Autosomal African admixture in Yemeni populations

Another ASHG 2010 abstract. Using CEU and Maasai reference populations, the authors estimate Yemenis average about 14.8% African admixture.

ASHG 2010 abstracts on Jewish genetics

Selected abstracts from the 2010 meeting of the American Society of Human Genetics.

ASHG 2010 abstract on archaic admixture in modern humans

Search abstracts for the upcoming meeting of the American Society of Human Genetics here.

Evidence for archaic admixture in contemporary non-African human populations. J. Long, R. Ferrucci, S. Joyce, K. Hunley Dept of Anthropology, Univeristy of New Mexico, Albuquerque, NM.

New, open access genetics journal

Investigative Genetics. Some of the areas of interest mentioned: forensic genetics, identity and lineage testing, personalized genetics, population genetics, evolutionary genetics, mechanisms of inheritance, ancient biomaterials, anthropological genetics, archaeogenetics. Mark Jobling will have a regular column. The inaugural issue includes the following paper.

Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations

the assays were used to screen 683 individuals from Southern Africa, including south eastern Bantu speakers (BAN), Khoe-San (KS) and South African Whites (SAW). Of the 61 haplogroups that the assays collectively resolved, 26 were found in the 683 samples. While haplogroup sharing was common between the BAN and KS, the frequencies of these haplogroups varied appreciably. Both groups showed low levels of assimilation of Eurasian haplogroups and only two individuals in the SAW clearly had Y chromosomes of African ancestry.

Redhead day 2010

Wikipedia: "Redheadday is the name of a Dutch summer festival that takes place each first weekend of September in the city of Breda, in the Netherlands."

Facts about redheads: "Red hair is seen on the heads of only less than one percent of people.in the world. Most redheads live in the U.K., Ireland, and former colonies of U.K. like Australia.

The highest percentage of natural Redheads in the world is in Scotland (13%), followed closely by Ireland with 10%. In the US, about 2% of the population are natural redheads.

Redheads are becoming rarer and could be extinct in 100 years, according to genetic scientists."

(Photo credit. More photographs.)

Free Access to Sage Journals until Oct 15th

More information here: "The next generation of SAGE Journals Online (SJO), SAGE's award-winning journal platform, is now live! To celebrate, free online access to must-have content back to 1999 is available until October 15, 2010" (via Jason Malloy).

David Sloan Wilson on kin selection and group selection

Open Letter to Richard Dawkins: Why Are You Still In Denial About Group Selection?

I do not agree with the Nowak et al. article in every respect and will articulate some of my disagreements in subsequent posts. For the moment, I want to stress how alone you are in your statement about group selection. Your view is essentially pre-1975, a date that is notable not only for the publication of Sociobiology but also a paper by W.D. Hamilton, one of your heroes, who correctly saw the relationship between kin selection and group selection thanks to the work of George Price. Ever since, knowledgeable theoretical biologists have known that inclusive fitness theory includes the logic of multilevel selection, which means that altruism is selectively disadvantageous within kin groups and evolves only by virtue of groups with more altruists contributing more to the gene pool than groups with fewer altruists. The significance of relatedness is that it clusters the genes coding for altruistic and selfish behaviors into different groups.

See earlier post for links to replies to Nowak et al. by Dawkins and others.

New(ish) blogs

Ahnenkult. According to the about page:

This blog is concerned with history, both human and natural, and race in its various senses. [] Ortu Kan is an Asiatic in the second decade of his life, temporarily in the West but not of it. His people’s language is Altaic (sensu Miller 1971).

Posts include: 'Were there Negritos on Taiwan?', 'Ushtettas as Tunisian "Australoids"', 'Cave-Dwelling Click Speakers in 16th-Century Mozambique'

The Anthroconservative Beacon. "A Daily Blog Dedicated to Upholding Conservative Principles Based on a Scientific Understanding of Human Nature" by "an Associate Professor in the State University of New York system."

HBD Talk. "Political Views from a Secular Humanist Perspective". Some have suggested this is Richard Hoste's new blog. I couldn't say. I skipped all the posts except the one on African blood in Arabs [Update: The person behind HBD Talk says he is not Hoste].

Miscellaneous links

HapMap 3 Consortium: Integrating common and rare genetic variation in diverse human populations

African signatures of recent positive selection in human FOXI1:

Conclusions: We present evidence for recent positive selection in the FOXI1 gene region in Africa. Climate might be related to this recent adaptive event in humans. Of the multiple functions of FOXI1, its role in kidney-mediated water-electrolyte homeostasis is the most obvious candidate for explaining a climate-related adaptation.

