central Asia and the Caucasus (but not into eastern Europe). In an attempt to explore diversity gradients within this signal, we investigated the haplotypic diversity associated with the ancestry components revealed by ADMIXTURE. Our simulations show that one can detect differences in haplotype diversity for a migration event that occurred 500 generations ago, but chances to distinguish signals for older events will apparently decrease with increasing age because of recombination. In terms of human population history, our oldest simulated migration event occurred roughly 12,500 years ago and predates or coincides with the initial Neolithic expansion in the Near East. Knowing whether signals associated with the initial peopling of Eurasia fall within our detection limits requires additional extensive simulations, but our current results indicate that the often debated episode of South Asian prehistory, the putative Indo-Aryan migration 3,500 years ago (see e.g., Abdulla15) falls well within the limits of our haplotype-based approach. We found no regional diversity differences associated with k5 at K = 8. Thus, regardless of where this component was from (the Caucasus, Near East, Indus Valley, or Central Asia), its spread to other regions must have occurred well before our detection limits at 12,500 years. Accordingly, the introduction of k5 to South Asia cannot be explained by recent gene flow, such as the hypothetical Indo-Aryan migration.

First, note that the k5 "light green" ADMIXTURE component does in fact extend into and throughout Europe (apart from Sardinia). The authors believe they've shown "k5" must have "spread" well before the Neolithic. What they've actually demonstrated is that ADMIXTURE (at least as used here) will not be the tool to disentangle complex recent population movements in Eurasia.

23andMe sale Monday

2011-11-26T14:45:00.001Z

For those who are interested.

"Huge" Genographic Project ancient DNA study underway?

2011-11-06T00:07:00.000Z

A reader forwards a comment posted to a mailing list yesterday by a project administrator attending FamilyTreeDNA's Houston conference:

Report from the mixer -- Spencer Wells was there and spoke enticingly of a huge ancient DNA research project that's been underway for some time, in which, instead of a simple replacement by incoming Neolithic populations, they are seeing wave after wave of peoples coming over thousands of years, each wave adding a stratum superimposed on those before it. The set of haplogroups seen in the earlier strata were not like the ones we see today. In particular he says mtDNA H was not there until a fairly recent, post-Neolithic date.

It's clear from already-published ancient DNA results that at least some sublineages of H were present in Neolithic Europe -- but H does seem to have become much more common since then.

He is still apparently clinging to a rather old date for R1b, though. He seems to think it had a major expansion about 10,000 years ago. Haven't genetic genealogists mostly been arguing for a considerably more recent time frame? I hope to see some R1b experts engage him in dialog on that point.

That's a 20,000 year step in the right direction. I won't begrudge him the other 5,000 years for now. I just hope the "huge" ancient DNA effort underway includes Y chromosomes. Another comment from the FTDNA conference:

Katherine, Emily, Joan and Bonnie are already tweeting from the FTDNAconference. Their Twitter accounts are: @khborges, @Genealem, @Luxegen and @Greenleafy
You can also follow the hashtag #FTDNA2011 though not all the tweets aregoing out with the hashtag. [. . .]
FTDNA has tested over 600,000 people.
The Genographic Project has 450,000 public participation samples and 75,000indigenous samples.
The Genographic Project has two Basque papers going into journals this weekand another paper which includes mtDNA haplogroup U5 is due out next year.

And a few more twitter comments:

khborges Katherine H. BorgesSW-Phase 1 of Geno is wrapping up. Phase 2 to begin #FTDNA2011

khborges Katherine H. Borges#FTDNA2011 #Genographic SW- 1 in 17 men in Med are descended from Phoenician traders

khborges Katherine H. Borges#FTDNA2011 #Genographic SW-East Asian human migration patterns follow the rivers

khborges Katherine H. Borges#FTDNA2011 #Genographic SW-10 papers are going off to the journals next week and about a dozen more in the pipeline

Luxegen Joan MillerSW - teaser - big announcement coming in Genographic project next year. #FTDNA2011

Jewish Liberalism: the Allinsmith Study

2011-11-04T14:14:00.001Z

Polling data is not kind to Moldbug's hilarious explanation for Jewish leftism. In a 1940s survey of eight religious denominations, Congregationalist respondents were least liberal. In Boston, high-SES Jews were more likely to vote for Adlai Stevenson for president in 1952 than low-SES non-Jews -- and low-SES non-Jews voted for Stevenson at twice the rate of high-SES non-Jews.

The degree of commitment of American Jews to liberalismis different from the degree of that commitment amongother religious groups. The difference is that the Jewishdevotion to liberalism is not correlated with economic oreducational status. This was demonstrated almost 20 yearsago by Wesley and Beverly Allinsmith.2
Toward the close of World War II, the Allinsmithsasked 8,820 members of eight religious denominationswhether they believed that the most important postwartask of the U.S. Government was to provide opportunityfor people to get ahead on their own or "to guarantee everyperson a decent and steady job and standard of living."
Nationally, 47% of the people questioned preferredsecurity to opportunity. As the percentage of manual workersin each denomination increased, the proportion favoringsecurity rose. Status, education and income were inverselyrelated to the choice of security. As one proceeded fromCongregationalists to Presbyterians to Episcopalians toMethodists to Lutherans to Baptists and finally to Catholics,the preference for security steadily increased from26% to 58%.
The Jews were the only exception to this rule. Althoughthey were a very high status group ranking first in occupationallevel, third in educational level and fourth in economiclevel, 56% of them preferred security to opportunity.This was almost as high as the Catholic preference forsecurity.
Moreover, within each of the eight religious denominations,the preference for opportunity was greatest amongthose with most education, highest status and best occupationallevel. Again, the Jews were the only exception.
The 1944 presidential vote also revealed this marked differencebetween Jewish and Gentile political behavior. Theupper-class and upper-middle-class Christian denominationsvoted heavily against Roosevelt and in favor of Republicanstandard-bearer Thomas Dewey. Only 31.4% of the Congregationalists,39.9% of the Presbyterians and 44.6% ofthe Episcopalians backed Franklin Delano Roosevelt. Themore working-class denominations, however, voted heavilyfor him, particularly the Catholics who were 72.8% in hisfavor. In terms of their combined educational, occupationaland status rank in the Allinsmith survey-that of second place-the Jews might well have been expected tovote Republican. Actually, they were 92.1% for Roosevelt.This overwhelming support was greater than that of anyof the Christian denominations. [. . .]
However, in the 1952 elections, despite the fact that theRepublican presidential candidate, Dwight D. Eisenhower,had led the Western coalition to victory over the Nazis,75% of the Jewish voters supported Adlai E. Stevenson, aman who had played no role of any importance in WorldWar II. There was no difference in the attitude of thecandidates toward Jewry or the state of Israel. The issuewas clearly one of moderation vs. liberalism. In a situationwhere American voters as a whole gave decisive support toEisenhower, three-fourths of the Jews backed his Democraticopponent. Moreover, interviews in depth of Bostonvoters showed that only 30% of the Gentiles with highsocioeconomic status, as against 60% of those with lowsocioeconomic status, backed Stevenson. Among BostonJews, 72% of those with high status voted for Stevenson.

Source: Nathaniel Weyl's The Jew in American Politics, pp. 6-8

Penny starting to drop for academics

2011-11-02T15:38:00.002Z

From "Ancient DNA suggests the leading role played by men in the Neolithic dissemination" (pdf):

The high frequency of G2a haplogroup in Neolithic specimens, whereas this haplogroup is very rare in current populations, also suggests that men could have played a particularly important role in the Neolithic dissemination that is no longer visible today. This would imply that intra-European migrations related to the metal ages may have strongly affected the modern gene pool.

I was intending to comment more, but for now I'll just mention:

(1) I agree with Jean M.: "MtDNA haplogroups were K1a (3), T2b (2), and one each of H3 and U5. Since it seems very likely that all of these except the U5 arrived in the Neolithic, I cannot agree with the conclusions of the authors that the spread of farming was male-led."

(2) The confirmed presence of E-V13 in Neolithic western Europe reinforces for me that those wanting to attribute the reported elevated levels of E-V13 in NE Wales to "Roman soldiers" or the like are probably mistaken.

Dental morphological evidence for European admixture in Mongolia and western China

2011-10-14T15:28:00.001+01:00

Lee, C. and Scott, G. R. (2011), Brief communication: Two-rooted lower Canines—A European trait and sensitive indicator of admixture across Eurasia. American Journal of Physical Anthropology, 146: 481–485. doi: 10.1002/ajpa.21585

With the exception of Carabelli's trait, the European dentition is better known for the morphological traits that it does not exhibit rather than the ones that it does. One root trait, however, runs counter to the characterization of reduced and simplified European crowns and roots. Although a rare trait in general, two-rooted lower canines are much more common in Europeans than in any other regional grouping and, given adequate sample sizes, can be useful in evaluating gene flow between Europeans and neighboring groups. In European samples, two-rooted lower canines consistently exhibit frequencies of 5–8%. In our sample from northern Spain, the trait attains a frequency of almost 10%. In contrast, in Sub-Saharan Africans the trait is virtually unknown while in Asian and Asian-derived populations, it varies between 0.0 and 1.0%. Here we show that two-rooted canine frequencies for new migrants along the western frontiers of China and Mongolia ranged from 0–4%. These data suggest European-derived populations migrated into western China (Xinjiang Province) and Mongolia (Bayan Olgii Aimag) sometime during the late Bronze age (1000–400 BCE). [. . .]
One of the major concerns of Alexandersen (1963)regarding two-rooted lower canines revolved around theissue of ‘‘atavism.’’ This term, rarely used today, begs thequestion of whether or not this double rooted form wascommon at one time, then disappeared, only to reappearsometime later. Swindler (1995) notes that ‘‘the deciduousand permanent canines in the majority of living primateshave a single root.’’ This suggests that two-rootedlower canines are not the ancestral condition in anthropoidsor hominoids. Rather, the phenotype is a derivedcondition, found primarily in recent human populationsdistributed across Western Eurasia.
The presence of the two-rooted canines in East Asiamay provide some clue as to the eastward migration ofnew populations into China and Mongolia. The largestnumbers of individuals with this trait are concentratedalong the western and northern frontiers of China andMongolia. Archaeological excavations support the largescale movement of people into this area during theBronze age (ca. 2200 BCE–400 BCE). Burial artifactsand settlement patterns suggest cultural and technologicalties to the Afanasevo culture in Siberia, which inturn is linked archaeologically, linguistically, and geneticallywith the Indo-European Tocharian populations thatappear to have migrated to the Tarim Basin ca. 4,000years ago (Ma and Sun, 1992; Ma and Wang, 1992; Malloryand Mair, 2000; Romgard, 2008; Keyser et al., 2009;Li et al., 2010).
The appearance of a new population on the westernfrontier also supports the findings of previous researchin cranial metrics, dental nonmetrics, and DNA. Usingcranial metrics and archaeological dating, Han (1994)hypothesized the earliest large-scale migration into westernChina occurred during the early Bronze age (2000BCE) from Central Asia or southern Siberia. Dental nonmetricdata also support multiple migrations into westernChina (Xinjiang Province) from Central Asia duringthe Bronze age to Iron age (Lee, 2007; Zhang, 2010).mtDNA studies on archaeological and modern populationsamples from Xinjiang Province show heterogeneousAsian and European genetic signatures dating from theBronze age to the present (Yao et al., 2004; Cui et al.,2010; Zhang et al., 2010; Li et al., 2010).
As the frequency of two-rooted canines is highest inEuropean samples and low to nonexistent in Asians, wepropose this trait was introduced into East Asia by Indo-European speaking groups or their affines crossing thewestern frontier of China and Mongolia. Further dataare needed to clarify aspects of these population movements,including the identity of the migrants, along withthe number, routes, and timing of the migrations.
Although two-rooted lower canines cannot offer theprecision of DNA in evaluating the ancestry in individualskulls, this trait is a sensitive indicator of admixturewherever Europeans come in contact with Asian orAfrican populations. As this distinctive trait can bescored with relative ease in large samples, it provides auseful supplemental tool in discerning gene flowbetween distantly related populations going back manymillennia.

Daniel MacArthur twitter commentary from CSHL Personal Genomes meeting

2011-10-14T15:18:00.001+01:00

This meeting took place a couple weeks ago -- dgmacarthur is presently posting from ICHG2011.

James Watson is asking a question. At least I think it's a question. #cshlpg
Yes, it was a question: hasn't ELSI just been a huge waste of money? Wait, no - he's back to talking again. #cshlpg

Manfred Kayser is talking about the genetics of human appearance, but his talk is untweetable. #cshlpg
Although Kayser's talk is untweetable it sounds as though a lot of this is close to publication - so stay tuned. #cshlpg

JV [Joris Veltman] discussing published analysis of de novo variants in mental retardation: http://bit.ly/olWpYK #cshlpg
JV: total number of de novo coding mutations is not higher in MR patients - but more likely to be in brain genes. #cshlpg

What fraction of the human genome is functional?

2011-10-14T15:02:00.000+01:00

What fraction of the human genome is functional?

Chris P. Ponting1,3 and Ross C. Hardison2,3

Abstract

Many evolutionary studies over the past decade have estimated ?sel, the proportion of all nucleotides in the human genome that are subject to purifying selection because of their biological function. Most of these studies have estimated the nucleotide substitution rates from genome sequence alignments across many diverse mammals. Some ?sel estimates will be affected by the heterogeneity of substitution rates in neutral sequence across the genome. Most will also be inaccurate if change in the functional sequence repertoire occurs rapidly relative to the separation of lineages that are being compared. Evidence gathered from both evolutionary and experimental analyses now indicate that rates of “turnover” of functional, predominantly noncoding, sequence are, indeed, high. They are sufficiently high that an estimated 50% of mouse constrained noncoding sequence is predicted not to be shared with rat, a closely related rodent. The rapidity of turnover results in, at least, a twofold underestimate of ?sel by analyses that measure constraint across the eutherian phylogeny. Approaches that take account of turnover estimate that the steady-state value of ?sel lies between 10% and 15%. Experimental studies corroborate the predicted rates of loss and gain of noncoding functional sites. These studies show the limitations inherent in the use of deep sequence conservation for identifying functional sequence. Experimental investigations focusing on lineage-specific, noncoding, and functional sequence are now essential if we are to appreciate the complete functional repertoire of the human genome.

http://genome.cshlp.org/content/early/2011/09/30/gr.116814.110.abstract

More excerpts from Chris Stringer's "The Origin of Our Species"

2011-10-07T08:21:00.002+01:00

I read this a few months ago, but never got around to posting anything on it.

On group selection:

However, more recently, biologists and anthropologists such as Paul Bingham and Samuel Bowles have returned to the issue by recruiting weaponry and genes to the cause of group selection. The argument goes that by joining together to use effective projectile weaponry, individual risks were reduced, and thus coalitions of warriors would have been advantageous for group defence and offence. Bingham proposed that this development would also have been important within societies by deterring free-riders who tried to reap the rewards of group membership without contributing their fair share of commitment to the associated costs or risks. However strong individually, they could soon be brought into line when faced with a coalition of spear-armed peers, who could act as general enforcers of within-group rules and solidarity. Bowles posited the idea that if Palaeolithic groups were relatively inbred and genetically distinct from each other, and warfare between groups was prevalent, then group selection via collaborative defence and attack could evolve and be maintained. Without warfare, a gene with a self-sacrificial cost of only 3 per cent would disappear in a few millennia, but with warfare, Bowles's model showed that even levels of self-sacrifice of up to 13 per cent could be sustained. He used archaeological data (although mainly post-Palaeolithic) to argue that lethal warfare was indeed widespread in prehistory, and that altruistic group-beneficial behaviours that damaged the survival chances of individuals but improved the group's chances of winning a conflict could emerge and even thrive by group selection. Moreover, the model could work whether the behaviour in question was genetically based or was a cultural trait such as a shared belief system. As mentioned above, Bowles's archaeological data do not come from the Palaeolithic, but there is one observation that does resonate with his views: the French archaeologist Nicolas Teyssandier has noted that the period of overlap of the last Neanderthals and first moderns in Europe was characterized by a profusion of different styles of stone points. This might reflect a sort of arms race to perfect the tips of spears, perhaps to hunt more efficiently, but equally, this could suggest heightened intergroup conflict.

On modern behavior:

In terms of innovation, we saw in chapter 1 that the apparently sudden florescence of the rich Upper Palaeolithic societies of Europe seduced many in the last century to consider that this period marked the real arrival of fully modern humans, even if areas like the Middle East or Africa had been rehearsal grounds for the revolution that was to be finally expressed in the caves of France. But as we have also seen, this Eurocentric viewpoint that the Cro-Magnons were the first "modern" people has been largely abandoned, although that is not to deny that something special did happen in the Upper Palaeolithic of Europe. If Africa was actually at the forefront of Palaeolithic innovations more than 40,000 years ago, why was that? As anthropologist Rob Foley has pointed out, the sheer size of Africa (one could easily fit China, India and Europe into its surface area), and its position straddling the tropics, certainly gave it advantages over any other area inhabited by early humans. The rapidity and repetition of climatic oscillations outside of Africa probably continually disrupted long-term adaptations by human populations in those regions. Thus Neanderthals in Europe and the descendants of Homo erectus in northern China were constantly faced with sudden range contractions and the extinction of large parts of their populations every time temperatures sank rapidly, as they often did. [. . .]
The complex climates of Africa may also explain why there seems to be no single centre of origin for the earliest signals of behavioural modernity. Perhaps North Africa (and the Middle East?) led the way 120,000 years ago, but as conditions deteriorated, populations there shrank back or even became extinct, as favoured environments rapidly vanished. Perhaps the torch of modernity was then kept alive further south at sites like Blombos and Klasies River Mouth, as conditions favoured that region for a while (give or take the interruption of events like the Toba eruption).Waves of population expansion and contraction could explain the brief but extensive florescence of the Still Bay culture with its rich symbolism, and the subsequent rise and fall of the Howieson's Poort with its innovative tiny hafted blades and engraved ostrich eggshells (recently described from Diepkloof rock shelter) more than 5,000 years later. And it is my guess (though we lack much data to support it) that East Africa became one of the next centres for behavioural evolution, about 60,000 years ago, as it was from there that modern humans (and their developing suite of modern behaviours) made their way out of Africa. [. . .]
The big picture is that we are predominantly of recent African origin, so is there a special reason for this? Overall, I think that the pre-eminence of Africa in the story of modern human origins was a question of its larger geographical and human population size, which gave greater opportunities for morphological and behavioural variations, and for innovations to develop and be conserved, rather than the result of a special evolutionary pathway. "Modernity" was not a package that had a unique African origin in one time, place and population, but was a composite whose elements appeared at different times and places, and were then gradually assembled to assume the form we recognize today.

On genetic evidence for archaic admixture:

Up to now, the big picture, from our autosomal, mitochondrial and Y-chromosome DNA, has generally lacked signs of introgression from other human species, although scientists such as John Relethford, Vinayak Eswaran, Henry Harpending and Alan Templeton have argued that indications were indeed there. Short branches in our gene trees, particularly in Y and mtDNA, have pointed to a simple, recent African origin, and simulations from mtDNA data of the level of possible Neanderthal and Cro-Magnon admixture had suggested that it was either zero or very close to zero. However, despite the fact that mtDNA and Y-DNA provide such clear genealogical signals, they constitute only about 1 per cent of our total DNA, and signs of hybridization were clearly lurking in the rest of our genome. [. . .]
A recent example of such work is the study by Jeffrey Wall and colleagues of 222 SNPs (see chapters 7 and 8) in the genes of people from West Africa (Yoruba), China and Europe. Many of the SNPs were tightly clustered, and so deviations from the expectation of them all sharing the same pattern of inheritance from a single recent African ancestral population should have shown up clearly. The majority met Out of Africa expectations, but analysis suggested that the populations did display unusual mutations in some genes, and these had different histories from each other, and when compared between the geographical samples. Wall argued that the most likely explanation was that there was not a single ancestral population for all the SNPs -- most fitted the bill, but some were apparently descended from ancestral groups that had been isolated from each other long enough to develop separate SNP mutational patterns, which had then been bequeathed in slightly different ways to the modern regional populations. Interestingly, although each showed a signal of some "archaic" (rather than recent African) genetic contribution, the strongest pattern was not in Europe (where the Neanderthals might have been the source), nor in China (where it might have come from Denisovans), but in West Africa -- a puzzling result. The work has been criticized because some of the anomalous genes might have developed via recent drift or strong selection, if the mutations were regionally advantageous, but enough have been found to convince sceptics like me that there probably was ancient admixture in Africa as well.

On Iwo Eleru:

West Africa, where the oldest known fossil, from the Iwo Eleru rock shelter in Nigeria, is thought to be less than 15,000 years old. This poorly preserved skeleton was excavated from basal sediments at Iwo Eleru in 1965 by archaeologist Thurstan Shaw and his team, and was associated with Later Stone Age tools. That latter fact alone would suggest a relatively young age, and a radiocarbon date on a piece of charcoal suggested an age of about 13,000 years. The skeleton, and particularly the skull and jaw, was studied in 1971 by Don Brothwell, my predecessor at the Natural History Museum, and he argued that while the specimen could be related to recent populations in West Africa, it actually looked rather different from them. I studied the skull for my Ph.D., with surprising results. I also found that it did not closely resemble recent African populations, but in its long and low shape it was actually closer to early moderns such as those from Skhul, and even to more primitive specimens such as Omo 2. This was decidedly odd for such a young skeleton, and so I recently collaborated in a new study of the specimen with archaeologist Philip Allsworth-Jones, dating expert Rainer Gruen and anthropologist Katerina Harvati. We first checked with Thurstan Shaw whether there were any hints that the skull could have been much older than previously suggested, and there were none. With the help of Nigerian archaeologist Philip Oyelaran, I obtained a fragment of bone from the skeleton and passed it to Gruen in order to check its age directly. His determination from a direct uranium-series age estimate is that the bone is unlikely to be older than 20,000 years, consistent with the stratigraphy, and associated archaeology and radiocarbon date. Finally, could Brothwell and I have been wrong about the unusual shape of the skull? Harvati used state-of-the-art geometric morphometric scanning techniques on an exact replica of the skull (which is now in Nigeria), and found, as we did, that it was quite distinct from recent African crania, and indeed from any modern specimen in her comparative sample. Her results placed the skull closest to late archaic African fossils such as Ngaloba, Jebel Irhoud and Omo 2 -- all thought to be at least 140,000 years old. So what does this mean? Because of the poor preservation of Pleistocene bones in West Africa, we have no other data on the physical form of the inhabitants of the region during the whole of the Pleistocene, so we have to be careful in interpreting an isolated specimen such as Iwo Eleru. But it does not seem to be diseased or distorted, and does indeed seem to indicate that Africa contained archaic-looking people in some areas when, and even long after, the first modern-looking humans had appeared. Support for this view comes from the work of anthropologist Isabelle Crevecoeur. Her restudy of the numerous Ishango fossils from the Congo has shown that these Later Stone Age humans were not only similar to Iwo Eleru in age, but also in the surprisingly archaic features found in their skulls, jaws and skeletons. [. . .]
Africa today has the greatest internal genetic variation of any inhabited continent, and its skull shapes show the highest variation. This is usually attributed to its greater size, larger ancient populations and deepest timelines for humanity. But could those timelines go back even further than we thought? Did the early modern morphology evolve gradually, and then spread outwards from a region like East Africa, completely replacing archaic forms within Africa, and then outside (as mtDNA data would suggest)? Or, could there have been a version of assimilation or multiregional evolution within Africa, with modern genes, morphology and behaviour coalescing from partly isolated populations across the continent? Given its huge size, complex climates and patchworks of environments, Africa could have secreted distinct human populations just as easily as the rest of the inhabited world. So was the origin of modern humans there characterized by long periods of fission and fusion between populations, rather than representing a sudden single event? And was the replacement of the preceding late archaic peoples not absolute, so that they were partly absorbed by the evolving moderns rather than completely dying out? In which case, did early Homo sapiens forms, and even the preceding species, Homo heidelbergensis, survive alongside descendant modern humans?

Possible reason we don't have pigmentation genes from Neanderthals:

If the interbreeding actually happened earlier, in a warmer region or a warmer period, maybe the Neanderthals involved were not light-skinned and cold-adapted European examples? In fact, the interbreeding might even have happened when people like those from Skhul-Qafzeh and Tabun were in the Middle East 120,000 years ago. If a thousand of those early moderns mixed with just fifty Neanderthals and then survived somewhere in Arabia or North Africa, could they have subsequently interbred with the Out of Africa emigrants 60,000 years later, and passed on their hidden component of Neanderthal genes?

Out of Eurasia

2011-10-07T07:51:00.000+01:00

From Chris Stringer's most recent book ("The Origin of Our Species"):

And the evidence from Dmanisi is now being added to this rethink, since the lack of very ancient fossil human evidence from Asia, apart from Dmanisi, is considered by archaeologists like Robin Dennell and Wil Roebroeks to reflect a lack of preservation and discovery, rather than a real absence. Combining the primitiveness of the Dmanisi specimens and tools with a similar view of the Liang Bua finds, it is argued that there was a widespread phase of human evolution in Eurasia about 2 million years ago, which is now only represented by the isolated Dmanisi and "Hobbit" fossils. This alternative scenario has a small-brained and small-bodied pre-erectus species, perhaps comparable to Homo habilis or even a late australopithecine, dispersing from Africa with primitive tools over 2 million years ago, reaching the Far East and, eventually, Flores. In Asia, this ancestral species then gave rise to the Dmanisi people and Homo erectus, while Dmanisi-like people reentered Africa about 1.8 million years ago, and evolved into later populations there -- including, eventually, Homo sapiens. So the orthodoxy of Out of Africa 1 is being challenged because of new evidence, and new interpretations of old evidence.

Ancestry.com's "Human Genetic Diversity Project"

2011-10-07T06:45:00.000+01:00

Ancestry.com will apparently be offering autosomal DNA testing soon. They just gave away 2000 free "upgrades" to people who had previously done Y or mtDNA tests through Ancestry DNA, evidently for a forthcoming service along the lines of 23andMe's Relative Finder.

What You'll Get
Your Genetic Ethnicity
By testing over 700,000 of your DNA markers, you'll see the mix of ethnicities you have in your genes and how they relate to your family tree.
More comprehensive DNA matching
Find more and closer relatives, overcome brick walls, confirm relationships and find common ancestors.Enhanced, simple web site tools

The consent form contains some additional details, which I haven't seen discussed elsewhere:

1. What is the research project?
The Ancestry DNA's Human Genetic Diversity Project ("The Project") will collect, preserve and analyze genetic information, genealogical pedigrees, historical records, surveys, and other information (collectively, "Information") from people all around the world in order to better understand human evolution and migration, population genetics, ethnographic diversity and boundaries, genealogy, and the history of our species. Researchers hope that the Project will be an invaluable genealogic tool for future generations and will engage the interest of a wide range of scholars interested in genealogy, anthropology, evolution, languages, cultures, medicine, and other topics. The Information will not be used for medical purposes in the treatment or diagnosis of any individuals. [. . .]
2. What information will be collected?
The Project will collect genetic, genealogical and health information that has been stripped of any personally identifiable information in order to study the history of our species. Genes are in your cells, and they are what make you different from anyone else. Some genes control things like the color of your hair or eyes. Genetic information includes your genotype that is discovered when Ancestry DNA processes your saliva or is otherwise provided by you to Ancestry DNA (the "Genetic Information") when you choose to use the Ancestry DNA service. Genealogical information is your pedigree, ethnicity, family history, and other information about you that is either provided by you or is gleaned from publicly available documents on Ancestry.com's website and other locations (the "Genealogical Information"). Health information includes self-reported information from you such as medical conditions, diseases, other health-related information, personal traits, and other information that is either provided by you or is gleaned from publicly available documents on Ancestry.com's website and other locations (the "Health Information").
In all cases for this Project, personally identifiable information about specific study participants (such as name and birth date) is removed from the Information before it is compiled as part of this Project.
The Project will take all of this information (that is already stripped of personally identifiable information) and compile it into a single data summary to minimize the possibility that any individual participant can be identified by any researcher or other individual from the Information.
3. How will the information be used?
Your Information will be combined with others and used to further the Project's objectives of increasing our understanding the components that define the history of our species. Discoveries made as a result of this research could be used in the study of genealogy, anthropology, evolution, languages, cultures, medicine, and other topics.

