Possible archaic African Y lineage

The paper has now been published: An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree

We report the discovery of an African American Y chromosome that carries the ancestral state of all SNPs that defined the basal portion of the Y chromosome phylogenetic tree. We sequenced ∼240 kb of this chromosome to identify private, derived mutations on this lineage, which we named A00. We then estimated the time to the most recent common ancestor (TMRCA) for the Y tree as 338 thousand years ago (kya) (95% confidence interval = 237–581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils. The extremely ancient age combined with the rarity of the A00 lineage, which we also find at very low frequency in central Africa, point to the importance of considering more complex models for the origin of Y chromosome diversity. These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans. The A00 lineage was discovered in a large database of consumer samples of African Americans and has not been identified in traditional hunter-gatherer populations from sub-Saharan Africa. This underscores how the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during the interpretation of the geographic location of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins.

Incomplete Y DNA results from two Corded Ware skeletons

The data:

The seemingly highly-confused interpretation offered by the authors:

Determining polymorphisms of SNP type from chromosome Y resulted in categorizing skeleton from grave no. 1 with very high probability into haplogroup G, whereas skeleton from grave no. 2 with very high probability into one of three haplogroups J, I or E*. Detailed results of determinations are included in the attached table 2. On the basis of the above mentioned expertise one can state that the skeletons are male individuals with no relationship between each other. [. . .]

An analysis of polymorphism of single nucleotide (SNP) of chromosome Y from genetic material derived from both burials has brought in different results than in the case of so far analyzed aDNA materials of burials of the Corded Ware culture or partly contemporary Beaker culture which revealed the presence of haplogroups R1a1 and R1b among them (Haak et al., 2008; Lee et al., 2012). In case of the dead from Wrocław-Jagodno genetic diversity of both individuals was observed. One of them does not have clearly determined haplogroup. We should reject his affiliation to paragroup E* characteristic mainly for Africa and identified among population of Bantu (Karafet et al., 2008). On the other hand, haplogroup J was probably formed about 30000 years ago in Arabian Peninsula and it is often identified as a indicator of the Neolithic demic diffusion associated with spreading agriculture (Semino et al., 2004, 1996). Its contemporary distribution covers mainly the area of Middle East and the Mediterranean Sea basin; it sporadically occurs in Central Europe. Latest analyses show that its spreading might be a marker of later migrations (Giacomo et al., 2004). Hence the most probable is acceptance of haplogroup I as a proper one for the examined individual. It is considered that it was developed between 15000 and 30000 years ago (Karafet et al., 2008) and its spreading is associated with the expansion of the Paleolithic Gravettian culture (Semino, 2000) or population from the beginning of Holocene (Rootsi et al., 2004). Thus we should think that this individual is most probably descendant of native hunting and gathering community. Haplogroup G, identified in the second individual, belongs to widespread multiethnic groups of Europe, Asia and northern Africa. This haplogroup is largely identified among analyzed aDNA materials from Europe including the early Neolithic in Spain and Germany and the late Neolithic in France. It is a serious factor supporting a conception of spreading of Neolithic from the area of Middle East (Haak et al., 2010; Lacan et al., 2011; Rootsi et al., 2012). It may indicate very complicated development processes of communities of the Corded Ware culture in which diverse populations participated – autochtonous deriving from hunting and gathering ancestors as well as Neolithic populations, genetically deriving from the Middle East areas but already living there since the beginning of Neolithic.

[Assessment of late Neolithic pastoralist's life conditions from the Wroclaw-Jagodno site (SW Poland) on the basis of physiological stress markers]

I see no basis whatsoever in the reported results for "categorizing skeleton from grave no. 1 with very high probability into haplogroup G". Possibly there is some miscommunication among the authors, or else a complete failure of logic. It appears the authors merely failed to exclude haplogroup G in sample 1 because of an unsuccessful test (and arbitrarily decided to make haplogroup G their "very highly probable" default assumption).

At the locations where both samples returned results, the only difference is at P25 (which we'll come back to). If I and J are possibilities for the haplogroup of sample 2, then possibilities for sample 1 include I, J, and G. [Edit: I originally wrote that among these choices haplogroup I would also be my guess, and it still is; but we shouldn't have to guess, and there are still other options not ruled out beyond I, J, and G.]. Note that if we ignore P25 (as the authors appear to have chosen to do), the Y haplotypes are identical at the available resolution and provide no basis for asserting the individuals are unrelated.

I'm not sure what to make of the fact that sample 1 shows CA and sample 2 shows C at P25. P25 exists in multiple copies in a palindromic region and is not the most reliable marker. But if in sample 1 any copy of P25 is A, it would suggest sample 1 is R1b.

Against this, the authors apparently take their results to indicate that sample 1 is ancestral for M207 (which would rule out R) and M45 (which would rule out P). [Update: removed speculation about errors due to strand issues. In this case, it should be safe to rule out R as a possibility for both samples, and to rule out P for skeleton 1 (though I'd still like to see comments from the authors about the "CA" at P25 for skeleton 1). The more fundamental point remains: more data will be needed to confidently assign haplogroups to these samples.]

Interesting-looking AAPA 2013 abstracts

Program here (pdf).

