race/history/evolution notes

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.

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.

For those who are interested.

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 FTDNA conference. Their Twitter accounts are: @khborges, @Genealem, @Luxegen and @Greenleafy

You can also follow the hashtag #FTDNA2011 though not all the tweets are going out with the hashtag. [. . .]

FTDNA has tested over 600,000 people.

The Genographic Project has 450,000 public participation samples and 75,000 indigenous samples.

The Genographic Project has two Basque papers going into journals this week and another paper which includes mtDNA haplogroup U5 is due out next year.

And a few more twitter comments:

khborges Katherine H. Borges SW-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 Miller SW - teaser - big announcement coming in Genographic project next year. #FTDNA2011

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 liberalism is different from the degree of that commitment among other religious groups. The difference is that the Jewish devotion to liberalism is not correlated with economic or educational status. This was demonstrated almost 20 years ago by Wesley and Beverly Allinsmith.2

Toward the close of World War II, the Allinsmiths asked 8,820 members of eight religious denominations whether they believed that the most important postwar task of the U.S. Government was to provide opportunity for people to get ahead on their own or "to guarantee every person a decent and steady job and standard of living."

Nationally, 47% of the people questioned preferred security to opportunity. As the percentage of manual workers in each denomination increased, the proportion favoring security rose. Status, education and income were inversely related to the choice of security. As one proceeded from Congregationalists to Presbyterians to Episcopalians to Methodists to Lutherans to Baptists and finally to Catholics, the preference for security steadily increased from 26% to 58%.

The Jews were the only exception to this rule. Although they were a very high status group ranking first in occupational level, third in educational level and fourth in economic level, 56% of them preferred security to opportunity. This was almost as high as the Catholic preference for security.

Moreover, within each of the eight religious denominations, the preference for opportunity was greatest among those with most education, highest status and best occupational level. Again, the Jews were the only exception.

The 1944 presidential vote also revealed this marked difference between Jewish and Gentile political behavior. The upper-class and upper-middle-class Christian denominations voted heavily against Roosevelt and in favor of Republican standard-bearer Thomas Dewey. Only 31.4% of the Congregationalists, 39.9% of the Presbyterians and 44.6% of the Episcopalians backed Franklin Delano Roosevelt. The more working-class denominations, however, voted heavily for him, particularly the Catholics who were 72.8% in his favor. In terms of their combined educational, occupational and status rank in the Allinsmith survey-that of second place-the Jews might well have been expected to vote Republican. Actually, they were 92.1% for Roosevelt. This overwhelming support was greater than that of any of the Christian denominations. [. . .]

However, in the 1952 elections, despite the fact that the Republican presidential candidate, Dwight D. Eisenhower, had led the Western coalition to victory over the Nazis, 75% of the Jewish voters supported Adlai E. Stevenson, a man who had played no role of any importance in World War II. There was no difference in the attitude of the candidates toward Jewry or the state of Israel. The issue was clearly one of moderation vs. liberalism. In a situation where American voters as a whole gave decisive support to Eisenhower, three-fourths of the Jews backed his Democratic opponent. Moreover, interviews in depth of Boston voters showed that only 30% of the Gentiles with high socioeconomic status, as against 60% of those with low socioeconomic status, backed Stevenson. Among Boston Jews, 72% of those with high status voted for Stevenson.

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

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.

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 the issue of ‘‘atavism.’’ This term, rarely used today, begs the question of whether or not this double rooted form was common at one time, then disappeared, only to reappear sometime later. Swindler (1995) notes that ‘‘the deciduous and permanent canines in the majority of living primates have a single root.’’ This suggests that two-rooted lower canines are not the ancestral condition in anthropoids or hominoids. Rather, the phenotype is a derived condition, found primarily in recent human populations distributed across Western Eurasia.

The presence of the two-rooted canines in East Asia may provide some clue as to the eastward migration of new populations into China and Mongolia. The largest numbers of individuals with this trait are concentrated along the western and northern frontiers of China and Mongolia. Archaeological excavations support the large scale movement of people into this area during the Bronze age (ca. 2200 BCE–400 BCE). Burial artifacts and settlement patterns suggest cultural and technological ties to the Afanasevo culture in Siberia, which in turn is linked archaeologically, linguistically, and genetically with the Indo-European Tocharian populations that appear to have migrated to the Tarim Basin ca. 4,000 years ago (Ma and Sun, 1992; Ma and Wang, 1992; Mallory and Mair, 2000; Romgard, 2008; Keyser et al., 2009; Li et al., 2010).

The appearance of a new population on the western frontier also supports the findings of previous research in cranial metrics, dental nonmetrics, and DNA. Using cranial metrics and archaeological dating, Han (1994) hypothesized the earliest large-scale migration into western China occurred during the early Bronze age (2000 BCE) from Central Asia or southern Siberia. Dental nonmetric data also support multiple migrations into western China (Xinjiang Province) from Central Asia during the Bronze age to Iron age (Lee, 2007; Zhang, 2010). mtDNA studies on archaeological and modern population samples from Xinjiang Province show heterogeneous Asian and European genetic signatures dating from the Bronze 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 in European samples and low to nonexistent in Asians, we propose this trait was introduced into East Asia by Indo- European speaking groups or their affines crossing the western frontier of China and Mongolia. Further data are needed to clarify aspects of these population movements, including the identity of the migrants, along with the number, routes, and timing of the migrations.

Although two-rooted lower canines cannot offer the precision of DNA in evaluating the ancestry in individual skulls, this trait is a sensitive indicator of admixture wherever Europeans come in contact with Asian or African populations. As this distinctive trait can be scored with relative ease in large samples, it provides a useful supplemental tool in discerning gene flow between distantly related populations going back many millennia.

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?

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

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?

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 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.

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.

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."

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.

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:

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.

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.

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."

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.