Previously, ancestry.com have advertised for a PhD population geneticist:

The right person will be using a huge dataset of information from all over the world, developing methods and experimental design to improve results in genotyping data to inform pedigrees. This is not (yet) for medical research and, as such, is not regulated by the FDA. [ . . .] We are mounting a major effort to use genomics to shed light on human diversity, origins and relatedness. The successful candidate will join our efforts to develop and apply analysis pipelines to exploit genotyping data in order to provide information about countries of origin, relatedness and apply genetic information to the construction of human pedigrees. In this position, you will develop, implement and improve methods to use SNP data to provide information on relatedness and genetic origins of humans. You will work closely with other biologists in analyzing data as well as with members of the product development team. This position offers an exciting opportunity to apply cutting edge computational approaches to an unprecedented, large-scale set of pedigreed human genome data. Characteristic duties will include: • Develop, benchmark and implement data analysis pipelines for SNP genotyping data • Evaluate significance of results and recommend changes in experimental design to improve results • Develop, benchmark and implement methods to use genotyping data to inform pedigrees. • Identify new experimental and/or analytic approaches that will improve the outcome of the study • Manage collaborations with laboratory and informatics staff • Successfully communicate scientific concepts to a diverse community of scientists and laypeople Key Responsibilities / Performance Requirements: • Doctorate degree in statistical genetics, population genetics, statistics or a related field. • Candidates should have a track record of productive research in statistical and population genetics • Experience in human population genetics and genotyping • Ability to manipulate large data sets • Programming skills in UNIX/LINUX operating systems, and fluency in standard genetic analytic software (such as R/Bioconductor, EIGENSOFT, MACH, PLINK, ADMIXMAP) • Experience in molecular biology and high-throughput environments would be a significant advantage. • Excellent organizational skills • Superior oral and written English communication skills required. • Must be able to manage multiple simultaneous long-term projects while meeting frequent project deadlines in a fast-paced environment. • Must be able to translate high-level biological questions into concrete tasks.

Denisovans: Homo erectus after all?

2011-09-27T11:21:00.001+01:00

Greg Cochran:

The new paper in Science about an Australian genome (An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia) hints at something new. Comments in the supplement (and by Ann Gibbon) suggest that the Denisovans may stem from Homo erectus, at least in part, rather than being a sister group to Neanderthals as suggested in the paper by Reich and Patterson back in December. In the supplement, the authors suggest that they may be a sister clade to the last common ancestor of Neanderthals and modern humans. Ann Gibbons say the same, concerning the Denisovan girl whose pinky we found: “She was not a modern human, but a descendant of Homo erectus, an ancestral species that left Africa almost 2 million years ago. “
Denisovan mtDNA is deeply diverged from modern human or Neanderthal mtDNA, while the Denisovan teeth found look strangely old-fashioned. Moreover, it now looks as if admixture between hominid subspecies is the norm rather than the exception. So, although Denisovans as an admixture between H. erectus and some branch of Neanderthals was always a possibility, evidence, signs, and portents are starting to make it look likely.

From the supplementary data (pdf) for the Aborigine genome paper:

Denisovans are more elusive. The term refers to a hypothetical population or possible species of archaic hominin, identified on the basis of ancient DNA, and with possible genetic affinities to both H. erectus and H. sapiens/neanderthalensis. They have been proposed as a sister clade to the last common ancestor of Neanderthals and modern humans.

"East Asian" mtDNA in Neolithic Hungary?

2011-09-27T11:02:00.000+01:00

I don't have access to the paper at the moment. According to Jean M:

The details have been added to Ancient Western Eurasian DNA. The team actually tested remains from:
Earliest Neolithic in Hungary, the Körös (N9a, C5, H? and a novel haplogroup 16235G, 16261T, 16291T, 16293G, 16304C)
Alföld (N1a, N9a, D1/G1a1, H?. The reported M/R24 is a partial result)
Final Neolithic Lengyel culture (H?)
9th-century AD Zalavár (H?)
16th-century AD Dobóruszka (U3)
19th-century mummies from Vác Dominician Church (H?, H12, N9a. Another mummy was tested, but produced different results for teeth and bone, presumably from contamination. I have not reported these results therefore)

Definitely interesting, but as John Hawks notes: "we need not maintain that the haplogroups presently common in East Asia have necessarily been there all that long."

Ötzi's Y-DNA haplogroup: G2a4

2011-09-15T03:16:00.002+01:00

A few days ago a commenter at Dienekes' posted that this information had been revealed by "Dr. Eduard Egarter-Vigl, Head of Conservation and Assistant to research projects of the Archaeological Museum in Bozen [. . .] in a documentary [Ötzi, ein Archäologie-Krimi] broadcast by 3sat on 10th august 2011." Now someone has uploaded the relevant clip:

Subtitles: "Since six months, the full decoding of the genome of the Iceman is done. [. . .] Certain genes that are relevant to the origin, Y-chromosome, for example, can be examined well. [. . .] And the haplogroup to which the Iceman belonged is the haplogroup G2a4. [. . .] And this group is known, that it is now very rare in Europe. Interestingly, it is still in Sardinia. Sardinia is as an island a so-called micro-isolate where the poulation has hardly changed and so has developed genetically fairly constant. But there is this haplogroup in Eurasian regions, ie those from which we know that Europe was actually populated."

Sample size equals one, but the presence of G2a and absence of R1b is consistent with previous ancient DNA findings for Neolithic western and central Europe.

Haplogroup C mtDNA in Caucasoids does not necessarily indicate "Mongoloid" admixture

2011-09-06T03:50:00.001+01:00

Dienekes writes:

Jean M links to a Master's thesis, which discovered the following:
While most of our samples possessed mtDNA haplotypes that can be linked to European and Near Eastern populations, three Neolithic and all three Bronze Age individuals belonged to mtDNA haplogroup C, which is common in East Eurasian, particularly South Siberian, populations but exceedingly rare in Europe. Phylogeographic network analysis revealed that our samples are located at or near the ancestral node for haplogroup C and that derived lineages branching from the Neolithic samples were present in Bronze Age Kurgans. In light of the numerous examples of mtDNA admixture that can be found in both Europe and Siberia, it appears that the NPR and South Siberia are located at opposite ends of a genetic continuum established at some point prior to the Neolithic. This migration corridor may have been established during the Last Glacial Maximum due to extensive glaciation in northern Eurasia and a consequent aridization of western Asia. This implies the demographic history for the European gene pool is more complex than previously considered and also has significant implications regarding the origin of Kurgan populations.
[. . .] The Dnieper-Donets population was described as robust Europeoid by Soviet anthropologists as was the Andronovo/Afanasevo tradition further east. It is interesting that Mongoloid admixture has been detected in both groups. I would not have guessed that this would have extended that far west and south. It seems that M. G. Levin may have been right when he stated that the Mongoloid elements penetrated far into eastern Europe.

I see no reason to believe the presence of haplogroup C indicates a "Mongoloid component". Stephen Oppenheimer sees C/Z mtDNA entering Mongoloids as part of an "intrusive" element "likely to have arrived from farther west in Asia, along with the eastern spread of the Upper Palaeolithic technology that appeared in Kara Bom in the Russian Altai 43,000 years ago." If this is correct, the presence of C in robust steppe Caucasoids would not be surprising. Oppenheimer has C/Z originating in western South Asia and entering Central Asia "round the western end of the Himalayas" 40-50,000 years ago, whereas Mongoloids (and "real" East Eurasian haplogroups) ultimately originate in SE Asia. Rather than indicating Mongoloid admixture "penetrated far into Eastern Europe", the presence of C mtDNA this early and this far west means one can't simply write off C and Z lineages in more easterly ancient Caucasoids (like some of those those buried at Xiaohe) -- or in Icelanders, for that matter -- as the product of Mongoloid admixture.

From Oppenheimer's Out of Eden:

There is still the puzzle of where those 'intrusive' founders of the Mongoloid Mammoth Steppe colony (C, X, and Z) came from in the first place, and which of the three possible corridors into the Mammoth Steppe they took. These three north Eurasian lines are very uncommon south of the Himalayas. The sister branches C and Z reach their highest rates in Siberia and Northeast Asia, and are hardly found farther south at all except in India, Mongolia, Central Asia, and Tibet. They stretch in a broad east-west continuum across the Asian Steppe, achieving significant rates in Central Asia and even as far west as Turkey. Group C even got to America via Alaska, yet their northerly distribution in East Asia suggests they could not have moved up north from South east Asia via China. Rather, they are more likely to have arrived from farther west in Asia, along with the eastern spread of the Upper Palaeolithic technology that appeared in Kara Bom in the Russian Altai 43,000 years ago. They belong to the Manju group, and their ultimate ancestors appear to come from Pakistan or India, having moved up the valley of the Indus via Kashmir or Afghanistan round the western end of the Himalayas. This all suggests that they moved in to the Asian Steppe between 40,000 and 50,000 years ago from west Central Asia. Consistent with the concept that C and Z spread east across the steppe with Upper Palaeolithic technology, Toomas Kivisild has estimated the age of C in Mongolia at 42,000 years. [. . .]
The complicated mitochondrial picture described above suggests that Mongoloids derive primarily from the south, while Central Asian people come mainly from a West Asian source, but combined with additional East and Southeast Asian sources in Central and Northeast Asia. This genetic evidence then supports the geographical theory of a three-pincer colonization of Central Asian from the Indo-Pacific coast about 40,000-50,000 years ago. The dissection of the various admixed genetic contributions to Northeast Asia clarifies and is consistent with the concept of an ultimately Southeast Asian origin of Mongoloids peoples.

Sex Chromosome Evolution and Medicine

2011-09-06T03:02:00.000+01:00

A talk from earlier this year by David Page. Slides available here (pdf).

Contra the view promoted by Bryan Sykes, the Y chromosome is not dying.

Greater policing required to enforce cooperation in "diverse" societies

2011-09-02T21:51:00.001+01:00

A Test of Evolutionary Policing Theory with Data from Human Societies (PLoS ONE):

In social groups where relatedness among interacting individuals is low, cooperation can often only be maintained through mechanisms that repress competition among group members. Repression-of-competition mechanisms, such as policing and punishment, seem to be of particular importance in human societies, where cooperative interactions often occur among unrelated individuals. In line with this view, economic games have shown that the ability to punish defectors enforces cooperation among humans. Here, I examine a real-world example of a repression-of-competition system, the police institutions common to modern human societies. Specifically, I test evolutionary policing theory by comparing data on policing effort, per capita crime rate, and similarity (used as a proxy for genetic relatedness) among citizens across the 26 cantons of Switzerland. This comparison revealed full support for all three predictions of evolutionary policing theory. First, when controlling for policing efforts, crime rate correlated negatively with the similarity among citizens. This is in line with the prediction that high similarity results in higher levels of cooperative self-restraint (i.e. lower crime rates) because it aligns the interests of individuals. Second, policing effort correlated negatively with the similarity among citizens, supporting the prediction that more policing is required to enforce cooperation in low-similarity societies, where individuals' interests diverge most. Third, increased policing efforts were associated with reductions in crime rates, indicating that policing indeed enforces cooperation. These analyses strongly indicate that humans respond to cues of their social environment and adjust cheating and policing behaviour as predicted by evolutionary policing theory.

Svante Paabo TED talk on Neanderthal admixture

2011-09-02T10:34:00.000+01:00

Posting without having watching watched it yet.

"Sharing the results of a massive, worldwide study, geneticist Svante Pääbo shows the DNA proof that early humans mated with Neanderthals after we moved out of Africa. (Yes, many of us have Neanderthal DNA.) He also shows how a tiny bone from a baby finger was enough to identify a whole new humanoid species."

Next PoBI paper should be more interesting

2011-09-02T09:45:00.000+01:00

Another ICHG/ASHG 2011 abstract:

People of the British Isles: An analysis of fine-scale population structure in a UK control population. S. Leslie1, B. Winney1, G. Hellenthal2, S. Myers2, A. Boumertit1, T. Day1, K. Hutnik1, E. Royrvik1, D. Lawson3, D. Falush4, P. Donnelly2, W. Bodmer1 1) Department of Oncology, University of Oxford, Oxford, United Kingdom; 2) Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom; 3) Department of Mathematics, University of Bristol, Bristol, United Kingdom; 4) Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
There is a great deal of interest in fine scale population structure in the UK, both as a signature of historical immigration events and because of the effect population structure may have on disease association studies. Although population structure appears to have a minor impact on the current generation of genome-wide association studies, it is likely to play a significant part in the next generation of studies designed to search for rare variants. A powerful means of detecting such structure is to control and document carefully the provenance of the samples involved. Here we describe the collection of a cohort of rural UK samples (The People of the British Isles), aimed at providing a well-characterised UK control population that can be used as a resource by the research community as well as providing fine scale genetic information on the British population. So far, some 4000 samples have been collected, the majority of which fit the criteria of coming from a rural area and having all four grandparents from approximately the same area. Three thousand samples were genotyped on the Illumina 1.2M and Affymetrix v6.0 platforms as part of WTCCC2. Using a novel clustering algorithm that takes into account linkage disequilibrium structure, approximately 3000 of the samples were clustered, using these comprehensive genotyping data, into more than 50 groups purely as a function of their genetic similarities without any reference to their know locations. When the appropriate geographical position of each individual within a cluster is plotted on a map of the UK, there is a striking association between clusters and geography, which reflects to a major extent the known history of the British peoples. Thus, for example, even individuals from Cornwall and Devon, the two adjacent counties in the southwestern tip of Britain, fall into different, but coherent clusters. Further details of this comprehensive analysis of the genetic structure of the People of the British Isles, together with a description of the provenance of the samples, will be give in the presentation. We believe that this is the first time that such a detailed fine scale genetic structure of a population of generally very similar individuals has been possible. This has been achieved through, on the one hand, a careful geographically structured collection of samples and, on the other hand, an approach to analysis that takes into account fully the linkage disequilibrium structure of the population.

An estimate of black admixture in white Americans

2011-09-02T09:26:00.000+01:00

An ICHG/ASHG 2011 abstract (below) reports some results from a study of the 23andMe database. I see various potential issues with the research as described in the abstract; but while the numbers are not definitive, these estimates are likely to be by far the most accurate to date. What's clear is the overwhelmingly huge majority of white Americans have zero black ancestry. All previous sensible analyses of genetic data agree, and any other result would be difficult to reconcile with American history -- however disappointing that might be to "Multiracial Voice"-types and race denialists.

In 2002, Mark Shriver claimed 30% of white Americans have on average about 2% African ancestry, the average for the population as a whole coming out to about 0.7%. Shortly thereafter, in a different interview, Shriver lowered his estimate, purporting "about 10 percent of [the European-American population] have some African ancestry". Subsequently, another principal of DNAprint revised the estimate still further downward: "Five percent of European Americans exhibit some detectable level of African ancestry". That too was an overestimate. 23andMe, examining the genomes of vastly larger numbers of people using thousands of times as many SNPs, estimates "about 2%" of "European Americans" have any detectable autosomal black ancestry. And three quarters of that 2% have only "about 0.5%" African ancestry (i.e., less than Shriver in 2002 claimed the average American carried).

Exceptions to the "One Drop Rule"? DNA evidence of African ancestry in European Americans. J. L. Mountain1, J. M. Macpherson1, C. B. Do1, B. T. Naughton1, R. A. Kittles2, N. Eriksson1 1) 23andMe, Inc, Mountain View, CA; 2) Institute of Human Genetics, University of Illinois at Chicago, Chicago, IL.
Genetic studies have revealed that most African Americans trace the majority (75-80%, on average) of their ancestry to western Africa. Most of the remaining ancestry traces to Europe, and paternal lines trace to Europe more often than maternal lines. This genetic pattern is consistent with the "One Drop Rule,” a social history wherein children born with at least one ancestor of African descent were considered Black in the United States. The question of how many European Americans have DNA evidence of African ancestry has been studied far less. We examined genetic ancestry for over 77,000 customers of 23andMe who had consented to participate in research. Most live in the United States. A subset of about 60,000 shows genetic evidence of fewer than one in 16 great-great-grandparents tracing ancestry to a continental region other than Europe. They are likely to consider themselves to be entirely of European descent. We conducted two analyses to understand what fraction of this group has genetic evidence of some ancestry tracing recently to Africa. We first identified individuals whose autosomal DNA indicates that they are predominantly of European ancestry, but who carry either a mitochondrial (mt) DNA or Y chromosome haplogroup that is highly likely to have originated in sub-Saharan Africa. Of the 60,000 individuals with 95% or greater European ancestry, close to 1% carry an mtDNA haplogroup indicating African ancestry. Of approximately 33,000 males, about one in 300 trace their paternal line to Africa. We then identified the subset of these European Americans who have estimates of between 0.5% and 5.0% of ancestry tracing to Africa. This subset constitutes about 2% of this set of individuals likely to be aware only of their European ancestry. The majority (75%) of that group has a very small estimated fraction of African ancestry (about 0.5%), likely to reflect African ancestry over seven generations (about 200 years) ago. We estimate that, overall, at least 2-3% of individuals with predominantly European ancestry have genetic patterns suggesting relatively deep ancestry tracing to Africa. This fraction is far lower than the genetic estimates of European ancestry of African Americans, consistent with the social history of the United States, but reveals that a small percentage of “mixed race” individuals were integrating into the European American community (passing for White) over 200 years ago, during the era of slavery in the United States.

Was there ever a Ruling Class? 1000 years of Social Mobility

2011-08-30T09:41:00.000+01:00

According to Gregory Clark, because of regression to the mean and the lack of any (e.g., racial) barrier preventing gene flow across classes, there was never a persistent ruling class in England.

Notes from a presentation by Clark last year containing "work in progress from a planned book on social mobility over the long run" (pdf):

What is the fundamental nature of human society? Is it stratified into enduringlayers of privilege and want, with some mobility between the layers, but permanentsocial classes? Or is there, over generations, complete mobility between all ranks inthe social hierarchy, and complete long run equal opportunity? [. . .]
This book systematically exploits a new method of tracing social mobility overmany generations, surnames, to measure the persistence of classes over as much as800 years, 24 generations. It looks at societies where surnames are inherited,unchanged, by children from fathers. In such cases they thus serve as a tracer of thedistant social origins of the modern population (and interestingly also as a tracer ofthe Y chromosome).
In this role surnames are a surprisingly powerful instrument for measuring longrun social mobility. The results they reveal are clear, powerful, and a shock to ourcasual intuitions.
(1) In England, where we can trace social mobility back to 1066 using surnames,there were never any long persistent ruling and lower classes for the indigenouspopulation: not in medieval England, and not now. About 5-6 generations were, andare, enough to erase most echoes of initial advantage or want. For the English classis, and always was, an illusion. Histories such as those of the Stanley family turn outto be rare exceptions, not the rule.
(2) Paradoxically, while England reveals complete long run mobility, the rates ofsocial mobility per generation, better measured by looking over multiple generations,turn out to be lower than is conventionally estimated. But the mathematics ofmobility is such that even such slow regression to the mean, over time, willcompletely erase initial advantage and want.
(3) The rate of social mobility in England was as high in the middle ages as it is now.The arrival of the whole apparatus of free public education in the late nineteenth century, and the elimination of nepotism in government and private firms, has notimproved the rate of social mobility.
(4) The extraordinarily complete long run mobility of England is likely typical ofother western European societies. But other countries, in contrast, do exhibitpersistent social classes over hundreds of years. In the US, for example, the Blackpopulation has persisted at the bottom of the social order, and the Jewish populationat the top. In Chile surname evidence shows the indigenous population hasremained at the bottom since the Spanish conquest of 1541. [. . .]
(7) Though parents at the top of the economic ladder in any generation in preindustrialEngland did not derive any lasting advantage for their progeny, there wasone odd effect. Surname frequencies show was that there was a permanent increasein the share of the DNA in England from rich parents before 1850. After 1850 afrequency effect operated, but in reverse. Surname frequencies show the DNA shareof families in England who were rich in 1850 declined relative to that of poorfamilies of the same generation by 2010. [. . .]
What is the meaning and explanation of these results? This is a much morecontentious and difficult area. The book argues for the following conclusions:
A. Why can’t the ruling class in a place like England defend itself against downwardsmobility? If the main determinants of economic and social success were wealth,education and connections then there would be no explanation of the consistenttendency of the rich to regress to the society mean. Only if genetics is the mainelement in determining economic success, if nature trumps nurture, is there a built-inmechanism that ensures the observed regression. That mechanism is theintermarriage of the rich with those from the lower classes. Even though there isstrong assortative mating, since this is based on the phenotype created in part bychance and luck, those of higher than average innate talent tend to systematicallymate with those of lesser ability and regress to the mean.
B. Racial, ethnic and religious differences allow long persisting social stratificationthrough the barriers they create to this intermarriage. Thus for a society to achievecomplete social mobility it must achieve cultural homogeneity. Multiculturalism isthe enemy of long run equality.

On the Normans:

We can even push back the study of mobility in medieval England to 1066 usingsurnames. In particular the Domesday book of 1086, and associated charters andother documents, allows us to identify a subset of English names which are ofNorman origin only, and which were held by the new ruling class installed byWilliam I (Keats-Rohan, 1999). These names include such well known Englishnames as Balliol, Baskerville, Darcy, Glanville, Lacy, Mandeville, Percy, Sinclair, andVenables. Most of these names were drawn from the home village of a member ofWilliam’s invasion force in Normandy, Brittany or Flanders. Thus Baskerville isfrom the village of Bacqueville in Normandy, Venables from Venables, Ivry fromIvry-la-Bataille. As the ruling class imposed by force in 1066, how quickly was thisgroup assimilated into the general population in medieval England?
A group of 236 names of this form was compiled. The frequency of thesenames in the later medieval population (1368-1449) was estimated at 0.9 percentbased on a sample of enrollment lists for English armies and garrisons. What was therelative representation of this conquering elite at Oxford university by the thirteenthcentury, assuming their name share in the general population was 0.9 percent?Figure 3.4 shows this by 20 year periods from 1180. In the thirteenth century thesesurnames were on average three times as frequent at the university as in the generalpopulation. However, their representation fell rapidly in the fourteenth century, sothat by the late fourteenth century these names were only about 10 percent morecommon at the university than in the general population. This would seeminglyimply that the Domesday elite of 1086 had by 1350, less than 300 years later,descended in status on average to the level of the general population. But we shallsee that there is contradictory evidence in this case. Among the fighting elite of1368-1449 the names of these original Norman warriors continue to be greatlyoverrepresented.

Another R1b paper

2011-08-26T19:37:00.002+01:00

The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269 (full text freely accessible):

Recently, the debate on the origins of the major European Y chromosome haplogroup R1b1b2-M269 has reignited, and opinion has moved away from Palaeolithic origins to the notion of a younger Neolithic spread of these chromosomes from the Near East. Here, we address this debate by investigating frequency patterns and diversity in the largest collection of R1b1b2-M269 chromosomes yet assembled. Our analysis reveals no geographical trends in diversity, in contradiction to expectation under the Neolithic hypothesis, and suggests an alternative explanation for the apparent cline in diversity recently described. We further investigate the young, STR-based time to the most recent common ancestor estimates proposed so far for R-M269-related lineages and find evidence for an appreciable effect of microsatellite choice on age estimates. As a consequence, the existing data and tools are insufficient to make credible estimates for the age of this haplogroup, and conclusions about the timing of its origin and dispersal should be viewed with a large degree of caution.

I find it hard to get too excited about this paper. As discussed previously, amateurs looking at more finely-resolved subclades using larger numbers of STRs do find trends in diversity that seem to point to an E. European origin for W. European R1b. I expect we'll have to wait a couple years, for overwhelming evidence to accumulate in the form of ancient DNA results and SNP-based dating, before seeing the correct route and timing of the entry of R1b into Europe widely agreed upon by academics. BBC article:

The extent to which modern Europeans are descended from these early farmers versus the indigenous hunter-gatherers who settled the continent thousands of years previously is a matter of heated debate. [. . .]
More than 100 million European men carry a type called R-M269, so identifying when this genetic group spread out is vital to understanding the peopling of Europe. [. . .]
A more recent origin for R-M269 than the Neolithic is also possible. But researchers point out that after the advent of agriculture, populations in Europe exploded, meaning that it would have been more difficult for incoming migrants to displace local people.

From the paper:

If the R-M269 lineage is more recent in origin than the Neolithic expansion, then its current distribution would have to be the result of major population movements occurring since that origin. For this haplogroup to be so ubiquitous, the population carrying R-S127 would have displaced most of the populations present in western Europe after the Neolithic agricultural transition.

Although the debate is commonly framed as Paleolithic vs. Neolithic, many lines of evidence suggest the correct answer is the third option: major post-Neolithic population movement.

Adaptive introgression of Denisovan HLA alleles across Asia?

2011-08-26T18:26:00.002+01:00

John Hawks:

If it turns out that we have widespread adaptive introgression in Asia today from Denisovans, that will change the game of studying the origins of these populations. Based on the genome-wide comparison, it looks like the genetic interaction that led to the habitation of Asia did not involve Denisovans, who contributed only to populations at the most eastern extreme of habitation in island Southeast Asia. But the only Denisovans we know about lived near the geographic center of the Asian landmass, not at the extreme southeastern extreme.
The HLA pattern may suggest a more widespread pattern of mixture across Asia, which was later overwritten by population movements of people who didn't have Denisovan ancestry. That means that the habitation of Asia was a process of successive migrations and replacements, which imperfectly covered up the evidence of archaic intermixture. The genes that remain as signs of this intermixture are those that had selective advantages in later populations.

The paper: The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans

Deary / Visscher IQ paper

2011-08-24T08:28:00.000+01:00

Those who read Sailer learned of this study a couple weeks ago. I've finally gotten around to looking at the actual paper, which seems convincing enough to me in doing what it says it does -- demonstrating "human intelligence is highly heritable and polygenic".

TGGP draws attention to comments by a blogger (Kevin Mitchell) who claims the paper "failed to establish the polygenic nature of the trait", but I don't see that Mitchell has a case. Mitchell:

I would interpret these findings very differently. What the authors do is analyse GWAS data in a very unusual way – they are not interested in finding specific SNPs affecting the trait, they simply use the SNPs to measure genetic relatedness between individuals.

As Mitchell then acknowledges, the paper does include a standard GWAS, the results of which are negative: at the level of individual SNPs not a single "replicable genome-wide significant association" is found. This is not surprising given the relatively small sample size and the (for me) expected polygenic nature of intelligence, but it (along with previous negative findings) tends to rule out any significant role for common variants of large effect in determining IQ.

The study uses SNPs across the genome to measure this relatedness and then shows it correlates with phenotypic similarity – i.e., the trait is heritable. We knew that already.
What they claim is that you can break down this effect by chromosome or by subregion. When they use the SNPs along longer chromosomes they seem to get a bigger effect – “explaining more of the phenotypic variance”. The inference is that thousands of SNPs, scattered across the whole genome, contribute to the trait or, more specifically to variance in the trait across the population (the implication is that they contribute to the value of the trait in individuals).
There is an alternative explanation for this effect, however, which is that using more SNPs simply gives a better estimate of genetic relatedness. So, the SNPs on chromosomes 1 (the longest) give a better estimate than those on chromosome 21 (the shortest) – they index relatedness with more precision. As a result, they correlate better with phenotypic similarity – this looks like you have “explained more of the variance”. In fact, getting such a signal from SNPs on chromosome 1 does not mean that any of the causal variants are actually on chromosome 1. Nor does the fact that such signals can be derived from anywhere in the genome mean that there are thousands of variants across the genome affecting the trait.