Natural selection acts to maintain diversity between Out of Africa and sub-Saharan African populations in genes related to neurological processes and brain development. JASON A. HODGSON1,5, ALI AL-MEERI2, CONNIE J. MULLIGAN3 and RYAN L. RAAUM4,5. 1Anthropology, New York University, 2Biochemistry and Molecular Biology, Sana'a University, Yemen, 3Anthropology, University of Florida, 4Anthropology, Lehman College and The Graduate Center CUNY, 5-, The New York Consortium in Evolutionary Primatology.

The Yemeni and Mozabite are closely related Out of Africa (OOA) populations from the Arabian Peninsula and North Africa respectively, while the Maasai are a sub-Saharan African (SSA) population. Using genome-wide SNP data (publicly available for the Mozabite and Maasai, and collected here for the Yemeni) we show the Yemeni to have ~7% and the Mozabite to have ~26% recent sub-Saharan admixture, while the Maasai have ~27% Middle Eastern admixture. We use an adaptation of the locus specific branch length method to look for the effects of natural selection on alleles introduced to the three populations through admixture. We specifically look for 1) the adaptive introgression of alleles from SSA into the Yemeni and Mozabite, 2) the adaptive introgression of alleles from OOA into the Maasai, 3) purifying selection of SSA alleles out of the Yemeni and Mozabite, and 4) purifying selection of OOA alleles out of the Maasai. We found correspondence in patterns of adaptive introgression and purifying selection between the populations for 18 genomic loci, all of which contain protein-coding genes. The correspondence in signatures of selection between three independent populations is strong evidence for natural selection, rather than the false positive signals common in genome-wide scans of selection. Strikingly, of the regions where purifying selection is acting to maintain diversity between the Out of Africa and sub-Saharan African populations, eight out of twelve genes with known ontologies are involved in neurological processes or brain development. A binomial test found this enrichment to be significant. This research was partially supported by NSF grant BCS-0518530.

Trivers-Willard effect in U.S. billionaires revisited

Revisiting a Sample of U.S. Billionaires: How Sample Selection and Timing of Maternal Condition Influence Findings on the Trivers-Willard Effect:

Based on evolutionary theory, Trivers & Willard (TW) predicted the existence of mechanisms that lead parents with high levels of resources to bias offspring sex composition to favor sons and parents with low levels of resources to favor daughters. This hypothesis has been tested in samples of wealthy individuals but with mixed results. Here, I argue that both sample selection due to a high number of missing cases and a lacking specification of the timing of wealth accumulation contribute to this equivocal pattern. This study improves on both issues: First, analyses are based on a data set of U.S. billionaires with near-complete information on the sex of offspring. Second, subgroups of billionaires are distinguished according to the timing when they acquired their wealth. Informed by recent insights on the timing of a potential TW effect in animal studies, I state two hypotheses. First, billionaires have a higher share of male offspring than the general population. Second, this effect is larger for heirs and heiresses who are wealthy at the time of conception of all of their children than for self-made billionaires who acquired their wealth during their adult lives, that is, after some or all of their children have already been conceived. Results do not support the first hypothesis for all subgroups of billionaires. But for males, results are weakly consistent with the second hypothesis: Heirs but not self-made billionaires have a higher share of male offspring than the U.S. population. Heiresses, on the other hand, have a much lower share of male offspring than the U.S. average. This hints to a possible interplay of at least two mechanisms affecting sex composition. Implications for future research that would allow disentangling the distinct mechanisms are discussed. [. . .]

A striking result of the current study, one implied by neither of the two initially stated variants of the TW hypothesis, is that heiresses have a considerably lower percentage of male offspring than heirs, self-made billionaires, and the general population. That is, for women, the observed effect is actually diametrical to the prediction made on the basis of the TW hypothesis. The difference in the proportion of male offspring between heiresses and heirs is, in fact, the highest difference observed in this study. Despite the large size of the effect and due to the low group size of 26 heiresses, however, it is only statistically significant when not controlling for multiple comparisons. Once this correction is applied, the difference remains only slightly above statistical significance in the logistic regression model. Future research should test whether this finding can be replicated with larger samples of elite women. [. . .]

These objections notwithstanding: What could drive this distinct finding for men and for women? A clue to an answer may be provided by the literature on the effect of various stressors on reducing the percentage of male offspring [13], [41]–[44], including occupational stress [38]. If stress and status both affect sex composition, at least two mechanisms may interact and confound each other in producing sex ratios in population subgroups. Could it be that heiresses, partners and spouses of self-made men, and those of male heirs have, on average, different work and career patterns and are thus exposed to various degrees of occupational stress? Specifically, heiresses may be more likely than the spouses of male billionaires to hold stressful leadership positions in companies they inherited from their parents.