Y Chromosomal Variation Tracks the Evolution of Mating Systems in Chimpanzee and Bonobo

Distinct patterns of mitochondrial genome diversity in bonobos (Pan paniscus) and humans:

Conclusions: Some variants of mitochondrially encoded subunits of the ATPase complex in humans very likely decrease the efficiency of energy conversion leading to production of extra heat.

Evolution Theory as the “Consilience” Ingredient of the Humanities:

The Humanities are awash with conflicting, baseless explanations of Human Nature. Sociology, Psychology, Rational Choice theory, Religion, Marxism, Feminisim–all fail in their EXPLANATORY power when tested for consistency when they butt up against the observable actions of real human beings on the Planet. [. . .] In his article Take The Evolution Challenge, David Sloan Wilson eloquently proposes that Evolution Theory be used as a Universal Solvent for all of these competing theories, burning away the accretions of years of constructivist and ideological fat and uncovering the truth.

How do we choose a mate? What scientists are learning from online dating.

Distinct genomic alterations in prostate cancers in Chinese and Western populations suggest alternative pathways of prostate carcinogenesis

How many journal articles have been published (ever)? / Twenty million papers in PubMed: a triumph or a tragedy?

Ancestral Health Symposium (August 5-6, 2011)

Stone Age Atlantis (2010)

A National Geographic documentary (watch online) on Doggerland, which I haven't watched yet.

Kin selection not dead

Explaining eusociality:

There's a slightly embarrassing paper out in Nature last week with E.O. Wilson on the list of authors that disparages inclusive fitness (the logic behind kin selection) and insists that (a) its explanatory power and contributions to evolutionary biology have been limited and (b) it can be ditched outright in favor of "standard natural selection theory". What is meant by this last phrase is not entirely clear, but what is clear is that the authors do not understand inclusive fitness and have completely overlooked the many ways in which it has illuminated us (sex ratio adjustment as the prime example). The authors have a section titled "Rise and fall of inclusive fitness theory", which is curious unless they are writing alt history fiction.

I am only going to comment briefly on the paper, because Jerry Coyne and Richard Dawkins have already chewed it up.

John Hawks agrees:

The weird part of the paper is the way it describes inclusive fitness as some kind of theoretical afterthought, useful only as an ad hoc explanation for eusocial insects. It contrasts the inclusive fitness concept with "standard natural selection" as if it were possible for organisms to erase the fact that they're related to each other! And the authors imply that they have fatally damaged the concept of kin selection.

It's so contrary to evolutionary theory, that I thought maybe I was missing something. But I've been spending time on another problem this week and haven't had time to follow it up.

Two new papers on the distribution of R1b subclades

Myres et al. (pdf):

present phylogeographically resolved data for 2043 M269-derived Y-chromosomes from 118 West Asian and European populations assessed for the M412 SNP that largely separates the majority of Central and West European R1b lineages from those observed in Eastern Europe, the Circum-Uralic region, the Near East, the Caucasus and Pakistan. Within the M412 dichotomy, the major S116 sub-clade shows a frequency peak in the upper Danube basin and Paris area with declining frequency toward Italy, Iberia, Southern France and British Isles.

The supplementary data contains more detailed information on the frequency and diversity of R1b subclades in various population samples. Dienekes comments.

The dating (and consequently the authors' specific attempts to link the spread of R1b to archaeological horizons) is likely badly off; the various subclades are probably much younger than calculated by the authors. It's also far from clear to me that R1b entered Europe via Anatolia (as opposed to a more northerly route). Either way, the Iberian Irish myth is still very dead.

I haven't read the Cruciani paper (pdf).

References:

Myres et al. A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe. European Journal of Human Genetics doi: 10.1038/ejhg.2010.146

Cruciani et al. Strong intra- and inter-continental differentiation revealed by Y chromosome SNPs M269, U106 and U152. Forensic Science International: Genetics doi:10.1016/j.fsigen.2010.07.006

Signatures of founder effects, admixture, and selection in the Ashkenazi Jewish population

The paper is free at the PNAS website. The raw data is available. The press release mentions:

In addition, a region on chromosome 12 showed selection in the Ashkenazi Jewish population but not Europeans. This area encompasses 18 genes but the investigators noticed that one of these, ALDH2, is important in alcohol metabolism, and genetic variation in ALDH2 has previously been shown to affect alcohol consumption, Bray says.