What Mitchell is claiming here is that the results could be explained by cryptic relatedness and/or population structure. However, the researchers address both issues, by excluding samples that appear to be related to other samples nearer than the level of 4th cousins and by including as covariates in their models the first few components of an MDS analysis. For non-close relatives in unstructured populations, how similar two individuals are on chromosome 1 tells us nothing about how similar they are on any other chromosome. Visscher was more explicit on this point in a commentary on the height paper:

What is the evidence that population structure is not causing the observed effects?
We took several steps to avoid population structure inflating the estimate of the variance explained by the SNPs. We excluded one individual from any pair that had an estimated relationship > 0.025 (approximately equivalent to between 3rd and 4th cousins). We fitted the first 20 principal components from the relationship matrix in the statistical model so that any population substructure that they picked up was excluded from the variance explained by the SNPs. Critically, we then estimated the correlation between the relationship matrices estimated from different chromosomes and did not find significant correlation. We tested a set of SNPs that are ancestry-informative in Europe for association with height and did not observe inflation of the test-statistics.
For the purpose of this paper, we performed an additional simulation experiment (inspired by comments from Dan Stram) by assuming that the causal variants were all carried on one set of chromosomes (odd numbers) and another set of chromosomes (even numbers) carried SNPs from which we estimated relatedness. If there is structure in the population then this would imply that a pair of individuals that are closely related on odd chromosomes will also be closely related on even chromosomes. We used the observed genotype data of 3,925 individuals and 295K SNPs as the basis of the simulation, and simulated 1,000 causal variants on the odd chromosomes with a total heritability of 80%. Then we performed a restricted maximum likelihood (REML) analysis of the simulated phenotypes on the genetic relationship matrix estimated from the SNPs on the even chromosomes. The estimates and standard errors (SEs) from 10 simulation replicates are shown in Table 1. Since REML estimates of variance are always positive, if the true variance explained is zero, we expect half the replicates to return an estimate of 0.0 and half to return an estimate with mean value 0.8 times the standard error. This is exactly what happened. Therefore we conclude (again) that there is no structure in the data that would inflate the estimate of the variance explained by the SNPs.

Steve Hsu correctly points out:

If I understand correctly, you want to claim that the observed population variation could be due to a few rare variants of large effect. But then it would be surprising for this study to have found .5 of the total variation to be associated with SNPs — compare to earlier studies using twins/adoptions/siblings that found narrow sense heritability of about .6 or so. I would not expect the rare alleles you hypothesize to be in good LD with SNPs (which are designed to tag common variants), so we would expect to lose a big chunk of the .6 additive heritability.
For example, in the Visscher paper on height they had to hand wave about imperfect LD to recover the full .8 or so of heritability. In this case the global fit comes out very close to .6, which suggests common rather than rare variants (at least, they are well tagged by SNPs). But if they are common variants their individual effect sizes must be small and there are a lot of them. Let me know if I am missing something.

Mitchell:

I don’t think the population variation is caused by “a few” rare variants – I think it is (or could be at least) caused by a larger number of rare variants – different ones in different people.

This is getting to be a pretty silly argument: "different ones in different people" would add up to a very large number, which sounds "polygenic" enough to me (regardless of how many people have the major allele at most variable sites). And again: rare variants will be tagged less effectively (if at all) by common SNPs, so the causal variants whose effects are being estimated in this study can't be too rare. The contribution of rare variants to variability in intelligence is likely largely on top of the effect identified here, and probably mostly negative: an unusually high number of rare, deleterious mutations will tend to interfere with brain development and diminish IQ; an unusually low number will result in a higher IQ on average, explaining at least in part the associations commonly found between intelligence and other markers of "good genes" (health, physical attractiveness, and so on). A priori, though, it makes no sense to expect this type of variation to be the only or overwhelming source of genetic variability in IQ. Clearly, a very large number of genes affect brain development, and I expect pretty much all of these genes to be polymorphic. It's also clear tradeoffs affecting IQ exist (such as between brain size and energy expenditure) and that specific IQ-influencing alleles will have varying effects on fitness in different times and places. So it seems obvious to me common variants should be expected to play a major role in inter-individual and inter-population IQ differences.

Incidentally, looking again at the supplementary material for the height paper recently, I noticed the following addition:

In the version of this supplementary file originally posted online, Supplementary Fig. 2a and 2b were incorrect. The legend stated that in Supplementary Fig. 2a, PC1 versus PC2 was plotted when in fact PC2 versus PC3 was shown. Similarly, in Supplementary Fig. 2b, PC4 versus PC5 was plotted rather than PC3 versus PC4 as stated. This error is purely graphical and does not in any way affect the results or conclusions presented in the article.

Dasein spotted the strange-looking PCA at the time. I didn't think it materially affected that paper's conclusion, but I'm pleased to see that confirmed and the issue resolved.

Y haplogroup R1b and light hair in Italy

2011-08-17T10:55:00.003+01:00

Via Italian Wikipedia.

Update addressing some questions/comments:

(1) The map specifically shows the frequency of blond hair; so yes the frequency of light hair in general will be higher.

(2) The map is adapted from Biasutti's Razze e popoli della Terra. The data was originally collected by Ridolfo Livi in 1859-1863.

(3) The Biasutti/Livi map shows a higher frequency of blond hair in Corsica than in Sardinia. In keeping with the apparent pattern elsewhere in Italy, the frequency of R1b appears to be markedly higher in Corsicans than in Sardinians (in this paper, "HG 1" in combination with "HG 22" roughly corresponds to R1b).

(4) "Does R1b necessarily correlate with light hair?" In Italy it pretty clearly does. If you mean am I suggesting a strict correspondence between light hair and haplogroup R1b, obviously I am not. Looking at Europe as a whole, I doubt much of a correlation exists. But the evidence is consistent with the bearers of R1b (or more specifically subclades of R-L11) being lighter than the previous inhabitants of Italy. This doesn't mean the original carriers of R-M417 and some subclades of I weren't probably also lighter-haired, or that as R1b spread throughout Europe and mixing occurred, R1b always remained associated with light hair. It does tend to add yet more weight against attempts to link R1b in Europe to migration of Neolithic farmers from Anatolia, but dispensing with that question for good awaits large, high-resolution studies of ancient and modern DNA.

"haplogroup R1b is found in some of it's highest concentrations among European peoples in Spain and Portugal -- two countries hardly known for blondes."

Within Iberia, though, it's certainly possible the pattern will hold. Among Iberians, Basques have some of the highest frequencies of both R1b and blondism. According to Coon: 'The French Basques are by no means all brunet; Collignon finds 22 per cent of blue eyes, 44 per cent of "medium," and 34 per cent of dark. Black hair is found in 7 per cent of the group, brown in 77 per cent, and light brown to blond in 16 per cent. Among the Spanish Basques the incidence of blondism is somewhat lower, but the Basques are still light when compared to most other inhabitants of Spain.'

Variance of R-P312 lineages highest in eastern Europe

2011-08-17T10:45:00.001+01:00

I take this as further evidence most R1b arrived in western Europe by way of eastern (but not southeastern) Europe:

For the last two years, whenever I've calculated variance by country for
R-P312 "All" I get results that match Myres' 2010 study in that France
always has a very high variance. One problem, however, is there just aren't
many R-P312 haplotypes available in our DNA projects with MDKA's from
East/Central Europe (anything east of Germany.)

With the advent of R-P312 subclade Z196 and additional testing, the number
of haplotypes is edging up so I ran the variance calculations again. To keep
the sample size up, I backed down to 37 or greater length haplotypes. I used
only the 25 non-multicopy markers and calculated sum of the variance
relative to a base = 1.0 to make it easier to compare. I express the caveats
that we still need larger samples, a better cross-section of Europe/W/SW
Asia and I'd prefer to use only 67 length haplotypes.

I was startled a bit to find East/Central Europe came up higher than France,
so I broke the countries out as best I could. It didn't change the essence
of the ranking.

Hungary_____________: Var=1.31 (N=15)
Baltic states_______: Var=1.24 (N=15)
Belarus/Russia/Ukrai: Var=1.23 (N=26)
Poland______________: Var=1.15 (N=26)
France______________: Var=1.12 (N=188)
Czech Rep.__________: Var=1.10 (N=12)
England_____________: Var=1.03 (N=540)
Nordic area_________: Var=1.02 (N=71)
Germany_____________: Var=1.01 (N=181)
Switzerland_________: Var=0.98 (N=43)
Italy_______________: Var=0.96 (N=60)
Ireland_____________: Var=0.94 (N=935)
Wales_______________: Var=0.93 (N=91)
Iberia______________: Var=0.92 (N=494)
Low Countries_______: Var=0.91 (N=43)
Scotland____________: Var=0.90 (N=463)

It's a bit of twist, but the variance runs just about polar opposite to the
frequency.

I've never been able to figure out how a Mediterranean route into Europe
worked for R-P312, at least when looking at the Y STR variance and the SNP
phylogenetic trail. It seems like the more data and the more resolution, the
more indications are that R-P312 moved east to west across the core of the
continent. We still don't have many R-P312 haplotypes from the Balkan
Peninsula, but if I add the Italian Peninsula together with Greece, Croatia,
Algeria and Malta I get this result:

East Mediterranean__: Var=0.90 (N=27)

If I just look at the Balkans, this is all we get. I don't think this is a
high enough count (only 4) to mean anything, but here it is:

Greece/Croatia______: Var=0.85 (N=4)

This is not to say that some R-L11* or R-M269 L11- uncles and cousins didn't
come across the boot of Italy and into Iberia at an early period, but I
don't think that's what happened with R-P312. Keep in mind, R1b in Western
Europe is about 96% R-L11 (P312 + U106 + L11*.)

It has always been perplexing that R-U106, R-P312 and R-L11 all have TMRCA
aging of about the same time, but (according to Myres) R-U106 showed higher
variance in the Baltic states than in Western Europe whereas R-P312 showed
higher variance in France. The jury is still out, but perhaps R-P312's
launching points are pretty close to U106's after all.

I wish we had more R-P312 data from the Near East, Anatolia and the
Caucasus. We know there is some R-P312 in Anatolia. I guess I should wish
for more Romanian data as well. We probably have to look deeper at the
R-L11* brothers in these areas as well as R-L23 L11- cousins.

Any new news on the R-U106 or R-L11* fronts?

Regards,
Mike

Recently-revealed structure in Y haplogroup R1a

2011-08-12T17:51:00.001+01:00

Posters at dna-forums.com using data from the 1000 Genomes Project to identify new Y subclades have arrived at the following structure below M417:

Early results from commercial and academic testing suggest the bulk of Central Asian, Middle Eastern, and South Asian R1a will turn out to be Z93+ and L342.2+. An academic, posting at dna-forums:

It appears that Z93 and Z95, which, according to the heuristic tree from the 1K genomes project, are above L342.2 do separate most of the Europeans who are ancestral for Z93 and Z95 from the Pakistanis, Indians, Iranians, Ashkenazi Levites and the Eastern Turks (probably Kurds). [. . .] We do have some very preliminary results on Z93 and Z95 that would indicate that almost all Balkan and East European R1a1's are ancestral for Z93 and Z95. Also most of Western Turkey but not Eastern Turkey. I think that the Tuscans who are derived for Z93 and Z95 must be originally of Ashkenazi ancestry (perhaps also the Iberian).

Note: Ashkenazi Levite R1a is L342.2+. I can see no reasonable grounds on which to propose the Z93+ L342.2- TSI and IBS samples are of Jewish origin. More from the academic:

Most Pakistanis are Z93/Z95. We haven't tested many Indians, but the few we have are Z93/Z95. We haven't genotyped any other Z or L SNPs on R1a1 backgrounds. What amazes me is the clear geographic bifurcation between Middle East/South Asian Z93/Z95 (and by inference L342.2) and European markers such as M458. This points to a vary old what we term vicariance pattern between Europe and the Middle East with respect to R1a1. Maybe the original source of R1a1 is somewhere in the middle such as Armenia or Turkey and some R1a1 moved to Europe to become M458 and other newly discovered L# lineages and other R1a1's move to Iran/Pakistan/India/Central Asia to become Z93/Z95. I think that this bifurcation occurred at least 10,000 years ago, but then of course we tend to use the evolutionary mutation rates on YSTRs.

Another poster points out: "Dividing by 3 [to bring the estimate more in line with real mutation rates] gives an age of 3300 years, almost exactly the estimate from Nordtvedt's spreadsheet." Someone else recently estimated the TMRCA for L342.2+ at around 3,600 years. So: if current patterns hold, the bulk of South Asian R1a unambiguously falls within European R1a variation. While I fully expect, when we eventually see results for these markers in large academic samples published, the papers will feature evolutionary mutation rates and less than parsimonious attempts to fit the distribution of M417 sublineages to archaeology, it's pretty clear to me Z93 and L342.2 originated on the Steppe within the past 4000 years or so and spread with Indo-Iranian.

Swedish McDonald's

2011-08-12T16:01:00.001+01:00

Open thread (7)

2011-08-12T15:59:00.000+01:00

Links, off-topic discussion, etc. Previous open threads: 1 2 3 4 5 6

Editorial and preliminary paper on People of the British Isles project

2011-08-12T14:50:00.001+01:00

Both freely accessible.

A British approach to sampling:

The acronym ‘PoBI’ may not yet be familiar to human geneticists in the way that ‘HGDP’, ‘WTCCC’ or ‘HapMap’ are, but a paper in this issue of EJHG1 that introduces the ‘People of the British Isles’ project to the scientific community aims to change this. The PoBI project will collect up to 5000 DNA samples from diverse regions of the British Isles, taking great care to sample individuals with several generations of ancestry in rural locations. These samples are intended to serve as controls for future medical genetic studies, and to provide insights into the peopling of the British Isles over the last few millennia. [. . .] Although readers will have to wait for future publications to discover the insights from these large-scale genetic analyses, the current paper describes the sampling strategy and initial 3865 samples in some detail, outlines an approach to investigating fine-scale population structure using surnames, and presents some preliminary genetic analyses of a handful of chosen loci. [. . .]
In addition to collecting blood, the project recorded surnames. Using data from a census performed in 1881, these were classified as ‘local’ or ‘non-local’, and the two classes examined separately. The authors then modelled a population such as that from central England as a mixture between south-western (taken to represent Ancient Britons) and eastern (Anglo Saxon) populations, and estimated the contribution of each population to the central England autosomal genotypes. These contributions differed between the local surname class (mostly eastern) and the non-local class (half and half), which the authors take as evidence of subtle population structure. Published genetic analyses using much larger numbers of markers have already detected low, but significant levels of genetic structure within Britain in more straightforward ways,4, 5 even with less stringently ascertained samples (Figure 1): Europe-wide south-east to north-west gradients extend into the British Isles. We can look forward to deeper insights into genetic differentiation and its causes when large-scale genetic analyses of the PoBI samples are available.
[. . .] anthropological and evolutionary geneticists should rejoice in the assembly of this resource, the foresight of The Wellcome Trust in funding the project over a decade or so, and hope that resources are available for establishing more cell lines and performing more genome-wide sequencing, so that both the full set of samples and their sequences can be made widely available.
It is obvious why British people interested in their ancestry, and medical geneticists working with British subjects should welcome PoBI, but why should others pay attention? PoBI will not provide information about global genetic diversity in the way that HGDP7 and HapMap8 do, but its microcosmic survey of genetic variation in a set of small islands off the western coast of the Eurasian continent is revealing the level of differentiation that builds up over millennia via events well documented by archaeology and history, so these alternative data sets can be compared to address questions about the initial peopling of the area, and its subsequent reshaping by internal and external forces. And if the characteristics of the British – politeness, eccentricity, or drunken loutishness, according to your viewpoint and experience – have any genetic basis, perhaps PoBI can provide a starting point for identifying it!

People of the British Isles: preliminary analysis of genotypes and surnames in a UK-control population:

There is a great deal of interest in a fine-scale population structure in the UK, both as a signature of historical immigration events and because of the effect population structure may have on disease association studies. Although population structure appears to have a minor impact on the current generation of genome-wide association studies, it is likely to have a significant part in the next generation of studies designed to search for rare variants. A powerful way of detecting such structure is to control and document carefully the provenance of the samples involved. In this study, we describe the collection of a cohort of rural UK samples (The People of the British Isles), aimed at providing a well-characterised UK-control population that can be used as a resource by the research community, as well as providing a fine-scale genetic information on the British population. So far, some 4000 samples have been collected, the majority of which fit the criteria of coming from a rural area and having all four grandparents from approximately the same area. Analysis of the first 3865 samples that have been geocoded indicates that 75% have a mean distance between grandparental places of birth of 37.3 km, and that about 70% of grandparental places of birth can be classed as rural. Preliminary genotyping of 1057 samples demonstrates the value of these samples for investigating a fine-scale population structure within the UK, and shows how this can be enhanced by the use of surnames.

Swedish population structure

2011-08-05T09:44:00.002+01:00

Via Dienekes, The Genetic Structure of the Swedish Population:

An analysis of genetic differentiation (based on pairwise Fst) indicated that the population of Sweden's southernmost counties are genetically closer to the HapMap CEU samples of Northern European ancestry than to the populations of Sweden's northernmost counties. [. . .] We have shown that genetic differences within a single country may be substantial, even when viewed on a European scale.

The paper is in PLoS ONE (i.e., it's open access). More:

The first principal component showed the presence of a north-south genetic gradient that was mainly driven by each northern county being different from other counties. [. . .]

The second principal component did not display a constant gradient across Sweden. The county with the lowest mean was Dalarna, with samples in the north-western parts of this county contributing with particularly low values. These patterns may be linked to Finnish or Norwegian ancestry, although the component most probably encompasses other signals arising from factors such as isolation and drift in the more remote parts of Dalarna county. A large wave of migration did take place from parts of today's Finland to Dalarna, Värmland and Gävleborg counties during the 16th and 17th centuries, with some settlers moving further west to Norway. The migrants, known as the “Forest Finns”, have today become fully assimilated into Norwegian and Swedish society with almost none speaking Finnish. As we conservatively removed samples that had Finnish ancestry to reduce the effect of ethnic Finns on the Swedish population stratification, we removed samples that had a substantial Finnish contribution. Indeed, the samples that had the most extreme values with respect to principal component 2 fell close to our cutoff used to define Finnish ancestry (Figure S10). What we see may therefore be the remnants of early Finnish migrations to Sweden. It could be that even after the removal of samples with Finnish ancestry, Finnish influx leaves its mark, consistent with a long history of Finnish migration to Sweden coupled with a high degree of admixture. However, when we applied the component to a set of Norwegian samples, they too had negative component values with a small number of samples being clear outliers in the negative direction (Figure S6). It is therefore possible that a portion of the component predicts Norwegian ancestry, or isolation and drift in the border areas that has left its mark in both populations, or a combination of these factors.

Population pairwise Fst values

The observed genetic differences between the southern national areas and counties are similar to what has been seen in the UK, when comparing southern England to Scotland, and the genetic differences between the southern national areas and North Middle Sweden (the approximate geographical center of the country) are similar to what has been observed between the UK and Ireland [9]. They are much smaller than the ones observed between regions in Finland where the Fst has been shown to be about an order of magnitude larger than what we observed among the southern Swedish national areas [7]. The genetic differences between Upper Norrland, the northernmost national area, and the southern and middle national areas were much larger than the genetic distances we observed between the southern national areas and the HapMap CEU founders, highlighting the extent of the distances. The genetic differences observed between the southern national areas and the northernmost one were larger than what has previously been observed between Swedes and Danes, and Swedes and the Dutch [5]. This puts the observed intra-Sweden genetic differentiation into perspective, showing that the genetic differences between the southern and northern parts of Sweden are of larger magnitude than those between a general sample of Swedes and samples from some other European countries and Americans of Northern European ancestry. [. . .]

The observed patterns of homozygosity further reinforce the picture of a genetic divide between the southern and northern parts of Sweden. While the differences in the number of extended homozygous segments were mostly small and non-significant for the southern national areas, the counties corresponding to the three northernmost national areas had a larger number of extended homozygous regions, suggestive of an increase in autozygosity. The northern national areas are much more sparsely populated than the southern with vast geographical distances between towns and villages, a fact that may have contributed to the observed loss of heterozygosity. [. . .]

The main south-north pattern detected in the principal component analysis may be the amalgamation of many separate factors. Immigration of continental Europeans, and Britons to the southern parts of Sweden may be one such factor, together with isolation and consecutive allelic drift and admixture with the indigenous Sami people in northern Sweden. [. . .]

The picture of the Swedish genetic structure presented here can only be considered as a historical snapshot. Immigration and movements around Sweden can alter the picture we have described considerably within the span of only a few generations. Within country population movement creates genetic diversity and breaks up existing structures. Immigration from other countries leads to new stratification of a vastly complex nature. With increased movements, homozygosity, due to a high degree of kinship with geographically local possible partners, may swiftly decrease.

Few of whites' best friends are black

2011-08-04T21:28:00.000+01:00

Friends for better or for worse: Interracial friendship in the United States as seen through wedding party photos (pdf):

Four findings stand out. First, the few survey estimates of close adult interracial friendships may overstate their actual prevalence, especially whites’ reporting of close friendships with blacks. My results show that very few whites have black friends who are close enough to be in their wedding party (3.7%), less than all previous estimates among adults. I reasoned that estimates of cross-race friendships for whites based on the wedding party photos would be lower than those based on existing survey measures because wedding parties include only the closest friends who may often have to conform to intergenerational norms about racial contact and the expectations of extended family. Wedding parties also limit the pool of friends to a small number and cannot be exaggerated out of normative pressure. Compared with what would be expected if there were homogenous opportunity for friendships, whites are most likely to have a close E/SE Asian friend and least likely to have a black friend. These results suggest that Jackman and Crane’s (1986: p. 460) declaration using data from 1979 still rings true: “only a tiny minority of whites could rightly claim that ‘some of their best friends’ are black.”

Second, I hypothesized that there would be an asymmetry, by race, of inviting a friend to be in the wedding party and being invited to be in a friend’s wedding party, with whites being invited more than they invite friends of other races. Adjusting for group size, whites and E/SE Asians are equally likely to invite and be invited, but whites invite blacks only half as much as blacks invite whites, and E/SE Asians invite blacks only one- fifth as much as blacks invite E/SE Asians. This finding is consistent with the notion that whites are less accepting of interracial friendships, a finding that is no longer detectable in survey-based attitudinal data.

More evidence of Sephardic ancestry in some new world Hispanic groups

2011-07-28T13:34:00.000+01:00

Velez et al. The impact of Converso Jews on the genomes of modern Latin Americans. Hum Genet. 2011 Jul 26. [abstract]

Modern day Latin America resulted from the encounter of Europeans with the indigenous peoples of the Americas in 1492, followed by waves of migration from Europe and Africa. As a result, the genomic structure of present day Latin Americans was determined both by the genetic structure of the founding populations and the numbers of migrants from these different populations. Here, we analyzed DNA collected from two well-established communities in Colorado (33 unrelated individuals) and Ecuador (20 unrelated individuals) with a measurable prevalence of the BRCA1 c.185delAG and the GHR c.E180 mutations, respectively, using Affymetrix Genome-wide Human SNP 6.0 arrays to identify their ancestry. These mutations are thought to have been brought to these communities by Sephardic Jewish progenitors. Principal component analysis and clustering methods were employed to determine the genome-wide patterns of continental ancestry within both populations using single nucleotide polymorphisms, complemented by determination of Y-chromosomal and mitochondrial DNA haplotypes. When examining the presumed European component of these two communities, we demonstrate enrichment for Sephardic Jewish ancestry not only for these mutations, but also for other segments as well. Although comparison of both groups to a reference Hispanic/Latino population of Mexicans demonstrated proximity and similarity to other modern day communities derived from a European and Native American two-way admixture, identity-by-descent and Y-chromosome mapping demonstrated signatures of Sephardim in both communities. These findings are consistent with historical accounts of Jewish migration from the realms that comprise modern Spain and Portugal during the Age of Discovery. More importantly, they provide a rationale for the occurrence of mutations typically associated with the Jewish Diaspora in Latin American communities.

Sorbs autosomally distinct from Germans

2011-07-28T13:12:00.002+01:00

Population-genetic comparison of the Sorbian isolate population in Germany with the German KORA population using genome-wide SNP arrays (abstract; provisional pdf):

Background
The Sorbs are an ethnic minority in Germany with putative genetic isolation, making the population interesting for disease mapping. A sample of N=977 Sorbs is currently analysed in several genome-wide meta-analyses. Since genetic differences between populations are a major confounding factor in genetic meta-analyses, we compare the Sorbs with the German outbred population of the KORA F3 study (N=1644) and other publically available European HapMap populations by population genetic means. We also aim to separate effects of over-sampling of families in the Sorbs sample from effects of genetic isolation and compare the power of genetic association studies between the samples.

Results
The degree of relatedness was significantly higher in the Sorbs. Principal components analysis revealed a west to east clustering of KORA individuals born in Germany, KORA individuals born in Poland or Czech Republic, Half-Sorbs (less than four Sorbian grandparents) and Full-Sorbs. The Sorbs cluster is nearest to the cluster of KORA individuals born in Poland. The number of rare SNPs is significantly higher in the Sorbs sample. FST between KORA and Sorbs is an order of magnitude higher than between different regions in Germany. Compared to the other populations, Sorbs show a higher proportion of individuals with runs of homozygosity between 2.5 Mb and 5 Mb. Linkage disequilibrium (LD) at longer range is also slightly increased but this has no effect on the power of association studies. Oversampling of families in the Sorbs sample causes detectable bias regarding higher FST values and higher LD but the effect is an order of magnitude smaller than the observed differences between KORA and Sorbs. Relatedness in the Sorbs also influenced the power of uncorrected association analyses.

Conclusions
Sorbs show signs of genetic isolation which cannot be explained by over-sampling of relatives, but the effects are moderate in size. The Slavonic origin of the Sorbs is still genetically detectable. Regarding LD structure, a clear advantage for genome-wide association studies cannot be deduced. The significant amount of cryptic relatedness in the Sorbs sample results in inflated variances of Beta-estimators which should be considered in genetic association analyses.

Dienekes releases ancestry analysis tool

2011-07-27T14:51:00.002+01:00

For people with 23andMe or Family Finder data (background; download). Don't take the component names too literally or assume this particular analysis is the final word, but the tool allows you to compare your personal results with those for various populations included in Dienekes' admixture runs. Definitely do not take the results from Dodecad Oracle mixed mode (which lists combinations of two populations that would produce admixture proportions most similar to yours) literally. It might be useful for people with more broadly mixed ancestry. But from what I'm seeing, people of Northwestern European ancestry will frequently be shown as, for example, 7/8 Scottish and 1/8 Italian, when they have minimal Scottish and no Italian ancestry. Dienekes acknowledges "mixed mode should be used with caution". I think it throws away too much information to ever have much precision within Europe. The future will be very large databases and assignment of individual segments to specific geographic locations.