Childhood intelligence is heritable, highly polygenic and associated with FNBP1L

New paper from Visscher, Deary, Plomin, and others, with results consistent with previous findings:

Intelligence in childhood, as measured by psychometric cognitive tests, is a strong predictor of many important life outcomes, including educational attainment, income, health and lifespan. Results from twin, family and adoption studies are consistent with general intelligence being highly heritable and genetically stable throughout the life course. No robustly associated genetic loci or variants for childhood intelligence have been reported. Here, we report the first genome-wide association study (GWAS) on childhood intelligence (age range 6-18 years) from 17 989 individuals in six discovery and three replication samples. Although no individual single-nucleotide polymorphisms (SNPs) were detected with genome-wide significance, we show that the aggregate effects of common SNPs explain 22-46% of phenotypic variation in childhood intelligence in the three largest cohorts (P=3.9 × 10(-15), 0.014 and 0.028). FNBP1L, previously reported to be the most significantly associated gene for adult intelligence, was also significantly associated with childhood intelligence (P=0.003). Polygenic prediction analyses resulted in a significant correlation between predictor and outcome in all replication cohorts. The proportion of childhood intelligence explained by the predictor reached 1.2% (P=6 × 10(-5)), 3.5% (P=10(-3)) and 0.5% (P=6 × 10(-5)) in three independent validation cohorts. Given the sample sizes, these genetic prediction results are consistent with expectations if the genetic architecture of childhood intelligence is like that of body mass index or height. Our study provides molecular support for the heritability and polygenic nature of childhood intelligence. Larger sample sizes will be required to detect individual variants with genome-wide significance. Molecular Psychiatry advance online publication, 29 January 2013; doi:10.1038/mp.2012.184.

Ethnic origins of US attendees of 2013 World Economic Forum in Davos

Starting from this list of Davos attendees, I've attempted to quickly classify the 711 "USA" individuals by racial or ethnic ancestry.

This is a very rough draft, but the initial breakdown I come up with is [29 Jan: made a few changes (see comments); updated percentages shown in brackets]:

[46.41%] 46.69% Northwestern European
[27.29%] 27.43% Jewish
6.05% Southern European
5.49% South Asian
[4.08%] 3.80% Middle Eastern
3.38% Latin America / Brazil
3.23% East Asian
2.25% Eastern European
1.55% Black
[0.28%] 0.14% North American Indian

Corrections are welcome. I've again defaulted to putting people in the NW European category. There may be a few false positives in the Jewish category, but there are probably more false negatives.

Full list below.

Molecular Markers Allow to Remove Introgressed Genetic Background

Molecular Markers Allow to Remove Introgressed Genetic Background: A Simulation Study.

PLoS One. 2012;7(11):e49409

Authors: Amador C, Toro MA, Fernández J

Abstract
The maintenance of genetically differentiated populations can be important for several reasons (whether for wild species or domestic breeds of economic interest). When those populations are introgressed by foreign individuals, methods to eliminate the exogenous alleles can be implemented to recover the native genetic background. This study used computer simulations to explore the usefulness of several molecular based diagnostic approaches to recover of a native population after suffering an introgression event where some exogenous alleles were admixed for a few generations. To remove the exogenous alleles, different types of molecular markers were used in order to decide which of the available individuals contributed descendants to next generation and their number of offspring. Recovery was most efficient using diagnostic markers (i.e., with private alleles) and least efficient when using alleles present in both native and exogenous populations at different frequencies. The increased inbreeding was a side-effect of the management strategy. Both values (% of native alleles and inbreeding) were largely dependent on the amount of exogenous individuals entering the population and the number of generations of admixture that occurred prior to management.

[. . .]  In all cases, the maximum NR was reached after three to four generations of management and, in cases with little introgression, the recovery was complete after just one generation of management (data not shown).

The number of exogenous individuals that entered the native population is also a key factor to determine the potential of success, with more exogenous individuals making the situation irrecoverable.

It must be pointed out that in scenarios with a long admixture period, the possibilities of recovery were quite low, even when using information from many markers [. . .]

The conclusion from the present study is that a relatively small number of markers can provide a good tool to remove undesired introgression from a population. The use of this information can lead to a substantial recovery, especially when the presence of diagnostic markers or alleles is higher in the population of interest than in the exogenous one. The importance of acting soon to avoid irrecoverable introgression of the exogenous genome is a main concern common to all methods (as in the pedigree approach) and it highlights the importance of prevention to control these populations as much as possible.

link

Mismodeling Indo-European Origins: The Assault On Historical Linguistics

Reply to some self-important dork whining about this talk at Dienekes':

"You simply cannot criticize a new, rapidly-evolving and improving model just based on its trivial, known shortcomings. Such a thing is ludicrous and paints a truly bad picture of the talk presenters."

I'm afraid your effeminate idea of proper protocol has no bearing on actual science. Gray and Atkinson's "innovation" is insisting that Bayesian phylogenetics with limited and sometimes questionable inputs of data can produce highly accurate and precise readouts of linguistic history that supercede all previous linguistic and archaeological knowledge. Their results may dazzle twits like you and appeal to those who find their results politically or ethnically congenial. But the first question a serious person would ask is how closely Gray and Atkinson's attempts at reconstruction recapitulate recent/known linguistic history. That they frequently fail to do so is extremely germane to the question of how much faith one should put in their deeper reconstructions.

Statistical models are not magic. Bayesian tree building is not magic. Even with large corpuses of genetic data, the "most likely" tree is often overwhelmingly likely to be wrong. For genetics, where there's an explosion of data with comparatively few human analysts and little or no historical context, such results are useful, being often the best we have until additional data and further refinements of models appear. On the other hand, in linguistics, where on the PIE question relatively many human analysts have been poring over a comparatively limited corpus for many decades, it's up to Gray and Atkinson to demonstrate they have something useful to contribute. Every indication says they do not.

Frank Salter on multiculturalism

Multiculturalism in the life of a society 7

23andMe price drop

For those interested: "23andMe Raises More Than $50 Million in New Financing / Company Sets Growth Goal Of One Million Customers, Reduces Price to $99 from $299"

The GenoChip: A New Tool for Genetic Anthropology

Preprint at arXiv:

The Genographic Project is an international effort using genetic data to chart human migratory history. The project is non-profit and non-medical, and through its Legacy Fund supports locally led efforts to preserve indigenous and traditional cultures. In its second phase, the project is focusing on markers from across the entire genome to obtain a more complete understanding of human genetic variation. Although many commercial arrays exist for genome-wide SNP genotyping, they were designed for medical genetic studies and contain medically related markers that are not appropriate for global population genetic studies. GenoChip, the Genographic Project's new genotyping array, was designed to resolve these issues and enable higher-resolution research into outstanding questions in genetic anthropology. We developed novel methods to identify AIMs and genomic regions that may be enriched with alleles shared with ancestral hominins. Overall, we collected and ascertained AIMs from over 450 populations. Containing an unprecedented number of Y-chromosomal and mtDNA SNPs and over 130,000 SNPs from the autosomes and X-chromosome, the chip was carefully vetted to avoid inclusion of medically relevant markers. The GenoChip results were successfully validated. To demonstrate its capabilities, we compared the FST distributions of GenoChip SNPs to those of two commercial arrays for three continental populations. While all arrays yielded similarly shaped (inverse J) FST distributions, the GenoChip autosomal and X-chromosomal distributions had the highest mean FST, attesting to its ability to discern subpopulations. The GenoChip is a dedicated genotyping platform for genetic anthropology and promises to be the most powerful tool available for assessing population structure and migration history.

Let's be clear: the "most powerful tool available for assessing population structure and migration history" is whole genome sequencing. The Genographic Project, which represents a large fraction of the global spending on its type of population genetics research, unnecessarily hobbled itself from the outset in hopes of pre-emptively appeasing rent-seeking shrill self-appointed advocates for "indigenous peoples". I don't think Spencer Wells and company thought they were giving up much, since the short-sighted original plan was to examine only uniparental markers. In that light, perhaps we can be thankful that they've come up with a way of sidestepping the restrictions they placed on themselves and generating at least some useful autosomal data.

Several steps were taken to ensure that the genetic results would not be exploited for pharmaceutical, medical, and biotechnology purposes. First, participant samples were maintained in a completely anonymous status during GenoChip analysis. Second, no phenotypic or medical data were collected from the participants. Third, we included only SNPs in noncoding regions without any known functional association, as reported in dbSNP build 132. Lastly, we filtered our SNP collection against a 1.5 million SNP data set containing all variants that have potential, known, or suspected associations with diseases.

But however they'd like to spin it there's nothing ideal about ignoring "functional" variation or limiting the number of SNPs tested. Razib has a bizarre post up at his Discover blog in which he confuses SNP ascertainment and "Ancestry Informative Marker" ascertainment, and I see that the authors of the paper themselves appear to be eliding the distinction. But the overwhelming majority of the "450 populations" from which "AIMs" were "ascertained" for the GenoChip had merely been typed on existing microarrays -- which goes no ways towards addressing the issue the Affymetrix Human Origins array was designed to address (putting together SNP panels with known ascertainment, starting by sequencing individuals from multiple populations). Ultimately, the most useful and complete picture of human genetic history will come from whole genome sequencing, which should be cheap enough within a few years for use by the Genographic Project. The question is have they permanently handicapped themselves from applying the actual best tool for their stated mission, or will we eventually see at least some whole genome data for their 75,000 indigenous samples (no doubt with at minimum coding regions redacted).

Protective buttressing of the human fist and the evolution of hominin hands

FIGHTING SHAPED HUMAN HANDS. Protective buttressing of the human fist and the evolution of hominin hands

The derived proportions of the human hand may provide supportive buttressing that protects the hand from injury when striking with a fist. Flexion of digits 2–5 results in buttressing of the pads of the distal phalanges against the central palm and the palmar pads of the proximal phalanges. Additionally, adduction of the thenar eminence to abut the dorsal surface of the distal phalanges of digits 2 and 3 locks these digits into a solid configuration that may allow a transfer of energy through the thenar eminence to the wrist. To test the hypothesis of a performance advantage, we measured: (1) the forces and rate of change of acceleration (jerk) from maximum effort strikes of subjects striking with a fist and an open hand; (2) the static stiffness of the second metacarpo-phalangeal (MCP) joint in buttressed and unbuttressed fist postures; and (3) static force transfer from digits 2 and 3 to digit 1 also in buttressed and unbuttressed fist postures. We found that peak forces, force impulses and peak jerk did not differ between the closed fist and open palm strikes. However, the structure of the human fist provides buttressing that increases the stiffness of the second MCP joint by fourfold and, as a result of force transfer through the thenar eminence, more than doubles the ability of the proximal phalanges to transmit ‘punching’ force. Thus, the proportions of the human hand provide a performance advantage when striking with a fist. We propose that the derived proportions of hominin hands reflect, in part, sexual selection to improve fighting performance.