Advice for women and men

2011-07-27T14:07:00.001+01:00

Some woman: "In the end, infertility can make you feel less human. As cultivated as we are, we hold on to a deep-rooted belief that our worth is tied to how well, and how much, we reproduce. I've seen women and men shrink like salted slugs during IVF treatment. [. . .] Many women are still listening to their bosses instead of their gynecologists and their guts. They still trust that their mid to late 30s is a fine time to start trying for children. True, they could get lucky. But the question should be asked: Would you prefer to have children earlier and naturally or later, by dosing yourself up with drugs, submitting to surgery and paying tens of thousands of dollars? [. . .] The first thing I'd like to tell women ages 26 to 34 is: Start having babies. I know it's not polite or funny. But I don't want others to go through what I'm going through now." (Holly Finn; My Fertility Crisis; We hear about fertility treatments when they're successful. But for millions of women, they mean regret, heartbreak, shame and silence.)

Winston Churchill: "There is no finer investment for any community than putting milk into babies" - radio broadcast, 1943. "You must have four children. One for Mother, one for Father, one for Accidents, one for Increase".

Julian Huxley: "If we want to maintain the race, at a high level, physically and mentally, everybody sound in body and mind should marry and have enough children to perpetuate their stock and carry on the race."

Ötzi (Tyrolean Iceman) genome coming "soon"

2011-07-22T21:14:00.001+01:00

Someone at a genealogical DNA forum posts a reply received from the Institute for Mummies and the Iceman in Bolzano, Italy: "The Iceman genome will be published soon including his Y haplogroup. You may understand that we cannot release any information in advance." The information is apparently scheduled to be released 'October 20-22, 2011, at the next Bolzano Mummy Congress called "Mummies from the Ice".'

Irish DNA Atlas project launched

2011-07-22T20:59:00.000+01:00

From an article in an Irish genealogy newsletter (pdf): "Over the past decade or so genealogists around the world have become increasingly intrigued by the possibilities afforded through the advances in genetic genealogy to augment or confirm our traditional record based research. This new group project is yet another first for Irish genealogy building on the Society’s unparalleled record of innovative projects and initiatives. The Society’s Director of Archival Services, Séamus O’Reilly, FGSI, will spearhead this new group project in conjunction with Dr. Gianpiero Cavalleri of the Royal College of Surgeons in Ireland aimed at promoting an awareness, appreciation and knowledge of genetic genealogy. The project will compile an Irish DNA Atlas through the collection of birth briefs and DNA samples. [. . .]

Dr. Cavalleri explained the objective of the project as ‘seeking to create a collection of DNA samples from individuals of Irish origin, which can then be used to explore human genetic variation in the Irish population. Understanding human genetic variation in the Irish population is required for two principal purposes; (1) to further our knowledge of the population history of Ireland and (2) to help us understand how genes influence health in Ireland.’ He said that ‘the diversity of the Irish genome is a valuable, yet largely unexplored, resource of the Irish nation. As an island population on the edge of Europe, Ireland has a rich cultural heritage that is the product of ancient migrations to the region. Understanding and preserving this history enriches our culture. Whilst historical records and archaeological studies have uncovered many wonderful aspects of Irish history, there are many questions left unanswered and DNA can help address these.’

The Aims of the Irish DNA Atlas are (1) To create a DNA collection that allows genetic analysis of population structure within Ireland, and ethnic groups across the island. Analysis of such a collection will reveal ancient demographic movements and inform on the ancestry of specific regions and ethnic groups within Ireland. (2) To create a DNA collection to act as controls in population based studies of health in Ireland. The Project aims to recruit individuals representing each of the 32 counties of Ireland. Each participant should have all eight great grandparents from that county – so that their DNA represents that particular region of Ireland. By recruiting people from every county the project hopes to build a “DNA atlas” of the island of Ireland. This new group project is not confined to GSI Members, anybody can participate. For further information or to participate please contact Séamus O’Reilly on Irish.DNA@familyhistory.ie"

Svante Paabo to sequence Upper Paleolithic (early modern) Europeans

2011-07-19T04:45:00.003+01:00

Paabo collected samples of 19,000 year old bone from Iberia and intends to test the theory that Northern Europeans derive from a Last Glacial Maximum refugium in SW Europe. This Franco-Cantabrian refuge will almost certainly turn out to be a much less important (though still real) source of ancestry for Northern Europeans than was assumed a few years ago. Results should be interesting.

El padre del genoma del neandertal investiga el enterramiento del Mirón:

Svante Pääbo, prestigioso científico en el campo de la Paleogenética, ha iniciado una colaboración con el Instituto Internacional de Investigaciones Prehistóricas de la Universidad de Cantabria para estudiar el enterramiento paleolítico que se exhumó en la campaña de 2010 en la cueva del Mirón, en Ramales de la Victoria. Invitado por el catedrático de la UC Manuel González Morales y por su colega norteamericano Lawrence G. Strauss, de la Universidad de Nuevo México, directores de los trabajos en la cueva del Mirón, Pääbo ha recogido muestras y conocido de primera mano este proyecto arqueológico.

Neandertales y sapiens

-¿Qué motivo le ha traído a Cantabria?

-El descubrimiento del pasado año de un enterramiento en la cueva del Mirón, un hallazgo muy singular e interesante para nosotros ya que esto nos permitirá contar con el ADN de esqueletos del Paleolítico Superior, de los que hasta ahora no disponíamos. He visitado la excavación y se trata de un yacimiento fascinante por la larga secuencia de ocupación que presenta.

-¿Qué puede aportar este hallazgo a sus proyectos de investigación?

-Nos interesa para poder analizar qué relación tiene este individuo de tiempos de la última glaciación con la población actual europea. Estimamos que tiene 19.000 años y ahora hemos tomado muestras para obtener el ADN y contar con una datación directa del hueso. Los isótopos nos permitirán conocer, entre otros aspectos, qué régimen alimenticio tenía, si consumía más carne o plantas... [. . .]

-¿Y sus próximos retos?

-En primer lugar, completar el mapa genómico del neandertal. En segundo lugar, conocer mejor quiénes eran los contemporáneos de los neandertales en el sudeste de Asia y en China; para ello estamos trabajando con los restos aparecidos en las cuevas de Denisova, al sur de Siberia. Y en tercer lugar, estamos estudiando los humanos modernos (sapiens sapiens) que reemplazaron a los neandertales.

-¿Qué teorías manejan al respecto?

-Existe la idea entre algunos geneticistas que la población del norte de la Europa actual procede del suroeste con motivo de la última glaciación hace 20.000 años. Se refugiaron allí para protegerse del frío. En el Magdaleniense Superior (Paleolítico Superior) parece que grupos de población volvieron al norte. Trataremos de aportar luz y ver si las poblaciones actuales de países como Holanda, Bélgica, Alemania... están relacionadas con individuos como éste del Mirón, sin comparten características genéticas.

Google translation below:

The father of the Neanderthal genome is investigating the burial Miron

Svante Pääbo, a renowned scientist in the field of palaeogenetics, has initiated a collaboration with the International Institute for Prehistoric Research at the University of Cantabria to study that Paleolithic burial unearthed in the 2010 campaign in the cave of Miron Branches in Victoria. Hosted by UC professor Manuel González Morales and his American colleague Lawrence G. Strauss of the University of New Mexico, managers work in the cave of Myron, Pääbo has collected samples and learned first-hand the archaeological project.

Neanderthals and sapiens

- What reason has brought him to Cantabria?

- Last year's discovery of a burial in the cave of Myron, a very unique and interesting finding for us because this will provide us with the DNA of the Upper Palaeolithic skeletons, of which so far did not have. I visited the excavation and is a fascinating field for the long sequence of occupation introduced.

- What can this finding to their research projects?

- We want to analyze what relationship this individual time of the last glaciation to the current European population. believe that is 19,000 years and now we have taken samples for DNA and have a direct dating bone. Isotopes allow us to know, among other things, why diet had, if consumed more meat or plants ... [. . .]

- And your next challenges?

-First complete Neanderthal genome map. Second, better know who were contemporaries of the Neanderthals in Southeast Asia and China, for we are working with the remains appeared in the Denisova cave in southern Siberia. And thirdly, we are studying modern humans (sapiens sapiens) who replaced the Neanderthals .

- What theories handle this?

- There is the idea among some geneticists that the people of northern Europe today is from the southwest because of the last ice age 20,000 years ago. They took refuge there to keep warm. In the Upper Magdalenian (Upper Paleolithic) it seems that populations north again. try to shed light and see if the current populations of countries like Holland, Belgium, Germany ... relate to individuals as it's Myron without sharing genetic characteristics.

The beautiful woman in medieval Iberia: Rhetoric, cosmetics, and evolution

2011-07-18T14:57:00.001+01:00

From a 2005 Ph.D. thesis by an Italian:

Literary portraits of the beautiful woman in medieval Iberia tend to emphasize several physical features, such as long, blond hair, or light-colored and hairless skin. This study examines the specific features of the beautiful woman in several major works and genres from medieval Iberia. It also traces the rhetorical sources of these portraits to the Classical and medieval Latin traditions, whose influence is evident in other early vernacular literatures of Europe. It then analyzes several medieval cosmetic treatises in Latin and in vernacular languages that attest to medieval women's beautifying practices, such as the use of hair-dyes, depilatories, and skin-whitening creams.

The comparison of the literary and cosmetic evidence shows a canonical view of feminine beauty that encompasses different cultural areas in medieval Iberia. This view is also consistent with ancient as well as with twenty-first century conceptions of beauty. The findings suggest that the ideal of feminine beauty in medieval Iberia is not unique, but rather a manifestation of near-universal male preferences shaped by sexual selection in the course of human evolution. [. . .]

Most cosmetic treatises devote considerable space to the maintenance of well-groomed, long, and healthy hair. They also include many recipes for hair-dyes (blond and black). In Spanish literature, blond hair appears to be more typical of learned poetry and appears to be associated with nobility: "rruvios, largos cabellos / segund doncellas d’estado" (Marqués de Santillana 11-12). In the cantigas it is not mentioned, and in the Andalusian and Arabic tradition hair is black, not without exceptions (see Chapter Three).

[Claudio Da Soller. The beautiful woman in medieval Iberia: Rhetoric, cosmetics, and evolution. University of Missouri - Columbia, 2005.]

Some left response to latest Gould exposure

2011-07-18T12:28:00.000+01:00

Nature editorial urges "caution when it comes to questioning the work of scientists who are no longer with us."

This month sees the latest episode: an assault on the work of US evolutionary biologist and celebrated author Stephen Jay Gould, who died in 2002. Although the critique leaves the majority of Gould's work unscathed, it carries a special sting because it deconstructs a posthumous attack that Gould launched on nineteenth-century physician Samuel Morton. In a 1978 paper (S. J. Gould Science 200, 503–509; 1978) and in his 1981 book The Mismeasure of Man, Gould argued that Morton's measurements of the cranial capacity of hundreds of skulls from worldwide populations, reported in works published between 1839 and 1849, were unconsciously biased, by what he claimed was the physician's prejudice that caucasians were more intelligent, and therefore would have larger skulls. As Gould was canny enough to realize, a charge of unconscious bias sticks faster in science than one of fraud.

Nature editor isn't seething with indignation at the temerity of Lewis et al., or anything. He just wishes they would have published this paper while Gould was alive. Gould can't be faulted for failing to ever acknowledge or respond to a similar paper published 23 years ago -- eight years before Gould brought out a "revised" edition of Mismeasure of Man -- since that undergraduate effort was a "more modest" one:

Just as important is the readiness of the scientific community to undertake such studies, and to see them through the sometimes difficult publication process. The criticism of Gould was rejected by the journal Current Anthropology, and spent eight months in the review process at PLoS Biology. And although an undergraduate did publish a more modest study scrutinizing Gould in 1988, it is remarkable that it has taken more than 30 years for a research group to check Gould's claims thoroughly. Did Gould's compelling writing and admirable anti-racist motivations help to delay scrutiny of his facts? Quite possibly, and this is regrettable. Although future historians will be happy to scrutinize our most persuasive and celebrated luminaries, today's scientists should not leave the job to them.

Jonathan "reads Madison Grant angrily" Marks takes a slipperier tack:

Gould’s analysis of Morton is widely read, frequently cited, and still commonly assigned in university courses (refs.). Morton has become a canonical example of scientific misconduct...
Let’s pause right there. Who says it’s an example of misconduct at all, much less a canonical one? Gould didn’t; Gould argued that Morton fudged unconsciously. I wrote chapters on “Bogus Science” and on “Scientific Misconduct” in my book, Why I Am Not a Scientist (their Ref. 4), and didn’t mention Gould’s treatment of Morton, and I mentioned Morton himself only in passing, as a phrenologist. (Perhaps unsurprisingly , that interest of Morton’s – the scientific aspects of head bumps – doesn’t get a mention in the new paper.)

So why didn’t I cite it as a canonical example of misconduct? Two reasons: First, Gould himself didn’t think it was; and second, even Gould’s argument for unconscious fudging had been convincingly challenged in a paper published in Current Anthropology 23 years ago (their ref. 14).[. . .]

So I will take away two lessons from this. First, about Stephen Jay Gould. Gould, like everybody else in science, tended to see what he was looking for. That’s a good science studies lesson. Second, about this paper. For the most part, it is paranoid positivist rhetoric mixed with slovenly-argued bombast, and a warmed-over critique of Gould, not a significant new contribution to knowledge. If it were, it might have been publishable in a real journal, like Current Anthropology.

So we have: (1) Gould never accused Morton of "misconduct" (2) no one ever took seriously as an example of bias in science Gould's wholly self-invented fantasy of Morton unconsciously mismeasuring "threateningly large black skulls" (3) everyone knows this aspect of Gould's work was already "convincingly challenged" by the 1988 paper (4) Gould was biased but that just proves Gould was right.

At least we know Marks and Nature editor didn't coordinate their responses.

Of course, the fact that people like Gould frequently seem incapable of or uninterested in scientific objectivity hardly constitutes a convincing argument that people like Morton are similarly handicapped.

Some links

2011-07-18T10:29:00.001+01:00

Ahnenkult: An Uyghur redhead

Peter Frost: Big Other? "It is even doubtful whether the east-west flow of ideas explains the rise of the European world to global dominance between 1500 and 1900—the main theme of Diamond’s book. This rise to dominance was fueled by a technological revolution that occurred largely in northwestern Europe [. . .] Europe took off economically and geopolitically only when it developed its own intellectual resources."

John Hawks: Where did Neanderancestors live? "I discussed this exact issue with David Reich last week. There is no strong fossil argument for an African ancestor at that time, Europe and West Asia are anatomically and archaeologically just as plausible. My inclination is to suspect Africa because of the deep genetic variation still retained in that population, but that variation could have been retained in other ways -- particularly since every scenario of human origins now must involve population mixture." Apparently continuing a twitter conversation: "With Ngandong date change last week, no H. erectus fossil is late enough to be part of a Denisovan population. [. . .] The hinge point in paleoanthropology right now is the European Middle Pleistocene. Neandergenes don't fit fossil record. That is, Neandergene analysis seems to rule out substantial Neandertal ancestry from Atapuerca et al. Instead, Neandergenes appear to derive from Africa after 250-400 kya. Is Atapuerca/Petralona/Arago a dead end? Or can we find a model that fits data and allows some substantially deeper Neandertal local ancestry? And while we're at it, can we get any Denisovan ancestry to be consistent with Asian Homo erectus? The Denisovan genome analysis seems to rule out any substantial mixture with Neandertals... ...but Okladnikov is literally 3 days' walk. There's simply no biogeographic barrier. The populations need not have been here at same time, but if not where were they? If we can't resolve the European Mid Pleistocene problem, fossils may never help with Denisovan problem."

Arthur R. Jensen and Frank Miele: Ratio Scale Measurement of Mental Processes by Means of Mental Chronometry (mp4 video)

Why is Google keeping a list of Jewish names? Anti-semitism, no doubt.

Tribe on Papua New Guinea meets white man for the first time

Light-skinned black women rated more attractive

2011-06-02T02:56:00.001+01:00

Shocking, perhaps, but here are interviewer ratings of black womens' attractiveness vs. skin color from wave 3 of Add health:

Variables:
Row H3IR1 S35Q1 PHYSICAL ATTRACTIVENESS OF R-W3
Column H3IR17 S35Q17 RESPONDENT SKIN COLOR-W3
Control BIO_SEX3 BIOLOGICAL SEX-W3
Filter H3OD4B(1) S1Q4B RACE-BLACK/AFRICAN AM-W3(=Marked)

Please make no unkind inferences concerning a possible relationship between degree of European admixture and attractiveness. The obvious conclusion is Kanazawa's critics were right: biased raters downgrade the beauty of African American women owing to their racism and brainwashed adherence to Eurocentric beauty standards. This insidious form of racism apparently extends to more literal sexual marketplaces:

Gwen and Alicia were especially coveted because of their skin color. In a rigid hierarchy that clinical psychologist Melissa Farley—founder of Prostitution Research & Education, a San Francisco–based think tank—calls “eroticized racism,” the “snow bunnies” (white girls) outclass the “ducks” (black girls). “Maybe one out of 50 callers would request a black or Latina,” says Caroline. “Most asked for ‘the girl next door’—a blonde, thin teenager with big breasts. That’s candy to ants.” [Sex Trafficking of Americans: The Girls Next Door]

I'll sheepishly admit I'm a longtime regular at strip clubs. I'll often get black strippers with slightly desperate looks on their faces sitting at my table trying really hard to be friendly to me hoping they can sell me a lap dance. Meanwhile the blonde strippers in the club don't even have to approach anyone; the male customers swarm the stage when they get up to dance. In a strip club it's kind of obvious who men find the most attractive. I admit this is not a scientific study, just my personal observation. [A comment at Mangan's]

Note: Kanazawa's methods may well be flawed. I personally wouldn't be comfortable drawing the conclusion he did based on the data he did. I actually expect racial differences (or similarities) in average rated physical attractiveness have little to do with actual sexual attraction/behavior. To the extent that ratings of physical attractiveness reflect subconscious judgments of youth, health, symmetry, and so on, we should be able to meaningfully rank attractiveness across races; but this does not make even an "attractive" black woman an ideal or preferred sexual partner for a normal white man. Sorry Severn (commenter at Mangan's who is flipping out about Kanazawa's "bad science" and who coincidentally says he has dated black women).

Neolithic Y DNA from Southwestern France

2011-05-31T23:00:00.001+01:00

A post by Dienekes brings to my attention a paper in PNAS, "Ancient DNA reveals male diffusion through the Neolithic Mediterranean route":

The Neolithic is a key period in the history of the European settlement. Although archaeological and present-day genetic data suggest several hypotheses regarding the human migration patterns at this period, validation of these hypotheses with the use of ancient genetic data has been limited. In this context, we studied DNA extracted from 53 individuals buried in a necropolis used by a French local community 5,000 y ago. The relatively good DNA preservation of the samples allowed us to obtain autosomal, Y-chromosomal, and/or mtDNA data for 29 of the 53 samples studied. From these datasets, we established close parental relationships within the necropolis and determined maternal and paternal lineages as well as the absence of an allele associated with lactase persistence, probably carried by Neolithic cultures of central Europe. Our study provides an integrative view of the genetic past in southern France at the end of the Neolithic period. Furthermore, the Y-haplotype lineages characterized and the study of their current repartition in European populations confirm a greater influence of the Mediterranean than the Central European route in the peopling of southern Europe during the Neolithic transition.

Note: contra the authors' assertion, lactase persistence was probably not carried by Neolithic central Europeans; the most common European LP-associated allele has been absent in all central European Neolithic samples tested to date.

Dienekes writes:

R-M269 which, because of its apparent young Y-STR age has been tied by some to either the Mediterranean or Central European Neolithic is conspicuous absently from both at the moment. It may yet surface in a Neolithic context, but its absence this late from a region where, today, it is abundant only adds to its mystery.

In fact, the amateur estimates using actual mutation rates put the spread of R1b into Western Europe clearly post-Neolithic.

R1b and LP in Western Europe are in all likelihood associated with the dispersal of Indo-European languages.

These findings add to ancient DNA evidence indicating large-scale post-Neolithic population replacement in Europe. Coon and other traditional physical anthropologists, it turns out, probably had a better handle on European prehistory 70 years ago than population geneticists did five years ago.

DNA tests show Ingmar Bergman not his mother's biological child

2011-05-28T02:12:00.000+01:00

Who was the mother of Ingmar Bergman?

The mystery is even greater given that Karin Bergman, who kept extensive diaries, recording both events and thoughts, was by all accounts unaware that Ingmar was not the child to whom she gave birth July 14,1918 but a surrogate child. [. . .]

The analysis, which reached her April 12, 2011, established with certainty that Ingmar Bergman was not the son of Karin Bergman, supporting Tillberg’s hypothesis about her own family. It is not yet certain who Bergman’s mother was, but a great deal of circumstantial evidence suggests that it was Tillberg’s grandmother, Hedvig Sjöberg (later Tillberg), who in July 1918 gave birth to a son in Stockholm who was immediately given up for adoption.

Racial differences in genetic load?

2011-05-18T19:51:00.001+01:00

Another point of confusion in Kanazawa's deleted post:

There are many biological and genetic differences between the races. However, such race differences usually exist in equal measure for both men and women. For example, because they have existed much longer in human evolutionary history, Africans have more mutations in their genomes than other races. And the mutation loads significantly decrease physical attractiveness (because physical attractiveness is a measure of genetic and developmental health). But since both black women and black men have higher mutation loads, it cannot explain why only black women are less physically attractive, while black men are, if anything, more attractive.

Actually, the ancestors of present-day non-Africans existed for the same amount of time as the ancestors of present-day Africans. Any racial differences in the number of deleterious variants per genome would need to be explained in terms of population differences in mutation rate, or strength of purifying selection, or some other relevant population genetics parameter.

A few years ago, an academic geneticist affirmative-action beneficiary made the opposite claim: that due to a population bottleneck, Europeans harbor more deleterious variation than Africans. John Hawks pointed out the impossibility of that study's conclusion around the time it was published:

What is amazing to me is that these same geneticists embrace hypotheses of population history that cannot possibly have happened. The other geneticists quoted in the article, Carlos Bustamante and his graduate student Kirk Lohmueller, wrote a paper earlier this spring arguing that deleterious mutations have reached high frequency in Europeans (moreso than Africans) because of a bottleneck during European history. The press reported this work as "Whites genetically weaker than blacks, study finds." The hypothesis in the paper is that protein-coding sites otherwise conserved in most mammals may differ among humans because of relaxed selection in a bottleneck.

Here's why they're wrong: their bottleneck is impossible. They propose that the European population was a small, isolated population of 5,700 effective individuals from 214,000 years ago up to the Last Glacial Maximum. I suppose I should take some encouragement that they believe Neandertals were European ancestors (because otherwise, where exactly would this small, isolated population of Europeans have lived). But it's still quite impossible -- it implies no gene flow between Africans and Europeans across that entire span. You see, that is the only way that genetic drift can lead to this kind of result -- large differences in frequencies between continents for hundreds of deleterious alleles. It takes a bottleneck of exceptional length, along with complete isolation.

In what has become a troubling trend, these details were hidden away in the online supplementary information of the paper.

Empirically, there seem to be no major racial differences in genetic load. Compared to whites, blacks have much higher rates of spontaneous abortion and infant mortality -- superficially consistent with higher genetic load among blacks -- and an early attempt in Brazil to assess racial differences in genetic load by examining the effects of inbreeding did conclude that blacks have more lethal equivalents. However, a subsequent Brazilian study, with better controls, found no racial differences in inbreeding load:

A new investigation using sib and cousin controls, made in the same Brazilian area where whites and nonwhites (mulattoes and Negroes) had before shown inbreeding loads of different magnitudes, failed to support these findings. Our present data show that the number of lethons is the same in both ethnic groups. A review of all investigations on Brazilian whites and nonwhites suggests that the number of lethons may be accepted as roughly 2 in both ethnic groups.

The total number of heterozygous deleterious genes carried per person in this population was estimated to be 8.71 +/- 3.92 (SD), which is not too different from estimates for several other racial groups.

Black women rated less physically attractive than other women; white men rated better looking than black men

2011-05-18T17:34:00.002+01:00

Via the isteve comments section, I learn of a now-deleted Psychology Today blog entry by Satoshi Kanazawa, headlined "Why Are Black Women Rated Less Physically Attractive Than Other Women, But Black Men Are Rated Better Looking Than Other Men?" Prissy, terrier-faced "science" blogger / wannabe PC enforcer PZ Myers helpfully includes a link to a pdf copy of the post. (PC's own reaction includes this amazing bit: "Good grief…shades of Francis Galton! For those of you who don't know, creepy old man Galton ogled women and judged them for looks[!].")

Kanazawa explains:

The physical attractiveness of each Add Health respondent is [rated] three times by three different interviewers over seven years.

From these three scores, I can compute the latent "physical attractiveness factor" by a statistical procedure called factor analysis. Factor analysis has the added advantage of eliminating all random measurement errors that are inherent in any scientific measurement. The latent physical attractiveness factor has a mean of 0 and a standard deviation of 1.

Kanazawa finds that black women are "far less attractive than white, Asian, and Native American women", while "races do not differ in physical attractiveness among men, as the following graph shows". In fact, the second graph clearly shows that white men have higher "mean latent physical attractiveness" scores than black men, and that the difference is statistically significant. Kanazawa goes on to write:

Black women are still less physically attractive than nonblack women net of BMI and intelligence. Net of intelligence, black men are significantly more physically attractive than nonblack men.

Inconveniently for black men and Kanazawa, the real world does not control for intelligence. Further, if the association between intelligence and physical attractiveness rests on some underlying "good genes" factor, it makes little sense to try to "control" for intelligence when comparing races. The intelligence and attractiveness of someone with average genes for his race are what they are.

23andMe sale Monday April 11

2011-04-10T22:32:00.001+01:00

Details here.

RE this blog: Busy right now, but more real posts coming eventually.

What are the genomic drivers of the rapid evolution of PRDM9?

2011-03-31T09:49:00.000+01:00

Ponting CP. What are the genomic drivers of the rapid evolution of PRDM9? Trends Genet. 2011 Mar 7. [Epub ahead of print] [abstract]

Mammalian Prdm9 has been proposed to be a key determinant of the positioning of chromosome double-strand breaks during meiosis, a contributor to speciation processes, and the most rapidly evolving gene in human, and other animal, genomes. Prdm9 genes often exhibit substantial variation in their numbers of encoded zinc fingers (ZFs), not only between closely related species but also among individuals of a species. The near-identity of these ZF sequences appears to render them very unstable in copy number. The rare sequence differences, however, cluster within ZF sites that determine the DNA-binding specificity of PRDM9, and these substitutions are frequently positively selected. Here, possible drivers of the rapid evolution of Prdm9 are discussed, including selection for efficient pairing of homologous chromosomes or for recombination of deleterious linked alleles, and selection against depletion of recombination hotspots or against disease-associated genome rearrangement.

Similarity in Recombination Rate Estimates Highly Correlates with Genetic Differentiation in Humans

2011-03-31T09:36:00.000+01:00

Laayouni H, Montanucci L, Sikora M, Melé M, Dall'Olio GM, et al. (2011) Similarity in Recombination Rate Estimates Highly Correlates with Genetic Differentiation in Humans. PLoS ONE 6(3): e17913. doi:10.1371/journal.pone.0017913

Recombination varies greatly among species, as illustrated by the poor conservation of the recombination landscape between humans and chimpanzees. Thus, shorter evolutionary time frames are needed to understand the evolution of recombination. Here, we analyze its recent evolution in humans. We calculated the recombination rates between adjacent pairs of 636,933 common single-nucleotide polymorphism loci in 28 worldwide human populations and analyzed them in relation to genetic distances between populations. We found a strong and highly significant correlation between similarity in the recombination rates corrected for effective population size and genetic differentiation between populations. This correlation is observed at the genome-wide level, but also for each chromosome and when genetic distances and recombination similarities are calculated independently from different parts of the genome. Moreover, and more relevant, this relationship is robustly maintained when considering presence/absence of recombination hotspots. Simulations show that this correlation cannot be explained by biases in the inference of recombination rates caused by haplotype sharing among similar populations. This result indicates a rapid pace of evolution of recombination, within the time span of differentiation of modern humans. [. . .]