Human hands have 'evolved for fighting'

Compared with apes, humans have shorter palms and fingers and longer, stronger flexible thumbs.

Experts have long assumed these features evolved to help our ancestors make and use tools.

But new evidence from the US suggests it was not just dexterity that shaped the human hand, but violence also.

Hands largely evolved through natural selection to form a punching fist, it is claimed.

''The role aggression has played in our evolution has not been adequately appreciated,'' said Professor David Carrier, from the University of Utah.

''There are people who do not like this idea but it is clear that compared with other mammals, great apes are a relatively aggressive group with lots of fighting and violence, and that includes us. We're the poster children for violence.'' [. . .]

''Individuals who could strike with a clenched fish could hit harder without injuring themselves, so they were better able to fight for mates and thus be more likely to reproduce,'' he said. [. . .]

To test the theory Prof Carrier conducted experiments with volunteers aged 22 to 50 who had boxing or martial arts experience.

In one, participants were asked to hit a punchbag as hard as possible from different directions with their hands in a range of shapes, from open palms to closed fists.

The results, published in the Journal of Experimental Biology, show that tightly clenched fists are much more efficient weapons than open or loosely curled hands.

A punch delivers up for three times more force to the same amount of surface area as a slap. And the buttressing provided by a clenched fist increases the stiffness of the knuckles fourfold, while doubling the ability of the fingers to deliver a punching force. [. . .]

''Human-like hand proportions appear in the fossil record at the same time our ancestors started walking upright four million to five million years ago. An alternative possible explanation is that we stood up on two legs and evolved these hand proportions to beat each other.''

Manual dexterity could have evolved without the fingers and palms getting shorter, he said. But he added: ''There is only one way you can have a buttressed, clenched fist: the palms and fingers got shorter at the same time the thumb got longer.''

Prof Carrier cited other evidence pointing to the role of fighting in the evolution of human hands.

:: No ape other than humans hits with a clenched fist.

:: Humans use fists instinctively as threat displays. ''If you are angry, the reflexive response is to form a fist,'' said Prof Carrier. ''If you want to intimidate somebody, you wave your fist.''

:: Sexual dimorphism, or the difference in body size between the sexes, tends to be greater among primates when there is more competition between males. In humans the difference is mainly in the upper body and arms, especially the hands. ''It's consistent with the hand being a weapon,'' said Prof Carrier.

In their paper the professor and colleague Michael Morgan, a University of Utah medical student, ponder on the paradoxical nature of the human hand.

''It is arguably our most important anatomical weapon, used to threaten, beat and sometimes kill to resolve conflict. Yet it is also the part of our musculoskeletal system that crafts and uses delicate tools, plays musical instruments, produces art, conveys complex intentions and emotions, and nurtures,'' they write.

''More than any other part of our anatomy, the hand represents the identity of Homo sapiens. Ultimately, the evolutionary significance of the human hand may lie in its remarkable ability to serve two seemingly incompatible but intrinsically human functions.''

War of words: The language paradox explained

New Scientist article (free copy) by Mark Pagel (via Jason Malloy's bookmarks). Some mostly worthwhile paragraphs precede the requisite pollyannaish-on-globalism denouement.

This highlights an intriguing paradox at the heart of human communication. If language evolved to allow us to exchange information, how come most people cannot understand what most other people are saying? This perennial question was famously addressed in the Old Testament story of the Tower of Babel, which tells of how humans developed the conceit that they could use their shared language to cooperate in the building of a tower that would take them to heaven. God, angered at this attempt to usurp his power, destroyed the tower and to ensure it would not be rebuilt he scattered the people and confused them by giving them different languages. The myth leads to the amusing irony that our separate languages exist to prevent us from communicating. The surprise is that this might not be far from the truth. [. . .]

Of course that still leaves the question of why people would want to form into so many distinct groups. For the myriad biological species in the tropics, there are advantages to being different because it allows each to adapt to its own ecological niche. But humans all occupy the same niche, and splitting into distinct cultural and linguistic groups actually brings disadvantages, such as slowing the movement of ideas, technologies and people. It also makes societies more vulnerable to risks and plain bad luck. So why not have one large group with a shared language?

An answer to this question is emerging with the realisation that human history has been characterised by continual battles. Ever since our ancestors walked out of Africa, beginning around 60,000 years ago, people have been in conflict over territory and resources. In my book Wired for Culture (Norton/Penguin, 2012) I describe how, as a consequence, we have acquired a suite of traits that help our own particular group to outcompete the others. Two traits that stand out are "groupishness" - affiliating with people with whom you share a distinct identity - and xenophobia, demonising those outside your group and holding parochial views towards them. In this context, languages act as powerful social anchors of our tribal identity. How we speak is a continual auditory reminder of who we are and, equally as important, who we are not. Anyone who can speak your particular dialect is a walking, talking advertisement for the values and cultural history you share. What's more, where different groups live in close proximity, distinct languages are an effective way to prevent eavesdropping or the loss of important information to a competitor.