Taking into account only the common hotspots shared by all populations within a given continental region, the proportion of shared hotspots between continental regions is maximum between Europe and Middle East and North Africa (0.52), Europe and Central South Asia (0.44) and between Middle East and North Africa and Central South Asia (0.41). These values are, as expected, much lower when considering Sub-Saharan African or East Asian populations (Table 4). An interesting outcome from this analysis is the number of hotspots common to non African human populations compared to Sub-Saharan Africans. The proportion of hotspots shared between these two groups is only 17.4%, which is a small proportion given the recent out of Africa origin of non African population, and also show that the pace of evolution of hotspots is substantial. Figure S3 shows, as an example, patterns of recombination rates for SNPs where a hotspot event was detected in at least one population. Most variation is observed between continental groups while there is a substantial pattern sharing among populations belonging to the same continental group. [. . .]

Recombination rate appears to be a rapidly changing parameter, indicating that the underlying factors shaping the likelihood of a recombination event, such as DNA sequences controlling recombination rate variation, also change. The change is strongly detectable also in terms of presence or absence of recombination hotspots even if at the present stage it is not possible to measure the relative importance between changes in intermediate recombination rates and the appearing or disappearing of recombination hotspots. This is consistent with recent data showing that allelic variants of PRDM zinc fingers are significantly associated with variability in genome hotspots among humans [8]. The results obtained in this work contribute to the growing perception of recombination not as fixed feature of the genome of a species, but as a phenotype with ample genetic variation.

Elite Afr-Am sprinters more admixed than Afr-Am non-athletes?

2011-03-22T03:47:00.000Z

Though hardly definitive, this study certainly lends no support to the notion that black dominance of short sprints in the US can be explained purely as a consequence of West African DNA.

The purpose of this study was to compare the mtDNA haplogroup data of elite groups of Jamaican and African-American sprinters against respective controls to assess any differences in maternal lineage. The first hypervariable region of mtDNA was haplogrouped in elite Jamaican athletes (N=107) and Jamaican controls (N=293), and elite African-American athletes (N=119) and African-American controls (N=1148). Exact tests of total population differentiation were performed on total haplogroup frequencies. The frequency of non-sub-Saharan haplogroups in Jamaican athletes and Jamaican controls was similar (1.87% and 1.71%, respectively) and lower than that of African-American athletes and African-American controls (21.01% and 8.19%, respectively). There was no significant difference in total haplogroup frequencies between Jamaican athletes and Jamaican controls (P=0.551 ± 0.005); however, there was a highly significant difference between African-American athletes and African-American controls (P<0.001). The finding of statistically similar mtDNA haplogroup distributions in Jamaican athletes and Jamaican controls suggests that elite Jamaican sprinters are derived from the same source population and there is neither population stratification nor isolation for sprint performance. The significant difference between African-American sprinters and African-American controls suggests that the maternal admixture may play a role in sprint performance.
[. . .]
Among African Americans, no individual haplogroup produced significant findings for Bonferroni-adjusted critical a of 0.003, presented in Table 3. Interestingly, the nonsub- Saharan paragroup was highly significant in overrepresentation within athletes. This may indicate an advantage possessed by more admixed individuals. While maternal admixture contributing any environmental and social advantages with regard to athletic training and development cannot be ruled out, further investigation into the amount of admixture in the autosomal genome is required to assess the overall non-African genomic component. In addition to assessing differences between athletes and controls in either group, the haplogroup distributions of Jamaican controls and African-American controls were also compared. These two populations were found to have significantly different haplogroup distributions (Po0.001), providing further mitochondrial evidence of different population histories. The matrilineal distribution of both athlete populations differs significantly, suggesting no discernable distribution of lineages indicative of elite sprinting in these genetically distinct groups of West African descent.

Reference: Deason et al. Scand J Med Sci Sports. 2011 Mar 16. doi: 10.1111/j.1600-0838.2010.01289.x. [Epub ahead of print]

Ethnic background of the British Royal family

2011-03-15T14:55:00.000Z

From the website of genealogist William Addams Reitwiesner, who died last year. The Ethnic ancestry of Prince William (b. 1982):

Every so often, someone will state that the British Royal Family is "not British", that they are instead "German" or "Foreign". Since this belief seems to be somewhat wide-spread, and since the genealogy of many members of the British Royal Family is fairly well known, it seemed to me that it would be fairly easy to quantify precisely how "British" or "non-British" the British Royal Family is. This webpage shows the results of my work.

[. . .] The definition of "ethnic group" I'm using, and the working definition most people seem to use when referring to someone's ethnicity, is that all of the known and/or traceable ancestors of the person in question were part of the indigenous population in a certain geographic location, where the inhabitants shared a common language, a common culture (including a common religion), and an exclusive mating population (i.e., the members of this group would only mate with other members of the same group). The person can then be considered to be a member of that "ethnic group". [. . .]

Another place where derived values can be adjusted is in my handling of one certain ethnic group. Long study of the genealogies of the European Royals can lead one (specifically, has led me) to the realization that the European Royals can be considered a separate ethnic group. The only way they differ from other ethnic groups is that they are not geographically discrete, but in other respects they meet all the qualifications of an ethnic group: their shared rituals, their shared language(s), etc., and (most significant from a genealogical / genetic perspective) their mating habits. Until fairly recently, the only acceptable mate for a Royal, male or female, was another Royal. Royal = non-Royal matings which resulted in Royal offspring are notable primarily for their scarcity. For this reason, I have described someone whose ancestry is exclusively or primarily from this Royal caste to be of the "Royal" ethnic group.

It's possible that you, the reader, may not wish to accept my definition of the "Royal" ethnic group, and would rather describe persons of the Royal caste by using one or another of the traditional ethnic group names. Feel free to do so. Since most of the "Royal" persons referred to below lived in what is now Germany, the most convenient traditional ethnic group name to refer to them would be "German". Simply add the values I refer to as "Royal" to the values I refer to as "German" and call the result "German". I, however, will maintain the distinction in the layouts below. [. . .]

Prince William of Wales:

35.327 148 437 5 % English
29.418 945 312 5 % Royal
14.404 296 875 % Scottish
5.383 300 781 25 % German
3.747 558 593 75 % Irish
3.320 312 5 % French
3.295 898 437 5 % Anglo-Irish
2.343 75 % Hungarian
0.781 25 % Armenian
0.585 937 5 % Dutch
0.292 968 75 % Danish
0.292 968 75 % Welsh
0.158 691 906 25 % Belgian
0.146 484 375 % Swedish
0.146 484 375 % Swiss
0.122 070 312 5 % Bohemian
0.097 656 25 % Lithuanian
0.097 656 25 % Russian
0.036 621 093 75 % Jersiaise
======================
100.0 %

A few links

2011-03-09T05:35:00.001Z

The Unsilenced Science: The Racial Controversy of a Violent Gene

Viking ancestry explored on the Isle of Man by researchers

Viking's first took up settlement on the Isle of Man at the end of the 8th century.

The research team will analyse Y chromosomes which are linked with surnames and then estimate proportions of Norwegian ancestry in these samples.

Recent adverse trends in semen quality and testis cancer incidence among Finnish men

These simultaneous and rapidly occurring adverse trends suggest that the underlying causes are environmental and, as such, preventable. Our findings necessitate not only further surveillance of male reproductive health but also research to detect and remove the underlying factors.

Genetic Genealogy and the Single Segment. One minor point of disagreement. The author writes:

What this means for genealogy on 23andMe is that for two people sharing one segment identical by descent there is no way to reliably estimate how far back the common ancestor was. Furthermore, no improvement in software can possibly change that, because the limitation is imposed by the genetics itself.

For relatively sparse databases and at present levels of testing resolution, this is more or less true. However, two things could potentially change this: (1) denser databases linked to pedigree information should allow small segments in living individuals to be attributed with high confidence to particular distant ancestors in many cases; (2) high-quality complete genome sequences should provide additional resolution, potentially allowing the level of relationship represented by a small segment to be estimated with greater precision (e.g. using STR haplotypes, recent/novel SNPs, and other sorts of variation not captured by SNP microarrays).

Open thread (6)

2011-03-03T10:29:00.000Z

Links, off-topic discussion, etc. Previous open threads: 1 2 3 4 5

Craniometric data support a mosaic model of demic and cultural Neolithic diffusion to outlying regions of Europe

2011-02-24T06:53:00.002Z

Full text is free:

The extent to which the transition to agriculture in Europe was the result of biological (demic) diffusion from the Near East or the adoption of farming practices by indigenous hunter–gatherers is subject to continuing debate. Thus far, archaeological study and the analysis of modern and ancient European DNA have yielded inconclusive results regarding these hypotheses. Here we test these ideas using an extensive craniometric dataset representing 30 hunter–gatherer and farming populations. Pairwise population craniometric distance was compared with temporally controlled geographical models representing evolutionary hypotheses of biological and cultural transmission. The results show that, following the physical dispersal of Near Eastern/Anatolian farmers into central Europe, two biological lineages were established with limited gene flow between them. Farming communities spread across Europe, while hunter–gatherer communities located in outlying geographical regions adopted some cultural elements from the farmers. Therefore, the transition to farming in Europe did not involve the complete replacement of indigenous hunter–gatherer populations despite significant gene flow from the Southwest Asia. This study suggests that a mosaic process of dispersal of farmers and their ideas was operating in outlying regions of Europe, thereby reconciling previously conflicting results obtained from genetic and archaeological studies.

Jean M comments:

Their results are remarkably neat, showing two clearly distinct lineages, with comparatively little inter-mixture, confirming the picture from the archaeology of the LBK, for example, which seems to indicate that farmers and foragers kept to their own zones.

This helps to explain why the presumed Neolithic Y-DNA haplogroups G, E and J do not dominate Europe today, and decline in frequency the further one moves from the Mediterranean. The farming pioneers in Europe, though initially successful, eventually encountered problems which led to population crashes. Then after the Neolithic, Europe had two great bursts of migration, both from fringe regions where farming had been adopted by foragers. One came from the European steppe in the Copper and Bronze Ages. The other was the spread of their Germanic and Slavic descendants in the Migration Period.

Most bizarre rationale for creating racial hybrids I've yet come across

2011-02-24T06:44:00.002Z

On the second-to-last page of The $1,000 Genome, Kevin Davies recounts noticing two small children running around at the GET (Genomes, Environments, Traits) Conference:

They turned out to be [. . .] the children of Jong Bhak, the director of the Personal Genomics Institute in Korea, and his American (Caucasian) wife. They were also the youngest members of the genome sequencing club. "We wanted to know how different two siblings can be," said Bhak. "Our hybrid kids can give us some easy confirmation on that. They are brothers, but their genetic makeup will be much more different from each other than any two random people in the same population."

Nothing says "family" like "more different from each other than any two random people in the same population." In fairness, I'm not sure if Bhak is attempting to celebrate this fact, or merely acknowledging a reality that the vast majority of multiracialists no doubt fail to grasp.

Further update on People of the British Isles project

2011-02-22T07:43:00.001Z

From their most recent newsletter (pdf):

We are pleased to tell you that we have just submitted our first scientific paper about the project. The main function of this paper is to announce PoBI to the scientific world and in it we show that, even with a relatively small number of samples and a few genetic markers, the samples we collected should be sufficient to detect genetic differences across the UK. [. . .]

One aspect that is of particular interest is the surnames we collected and we have spent some time with our collaborators at UCL (Professor Paul Longley and his group) dividing them into local and non-local surnames. The figure on the left shows a couple of examples. The idea is that individuals whose surname is local to an area are more likely to have family in that area for many generations than individuals whose surnames are found all over the country. This is obviously a generalisation, but it does seem that there are some genetic differences between sets of volunteers with local surnames and sets with non-local surnames and we are really looking forward to analysing all the data rather than just the small subset we have been studying so far. [. . .]

Our next priority is to analyse the 1.3 million genetic markers that have been typed on 3,000 of our volunteers [. . .] The data we analyse from these samples should shed light on the genetic impact of the different historical incursions into Britain. It is an extremely large data set and so it will take a while to analyse and write up. As mentioned in our last newsletter, 100 of our samples are having their complete DNA sequenced by the 1,000 Genomes Project (www.1000genomes.org) and it should not be too long before that very valuable information becomes available to us. [. . .]

As you will know from the last newsletter, the Wellcome Trust has given us funding for a further five years to look for genes involved in normal traits. The main focus is on facial features, but other traits include handedness, taste perception and skin colour. We have been going back to our volunteers to collect these data. We take 3D photographs of each volunteer’s face in order to identify genes involved in the control of particular facial features. Over the last 18 months, we have collected 475 such photographs and are beginning to analyse them with our collaborators in Surrey (Professor Josef Kittler and his group).

Last newsletter (pdf):

There is a great deal of interest in the genetics of facial features and, in addition, the frequency of genetic variants for facial features may well differ significantly between different parts of the UK. We will also be collecting data on a variety of other normal features including height, hair and skin colour, handedness, milk tolerance, musical preferences and perfect pitch, taste and smell preferences and features of the hand.

Victor Mair talk on Tarim Basin Mummies

2011-02-22T00:00:00.001Z

Part of a series of lectures related to the "Secrets of the Silk Road" exhibition at the University of Pennsylvania Museum of Archaeology and Anthropology. The mummy and artifacts abruptly pulled from the exhibition by the Chinese government before it opened are back for now.

1000 Genomes Pilot Data Suggests Recent Selective Sweeps Rare in Human Lineage

2011-02-18T09:32:00.003Z

Via GenomeWeb Daily News:

"Our findings suggest that recent human adaptation has not taken place through the arrival and spread of single changes of large effect, but through shifts of frequency in many places of the genome," co-senior author Mary Przeworski, a human genetics, ecology, and evolution researcher at the University of Chicago, said in a statement. "It suggests that human adaptation, like most common human diseases, has a complex genetic architecture."

Przeworski et al. Classic Selective Sweeps Were Rare in Recent Human Evolution. Science 18 February 2011: vol. 331 no. 6019 pp. 920-924. DOI: 10.1126/science.1198878

Efforts to identify the genetic basis of human adaptations from polymorphism data have sought footprints of “classic selective sweeps” (in which a beneficial mutation arises and rapidly fixes in the population).Yet it remains unknown whether this form of natural selection was common in our evolution. We examined the evidence for classic sweeps in resequencing data from 179 human genomes. As expected under a recurrent-sweep model, we found that diversity levels decrease near exons and conserved noncoding regions. In contrast to expectation, however, the trough in diversity around human-specific amino acid substitutions is no more pronounced than around synonymous substitutions. Moreover, relative to the genome background, amino acid and putative regulatory sites are not significantly enriched in alleles that are highly differentiated between populations. These findings indicate that classic sweeps were not a dominant mode of human adaptation over the past ~250,000 years.

[. . .]

This conclusion does not imply that humans have experienced few phenotypic adaptations, or that adaptations have not shaped genomic patterns of diversity. Comparisons of diversity and divergence levels at putatively functional versus neutral sites, for example, suggest that 10 to 15% [and possibly as many as 40% (29)] of amino acid differences between humans and chimpanzees were adaptive [e.g., (30)], as were 5% of substitutions in conserved noncoding regions (22, 29) and ~20% in UTRs (22). Given the paucity of classic sweeps revealed by our findings, an excess of functional divergence would point to the importance of other modes of adaptation. One way to categorize modes of adaptation is in terms of their effect on the allele frequencies at sites that affect the beneficial phenotype. In this view, classic sweeps bring new alleles to fixation; selection on standing variation or on multiple beneficial alleles brings rare or intermediate frequency alleles to fixation; and other forms of adaptation, such as selection on polygenic traits, increase or decrease allele frequencies to a lesser extent. Such changes in allele frequencies can decrease variation at closely linked sites—to a lesser extent than in a full sweep—and might therefore contribute to a reduction in diversity near functional elements (31) as well as to excess divergence. Alternatives to classic sweeps are likely for parameters applicable to human populations (7, 32); in particular, many phenotypes of interest are quantitative and plausibly result from selection at many loci of small effect (8).

An important implication is that in the search for targets of human adaptation, a change in focus is warranted. To date, selection scans have relied almost entirely on the sweep model, either explicitly (by considering strict neutrality as the null hypothesis and a classic sweep as the alternative) or implicitly (by ranking regions by a statistic thought to be sensitive to classic sweeps and focusing on the tails of the empirical distribution). It appears that few adaptations in humans took the form that these approaches are designed to detect, such that low-hanging fruits accessible by existing approaches may be largely depleted. Conversely, the more common modes of adaptation likely remain undetected. Thus, to dissect the genetic basis of human adaptations and assess what fraction of the genome was affected by positive selection, we need new tests to detect other modes of selection, such as comparisons between closely related populations that have adapted to drastically different environments [e.g., (33)] or methods that consider loci that contribute to the same phenotype jointly [e.g., (34)]. Moreover, if alleles that contribute to recent adaptations are often polymorphic within a population, genome-wide association studies should be highly informative.

DNA USA: A Genetic Biography of America

2011-01-25T13:31:00.001Z

Apparently not due out for another year, but here's what Bryan Sykes has been working on:

The best-selling author of The Seven Daughters of Eve now turns his sights on the United States, one of the most genetically variegated countries in the world. From the blue-blooded pockets of old-WASP New England to the vast tribal lands of the Navajo, Bryan Sykes takes us on a historical genetic tour, interviewing genealogists, geneticists, anthropologists, and everyday Americans with compelling ancestral stories. His findings suggest: Of Americans whose ancestors came as slaves, virtually all have some European DNA. Racial intermixing appears least common among descendants of early New England colonists. There is clear evidence of Jewish genes among descendants of southwestern Spanish Catholics. Among white Americans, evidence of African DNA is most common in the South. European genes appeared among Native Americans as early as ten thousand years ago. An unprecedented look into America's genetic mosaic and an impressive contribution to how we perceive race, this is a fascinating book about what it means to be American.

Also of possible interest: Viking DNA: The Wirral and West Lancashire Project (Stephen Harding, Mark Jobling, Turi King); Surnames, DNA, and Family History (George Redmonds, Turi King, David Hey).

Some links

2011-01-21T19:34:00.000Z

Ahnenkult: Miscellaneous musings on the Ainu; race quotes

Hail: USA’s Total Fertility Rates by Race, 1980-2008; The Decline of Abortion

Genetic Future: On sharing genes with friends

Forward: Newer DNA Tests Uncover Hidden Jewish Bloodlines

JASON: The $100 Genome: Implication for the DoD (US Department of Defense) (pdf)

Genome Res.: Adaptive selection of an incretin gene in Eurasian populations

Haplotype structure analysis suggests that the derived allele at rs2291725 arose to dominance in East Asians ~8100 yr ago due to positive selection. The combined results suggested that rs2291725 represents a functional mutation and may contribute to the population genetics observation. Given that GIP signaling plays a critical role in homeostasis regulation at both the enteroinsular and enteroadipocyte axes, our study highlights the importance of understanding adaptations in energy-balance regulation in the face of the emerging diabetes and obesity epidemics.

PLoS ONE: Dissecting the Within-Africa Ancestry of Populations of African Descent in the Americas

MBE: The Genetic Structure of Domestic Rabbits

Patterns of genetic variation suggest a single origin of domestication in wild populations from France, supporting historical records that place rabbit domestication in French monasteries.

Am J Hum Biol.: Substantial variation in qPCR measured mean blood telomere lengths in young men from eleven European countries

Controlling for age and case-control status, telomere lengths averaged 10.20 kilobases (interpolated from qPCR measures) across study centers and ranged from 5.10 kilobases in Naples, Italy to 18.64 kilobases in Ghent, Belgium-a greater than threefold difference across populations.

La antropología física y los «zoológicos humanos»: exhibiciones de indígenas como práctica de popularización científica en el umbral del siglo XX

All along the nineteenth century different anthropological exhibitions were held in many countries, in which people from a number of indigenous communities, especially transported from their homeland for the occasion, were exhibited publicly, both for citizenship's instruction and for specialists's "in vivo" studies on human biology. This paper presents a brief description of some of these scientific shows, and tries to relate them to contemporary human biology theories.

NYT: Heavy Doses of DNA Data, With Few Side Effects

John Hawks: Genomes too cheap to meter

J Pers Soc Psychol.: To be liked versus respected: Divergent goals in interracial interactions

Pervasive representations of Blacks and Latinos as unintelligent and of Whites as racist may give rise to divergent impression management goals in interracial interactions. We present studies showing that in interracial interactions racial minorities seek to be respected and seen as competent more than Whites do, whereas Whites seek to be liked and seen as moral more than racial minorities do.

Norwegian foundation plans ancient DNA analysis of Rollo descendants

2011-01-21T18:40:00.002Z

The Explico Historical Research Foundation:

will attempt to find out if Rollo the Viking [male line ancestor of William the Conqueror] was Danish or Norwegian to settle a dispute that has been going on for centuries in Scandinavia. This we will do by retrieving DNA from corpses of his descendants.

They say they "hope to be able to perform our analysis by Easter 2011." The foundation's other projects include searching for remnants of the Celts in Turkey and Goths north of the Black Sea. More:

- Successfully conducted research on the Easter Island, proving South American origin for parts of the Easter Island population through genomic HLA typing. This research indicates strongly that some of the original Easter Island inhabitants some how migrated to the island from the east, from South America, and not only from Polynesia in the west, which has been the official story of Easter Island immigration. The research report by professor Erik Thorsby can be read here.

- On the Canary Islands contributed to the understanding of how the Canary Islands were originally settled and by whom (Pereira et al: Population expansion in the North African Late Pleistoscene signalled by mitochondrial DNA haplogroup U6. BMC Evolutionary Biology 2010 10:390). Also, DNA from a Royal Native lineage on the Canary Island La Gomera proves a connection most likely with the Basque, North Portugal or a British 'Celtic' connection.

- In Normandy, in our search for famous historical figures, closed in the lead on the patriach of William the Conqueror, the great Viking giant Rollo, in order to solve a close to thousand year old riddle about his origin. To be continued..

- In the Ukraine on Crimea and the Black Sea coast of Azov our successful 2006 expedition work is now continued in the labs, hopefully providing us with new vital knowledge on the ancient Greeks, who they were and whom today are most closely related to them.

- In the Caribbean we have worked hard on finding the DNA and especially the Y-chromosome lineage of Christopher Columbus' heritage. This work now seems to have paid off, giving us the opportunity to make new revelations about one of the worlds greatest explorers.

- Established good contact and made all preparations ready for field work in Northern Africa. We are awaiting the neccesary permissions to continue our scientific work in the Atlas Mountains.

- Continued our work in the different fields of expertise involving new technologies and our constant search for new discoveries. We are currently involved in projects in the Caribbean, the Ukraine, in Peru, Russia, Spain, France, Turkey, on Greenland and in Scandinavia. The new technologies we continue to make use of are foremost DNA and the mapping of Human Migrations and Georadar instruments for discovering treasures underground.

(Via the GENEALOGY-DNA list.)

Open thread (5)

2011-01-21T18:02:00.000Z

For links, comments, suggestions, etc. Previous open threads: 1 2 3 4

Not skin deep

2011-01-19T16:05:00.001Z

Basque communist Maju thinks this study indicates "patterns of inter-population differentiation are stronger in the genes of appearance mostly" and "the actual underlying differences between populations [. . .] are invariably much smaller than it looks".

But this is not what the paper shows at all. The single most highly population-differentiated gene group in the authors's analysis relates to pituitary gland development. Next comes dorsoventral neural tube patterning. Then some low-level cellular functions, more brain development, sperm motility and development, and thyroid gland development. Pigmentation comes about halfway down the list and hair follicle development below that.

The placement of pituitary- and thyroid-related genes near the head of the list brought to mind Carleton Coon's comments on endocrines and racial differences in temperament.

Why a dominant China could spark tribal warfare

2011-01-19T05:16:00.001Z

A commenter links to an article in Foreign Policy which argues:

With China's new prominence in global affairs, the Han race, which constitutes 90 percent of the Chinese population, is suddenly the most dominant cohesive ethnic group in the world -- and it is seeking to remain that way through strategic alliances, aggressive trade policy, and attacks on racial minorities within the country's boundaries. The less tribally cohesive, more fragmented West is, meanwhile, losing out. [. . .]

Such primitive racial instincts were supposed to be long ago passé: We're supposed to be living in Thomas Friedman's "flat" world or Kenichi Ohmae's "borderless world." By now, supposedly, everyone is increasingly interconnected and undifferentiated. Affairs should be managed neatly by deracinated professionals, working on their iPads from Brussels, Washington, or any of the other "global" capitals.

But most people do not really see themselves as members of a large multinational unit, global citizens, or "mass consumers." Instead the drivers of history remain the essentials: the desire to feed one's family, support the health of the tribe, and shape the immediate community. The particularistic continues to trump the universalistic.

On differences within Europe:

The new tribalism is also increasingly evident in Europe. Just a few years ago Europhiles like French eminence grise Jacques Attali or left-wing author Jeremy Rifkin could project a utopian future European Union that would stand both as a global role model and one of the world's great powers. Today, Rifkin's ideal of a universalistic "European dream" is collapsing -- a process accelerated by the financial crisis -- as the continent is torn apart by deep-seated historical and cultural rifts.

Europe today can best be seen as divided between three cultural tribes: Nordic-Germanic, Latin, and Slavonic. In the north, there is a vast region of prosperity, a zone of Nordic dynamism. Characterized by economies based on specialized exports, a still powerful Protestant ethic, and a culture that embraces authority, these countries -- including Scandinavia, the Netherlands, Germany, and, arguably, the Baltic states -- are becoming ever more aware of the cultural, fiscal, and attitudinal gulf between them and the southern countries.

At the same time, the attempt to build a new European identity fused with immigrants appears to be failing. As Chancellor Angela Merkel noted, Germany has failed at "multi-culturalism." Such sentiments may be reviled by the media, academics, and even business leaders in Northern Europe, but they are clearly popular at the grassroots. Once considered paragons of liberalism, countries such as Denmark and the Netherlands have incubated potent anti-immigration movements.

In a world dominated increasingly by Asia, northern Europe cannot be anything more than a peripheral global power, which may explain its new introversion. Instead these resilient cultures more accurately represent a revival of the old Hanseatic League, a network of opportunistic and prosperous trading states that ringed the North and Baltic seas during the 13th century. This new league increasingly battles over issues of trade and fiscal policy, often with ill-disguised contempt, with the southern European countries I call "the Olive Republics": a region typified by dire straits, with rapidly aging populations, enormous budget deficits, and declining industrial might. Southern Europe now constitutes a zone of lassitude that extends from Portugal and Spain through the south of France, Italy, the former Yugoslavia, Greece, and Bulgaria.

The last European tribe includes the Slavic countries, centered by Russia but extending to parts of the Balkans as well, places like Ukraine, Belarus, Serbia, and Moldova that historically have looked east as well as west and are currently defined by shrinking populations and weak democratic institutions. A historic pattern of Russian domination is evident here, based in large part on a revived Slavic identity that embraces similarities in religion, culture, history, and language with countries living under Russia's shield. In this sense the czars are back, not a great development for the rest of the world or for the fading chimera of a "common European home."

What does this resurgence of tribalism mean to the foreign policy community? Clearly more attention needs to be played to such issues as cultural vibrancy, birthrates, and economic "animal spirits." In some sense, we need to return to the perspectives of ancient writers like Herodotus and Ibn Khaldun, who attributed the rise and fall of nations to the vitality of what the latter called "group feeling."

Tribalism will also threaten the efficacy of international organizations, which tend to assume common interests between groups. Instead we have to think of future international cooperation in more traditional terms, balancing distinct sets of tribal interest. As tribes continue to pursue their own interests ever more zealously, the idealistic rhetoric of multinational organizations will become ever more risible. The way China and other developing countries snarled up the Copenhagen climate conference reflects this shift.

From here, the article degenerates as Kotkin asserts Anglo-American exceptionalism in regard to "successful" multiracialism, claiming: "It is in the melding of many into one dynamic culture that the Anglosphere may retain a powerful influence over our emerging world of tribes."

The wigger mindset

2011-01-19T04:53:00.000Z

A reader forwards a reference to this passage by Hebrew wigger / wigger expert William Upski Wimsatt. In line with my own perception of what motivates these types, Wimsatt acknowledges "romanticization of blacks was also a way to elevate myself":

Midway through grammar school I made a discovery. Michael Jackson, Prince, and most of the other rock stars I stood admiring one day in the record store display window were black. From this massive insight followed others. Practically all of the wittiest, the coolest, the strongest, the most agile, and the most precocious kids I knew were black (in part this was because most of the whites I knew were unusually dull and spoiled). In the locker room, the black boys really did seem to have bigger dicks. Although it has been proven untrue scientifically, you couldn't have told me that at the time. Next to them my voice was flat, my personality dull, my life-style bland, my complexion pallid. I didn't yet know race was the national obsession. I thought obsessing about blacks was, like masturbation, my dirty little secret.

As embarrassing as all of this was, its importance shouldn't be overlooked. The most promising thing about spilled milk is that it has ventured from its container. The most promising thing about the Cool White, the white b-boy, the wannabe (or to update Norman Mailer's term, the white nigga), is that he is defying in some way the circumstances of his birth. He harbors curiosity and admiration for a people his people have stepped on. He lives by his fascinations rather than his habits, his awkwardness rather than his cool. But it is the desire to be cool that drives him. And it is this desire--not only his guilt--that blacks must use to judo some of his power away from him.

My romanticization of blacks was also a way to elevate myself. If blacks were the superior race, then by association I too was superior. This conceit, shared by all white niggas, is founded on (what seems to us) our rare ability to mingle with blacks who other whites find inaccessible. In fact, we flatter ourselves; fitting in requires no uncommon talent. The main reason more whites don't become white niggas--instead of just white rap fans--is that getting down with blacks, like any relationship, requires that precious, ego-endangering resource: effort.

Why does head form change in children of immigrants? A reappraisal.

2011-01-17T05:15:00.000Z

Greater population differences for some functional genes

2011-01-17T04:33:00.003Z

Different level of population differentiation among human genes:

Background
During the colonization of the world, after dispersal out of African, modern humans encountered changeable environments and substantial phenotypic variations that involve diverse behaviors, lifestyles and cultures, were generated among the different modern human populations.

Results
Here, we study the level of population differentiation among different populations of human genes. Intriguingly, genes involved in osteoblast development were identified as being enriched with higher FST SNPs, a result consistent with the proposed role of the skeletal system in accounting for variation among human populations. Genes involved in the development of hair follicles, where hair is produced, were also found to have higher levels of population differentiation, consistent with hair morphology being a distinctive trait among human populations. Other genes that showed higher levels of population differentiation include those involved in pigmentation, spermatid, nervous system and organ development, and some metabolic pathways, but few involved with the immune system. Disease-related genes demonstrate excessive SNPs with lower levels of population differentiation, probably due to purifying selection. Surprisingly, we find that Mendelian-disease genes appear to have a significant excessive of SNPs with high levels of population differentiation, possibly because the incidence and susceptibility of these diseases show differences among populations. As expected, microRNA regulated genes show lower levels of population differentiation due to purifying selection.

Conclusion
Our analysis demonstrates different level of population differentiation among human populations for different gene groups.

Provisional pdf.

Blonde women earn more, have husbands who earn more

2011-01-09T01:24:00.000Z

David W. Johnston. Physical Appearance and Wages: Do Blondes Have More Fun? (Economic Letters 108, s. 10-12):

Our data source is the 1979 cohort of the National Longitudinal Survey of Youth (NLSY79). [. . .] We limit our sample to Caucasian women aged 25 and over. [. . .] Regression results indicate that blonde women receive a wage premium equivalent in size to the return for an extra year of schooling. A significant blondeness effect is also evident in the marriage market. Blonde women are no more or less likely to be married; but, their spouse's wages are around 6% higher than the wages of other spouse's.

Twenty-eleven

2011-01-09T00:53:00.002Z

I'll skip the predictions (you're welcome to post your own), and just post a bit more information on a few projects that should be announcing results this year:

(1) Otzi genome. Here's a 9 minute podcast from Life Technologies containing a few more details:
- "above 5X coverage"
- "looking at potentially medically-relevant SNPs"
- "this individual living over 5000 years ago would represent an ancestor for, we think, a significant proportion of the European population."
- "looking at his ancestry and indeed trying to determine exactly where is he from"

(2) People of the British Isles Project. A movie from the Wellcome Trust:

Most interestingly, the project is now collecting phenotypic data, including skin color, and taking 3-d facial photographs. Bodmer: "The next stage of our study, we're now taking pictures of people's faces so we can analyze components statistically [. . .] and then look for the genetic features behind that. What are the genes, what are the variations that determine facial features. Will it be possible to reconstruct from a piece of DNA what a person really looked like."

(3) 1000 Genomes Project. Another short film by the Wellcome Trust:

Chris Tyler-Smith: "[The project has] told us that natural selection has influenced virtually every part of our genome [. . .] we've now got a catalog of some thousands of genes that we think have been specifically positively selected in our fairly recent history."

Evidence for Homo erectus genes in Papuans (and Chinese)?

2010-12-22T15:01:00.007Z

Steve Sailer says he's "been alerted that there should be science news soon of a caliber comparable to the recent human-neanderthal inter-mating story." At Gene Expression, Greg Cochran calls attention to a comparison in the supplementary material of the Neanderthal genome paper showing "San closer to Han+French than to" Papuans. The San are also shown to be closer to the French than to the Chinese (and the Papuan closer to Han than French), though to a lesser degree. In addition, the San are shown to be closer to Han+French than to Yorubans, perhaps reflecting archaic admixture among West Africans; on the other hand, Yorubans are closer to non-Africans than to San.

Incidentally, this last point is in keeping with Kalinowski's assertion based on autosomal STR data. But as before I'm inclined to attribute any increased similarity between Negroids (as opposed to Bushmen) and non-Africans to back-migration from Eurasia to Africa, given that Y chromosomes likely of ultimate Eurasian origin (namely, E, and to a much lesser extent R1b, lineages) predominate among Negroids, while among Bushmen older clades predominate.

Update: A commenter passes on a link to a Google translation of a Spanish newspaper article reporting that Paabo and friends have sequenced the genome of the Denisova hominin, evidently a Homo erectus, and found evidence that genes related to the specimen persist in Melanesians. Update 2: Links are now dead (I assume the story is still supposed to be under embargo); see below for Google translation. Update 3: Much more information on this story is now available elsewhere, of course.

Describe the genome of a new hominid

An international study, led by the Max Planck Institute in Germany and involving the Universitat Pompeu Fabra (UPF) has described the genome of a new hominid, Denisova, who shared a common origin with the Neanderthals.

December 22, 1910 - Barcelona - Ep

The study "Genetic history of an archaic group homin from Denisova Cave in Siberia ', to be published in the journal' Nature ', part of the mitochondrial DNA analysis of a finger bone 30,000 years ago found in a cave in Denisova, in Southern Siberia in Russia, which contained a rare genetic sequence suggesting that it was a form of ancient hominid not yet described.

The latest analysis of the nuclear genome of the extinct hominid and morphology of a tooth from the same specimen suggests a different story. The researcher of the Institute of Evolutionary Bilogía Marquet-Bone Toms UPF studied regions of the genome structural variants that are linked to some human diseases indicate that the genome of Denisovanes is more archaic than that of other hominids, as it shares some features with the chimpanzee genome.

On this basis, the Denisovanes seem to have been a group of hominids who shared a common origin with the ancient Neanderthals, but later had a different evolution. Unlike the Neanderthals, the Denisovanes not contribute to all Eurasian genes today.

However, appear to be closely related to modern populations in Melanesia, a region of Oceania, which suggests that there was interbreeding with the antepsados of the Melanesians. In fact, the current Melanesians are between 4% and 6% of the genetic material Denisovanes extinguished. The discovery of Denisovanes south of Siberia suggests that this group occupied much of Asia during the late Pleistocene - about 50,000 years ago -.

After DNA analysis, researchers have deduced that the Denisova finger bone belonged to a girl between 6 and 7, who belonged to a group of common genetic origin with Neanderthals, while showing a different population history to this group.

The analysis of a tooth of same specimen, shows a different morphology of Neanderthals and modern humans are more like the old forms of Homo erectus and Homo habilis. Specifically, Denisova genome suggests a complex picture of genetic interactions between the ancestors of humans and other groups of hominids that lived at that time.

The computer program STRUCTURE does not reliably identify the main genetic clusters within species

2010-12-21T13:57:00.000Z

Says this guy. While the author seems to be motivated by race-denialism, I think he's probably right that "forcing STRUCTURE to place individuals into too few clusters" can lead to non-optimal results (which would be consistent with what Dienekes appears to be finding). Certainly, contra Rienzi's railing against "incompetent amateurs, with their K=15 ADMIXTURE plots and clustering with up to 124 components", there's no reason to assume that in general runs with lower K will give more meaningful or accurate results than runs with higher K using programs like STRUCTURE and admixture.

I'm not terribly interested in Kalinowski's specific attempt to prove that African farmers are genetically closer to Europeans than to African hunter gatherers, but two things: (1) if this is true, I'd say it's much more likely to be attributable to back-migrations from Eurasia than to Europeans being descended from "African farmers"; (2) I enjoyed the section of the article in which the author promotes neighbor-joining trees as a superior method for visualizing relationships between populations, only to go on to explain that "even a tree with a R2 of 0.98 does not accurately depict all of the relationships between populations" since it still "depicts all sub-Saharan African populations as being more similar to each other than to European populations."

Reference: KALINOWSKI ST (2010) The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure. Heredity (Published online). pdf

Google ngrams

2010-12-21T11:03:00.000Z

"dumb blonde"

"fair and handsome" vs. "dark and handsome"

"melting pot"

"immigrant stock"

"nation of immigrants"

Use ngrams tool here or see Science paper here.

The Denisova hominin need not be an out of Africa story

2010-12-17T08:48:00.028Z

I had a similar reaction when the original article was published, but this piece in the Journal of Human Evolution makes a much more extensive and better-argued case:

The recent retrieval of a complete mitochondrial (mt) DNA sequence from a 48–30 ka human bone from Denisova (Siberia) (Krause et al., 2010) is a remarkable achievement fully deserving international acclaim. Without wishing to detract from this feat, however, we wish to challenge their conclusion that the Denisova hominin “derives from a hominin migration out of Africa [ca. 1.0 Ma] distinct from that of the ancestors of Neanderthals and of modern humans” (Krause et al., 2010: 894). In addition, we challenge their assumption that the ancestors of the Neanderthals left Africa between 500–300 ka. In our view, alternative interpretations of the evidence are available and should be considered.

Longer excerpts below:

Did the Denisova hominin derive from “a hominin migration out of Africa [ca. 1.0 Ma] distinct from that of the ancestors of Neanderthals and of modern humans” (Krause et al., 2010: 894)?

In support of Krause et al. (2010), there is evidence of hominin dispersals from Africa after the first documented appearance of Homo erectus ca. 1.75 Ma and before 0.5 Ma. Mammalian dispersals from Africa were much easier in the Early Pleistocene than during the Middle Pleistocene (see below) [. . .]

Although hominins could therefore have dispersed from Africa ca. 1.0 Ma, as suggested by Krause et al. (2010), we also need to bear in mind both the small number of relevant African finds from the late Early Pleistocene and the virtual absence of fossil skeletal evidence from the 5,500 miles of continental Eurasia (i.e., excluding Java) between Spain and China (a gap equivalent to the distance from London to Johannesburg). In Africa, the crania from Buia (0.9 Ma) and Daka (ca. 1 Ma) are the most relevant to understanding whatever might have been happening in Asia. Neither are straightforward examples of African H. erectus; [. . .] Neither specimen has obvious counterparts in Asia. Within Eurasia, the fossil hominin evidence from Southwest Asia – the cross-roads between Africa and Europe, but also the “black hole of palaeoanthropology” (Dennell, 2009:192) – between 1.5–0.5 Ma is limited to a few incisors from ‘Ubeidiya, one of which has been identified as H. erectus (Belmaker et al., 2002). The earliest European hominin evidence is the mandible from the Sima del Elefante (ca. 1.3 Ma) (Carbonell et al., 2008) and an assemblage of >150 specimens from the Gran Dolina TD6 level, ca. 0.8–1.0 Ma ([Falguères et al., 1999] and [Berger et al., 2008]) that is attributed to Homo antecessor ([Carbonell et al., 1995], [Carbonell et al., 2008] and [Bermúdez de Castro, 1997]). Putting aside discussions about its taxonomic distinctiveness (e.g., [Lahr and Foley, 1998], [Rightmire, 2008] and [Hublin, 2009]; but also see [Bermúdez de Castro, 1997], Bermúdez de Castro, 2003 J.M. Bermúdez de Castro, M. Martinón-Torres, S. Sarmiento and M. Lozano, Gran dolina-TD6 versus Sima de los Huesos dental samples from Atapuerca: evidence of discontinuity in the European Pleistocene population?, J. Archaeol. Sci. 30 (2003), pp. 1421–1428. Article | PDF (226 K) | View Record in Scopus | Cited By in Scopus (14)[Bermúdez de Castro, 2003], [Delson et al., 2000], [Mounier et al., 2009] and [Stringer, 2009]), morphologically, the European Early Pleistocene populations currently represented by the Sierra de Atapuerca hominins are closer to Early Pleistocene hominins from Asia than those from Africa ([Carbonell et al., 2005], [Carbonell et al., 2008] and [Martinón-Torres et al., 2007]). Archaeologically, the absence of any Acheulean artefacts at Atapuerca would make a Eurasian origin more likely, as hominins dispersing from the Levant after 1.4 Ma would be expected to retain an Acheulean technology. The Chinese evidence ca. 1 Ma is limited to the cranium from Lantian (Gongwangling), for which an age of 1.15 Ma is most commonly cited (An and Ho, 1989), and the two crania from Yunxian, which probably date to 0.8–1.0 Ma. Both have previously been assigned to H. erectus (Wu and Poirier, 1995). Work in progress indicates that the Gongwangling cranium is likely significantly older than 1.15 Ma and nearer in age to that of Dmanisi, and is thus not relevant here. With a cautionary note due to the high distortion of this fossil, the Yunxian crania may show affinities with Homo heidelbergensis ([Stringer, 2002] and [Etler, 2010]; see below), may or may not be derived directly from the population represented by the Gongwangling specimen, and may not be ancestral to the better known H. erectus population at Locality 1, Zhoukoudian.

Although hominins could therefore have dispersed from Africa ca. 1.0 Ma, as suggested by Krause et al. (2010), large-scale dispersals also occurred within Eurasia in the Early Pleistocene. [. . .] Under conditions of repeated fragmentation and recombination, part of the European Early Pleistocene population’s gene pool could have developed in isolation as a separate deme and persisted in time. The mid-Middle Pleistocene dates (0.45 +0.05/−0.10 Ma) for Ceprano (Muttoni et al., 2009), tentatively assigned to H. antecessor (Manzi et al., 2001) because of its primitive morphology and lack of Neanderthal traits (see also Manzi et al., 2010), could support this scenario. Within this frame, 1.0 Ma DNA from Denisova could be another example of lineage persistence in time. Interestingly, the Yunxian evidence has recently been cited as an “ideal candidate” for the ancestor of both the Denisova hominin and H. heidelbergensis in both Europe and Africa, and thus it may also imply a large-scale dispersal westwards after 1.0 Ma (Etler, 2010). Therefore, whilst a dispersal event out of Africa may have occurred ca. 1.0 Ma, dispersal events within Eurasia seem at least as likely. As there is no ancient DNA evidence from Eurasian populations of H. antecessor, H. heidelbergensis, and East Asian H. erectus, it is thus a massive assumption that the source of the Denisova mtDNA was necessarily African.

Did H. heidelbergensis leave Africa ca. 500–300 ka?

A popular scenario is that H. heidelbergensis originated in Africa; some groups left ca. 500 ka, dispersed into Europe and possibly India (Cameron et al., 2004), and thereby introduced an Acheulean bifacial technology into these regions (e.g., Klein, 2009). [. . .] There are several reasons for expressing caution over this scenario. First, archaeologically, there is no need to postulate an immediate African origin for the Acheulean in Europe or India ca. 500 ka, as an Acheulean hand-axe and cleaver tradition with clear African affinities is evidenced at GBY, Israel, ca. 780 ka. The Levant is a far more likely starting point for the Acheulean of Europe and India after 500–600 ka than an East African one. There is also no clear evidence that later Levallois technologies in Eurasia were African in origin (contra Foley and Lahr, 1997), and not independent, indigenous developments within those areas where Acheulean bifacial technologies were used (Tuffreau, 1995). Second, the ambiguities and limitations of the Middle Pleistocene hominin record preclude firm inferences about these events. [. . .] Because the absolute dating of key specimens attributed to H. heidelbergensis or Homo rhodesiensis is still problematic, the relative dating of specimens remains unclear: obvious examples are Kabwe and Sima de los Huesos. At present, it is not even unequivocally clear that the earliest example of H. heidelbergensis (if considered as an Afro-Eurasian lineage) is African rather than European or East Asian. [. . .] As examples of the range of current interpretations on offer, one can argue either that H. heidelbergensis originated in sub-Saharan Africa and dispersed as far as China ([Stringer, 1990], [Stringer, 2002] and [Rightmire, 2001]), or that it originated in China and eventually dispersed as far as sub-Saharan Africa (Etler, 2010)! Alternatively, it has been suggested that African specimens such as Bodo, Kabwe, and Ndutu should be classified as H. rhodesiensis ([McBrearty and Brooks, 2000] and [Hublin, 2001]), and seen as distinct from H. heidelbergensis, which is thus restricted to Eurasia. Consistent with that suggestion, a SW Asian origin of H. heidelbergensis has been proposed, possibly with some traits shared with H. antecessor ([Martinón-Torres et al., 2006], [Martinón-Torres et al., 2007], [Gómez-Robles et al., 2007], [Bermúdez de Castro, 2008], [Carbonell et al., 2008] and [Dennell, 2009]). Here, we are not advocating any one of these scenarios but aim only to point out that there are several alternatives to the one presented by Krause et al. (2010). Based on the differences in the genetic diversity of H. sapiens and H. neanderthalensis (e.g., [Orlando et al., 2006], [Green et al., 2010] and [Krause et al., 2010]), future genetic studies might contribute to this debate by analysing the theoretical genetic models behind “Africa into Eurasia” and “Eurasia into Africa” scenarios.

The third line of evidence requiring interpretive caution includes faunal data, which indicate that Africa and SW Asia were probably largely isolated by the Saharan-Arabian desert barrier between 500–300 ka. [. . .]

We suggest, therefore, that the evidence that the ancestors of Neanderthals dispersed out of Africa between 500–300 ka is, contra Krause et al. (2010), equivocal on chronometric and morphological grounds, and improbable on archaeological and faunal grounds. [. . .]

Summary

As outlined above, we urge caution over both the interpretative framework of Krause et al. (2010) and their main conclusion. The evidence that the ancestors of Neanderthals (i.e., H. heidelbergensis) left Africa ca. 500–300 ka is currently inconclusive, and the origin of H. heidelbergensis remains enigmatic. Whilst dispersals out of Africa might have occurred ca. 1.0 Ma, large-scale dispersals within Asia were also probable, and thus an Asian origin of the Denisovans cannot be excluded. These issues cannot be resolved without substantial improvements in the dating of key specimens, without an enlarged Asian fossil hominin record (particularly from SW Asia), and without a much more detailed Middle Pleistocene climatic record from SW Asia and NE Africa. Although the Denisova evidence is undoubtedly a fascinating piece in the jigsaw puzzle of human origins, it would be premature at present to determine the part of the picture to which it belongs.

China spying on deCODE?

2010-12-16T10:55:00.000Z

Wikileaks: US Says Chinese Spies Operate in Iceland

Chinese authorities are believed to be spying on companies involved in genealogy and medical research in Iceland, as stated in documents sent by the US Embassy in Reykjavík to the US Foreign Service in Washington, leaked by Wikileaks.

This is stated in a report from February 26, 2009, which is marked as “confidential”. Copies of it were sent to the CIA, FBI and DIA, Fréttabladid reports.

In another report from December 24, 2009, also marked as “confidential”, an annual meeting of the US Embassy’s counter-spying group directed by the ambassador’s substitute Sam Watson is covered.

The report states that US authorities believe that their Chinese counterparts have continued with their intellectual spying in Iceland, by means of human intelligence and with technical equipment, such as bugging telephone lines and breaking into databases on the internet.

deCODE employs a Chinese national as "Vice President of Statistics", but Kari Steffanson is unconcerned on that front since the employee "has lived here for 14 years and considers Iceland his home".

Ethnic origins of Quebec regional populations estimated from genealogy

2010-12-03T03:50:00.000Z

Tables from Admixed Ancestry and Stratification of Quebec Regional Populations:

Population stratification results from unequal, nonrandom genetic contribution of ancestors and should be reflected in the underlying genealogies. In Quebec, the distribution of Mendelian diseases points to local founder effects suggesting stratification of the contemporary French Canadian gene pool. Here we characterize the population structure through the analysis of the genetic contribution of 7,798 immigrant founders identified in the genealogies of 2,221 subjects partitioned in eight regions. In all but one region, about 90% of gene pools were contributed by early French founders. In the eastern region where this contribution was 76%, we observed higher contributions of Acadians, British and American Loyalists. To detect population stratification from genealogical data, we propose an approach based on principal component analysis (PCA) of immigrant founders' genetic contributions. This analysis was compared with a multidimensional scaling of pairwise kinship coefficients. Both methods showed evidence of a distinct identity of the northeastern and eastern regions and stratification of the regional populations correlated with geographical location along the St-Lawrence River. In addition, we observed a West-East decreasing gradient of diversity. Analysis of PC-correlated founders illustrates the differential impact of early versus latter founders consistent with specific regional genetic patterns. These results highlight the importance of considering the geographic origin of samples in the design of genetic epidemiology studies conducted in Quebec. Moreover, our results demonstrate that the study of deep ascending genealogies can accurately reveal population structure. Am J Phys Anthropol, 2010. [. . .]

Time of arrival and origins of the founders

In the genealogies of the 2,221 subjects sampled, we identified a total of 7,798 immigrant founders (Table 1 and Fig. 2A). Among these founders, there were 2.6 times as many males as females (Fig. 2B), consistent with the skewed male-to-female ratio among the first settlers of Nouvelle-France (Charbonneau et al., 1993). Seventy-two percent of the immigrant founders settled during the French Regime (1608–1760) and 24% came in two major waves of immigration, the first between 1663 and 1673 and the second a hundred years later between 1755 and 1765 (Fig. 2B, Supporting Information Fig. S2 and Table S2). The first wave corresponds to the arrival of French women, the so-called ‘‘Filles du Roy’’ who were sent from France to encourage stable family-based settlement in Nouvelle-France (Charbonneau et al., 1993). The second wave coincides with the British Conquest. It included Acadians escaping deportation by the British from their original settlements in Acadia as well as French soldiers who stayed in Quebec once the war ended (Charbonneau et al., 2000).

Sixty-eight percent of the immigrant founders came from France. French founders represent the vast majority of Europeans who settled before the British Conquest (Fig. 2C - Supporting Information Table S3). Only 3% of the founders married before 1700 did not originate directly from France. The proportion of such founders increased to 35% in the period from 1700 to 1760. Acadians represent 14% of all the immigrant founders (Fig. 2C - Supporting Information Table S3). The remaining founders of known origin came from Great- Britain (4%), Germany (2%), Ireland (3%), other European countries (1%) and other American locations (besides Acadia) (4%) (Supporting Information Table S3). Amerindian origin was documented for one per cent of founders. Overall, the period of arrival and origins of the immigrant founders appearing in the genealogical ascendance of our contemporary sample well reflected those of the pioneer immigrants that settled in Quebec prior to the British Conquest (Charbonneau et al., 2000).

Partitioning of founders among regions

Not every founder contributed descendants to all regions of Quebec. One fifth of the founders (n 5 1,612; 20.7%) were common, that is, they contributed to all eight regions of Quebec (Fig. 2A). More than half of the founders (n 5 4,330; 55.5%) contributed to 2–7 regions and more than one fifth (n 5 1,856; 23.8%) were specific to only one region (Fig. 2A). All founders common to all eight regions married during the French rule and 97.2% of them before 1700. By contrast, 70% of the specific founders arrived after the installment of the British rule in 1760. We observed a negative correlation between founders’ arrival time and the number of regions where they have descendants (Pearson’s r 5 20.6, P-value \ 2.2 3 10216).

Mosaic origins of Quebec regional populations

Nearly 90% of the regional gene pools were contributed by French founders (Table 2) and 2–6% by Acadians, who are second in numerical importance. Other groups of immigrant founders each contributed 2% or less. These proportions were similar across regions except for the East where the genetic contribution of French founders was reduced (76%) to the advantage of Acadian (11%), British (3.4%), and American founders (3.5%). Despite the elevated contribution of French founders, the subjects from our sample were nearly all admixed: on average, each genealogies contained immigrant founders from 6.75 distinct origins. While virtually all genealogies (99.1%) had at least one founder originating from France (Table 3), founders of other origins also appeared in a large proportion of the genealogies: British in 93% of genealogies, Acadian in 79% and notably, Amerindian in 47%.

Differential contribution of early and late founders

[. . .] All regional populations of Quebec (except for the North of Montreal) had a minimum of a third of their gene pools descending from the earliest founders, defined as those founders who married before the first major immigration wave of 1660 (Supporting Information Table S4). These founders were mostly French, represented 9.3% of all founders (Supporting Information Table S2) and 93% of them were found in at least six out of eight regions (75% common to all regions). For the North-East and Quebec City ancestors, the contribution of the earliest founders was even higher, increasing over time up to 50% and 44%, respectively. This increase is not compatible with a simple model of population expansion (Supporting Information Fig. S5). Even if we assume that the rate of migration tends to zero, the contribution of the earliest founders is expected to stabilize and not to increase. For the North-East and Quebec City area, it suggests that the earliest founders had on average a higher number of descendants than expected under the assumption of uniform reproductive success of all founders. This points to a higher reproductive success of the earliest founders and their descendants throughout the period.

A substantial fraction of regional gene pools was also explained by founders married between 1660 and 1700 (Figs. 4A,B and Supporting Information Fig. S4). These founders represented 32% of all founders (Supporting Information Table S2), were mostly French (97%) and had a lower regional representation than the earliest founders with 74% appearing in at least six regions (40% common to all eight regions). However, the fraction of the gene pool explained by the 1660–1700 founders differed across regions as it decreased to the profit either of the earliest founders (in the Quebec City area and North- East) and/or of latecomers, arrived after 1700 (in all regions). Notably, the East region displayed the highest contribution of late founders (Supporting Information Fig. S4) who are more specific and have more diversified origins (Table 2).

New England self-perception circa 1810

2010-12-02T07:01:00.001Z

Some fairly random excerpts from Timothy Dwight's Travels in New England and New York (4 vols., 1821–1822).

Character of the inhabitants of Boston.