In support of this idea, I have found anthropological accounts of tribes deciding to change their language, with immediate effect, for no other reason than to distinguish themselves from neighbouring groups. For example, a group of Selepet speakers in Papua New Guinea changed its word for "no" from bia to bune to be distinct from other Selepet speakers in a nearby village. Another group reversed all its masculine and feminine nouns - the word for he became she, man became woman, mother became father, and so on. One can only sympathise with anyone who had been away hunting for a few days when the changes occurred.

The use of language as identity is not confined to Papua New Guinea. People everywhere use language to monitor who is a member of their "tribe". We have an acute, and sometimes obsessive, awareness of how those around us speak, and we continually adapt language to mark out our particular group from others. In a striking parallel to the Selepet examples, many of the peculiar spellings that differentiate American English from British - such as the tendency to drop the "u" in words like colour - arose almost overnight when Noah Webster produced the first American Dictionary of the English Language at the start of the 19th century. He insisted that: "As an independent nation, our honor [sic] requires us to have a system of our own, in language as well as government."

The Myth of American Meritocracy: How corrupt are Ivy League admissions?

Via Sailer. Note: the article is by Ron Unz, though in this case his numbers appear consistent with my own impressions and previous knowledge.

The Myth of American Meritocracy:

The evidence of the recent NMS semifinalist lists seems the most conclusive of all, given the huge statistical sample sizes involved. As discussed earlier, these students constitute roughly the highest 0.5 percent in academic ability, the top 16,000 high school seniors who should be enrolling at the Ivy League and America’s other most elite academic universities. In California, white Gentile names outnumber Jewish ones by over 8-to-1; in Texas, over 20-to-1; in Florida and Illinois, around 9-to-1. Even in New York, America’s most heavily Jewish state, there are more than two high-ability white Gentile students for every Jewish one. Based on the overall distribution of America’s population, it appears that approximately 65–70 percent of America’s highest ability students are non-Jewish whites, well over ten times the Jewish total of under 6 percent.

Needless to say, these proportions are considerably different from what we actually find among the admitted students at Harvard and its elite peers, which today serve as a direct funnel to the commanding heights of American academics, law, business, and finance. Based on reported statistics, Jews approximately match or even outnumber non-Jewish whites at Harvard and most of the other Ivy League schools, which seems wildly disproportionate. Indeed, the official statistics indicate that non-Jewish whites at Harvard are America’s most under-represented population group, enrolled at a much lower fraction of their national population than blacks or Hispanics, despite having far higher academic test scores. [. . .]

Just as striking as these wildly disproportionate current numbers have been the longer enrollment trends. In the three decades since I graduated Harvard, the presence of white Gentiles has dropped by as much as 70 percent, despite no remotely comparable decline in the relative size or academic performance of that population; meanwhile, the percentage of Jewish students has actually increased. This period certainly saw a very rapid rise in the number of Asian, Hispanic, and foreign students, as well as some increase in blacks. But it seems rather odd that all of these other gains would have come at the expense of whites of Christian background, and none at the expense of Jews.

Furthermore, the Harvard enrollment changes over the last decade have been even more unusual when we compare them to changes in the underlying demographics. Between 2000 and 2011, the relative percentage of college-age blacks enrolled at Harvard dropped by 18 percent, along with declines of 13 percent for Asians and 11 percent for Hispanics, while only whites increased, expanding their relative enrollment by 16 percent. However, this is merely an optical illusion: in fact, the figure for non-Jewish whites slightly declined, while the relative enrollment of Jews increased by over 35 percent, probably reaching the highest level in Harvard’s entire history. Thus, the relative presence of Jews rose sharply while that of all other groups declined, and this occurred during exactly the period when the once-remarkable academic performance of Jewish high school students seemed to suddenly collapse. [. . .]

Each year, the Ivy League colleges enroll almost 10,000 American whites and Asians, of whom over 3000 are Jewish. Meanwhile, each year the NMS Corporation selects and publicly names America’s highest-ability 16,000 graduating seniors; of these, fewer than 1000 are Jewish, while almost 15,000 are non-Jewish whites and Asians. Even if every single one of these high-ability Jewish students applied to and enrolled at the Ivy League—with none going to any of America’s other 3000 colleges—Ivy League admissions officers are obviously still dipping rather deep into the lower reaches of the Jewish ability-pool, instead of easily drawing from some 15,000 other publicly identified candidates of far greater ability but different ethnicity. [. . .]

The situation becomes even stranger when we focus on Harvard, which this year accepted fewer than 6 percent of over 34,000 applicants and whose offers of admission are seldom refused. Each Harvard class includes roughly 400 Jews and 800 Asians and non-Jewish whites; this total represents over 40 percent of America’s highest-ability Jewish students, but merely 5 percent of their equally high-ability non-Jewish peers. It is quite possible that a larger percentage of these top Jewish students apply and decide to attend than similar members from these other groups, but it seems wildly implausible that such causes could account for roughly an eight-fold difference in apparent admissions outcome. Harvard’s stated “holistic” admissions policy explicitly takes into account numerous personal characteristics other than straight academic ability, including sports and musical talent. But it seems very unlikely that any remotely neutral application of these principles could produce admissions results whose ethnic skew differs so widely from the underlying meritocratic ratios.