Dear Sir,

Having presented to you an imperfect picture of Boston, I will now attempt to exhibit the character of its Inhabitants.

The Bostonians, almost without an exception, are derived from one country and a single stock. They are all descendants of Englishmen ; and of course are united by all the great bonds of society ; language, religion, government, manners and interests. You will easily believe therefore, that they exhibit as much unity of character, as can accord with the nature of free and civilized society. With a very small number of exceptions, they speak the English language in the English manner; are protestants, hold the great principles of English liberty ; are governed voluntarily by the English common law, and by statutes, strongly resembling those of Great Britain, under a Constitution, essentially copied from the British, and by courts in almost every respect the same. Their education, also, differs very little in the school, the shop, the counting-house, or the University. Although they are Republicans, and generally Congregationalists ; they are natively, friends of good order, and firm government; and feel the reputation of Old Massachusetts in much the same manner as an Englishman feels the honour of Old England.

You will remember, that every New-Englander, with hardly an exception is taught to read, write, and keep accounts. By means of this privilege knowledge is probably more universally diffused, here, than in any other considerable town in the world. A great number of the inhabitants, also, have been liberally educated. In examining a Catalogue of the members of the University in Cambridge, a short time since, I observed that about one fourth of the whole number were natives of Boston. Persons of this character, from the state of society, mix more freely, and converse more generally than in other countries, with those of every class. Hence, also, information is more universally diffused.

On Essex County:

As Lynn is the last town in the County of Essex, lying on our road, it will not be improper here, to make some general observations concerning this County.

The County of Essex is the North-Eastern corner of Massachusetts-proper ; and is not far from forty miles long and twenty-fire broad. Its form is triangular : Salisbury being the North-Eastern, Methuen the North-Western, and Lynn the Southern, angles. On the Eastern side it is washed by the ocean. On the Western, it is bounded by the County of Middlesex, and on the Northern, by the Counties of Rockingham and Hillsborough in New-Hampshire. Essex may all be considered as an ancient settlement, and no County in Massachusetts, except Suffolk, which is composed almost wholly of Boston, is equally populous. In 1790 it contained seven thousand six hundred and forty-four dwelling-houses, ten thousand eight hundred and eighty-three families, and fifty-seven thousand nine hundred and thirteen inhabitants. There are about four hundred and fifty-three square miles in this County. [. . .]

In 1810 the whole number of inhabitants in this County was seventy-one thousand eight hundred and eighty-eight.*

Salem, Newburyport, Gloucester, Marblehead, Beverly, Havfihill and Manchester are commercial, and fishing, towns ; and contained, together, in 1800, thirty-three thousand six hundred and twenty inhabitants. To these may be added from Ipswich, Amesbury, Salisbury, Bradford, &c. enough to make the number forty thousand : a greater number, than are employed in this business in any County of the United States; if we except the cities of Philadelphia and New-York. The commerce of this County is very great: and the fish caught, and exported, by its inhabitants, are more, it is believed, than one half of all, which are exported from the Union. Its wealth is proportionally great. Of every thousand pounds, raised by a State tax, this County pays £193 13s. 7d.: almost a fifth part of the whole : and this proportion probably falls short of its wealth, compared with that of every other County, except Suffolk. The surface of this County is generally pleasant; the soil in most places pretty good ; and the agriculture creditable to the inhabitants. The farmers are, accordingly, in good thrift. No County in the United States is believed to be more friendly to literature ; and perhaps none is more distinguished for its morals.

Essex was made a County, when the Colony of Massachusettsbay was first divided.

From the preface:

In both New-England, and New-York, every man is permitted, and in some, if not all the States, is required to possess fire arms. To trust arms in the hands of the people at large has, in Europe, been believed, and so far as I am informed universally, to be an experiment, fraught only with danger. Here by a long trial it has been proved to be perfectly harmless: neither public nor private evils having ever flowed from this source, except in instances of too little moment to deserve any serious regard. If the government be equitable ; if it be reasonable in its exactions; if proper attention be paid to the education of children in knowledge, and religion, few men will be disposed to use arms, unless for their amusement, and for the defence of themselves and their country. The difficulty, here, has been to persuade the citizens to keep arms; not to prevent them from being employed for violent purposes. [. . .]

The conversion of a wilderness into a desirable residence for man is an object, which no intelligent spectator can behold without being strongly interested in such a combination of enterprise, patience, and perseverance. Few of those human efforts, which have excited the applause of mankind, have demanded equal energy, or merited equal approbation. A forest, changed within a short period into fruitful fields, covered with houses, schools, and churches, and filled with inhabitants, possessing not only the necessaries and comforts, but also the conveniences of life, and devoted to the worship of Jehovah, when seen only in prophetic vision, enraptured the mind even of Isaiah; and when realized, can hardly fail to delight that of a spectator. At least, it may compensate the want of ancient castles, ruined abbeys, and fine pictures. This is a subject, which, hitherto, has scarcely found a place in the productions of the press; and will be imperfectly comprehended by those, who have not seen the process extensively, and examined it with interest.

These considerations furnish a partial answer to the question, mentioned above. An additional reason for undertaking the pres. I work, as has already been hinted, was the injustice done to these countries by European travellers. The United States have been regarded by this class of men as fair game, to be hunted down at pleasure. Nor have travellers alone entered the chase. Other writers, particularly literary journalists, have united with them in the pursuit; and, it must be acknowledged, with sufficient keenness.

New-England has been the object of this persecution from its infancy. The spirit, which drove our ancestors to these shores, followed them across the Atlantic; and from that time to the present has endeavoured to satiate itself by calumniating both them and their descendants. Hardly an attempt has, in the mean time, been made towards their defence. Silence under such aspersions is easily construed into a confession of their truth. To resist this construction, and the injustice to which it owes its origin, is unquestionably one of the duties, incumbent on the natives of New England. [. . .]

Two fifths, therefore, of the white population of the American Republic, its only real strength, are included in the Northern States. [. . .]

The attachment felt by every man to the land, which gave him birth, and which invests it in his mind with a peculiar importance, will be rationally supposed to have enhanced these considerations in my own. If a Laplander believes the frosty region around him to have been the seat of Paradise ; and an Icelander can find a comfortable life no where, but in the dreary island in which he was born ; it cannot be thought strange that a native of New England should feel a part of the same interest in the scenes, which have accumulated so many, and so various, enjoyments around himself, and all who have been dear to him, from his earliest remembrance.

At the same time, this was a task, which no other person appeared likely to perform. I am not acquainted with a single American, who has travelled through these States for the purpose of examining, and describing them. Multitudes of my countrymen make many journeys of pleasure, as well as of business ; but, none or certainly very few, designed for this kind of investigation. What was observed to me and my companions at Provincetown, that "we were the first persons, who had ever travelled over that peninsula from motives of curiosity," might have been said with much propriety of many other parts of the countries which I have visited. Had not the object fallen incidentally in my way; this account would never have been begun.

These letters are addressed to an English gentleman. Sufficient reasons for adopting this address will, it is believed, appear from the letters themselves. I wish it, however to be understood, that they are written for my own Countrymen. From the numerous errors, published in Great Britain concerning American subjects, of the most obvious nature, and such as seem hardly to admit of mistake, it is naturally concluded, that few persons in that Island feel any wish to become acquainted with the situation of the United States, or with the real character of their inhabitants. By the government, indeed, we must, from the extent of our territory, our local circumstances, our population, and our commerce, be considered as possessing a degree of political importance; and by the merchants of Liverpool, and the manufacturers of Manchester, Birmingham, and Sheffield, we may be regarded with some attention as customers. But, except by the religious part of the British nation, we seem to be chiefly unknown, or forgotten, in the character of rational beings; or known, and remembered, almost only to be made the objects of contempt, and calumny. A book, which professes nothing more than to give a description of a country and a people, regarded in this manner, can form no claims on the attention of those, by whom the subjects of which it treats, are thus estimated. It may indeed be read, or at least reviewed, by some or other of the literary journalists of Great Britain. From these gentlemen, Americans, and their writings, have customarily met with one kind of treatment only. I neither claim, nor wish, any exemption from the common lot of my countrymen.

The remarks on several works, published by European travellers concerning the American States, particularly concerning New-England and New-York, were demanded by the nature of my design. The account, which I proposed to give, would have been incomplete, had not so many of their errors been pointed out, as to shew that reliance cannot safely be placed on their representations. Most of these errors were probably unintentional. On some I cannot put this construction.

Charges preferred against the Colonists of New-England, examined; viz. their separation from the Church of England ; their Superstition ; their Rigidness; their observance of the Sabbath with Jewish rigour; their adoption of the Municipal Law of the Jews; their resistance to the British Government; their oppression of the Aborigines.:

Dear Sir,

You will undoubtedly believe, that the censures, which I have heretofore mentioned as so extensively cast upon the early settlers of New-England, were not wholly unmerited. I admit the rationality of this conclusion, and will now proceed to make some observations concerning what I deem the faulty side of their character. This I will endeavour to do without partiality.

In their separation from the Church of England I think them justifiable ; although, for myself, I should find no difficulty in worshipping under a conscientious and Evangelical minister of that Church ; nor feel any considerable embarrassment in conducting, for a congregation, who seriously chose it, their worship according to the prescriptions of her Liturgy. It is true, I do not think this the best mode of conducting public worship. Still, I think it a good one ; and fully believe, that it has proved the means of conversion, and of distinguished moral excellence, to very great multitudes of my fellow men. I will go farther, and acknowledge cheerfully, what I really believe, that the English Church has done more than most others, to promote the cause of Christianity. I will acknowledge also, that our ancestors were more solicitous about the surplice, and the ceremonies, than their importance required; if, indeed, these were the real causes of their solicitude. Provided a minister is dressed with decency, I am perfectly willing, that he should regulate his own dress. If my neighbour chooses to worship, kneeling; whether I myself kneel or stand, I shall certainly not disturb him. Against the use of the sign of the Cross in Baptism I should certainly object; but could bave worshipped very quietly with those, who used it, if I found in them no other, or greater, errours. I could have submitted to the Ecclesiastical government of a Bishop : for I believe a Bishop to be an authorised minister of the Gospel: although I cannot find a single trace of the Prelatical character in the New Testament ; and fully believe the declaration, made in the " Institution of a Christian Man ;" (a work, approved by your King and Parliament, and the main body of your Clergy;) that " in the New Testament there is no mention made of any other degrees, but of Deacons or Ministers, and of Presbyters or Bishops." Still many of your own Prelatical Bishops have rendered such important service to Christianity, that I cannot hesitate to regard them with high respect. Generally, I should never quarrel with a LowChurch-man, on account of his principles; but should never expect to harmonize very cordially with those of a Jacobite. Had I been born under the ministry of the late Mr. Milner, of Hull; the late Mr. Walker, of Truro ; or of any one among multitudes, whom I could name in your Church; I should probably have considered myself as placed in desirable circumstances for the attainment of eternal life.

But I could not have submitted to the edicts of the first, or of the second, James. I could not have submitted to the dominion of Archbishop Laud. I could not submit to any man, requiring of me the profession of doctrines, which I did not believe ; or conformity to worship, which the Scriptures have not enjoined. The Ablutions of the Pharisees were trifles, in a great measure harmless, so long as they were regarded in the character of things, which might be conveniently done. But, when they were enjoined upon others, and were announced to be binding upon the conscience ; they became fraught with danger and mischief.

God alone is Lord of the conscience; and nothing, but what He has required, can become an Institution in the religious sense. This is a field, into which man cannot enter without intrusion. Here neither King nor Pontiff, neither Parliament nor General Council, have either rights, or powers. A religious law can be formed only by Divine Authority; and can be found only in the Scriptures. Those, who "teach for doctrines the commandments «f men," will ever worship God in vain. With these views, I should certainly have been a non-conformist. Were I now to censure your Church; my objections would principally lie against her dereliction of her articles, the relaxation of her discipline, and the legalized introduction of civil and military officers, as such, to her Eucharist. This, your King and Parliament have no right to require. To this, your Clergy cannot, so far as I see, conscientiously submit. When, therefore, you feel, hereafter, disposed to censure the early settlers of New-England for suffering none to hold public offices, beside Professors of religion; remember, that they followed, with more good sense, and incomparably more consistency with the dictates of religion, the plan, marked out by your own Government. Your Government required all its officers to partake of the Lord's Supper. These men chose their officers out of such, as could lawfully partake of this ordinance.

The settlers of New-England fled from persecution. Every Government in the Christian world claimed, at that time, the right to control the religious conduct of its subjects. This claim, it is true, finds no warrant in the Scriptures. But its legitimacy had never been questioned, and therefore never investigated. All, that was then contended for, was, that it should be exercised with justice and moderation. Our ancestors brought with them to America the very same opinions concerning this subject, which were entertained by their fellow-citizens, and by all other men of all Christian countries. As they came to New-England, and underwent all the hardships, incident to colonizing it, for the sake of enjoying their religion, unmolested; they naturally were very reluctant that others, who had borne no share of their burdens, should wantonly intrude upon this favourite object, and disturb the peace of themselves and their families. With these views, they began to exercise the claim, which I have mentioned ; and, like the people of all other countries, carried the exercise to lengths, which nothing can justify. But it ought ever to be remembered, that no other civilized nation can take up the first stone to cast against them. An Englishman, certainly, must, if he look into the Ecclesiastical annals of his own country, be forever silent on the subject. It ought also to be remembered, that they scrupulously abstained from disturbing all others; and asked nothing of others, but to be unmolested at home.

They have been accused of Superstition. In some degree, I think this accusation just. To what nation is it not applicable? Their descendants hung the witches at Salem; and for this conduct merited the severest censure. Look into the records of your own Courts; and you will be obliged, for the same reason, to fasten the same censure upon your own country. This, you will say, does not at all excuse the people of New-England. You say it justly. Still it shows, that the New-England people were as little stained with this guilt, as those, who with no little indecency exult over their faults and errours.

It ought to be here observed, that a belief in the existence, and power, of witches, although unwarranted either by reason, or Revelation, has been the universal belief of man. From causes, which I may find an opportunity to mention elsewhere, it is probably true, that no people on the globe, at the present time, give so little credit to things of this imaginary nature, as the people of this very country. Even Conjurers and Fortunetellers, who so easily fascinate the curiosity of mankind, and acquire an importance in the eye of fancy, which reasonVeprobates, are generally regarded, here, with contempt and ridicule.

Rigidness is connected, of course, with superstition; and is perhaps always attendant, also, upon a state of controversy, whether real or apprehended. Where we feel ourselves in danger of being attacked, we are apt to be on our guard against the invader. Where demands, in our apprehension unfounded and unreasonable, are either made upon us, or expected, we fortify ourselves, watchfully, against every compliance. What in other circumstances we should cheerfully yield, in these we strenuously refuse ; and, sedulously attentive to the main object, are little solicitous concerning our subordinate measures, whether reasonably or rigid, whether moderate or excessive. The Settlers of New England came to America precisely in these circumstances. They left Great Britain with a strong and habitual sense of the inequitable controversy, which for many years they had been forced to sustain. Men, who leave their country, and lose their all for the sake of their religion, must be supposed to be unbending. The contention, which drove them from home, followed them across the Atlantic ; varied, indeed, in its form, but the same in its nature ; opposed to the same principles, and threatening the same interests. Of the rectitude of these principles, generally, they had every reason to be satisfied; and of the value of these interests they had strong, and even noble, conceptions. They watched both, therefore, with an ardour, which nothing could impair, and a vigilance, which nothing could fatigue. In such circumstances no men would be remiss: and virtuous men could hardly (ail, infirm as our nature is, to be unnecessarily exact.

They have been censured for observing the Sabbath with a Jewish rigour. If this intends, that they re-enacted the Jewish penalties for the non-observance of this sacred day ; the charge is untrue. If it intends, that they regarded the day as sacred, and as required by the Universal Lawgiver to be wholly consecrated to religion, except so far as its hours are demanded for necessary and charitable employments; the charge is true, but ceases to convey a censure. In this there is nothing rigid; unless we choose to attribute rigidness to the Creator: for it is nothing more than He has required. The creed of these men was in substance the same with that of your own Church, and that of the Protestant Churches generally. By those Churches, therefore, it will not be censured. To the doctrines and duties, involved in it, they adhered, I acknowledge, with a strictness not very common. In some particulars they were unnecessarily exact: and in some others perhaps less catholic, than the most enlightened spirit of the Gospel would dictate. At the same time, a strict adherence to the commands of God, and the duties of religion, even when attended with some disagreeable peculiarities, cannot fail to receive both the respect and the applause, of every virtuous man.

The Settlers of New-England have been also censured for adopting, to a considerable extent, the municipal law of the Jews, Justice demands that they be acquitted from all intention of making the Jewish law their own permanent system of regulations. That they had no apprehension of any obligation, under which themselves, or other christians, lay to obey this law, as their own civil code, is evident from the fact, that they departed from it, immediately, to a great extent; and afterwards varied from it still farther, as their own circumstances required. They reverenced it, indeed, as christians feel themselves bound to reverence every Institution of God. At the same time, the mildness and humanity, so conspicuous in many of its regulations, recommended it strongly to their esteem and attachment. To lessen the number of human actions, of which death is made the retribution, from one hundred to fourteen must have been a delightful employment to a benevolent legislator; and any means, of sufficient authority to give effectual aid in the accomplishment of such a work, must have been welcomed with ardour. The Jewish municipal law was, without a question, designed exclusively to regulate the public concerns of that nation. Still, its great principles of equity are now found in the Statutes of every enlightened people ; and constitute the basis of all its penal regulations. Our Ancestors differed from other civilized people, with respect to this subject, more in professing their design, than in carrying it into execution. They were, perhaps, too fondly attached to the Jewish System; but should not, I think, be deeply censured for this attachment by a nation, which, for some years, has, in its penal code registered one hundred and seventy-six crimes, as objects of capital punishment.

Perhaps you will number, also, their resistance, on various occasions, to the British Government in the list of their faults. That men, who had smarted so severely under that Government in their native Country, should be jealous of its intrusions upon their happiness and safety in this, cannot be thought surprising. At the same time, they came to New-England with a full conviction, that they were subject, so far as their domestic affairs were concerned, to no external jurisdiction, beside that of the British Crown. While they lived in England ; they regarded it, with all other Englishmen, as their native, indefeasible right to be subject to no laws, except those which were made by their own Representatives. When they came to America; they believed themselves, and were often declared by the Crown, to bring with them all the rights of Englishmen; and, of course, this, which was the basis of all others. It is not strange, therefore, that they should mark every invasion of this right! with extreme jealousy, and resist it strenuously with all the means in their power. For myself, I regard this conduct as highly honourable; and cannot easily believe, that it will be censured by any genuine Briton. Where would have been the liberty of your country ; had not the same spirit steadily animated the breasts of its inhabitants ?

That some excesses attended this resistance, at times, cannot be denied. Should you feel disposed to criminate the authors of them with severity, let me request you to turn over the pages of your own history, and see whether you do not find excesses recorded there, equal in number and degree, generated by provocations of no greater magnitude, and vindicablc only on the same principles.

The last charge, which I at present remember, and which has been frequently urged against these Colonists, and, like several others, has been often reiterated on this side of the water, is their abuse of the Aborigines. This charge is derived either from ignorance or injustice. The annals of the world cannot furnish a single instance, in which a nation, or any other body politic, has treated its allies, or its subjects, either with more justice, or more humanity, than the New-England Colonists treated these people. Exclusively of the Country of the Pequods, the inhabitants of Connecticut bought, unless I am deceived, every inch of ground, contained within that Colony, of its native Proprietors. The people of Rhode-Island, Plymouth, Massachusetts, and New Hampshire, proceeded wholly in the same equitable manner. Until Philip's war in 1675, not a single foot of ground in New England was claimed, or occupied, by the Colonists on any other score, but that of fair purchase. The war with the Pequods, that with Philip, and that with the Narrhagansetts, were all merely defensive, on the part of the Colonists. The savages were the aggressors in each of them. The Colonists used every hopeful and reasonable measure to avoid them. This you will not question, if you remember, that they dreaded these wars as not improbable means of their own destruction. To the lands of these people the conquerors had the usual right of conquest; with this additional circumstance in their favour, that the original inhabitants almost entirely deserted them. Such of them, as remained, have had lands amply sufficient for their maintenance, secured to them by the laws of the Colonists, down to the present time. Nor were they only secured from intrusion and violence; but also from the purchase, to which themselves would have easily and imprudently yielded, and which would have been accomplished by unprincipled individuals. At the same time, Agents have regularly been appointed for the management of their affairs, who have usually been men of respectability, and have periodically rendered an account of their agency to the Government. These Gentlemen have, in almost all instances, treated the Indians with unimpeachable equity, and with an honourable spirit of benevolence.

The prices, paid for these lands, will necessarily seem to an European who cannot possibly realize the little value of a tract, forming a mere speck in a boundless forest, to have been wholly inadequate; and the result of fraud, and superiour skill, on the part of the purchaser. Nothing is farther from the truth. The land was literally worth no more, than the sum paid for it. Land in America may be advantageously regarded by an European, as having been at the settlement of this Country, like water in his own; valuable in itself; but too abundant to become the subject of price. The present value of lands, here, does not ordinarily exceed that of the labour, which has been employed on them.

I have now recited all the chief topics of accusation against the Colonists of New-England. You will, I think, cheerfully agree with me, that there are not many communities, of which a fair portrait would present fewer disagreeable features.

I am Sir, yours, &c.

Excellencies of the Colonists of New-England ; viz. their Enterprise and Industry —their love of Science and Learning—their love of Liberty—their Morality— their Piety.:

Dear Sir,

It can scarcely be called fair dealing, for a writer, when giving the character of a people, to recite their faults, without exhibiting at the same time their good qualities. You will permit me, therefore, to perform this part of my duty in a summary manner.

The Enterprise of the original Colonists is sufficiently conspicuous in the story, already told of their first settlement in this country; and may be much more perfectly seen in the ampler accounts of that undertaking given by Neal, Governour Hutchinson, Mr. Prince, Dr. Trumbull, Dr. Belknap, Dr. Morse, Dr. Holmes, and Tarious others. A more hardy effort, begun with more discouraging prospects, and executed with smaller means, more unruffled patience, and more immoveable perseverance, has rarely been made by man. There is no account in the annals of Colonization, in which the principal actors have left fewer memorials behind them, calculated to awaken the regret of mankind, or to call forth a blush on the faces of their descendants; or more fitted to command the admiration, and applause of both. No sober New-Englander can read the history of his country, without rejoicing, that God has caused him to spring from the loins of such Ancestors, and given him his birth in a country, whose public concerns were entrusted to their management.

The same enterprising character, justice obliges me to say, has been exhibited by their descendants, of every generation. Their efforts against the Pequods; Philip and his associates; the Narrhagansetts ; the Canadian French; the Island of Cape Breton ; and the British forces at Lexington, Breed's Hill, Stillwater, and elsewhere; were such, as any nation in similar circumstances would be proud to see written on the pages of its own history. Of them all it is an honourable characteristic, that not one was undertaken for purposes of revenge, plunder, or victory; but merely from necessity, and self-defence: a necessity, created by their adversaries ; a self-defence, on which they could with confidence ask the blessing of God. By what other people can this be said ?

A Gentleman of great respectability in the State of New-York, and of Dutch extraction too, being asked in a late critical period by a circle of his friends, what measures he would advise them to take, replied, "Go with the people of New-England. So far as I can find, God has never forsaken that country."

Were you an American; and had you with me traversed the several settlements, made by the people of New-England in its immense forests ; had you traced the hardships, and discouragements, with which these settlements were made ; had you seen the wilderness converted by them into fruitful fields; had you surveyed the numerous, cheerful, and beautiful towns and villages, which under their forming hand have sprung up in a desert; you would regard this mighty work as an unanswerable, and delightful, proof of both the Enterprise, and the Industry, of this extraordinary people.

Nor is their Enterprise less conspicuous in their commercial undertakings. The spirit of commerce was brought to this country in the ship, which wafted the first settlers of Plymouth over the Atlantic. Trade was opened by them with the Indians the first summer after their arrival. From that period to the present it has been regularly extended; so that ships from New-England have, for a considerable time, visited every commercial part of the globe. They catch whales in the Southern Atlantic, and in (.he Southern Pacific, as well as in the seas of Greenland. They carry to China seal-skins from Massafuero, sea-otters from Nootka sound, and sandal wood from the Sandwich Islands. I have seen a sloop, of no great size, which has circumnavigated the globe; and a ship, which has performed this navigation three times.

All these facts prove their Industry, no less than their Enterprise.

Their love of Science and Learning, is amply evinced by the fact, that they have established parochial schools at such near distances, as to give every child in this country, except in very recent settlements, an ample opportunity of acquiring the Knowledge of reading, writing, and Arithmetic: a work, which cost the people of Scotland the labours of a century. Yet the schools of Scotland are far less numerous, less conveniently disposed, and less liberally endowed. Grammar schools, also, they established in all their towns, containing one hundred families. A College they founded at Cambridge in 1638: about eight years after the first landing of the Massachusetts colony. Another was proposed in Connecticut; and another in New-Haven, then a distinct colony, not long after. But both were given up from an apprehension, that the whole country was barely sufficient to support one : an apprehension, undoubtedly well founded. Since that period, their descendants have founded seven others: Yale College, at NeW-Haven in Connecticut; Dartmouth College, at Hanover in New-Hampshire ; Brown College, or, University, at Providence in Rhode-Island; Williams College, at Williamstown in Massachusetts ; Bowdoin College, at Brunswick in the District of Maine ; a College at Middlebury, and another at Burlington, both in Vermont. In these seminaries there are regularly more than eight hundred students. In addition to this, they have established 3. great number of Academies ; schools of a superiour character ; where students are fitted for the Colleges, or receive an English education, of a higher cast than that, which can be obtained at the parochial schools. These things, it is presumed, cannot be said of any country, of the same wealth and population.

Their Love of Liberty will not be questioned. It ought to be observed, that they are the only people on this continent, who originally understood, and have ever since maintained, the inseparable connection between Liberty and good order; or who practically knew, that genuine freedom is found only beneath the undisturbed dominion of equitable laws.

The Morality of these people may be fairly estimated from the following facts. There have been fewer capital crimes committed in New-England since its settlement, than in any other country on the globe, (Scotland perhaps excepted,) in proportion to the number of its inhabitants. Half, or two thirds, of these inhabitants sleep, at the present time, without barring or locking their doors. Not more than five duels have been fought here, since the landing of the Plymouth Colony. During the Revolutionary War, although party-spirit rose to the highest pitch, and although New-England contained at that time about one million of people, but one man suffered death by the hand of violence, and one more, by the decision of a Court of Justice. During the last fourteen years, I have travelled not far from twelve thousand miles, chiefly in New-England and New-York; and in this extensive progress have never seen two men employed in fighting. Nor do I remember more than one instance of this nature, which fell under my own eye, during my life. That many such have happened, I cannot doubt. But, had they been frequent, they must, I think, have occurred at times, when I was present: for I have not lived in a cloister.

Of the Piety of the New-England people their accusers have furnished abundant evidence. Change the words Superstition, Fanaticism, Enthusiasm, and Bigotry, into Piety; (the thing almost invariably meant by them all;) and you will find from their enemies themselves ample testimony, that the objects of their calumny were distinguished for this superiour kind of excellence. The numerous Churches in this country, a great part of them good, and many of them handsome, buildings, are a strong illustration of the spirit of the inhabitants concerning the subject of Religion. The number of these structures already exceeds fourteen hundred; and is annually increasing. In almost every part of the country, except where the settlements are quite new, they are found at the distances of five, six and seven miles; and with their handsome spires and cupolas, almost universally white, add an exquisite beauty to the landscape, and perpetually refresh the eye of a traveller.

I have now given you both sides of this subject; and, if I mistake not, without an intention to enhance either. Having the picture before you, with its light and shade, your own taste must determine concerning the beauty, and deformity of the features.

Yours, &c.

On New Haven:

The slate of Society in this Town is, I think, remarkably happy. The inhabitants, taken together, are not inferiour to those of any town, with which I am acquainted, in intelligence, refinement, morals, or religion. Both sexes are, to a great extent, well informed ; much less ceremonious, and perhaps somewhat less polished, but not less refined, than those of the larger cities in this country. Their morals, at the same time, are of a superiour cast; and their religion much more predominant. A general spirit of good neighbourhood prevails among all classes, which nothing, hitherto, has seriously interrupted. An extensive revival of religion, within a few years past, has added not a little to the pleasures, furnished by society in New-Haven. The Churches are regularly full: and an interest is apparently felt in the concerns of religion, which cannot fail of being grateful to the mind of a good man. Rarely is a more beautiful object presented to the eye ; (I have never met with one;) than the multitudes, crossing the Green in different directions to the House of God. A general softness and civility of manners also prevails among the inhabitants of every class. Their hospitality is honourable to them ; and is not excelled in New-England, unless in some of the towns along the Eastern shore of Massachusetts.

Few places in the world present a fairer example of peace, and good order. Disturbances are unknown. Even private contentions scarcely exist. I recollect but a single instance, in which a store, and not one, in which a house, has been broken open during the fifteen years, in which I have resided in this town.* This good order of the inhabitants is the more creditable to them, as the police of the town is far from being either vigorous, or exact.

Miscellaneous links

2010-12-01T01:12:00.002Z

Polako: Locating and visualizing minority non-European admixtures across our genomes

Dienekes: Clusters galore: extremely fine-scale ancestry inference

Rienzi fumes about Dienekes' description of his own efforts as "cutting edge" and explains:

In my opinion, Dienekes and Doug McDonald and Polako should be commended for attempting to further our understanding of human genetic diversity. They are trying to broaden our understanding. Hopefully, all three gentlemen are self-aware enough to know that their "findings" are at best tentative, should be interpreted cautiously, and await confirmation in the literature.

This is not how science works. Anyone can download the software and reference data Dienekes is playing with and attempt to verify or impugn his results. Certainly some amateurs make ridiculous claims based on faulty analyses. So do some commercial entities and published academics. If you're not able to assess Dienekes' work on it's own merits, you're not in a better position to do so with comparable research merely because it has passed "peer review". One can certainly choose to ignore results generated by amateurs if one pleases, but choosing to do so has no bearing on the validity of the results.

Hail: The Blackest Surnames in the USA; The Hated Richard Nixon’s Ancestry

Another theory on the origin of blond hair:

Many traits have been investigated for their role in attractiveness, but one question has repeatedly captured the attention of researchers down the years – why do many men prefer blondes? Over time, many explanations have been put forward. It has been suggested that men prefer rounder faces and that blonde hair is kinder to the outline of the face, or that natural blondes have softer skin, which men find attractive. Another suggestion is that blondes were a genetic mutation which men evolved to value as a status symbol because of the original scarcity.

But according to research out of the University of California, the answer is that blonde hair, like the peacock's tail or the rooster's bright-red plumage, is a sign of fitness. The evolutionary reason why men are attracted to blondes is that the hair and skin colour make it easier to spot problems. Anaemia, jaundice, skin infections, cyanosis (a sign of heart disease) and some other conditions, are, these researchers say, much easier to detect in fair-skinned individuals than in brunettes.

Genetic Evidence for Multiple Biological Mechanisms Underlying In-Group Favoritism

The best-fitting model revealed that a biological mechanism facilitates affiliation with arbitrary groups and exists alongside essentialist systems that evolved to process salient cues, such as shared beliefs and ancestry.

7 Ways the Mafia Made the U.S. a Better Place

2010-11-26T08:12:00.000Z

TGGP drops a link to an article (republished by the ever-daring LewRockwell.com) by a HuffingtonPost contributor who fancies himself a purveyor of "Renegade History". Thaddeus Russell says America has Jewish and Italian gangsters to thank for:

Jazz music
Las Vegas
Hollywood
Racial mixing
"Gay liberation"

I especially enjoyed Russell's retelling of how plucky Jewish gangsters and movie makers warded off attempts by Thomas Edison's thugs to defend Edison's intellectual and physical property:

Soon after he invented the motion picture camera and projector, Thomas Edison formed his own movie production and distribution company. In 1908, Edison joined with nine other film companies to form the Motion Picture Patents Company, a monopoly that attempted to control the making, distribution, and showing of all movies in the United States. Edison and "The Trust" pledged to make only movies that promoted wholesome, Christian, and "American" values. But on the Lower East Side, a group of entrepreneurial Jewish immigrants used Edison's inventions to produce and screen their own films, which were shown in thousands of nickelodeons – five-cent movie theaters – in working-class neighborhoods all over the country. These "outlaw" filmmakers started out as vaudeville and burlesque promoters, and many of their movies were sexier, more violent, and far more entertaining than the bland fare put out by the Edison monopoly.

The great inventor was furious that "Jewish profiteers" were stealing his patent, getting rich from it, and using it to spread "smut" across America. So too were law enforcement officials. In 1907 a judge in Chicago wrote that the nickelodeons "caused, indirectly or directly, more juvenile crime coming into my court than all other causes combined." Shortly thereafter the Chicago city council passed an ordinance granting power to the chief of police to censor motion pictures played in the city. In New York in 1907, soon after the police commissioner recommended that nickel shows be wiped out entirely, Mayor George McClellan was so moved by the evidence of immoral motion pictures polluting the minds of his citizens that on Christmas Day he ordered that all of the illicit motion picture houses be shut down.

Moral condemnations and court injunctions didn't stop the proliferation of nickelodeons that showed unseemly fare and violated Edison's patent, so the inventor and his colleagues hired squads of thugs to shut them down. They seized film, beat up directors and actors, forced audiences out of theaters, smashed the nickelodeon arcades and set fire to entire city blocks where they were concentrated. But fortunately for the Jewish renegades, they lived and operated in neighborhoods where hundreds of soldiers stood ready and able to protect them – men like "Big" Jack Zelig, "Lefty Louie" Rosenberg, "Gyp the Blood" Horowitz, Joe "The Greaser" Rosenzweig, and the leaders of the notorious Yiddish Black Hand, Jacob "Johnny" Levinsky and "Charley the Cripple" Vitoffsky. There were even women ready for the fight – fierce, well-armed "gun-mols" like Bessie London, Tillie Finkelstein, Birdie Pomerantz, and Jennie "The Factory" Morris.

Cameras, projectors, film, and sound equipment disappeared from the storerooms of Edison companies and showed up on makeshift movie lots on the Lower East Side. Bullets rained down on the Trust's enforcers from the rooftops of nickelodeons. And massive fires destroyed the Edison distributors' warehouses in the Bronx, Philadelphia, and Chicago. By 1915 the Trust had disbanded and the outlaw filmmakers moved west, where they could make bigger and better movies. Who were the men who, with the help of their nicknamed friends, fought Thomas Edison and the law and won? They were Marcus Loew of Loews Theatres and Metro-Goldwyn-Mayer, Carl Laemmle of Universal Pictures, Adolph Zukor of Paramount Pictures, William Fox of Twentieth-Century Fox, and the brothers Harry, Albert, Sam, and Jack Warner.

As for racial mixing and "gay liberation":

And then there were the dance halls that became all the rage in the 1910s and 1920s. Most were owned by Jewish or Italian immigrants, many of whom were affiliated with Jewish or Italian crime syndicates. The mixing of races in the dance halls was so prevalent that the Ku Klux Klan, which reached a membership of nearly 5 million by the middle of the 1920s, devoted much of its energy to destroying them. In hundreds of towns and cities where the Klan had organizations, it conducted campaigns against dance halls, which they called "vile places of amusement." They lobbied local governments to regulate or shut down dance halls and often, when that wasn't successful, they burned them down.

Though famous for their ultra-masculinity, gangsters were nonetheless instrumental in fostering and protecting the gay subculture during the hostile years of World War II and the 1950s. Vito Genovese and Carlo Gambino, leaders of the largest and most powerful crime families in New York, began investing in gay bars in the early 1930s.

By the 1950s, most of the gay bars in New York were owned by the mob. Because of the mafia's connections with the police department and willingness to bribe officers, patrons of mob-owned bars were often protected from the police raids that dominated gay life in the 1950s. The Stonewall Inn on Christopher Street in Greenwich Village had been a straight restaurant and a straight nightclub for many years when it was purchased in 1966 by three associates of the Genovese family and converted into a gay bar.

Many of the Mafiosi who managed the Stonewall and other gay clubs were themselves gay. The Stonewall's manager was a man named Ed "The Skull" Murphy, a lifelong hood and ex-convict who chose to work as a bouncer at many of New York's first gay clubs because he found it an easy way to meet and have sex with men. Murphy was also known for his fondness for black and Latino men, which contributed to the Stonewall's reputation as the most racially diverse bar – gay or straight – in New York City.

The famous raid on the Stonewall in 1969 that gave rise to the Gay Liberation movement was actually part of a federal sting operation directed at the mob. The New York Police Department was not notified of the operation until the last minute, when it was forced by federal officers – who, unlike the city cops, were not on the mob payroll – to conduct the raid. Over the next decade, Murphy and the Genovese family funded the Gay Pride marches that became annual, international demonstrations of sexual freedom, and Murphy rode the route every year in an open-top car wearing a crown and a sash that declared him "The Mayor of Christopher Street."

23andMe sale today (24 November)

2010-11-24T01:51:00.001Z

For those who are interested, according to someone on twitter:

DIYgenomics: @23andMe $99 discount returns; code B84YAG to be live 10 AM Wednesday for the new v3 chip

The updated chip is said to be the Illumina OmniExpress Plus:

The original press release described a chip with coverage of 733,202 markers, while the enhanced "Plus" version appears to cover greater than 900,000 markers. Either way, it is a significant upgrade from the previous 580,000 SNPs.

Update: Discount code works. New chip tests 1,000,000+ SNPs.

Conferences

2010-11-16T00:25:00.000Z

PDF slides of some presentations from Family Tree DNA's "6th International Conference on Genetic Genealogy", which took place at the end of October: Family Finder: Looking Under the Hood; Family Finder & Population Finder; "Inferring Genetic Ancestry: Oppourtunities, Challenges, and Implications"; IT Roadmap 2010; Predicting Individual Ancestry Using Genome-wide Genetic Data; Summarizing and Anticipating the Next Decade with NRY, mtDNA, and Autosomal DNA; Walk Through the Y Project.

Michael Hammer (according to an attendee): "village of origin can and will be done in the future as the database grows".

The 60th Annual ASHG meeting was held November 2-6 in Washington, D.C. A 23andMe employee comments and links to other coverage (see end of post) here. Video and slides from a 1000 Genomes Project tutorial here.

According to Luke Jostins:

at Biology of Genomes conference in May of next year; we’ll be putting out a large (~1100) sample dataset from around a dozen populations. These will be based on low-coverage whole-genome and high-coverage exome data on every sample, along with >2M genotypes from the Omni2.5 chip, to create a very high-quality set of data. Lots of work is going into putting together combined SNP, indel and CNV calls as nicely phased haplotypes. This dataset should be a massive boon to association studies

This should also provide an additional public source of data for people undertaking projects like Polako's and Dienekes'.

CF mutant heterozygote advantage in heavy metal exposure

2010-11-13T09:12:00.006Z

Teeth and leg bones from Iron Age people are showing a 21st century scientific-research team that there might be an evolutionary silver lining to the gene defects that cause cystic fibrosis (CF)

DNA analysis of ancient archeological finds is revealing that some CF gene defects may protect those who carry them from lead and other metal poisoning, or perhaps tuberculosis. [. . .]

Since the protective CF gene mutation is so common among people living in or coming originally from central and Western Europe, Farrell suspects that the mutation first arose in that part of the world, very likely in early Celtic populations. [. . .]

To understand what in the environment could cause the mutated CF gene to occur in the first place, Farrell turned to ancient burial remains. Evidence from his earlier studies already showed that transgenic mice carrying the gene might be resistant to lead toxicity. He wanted to see if there were links to people living in Europe during the Iron and Bronze Ages.

“This was an era in which people were exposed to toxic heavy metals for the first time in history,” he says. [. . .]

The first analyses are showing that specimens containing CF gene defects were not affected by lead or other metal poisoning, hinting at the mutation’s protective advantage. The specimens also contained very little tuberculosis. The scientists can’t pinpoint exactly where the first CF carrier may have lived, but they think current day Austria is a good candidate.

Via Jean M. The manuscript is freely available at Nature Precedings: Discovery of the Principal Cystic Fibrosis Mutation (F508del) in Ancient DNA from Iron Age Europeans

Icelandic C1 distinct from Amerindian and Asian subclades

2010-11-13T06:40:00.000Z

A new subclade of mtDNA haplogroup C1 found in icelanders: Evidence of pre-columbian contact?

Although most mtDNA lineages observed in contemporary Icelanders can be traced to neighboring populations in the British Isles and Scandinavia, one may have a more distant origin. This lineage belongs to haplogroup C1, one of a handful that was involved in the settlement of the Americas around 14,000 years ago. Contrary to an initial assumption that this lineage was a recent arrival, preliminary genealogical analyses revealed that the C1 lineage was present in the Icelandic mtDNA pool at least 300 years ago. This raised the intriguing possibility that the Icelandic C1 lineage could be traced to Viking voyages to the Americas that commenced in the 10th century. In an attempt to shed further light on the entry date of the C1 lineage into the Icelandic mtDNA pool and its geographical origin, we used the deCODE Genetics genealogical database to identify additional matrilineal ancestors that carry the C1 lineage and then sequenced the complete mtDNA genome of 11 contemporary C1 carriers from four different matrilines. Our results indicate a latest possible arrival date in Iceland of just prior to 1700 and a likely arrival date centuries earlier. Most surprisingly, we demonstrate that the Icelandic C1 lineage does not belong to any of the four known Native American (C1b, C1c, and C1d) or Asian (C1a) subclades of haplogroup C1. Rather, it is presently the only known member of a new subclade, C1e. While a Native American origin seems most likely for C1e, an Asian or European origin cannot be ruled out. Am J Phys Anthropol, 2010.

The logic and evidence behind the authors' assertion that "a Native American origin seems most likely" is wanting; I find it much more likely C1 entered Iceland via Europe. Scientists will need to look elsewhere to explain Björk.

The 11 mutations that differentiate the Icelandic C1 sequences from the C1 root are in the upper range of mutation counts that differentiate the other C1 sequences from the root. [. . .]

A simple [polite way of saying retarded] argument in favor of a Native American origin of C1e is the fact that three of the four previously characterized C1 subclades are associated with these groups and the vast majority of C1 sequences in the literature have been sampled from individuals of Native American ancestry. [. . .]

The German sequence (Pfeiffer et al., 2001) represents a perfect match to the Icelandic C1e for the short HVS1 fragment spanning sites 16024–16365. This raises the intriguing, but perhaps unlikely, hypothesis that C1e is a European-specific subclade of C1, following the precedent of the European and Native American subclades of mtDNA haplogroup X2 (Brown et al., 1998; Reidla et al., 2003). However, given the dense sampling of mtDNA variation in European populations, it is clear that C1e is exceedingly rare, a fact that weighs against a hypothesis of antiquity in Europe.

The frequency of C1 in a sample of 1538 Icelandic mtDNA sequences was 0.26%. Coincidentally, another abstract that recently appeared in PubMed is that of a Russian publication reporting:

The role of natural selection in the evolution of human populations from Northeastern Eurasia was studied. Selection for the regions-specific haplogroup C was demonstrated.

Update on People of the British Isles project

2010-11-13T01:40:00.000Z

A reader forwarded me this message, posted to a mailing list by a third party:

One of my project members wrote to one of the organisers of the People of the British Isles Project to find out a few more details. He was told the following:

"The data will be made publicly available after we have done some analyses, and so anyone should be able to get hold of it when it is!

As for SNPs, we have had 3,000 samples typed on a large scale (about 1.2M SNPs, of which something like 2,000 are on the Y-chromosome). There are about 150 or so that are on the y-chromosome consortium tree, so hopefully we should get quite a lot of information out of the analyses!"

That should make a big difference to Population Finder and all the other admixture tests. Perhaps those of us who already know that we are of 100% British origin might then actually get some meaningful results. The Orkney Islands are not exactly a good proxy for the entire British Isles!

The website is showing a total of 4214 samples collected.

Amerindian admixture in Gaspesia (Franch Canadia)

2010-11-13T01:28:00.001Z

When Genetics and Genealogies Tell Different Stories-Maternal Lineages in Gaspesia

Data from uniparentally inherited genetic systems were used to trace evolution of human populations. Reconstruction of the past primarily relies on variation in present-day populations, limiting historical inference to lineages that are found among living subjects. Our analysis of four population groups in the Gaspé Peninsula, demonstrates how this may occasionally lead to erroneous interpretations. Mitochondrial DNA analysis of Gaspesians revealed an important admixture with Native Americans. The most likely scenario links this admixture to French-Canadians from the St. Lawrence Valley who moved to Gaspesia in the 19th century. However, in contrast to genetic data, analysis of genealogical record shows that Native American maternal lineages were brought to Gaspesia in the 18th century by Acadians who settled on the south-western coast of the peninsula. Intriguingly, within three generations, virtually all Métis Acadian families separated from their nonadmixed relatives and moved eastward mixing in with other Gaspesian groups, in which Native American maternal lines are present in relatively high frequencies. Over time, the carriers of these lines eventually lost memory of their mixed Amerindian-Acadian origin. Our results show that a reliable reconstruction of population history requires cross-verification of different data sources for consistency, thus favouring multidisciplinary approaches.

I haven't read the article, so I have no idea on what basis the authors assert DNA results specifically pointed to "French-Canadians from the St. Lawrence Valley who moved to Gaspesia in the 19th century" as the most likely source of the admixture; but I'm all in favor of integrating DNA results with genealogical records in studies of this sort.

Ancestry analysis method

2010-11-01T16:41:00.002Z

Jombart T, Devillard S, Balloux F. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet. 2010 Oct 15;11(1):94.

BACKGROUND: The dramatic progress in sequencing technologies offers unprecedented prospects for deciphering the organization of natural populations in space and time. However, the size of the datasets generated also poses some daunting challenges. In particular, Bayesian clustering algorithms based on pre-defined population genetics models such as the STRUCTURE or BAPS software may not be able to cope with this unprecedented amount of data. Thus, there is a need for less computer-intensive approaches. Multivariate analyses seem particularly appealing as they are specifically devoted to extracting information from large datasets. Unfortunately, currently available multivariate methods still lack some essential features needed to study the genetic structure of natural populations.

RESULTS: We introduce the Discriminant Analysis of Principal Components (DAPC), a multivariate method designed to identify and describe clusters of genetically related individuals. When group priors are lacking, DAPC uses sequential K-means and model selection to infer genetic clusters. Our approach allows extracting rich information from genetic data, providing assignment of individuals to groups, a visual assessment of between-population differentiation, and contribution of individual alleles to population structuring. We evaluate the performance of our method using simulated data, which were also analyzed using STRUCTURE as a benchmark. Additionally, we illustrate the method by analyzing microsatellite polymorphism in worldwide human populations and hemagglutinin gene sequence variation in seasonal influenza.

CONCLUSIONS: Analysis of simulated data revealed that our approach performs generally better than STRUCTURE at characterizing population subdivision. The tools implemented in DAPC for the identification of clusters and graphical representation of between-group structures allow to unravel complex population structures. Our approach is also faster than Bayesian clustering algorithms by several orders of magnitude, and may be applicable to a wider range of datasets.

Website: http://adegenet.r-forge.r-project.org/

Demographic simulation framework

2010-11-01T16:41:00.000Z

Ray N, Currat M, Foll M, Excoffier L. SPLATCHE2: a spatially-explicit simulation framework for complex demography, genetic admixture and recombination. Bioinformatics. 2010 Oct 17.

SUMMARY: SPLATCHE2 is a program to simulate the demography of populations and the resulting molecular diversity for a wide range of evolutionary scenarios. The spatially-explicit simulation framework can account for environmental heterogeneity and fluctuations, and it can manage multiple population sources. A coalescent-based approach is used to generate genetic markers mostly used in population genetics studies (DNA sequences, SNPs, STRs, or RFLPs). Various combinations of independent, fully or partially linked genetic markers can be produced under a recombination model based on the ancestral recombination graph. Competition between two populations (or species) can also be simulated with user-defined levels of admixture between the two populations. SPLATCHE2 may be used to generate the expected genetic diversity under complex demographic scenarios and can thus serve to test null hypotheses. For model parameter estimation, SPLATCHE2 can easily be integrated into an Approximate Bayesian Computation (ABC) framework. Availability and Implementation: SPLATCHE2 is a C++ program compiled for Windows and Linux platforms. It is freely available at www.splatche.com, together with its related documentation and example data. CONTACT: mathias.currat@unige.ch.

Masculinity, skin color, and male facial attractiveness

2010-10-29T16:34:00.002+01:00

Does Masculinity Matter? The Contribution of Masculine Face Shape to Male Attractiveness in Humans (PLoS ONE):

The proposal [. . .] that masculine men are immunocompetent and attractive – underpins a large literature on facial masculinity preferences. Recently, theoretical models have suggested that current condition may be a better index of mate value than past immunocompetence. This is particularly likely in populations where pathogenic fluctuation is fast relative to host life history. As life history is slow in humans, there is reason to expect that, among humans, condition-dependent traits might contribute more to attractiveness than relatively stable traits such as masculinity. [. . .]

The relationship between masculinity and attractiveness was assessed in two samples of male faces. Most previous research has assessed masculinity either with subjective ratings or with simple anatomical measures. Here, we used geometric morphometric techniques to assess facial masculinity, generating a morphological masculinity measure based on a discriminant function that correctly classified >96% faces as male or female. When assessed using this measure, there was no relationship between morphological masculinity and rated attractiveness. In contrast, skin colour – a fluctuating, condition-dependent cue – was a significant predictor of attractiveness.

The authors point out problems with attempts to assess the affect of masculinity on facial attractiveness that rely on human ratings of perceived masculinity or digital manipulation of photographs: (1) for rated masculinity, "subjective judgments of masculinity are based on factors other than just morphological masculinity"; (2) with morphing techniques, factors potentially more important than masculinity in determining real world attractiveness are not allowed to vary, and a preference for averageness might result in participants systematically preferring more or less masculine morphs even if women are completely indifferent to masculinity. As for the effects of skin color, in this sample:

The regression retained only skin yellowness as a predictor of attractiveness, and the effect of skin yellowness was positive and highly significant (F(1,71) = 10.806, Beta = .366, t = 3.287, p<.002). Skin lightness, redness and morphological masculinity did not significantly predict attractiveness (all p>.114, see Table 1).

Other studies have also found increased skin lightness and redness associated with perceived health and attractiveness. The association of yellowness with attractiveness "may be attributable to dietary carotenoid deposition in the skin. This suggests that carotenoids, which are involved in health signaling (Massaro et al. 2003; Saks et al. 2003) and sexual selection (Eley 1991; MacDougall and Montgomerie 2003; Massaro et al. 2003) in many species of birds and fish, may also affect the appearance of health in humans."

Race and physical attraction

2010-10-28T15:38:00.000+01:00

A commenter links to a 2007 neuropolitics.org post ("Who Are The Caucasians Attracted To? Politics, Religion, and Physical Attraction") that reports the following survey results. As expected, "white females were more attracted to whites than are white males".

Political Cohort	Sex	No Racial Pref	White	Asian	Black	Hisp anic
NP	F	37.7%	47.5%	6.6%	0.0%	4.9%
VL	F	47.2%	36.5%	3.4%	3.9%	3.4%
L	F	38.7%	46.2%	2.0%	2.0%	3.5%
LB	F	35.1%	55.4%	2.7%	1.4%	1.4%
M	F	32.5%	55.0%	2.5%	2.5%	2.5%
C	F	20.4%	68.6%	3.7%	1.5%	2.2%
VC	F	14.6%	75.0%	0.0%	2.1%	2.1%
NP	M	40.7%	35.7%	15.7%	1.4%	2.9%
VL	M	32.1%	35.8%	15.5%	1.6%	3.4%
L	M	37.8%	39.9%	12.7%	2.1%	4.5%
LB	M	29.2%	46.7%	12.2%	2.8%	4.4%
M	M	31.7%	49.5%	11.5%	1.4%	3.7%
C	M	20.5%	59.9%	10.0%	0.5%	6.2%
VC	M	17.0%	70.0%	6.7%	0.9%	4.0%

The
Races Whites are Most Attracted To
(NP=Nonpolitical,VL=Very Liberal, L=Liberal, LB=Libertarian,M=Moderate,
C=Conservative, VC=Very Conservative) (F=Female, M=Male)

Another observation: "In general, the more liberal a white male is, the more likely they will indicate they are physically attracted to Asians."

From a different article on the same page:

In 2005, we had speculated that the testosterone-estrogen ratios of Liberal males and females were closer to each other than the Conservative males and females, who were more skewed towards either the testosterone or estrogen sides of the scale, respectively. This proposal is looking more reasonable today. [. . .]

Our current evidence indicates that white Liberal males are less likely to pass on their genes than are the white Conservative males, as the Conservatives report higher rates of both pair-bonding and heterosexual sex. Further, this tendency is exacerbated among Caucasians, as the white females, on average, are more likely to mate with Conservative males than with Liberal males.

However, all is not lost for the Liberal males. Liberal females heavily apply political and religious cues in mate selection, and have a strong preference for Liberal males, and seem to be more averse to prominent androgen features in mate selection. The rise of the low-testosterone male, so instrumental in the development of science, technology, and the arts, has been highly reliant on a subpopulation of females keeping them in the mating game.

(Note: I don't believe "low-testosterone males" contributed disproportionately to science and technology. The opposite seems more likely to be true.)

Miscellaneous links

2010-10-28T15:37:00.000+01:00

Mangan on Transparency International's World Corruption Index

A One-Way Human Mission to Mars:

There are many reasons why a human colony on Mars is a desirable goal, scientifically and politically. The strategy of one-way missions brings this goal within technological and financial feasibility. Nevertheless, to attain it would require [. . .] a return to the exploration spirit and risk-taking ethos of the great period of Earth exploration, from Columbus to Amundsen, but which has nowadays being replaced with a culture of safety and political correctness.

The origin of Eastern European Jews revealed by autosomal, sex chromosomal and mtDNA polymorphisms.

The Lost Tribes of Europe ("As national borders blur, the Continent's original minorities are fighting to reclaim their ancient cultures and identities")

Steve Sailer mentions: "a video of part of the amazing 1983 documentary First Contact with footage of the arrival of Australian explorers in the highlands of New Guinea around 1930."

Cranial differentiation of eastern and western pygmies

2010-10-28T14:27:00.000+01:00

Diversity among African Pygmies (PLoS One):

Thirty three-dimensional (3D) landmarks registered with Microscribe in four cranial samples (Western and Eastern pygmies and non-pygmies) were obtained. Multivariate analysis (generalized Procrustes analysis, Mahalanobis distances, multivariate regression) and complementary dimensions of size were evaluated with ANOVA and post hoc LSD. Results suggest that important cranial shape differentiation does occur between pygmies and non-pygmies but also between Eastern and Western populations and that size changes and allometries do not affect similarly Eastern and Western pygmies. [. . .] Although not directly related to skull differentiation, the diversity among pygmies would probably suggest that the process responsible for reduced stature occurred after the split of the ancestors of modern Eastern and Western pygmies.