One datapoint strengthening this suspicion of admissions bias has been the plunge in the number of Harvard’s entering National Merit Scholars, a particularly select ability group, which dropped by almost 40 percent between 2002 and 2011, falling from 396 to 248. This exact period saw a collapse in Jewish academic achievement combined with a sharp rise in Jewish Harvard admissions, which together might easily help to explain Harvard’s strange decline in this important measure of highest student quality. [. . .]

It is important to note that these current rejection rates of top scoring applicants are vastly higher than during the 1950s or 1960s, when Harvard admitted six of every seven such students and Princeton adopted a 1959 policy in which no high scoring applicant could be refused admission without a detailed review by a faculty committee.78 An obvious indication of Karabel’s obtuseness is that he describes and condemns the anti-meritocratic policies of the past without apparently noticing that they have actually become far worse today. An admissions framework in which academic merit is not the prime consideration may be directly related to the mystery of why Harvard’s ethnic skew differs in such extreme fashion from that of America’s brightest graduating seniors. In fact, Harvard’s apparent preference for academically weak Jewish applicants seems to be reflected in their performance once they arrive on campus.79

Related: "Merit" in elite college admissions

Racial Intermarriage and Household Production

For the edification of Whiskey and SeanTodRoy (pdf):

ASHG 2012 twitter copy/paste

Charley Farley ?@charley_farley Very cool PoBI talk from Leslie. I'm one of the red squares - Anglo-Saxon/pre-Roman British admix. Incredible UK structure #ASHG2012

Nick Eriksson ?@nkeriks Lovely talk by Stephen Leslie about fineSTRUCTURE and the fine structure of UK populations. learned lots about UK history. #ASHG2012

Luke Ward ?@luke__ward M.Wilson Sayres: Ultralow Y diversity due not only to diff reproductive success of sexes but also selection, both coding+noncoding #ashg2012

Yaniv erlich ?@erlichya WS: selection on the Y chromosome does not only act on the coding regions. #ASHG2012

Yaniv erlich Yaniv erlich ?@erlichya WS: reproductive success difference between male&female is not enough to explain the genetic signal from the Y chromosome #ASHG2012

Yaniv erlich ?@erlichya I am exited to hear Wlson Sayres talk about the Y chromosome! One of my favorite chromosomes #ASHG2012

23andMe ASHG 2012 poster presentations

Here. From "Genome wide association study of sexual orientation in a large, web-based cohort" (pdf):

Our GWAS results did not identify any genetic loci reaching genomewide significance at p < 5 x 10-8 among men or women. Among men, the peak (non-significant) hit was in chromosome 8q12.3 (chr8:63532921 in NKAIN3, p= 7.1 x 10-8).

More interesting (if generally unsurprising) are the phenotypic associations:

We examined the correlation between sexual identity and ~1000 phenotypes already characterized in the 23andMe database through other surveys. These analyses are preliminary; we have not checked for outliers or confounders beyond what is listed in the methods. We replicated previous findings showing a positive association between lesbians and alcoholism, and between lesbians and gay men and several psychiatric conditions.

A commenter at the 23andMe blog:

The phenotypic information is interesting if I’m reading it correctly: Gay men are less likely to to have played common US sports, and are more likely to cry easily or to have had liposuction. Lesbians are less likely to shave their legs. Surprisingly, gay men are less likely to be atheist or agnostic.

"New" R1a1 SNPs

New Y-chromosome binary markers improve phylogenetic resolution within haplogroup R1a1:

Despite the limited data available for Z280 and Z93, some general inferences can be drawn from the geographic distributions of these two haplogroups. The R1a1- Z280 subclade is a strong candidate for covering the R1a1a* (xM458) in Eastern Europe, which was found in high frequency by Underhill et al. (2010).The tested set of 53 Malaysian Indian samples presented 100% frequency for the R1a1-Z93 subclade, without co-existence Z280 or M458 sub-haplogroups. Inner and Central Asia seem to be the overlap zones for the R1a1-Z280 and R1a1-Z93 chromosomes as both forms were observed at low frequencies. This is again consistent with the observations described for R1a1a* spread in Central Asia and in the Altai region by Underhill et al. (2010). This pattern suggests that the origin of R1a1-M198 arguably occurred somewhere between South Asia and Eastern Europe. Potential candidates could be the Eurasian Steppes (Ukraine – Southern Russia – Kazakhstan – Caucasus) or the Middle East. European populations showed higher M458 and Z280, whereas Asian populations presented higher Z93 frequencies, indicating that the new markers can be effectively used to distinguish between the European and Asian branches of the haplogroup R1a1-M198. [. . .]

The coalescent time calculated by us for R1a1-M458 carriers is consistent with the age calculated by Underhill et al. (2010) in Europe yielding 7.3 KYA versus 7.9 KYA (thousands of years ago). Underhill et al. (2010) also noted the potential association of R1a1-M458 with the Linear Pottery Neolithic culture in the territory of present-day Hungary—this observation is supported by our data. The TMRCA calculated for R1a1-Z280 diversification (10.3 KYA) is approximately in agreement with the estimation of Underhill et al. (2010) for R1a1a*(xM458) chromosomes in Eastern Europe ( 11 KYA). However, the coalescent age of 10.3 KYA for R1a1- Z93 chromosomes in this study is lower than that of populations of the Indus Valley (14 KYA) for the STR associated diversity of R1a1a*(xM458) chromosomes calculated by Underhill et al. (2010).

Of course, these markers and other markers defining additional layers of structure under M417 have been known for over a year. Budgetary constraints and the magic of peer review combine to render this paper relatively uninformative. One of the authors explains:

I have to agree with all, but those who never tried to push an article through a serious academic journal has no idea how difficult this is. The first version was submitted like 1 year ago, and also contained pedigree rates plus 500+ FTDNA samples from different ethnic groups. But unfortunately the reviewers were so narrow-minded that we had finally to drop all FTDNA samples plus the pedigree calcs.

Personally I also do not consider Zhiv. rate valid, but I had to accept this compromise to get the paper accepted. Anyway, as Lukasz pointed out, the main goal was to introduce Z93 and Z280 into the "academic circles" so in the future we may have a comprehensive paper from a more wealthy lab. The Budapest forensics are not full of money so we had no chance to have more than 12 markers tested and "low-chance SNPs" like Z284 in Hungary. Actually we submitted the first draft before Z283 was established securely on the FTDNA tree so we could not include it later...

My comments from last year on the dna-forums postings of an Underhill(lab that brought us Zhivotovsky "evolutionary" mutation rates)-affiliated academic stand:

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.

Again: the most straightforward interpretation of the evidence is that Z93 is a relatively young branch of an evidently European lineage. Accurate, unbiased dates using SNPs instead of STRs should be here soon enough, definitively settling this and other issues.

Moment Magazine's great (Jewish) DNA experiment

23andMe:

In September, Moment Magazine got all nerdy and wrote about their Great DNA Experiment, in which they look at the 23andMe results of 15 notable Americans of Jewish ancestry and make some interesting genetic connections. It’s a good illustration of how our DNA can tell us about our interconnectedness.

The piece shows it’s not “six degrees” that separates these individuals from each other, but, in all but one case, no degrees of separation. This means that these individuals are all directly related to one another, albeit in most cases distantly. This was also news to the 15 participants.

All but one of the individuals has Ashkenazi Jewish ancestry. The one exception is Linda Chavez, the political commentator, who descended from Conversos, indivduals of Jewish and Muslim ancestry who converted to Catholicism during the Inquisition. Her ancestors eventually settled in New Mexico. But even in her case, although she isn’t directly related to any of the group, she is connected to each of the others individuals focused on in the piece by just one other individual in the 23andMe database.

The connections shown in the article are what prompted The New York Times columnist David Brooks and NPR “All Things Considered” host Robert Siegel to joke about learning they were distant cousins, sharing a common ancestor several generations back. Brooks kidded that he was “most surprised that our ancestors worked together on National Schetl Radio, on a program called ‘All Pogroms Considered.’” (Maybe the line needs a drum roll to work.)

The article shows the genetic connections between people like Mayim Bialik, the actress on the Big Bang Theory, and Stephen Dubner, co-author of Freakonomics. Or the connections between NPR’s Siegel, and Harvard Law professor, Alan Dershowitz, or his connections to 23andMe’s CEO’s mother Esther Wojcicki, a journalist and teacher. The magazine shows the connections and the amount of shared DNA, measured in centimorgans (cMs), to illustrate the “relatedness” of any two individuals. More closely related individuals share more DNA.

In the full article at the Moment Magazine website we also learn, for example, that Stephen Dubner's "first cousin once removed was Ethel Greenglass, wife of Julius Rosenberg", or that "Esther Wojicki's maternal-grandparents gave each of the boys among their 13 children a different surname in order to help them avoid conscription in the Russian army".

Our findings are typical of what geneticists would expect from a group of people of mostly Ashkenazi Jewish origin, says 23andMe's Mike Macpherson. Today's Ashkenazi Jews descend from approximately 25,000 ancestors who survived plagues and massacres in the 12th and 13th centuries. Survivors of these "bottlenecks" and other similar occurrences then married one another, sharing their DNA with millions of descendants.

Miscellaneous links

Mangan's is back.

New video depicts human migration across generations

A new video created by Whitehead Institute in collaboration with the genealogical website Geni.com shows the births of millions people, from the Middle Ages through the early 20th Century, as single dots on a black background. As time advances, those births define the coastlines and countries of Europe and Great Britain, then the Pilgrims’ voyage to the New World, the migration to Australia, the overland expansion of the United States through the Oregon Trail and Gold Rush, and the founding of Johannesburg, South Africa. [. . .]

In the future, Erlich and Daniel MacArthur, a Group Leader in Genetics at Massachusetts General Hospital and the Broad Institute, will be partnering with Geni to delve even deeper into the information submitted to the world’s largest collaborative genealogical website.

Richard III skeleton reveals 'hunchback king'

DNA tests are expected to take 12 weeks. The team will compare samples from the skeletal remains with the DNA of a direct descendant of the king's sister, Michael Ibsen, 55, a Canadian furniture maker who lives in London.

Biology and ideology: The anatomy of politics / From genes to hormone levels, biology may help to shape political behaviour.

Four Species of Homo You’ve Never Heard Of (not a profile of the writers and editors Counter Currents)