"This is consistent with historical and modern reports of lower alcoholism rates in Jews, although social and religious practices are also thought to play a role," he says. "However, a more detailed analysis of variants in the ALDH2 gene would be necessary to show a mechanistic link."

The abstract refers to ALDH2 as a genomic region under selection that accounts for "alcohol tolerance", but the Jewish version in fact confers alcohol intolerance:

Reduction in activity of the mitochondrial aldehyde dehydrogenase 2 (ALDH2) enzyme due to genetic deficiency causes reactions related to alcohol consumption and lowers the risk of alcoholism.

The authors suggest that the proliferation of the defective ALDH2 version among Jews may be incidental to selection on a different gene:

The mechanism driving selection of the ALDH2 locus is unknown, but a plausible target of selection also within this selected region is the TRAFD1/FLN29 gene, which is a negative regulator of the innate immune system, important for controlling the response to bacterial and viral infection (49). TRAFD1/FLN29 may have conferred a selective advantage in the immune response to a pathogen, perhaps near the time that the Jews returned to Israel from their Babylonian captivity. Despite the unclear selective mechanism, this remains a remarkable example of a putatively selected region accounting for a known population phenotype.

Reference: Bray et al. Signatures of founder effects, admixture, and selection in the Ashkenazi Jewish population. PNAS. Published online before print August 26, 2010, doi: 10.1073/pnas.1004381107

Miscellaneous links

Blaine Bettinger: Sequencing the Genome of Sitting Bull and Other Famous People

John Hawks: French Neolithic discontinuities

John Hawks's bibliography database and citeulike feed

Human migrations and genetics

Priestly Celibacy: A Venerable Tradition, And A Serious Mistake

Another intra-European AIMs paper

Drineas P, Lewis J, Paschou P (2010) Inferring Geographic Coordinates of Origin for Europeans Using Small Panels of Ancestry Informative Markers. PLoS ONE 5(8): e11892.

Analyzing 1,200 individuals from 11 populations genotyped for more than 500,000 SNPs (Population Reference Sample), we present a systematic exploration of the extent to which geographic coordinates of origin within Europe can be predicted, with small panels of SNPs. Markers are selected to correlate with the top principal components of the dataset, as we have previously demonstrated. Performing thorough cross-validation experiments we show that it is indeed possible to predict individual ancestry within Europe down to a few hundred kilometers from actual individual origin, using information from carefully selected panels of 500 or 1,000 SNPs. Furthermore, we show that these panels can be used to correctly assign the HapMap Phase 3 European populations to their geographic origin. [. . .] It is also worth noting that the largest average error was in the German samples and that the most accurately predicted populations were the Southern European and Irish ones. [. . .] Interestingly, within Europe, individual origin seems much easier to predict along the North to South axis than along the East to West axis. This could indicate increased gene flow along the latter axis.

Estimated coordinates for the CEU sample (Utah whites):

Two old papers on Tarim Basin mummies / crania

Now available online at the Sino-Platonic Papers website.

Dolkun Kamberi, "The Three Thousand Year Old Charchan Man" Sino-Platonic Papers, 44 (January, 1994)

The male would have been two meters tall when living (see color plates I and IIa); the corpse was lying on its right side with legs bent and propped up by a small piece of wood (perhaps to promote preservation by means of circulation of air around the corpse). The hair, eyelashes, beard and chest hair were intact and traces of makeup (ocher spiral sun-symbols) could be seen on the face. The presence in the tomb of two small bone spoons with dried ocher pigment in them may indicate that the makeup was applied after death. The male's head hair was yellowish brown half gone to white;

Note: More recent estimates put Cherchen Man's height closer to 5'9".

HAN Kangxin: "The Study of Ancient Human Skeletons from Xinjiang, China" Sino-Platonic Papers, 5 1 (November, 1994)

Between 1920 and 1940, only three foreign scientists published completed research in this area. They are: Arthur Keith of England (1929), Carl-Herman Hjortsjo and Ander Walander of Germany (1924) and A.N. Iuzefovich of the USSR (1949). A total of twenty skulls were described. Five came from the northern part of the Taklamakan Desert and Keith thought they characterized the "Loulan racial type." Eleven skulls were collected by Sven Hedin from near Luobubo (Lopnor) in 1928 and 1934, and have been subdivided into three groups (Nordic, Chinese, and Alpine) by Hjortsjo and Walander. The remaining skulls also came from the Luobubo (Lopnor) area and exhibit Mongoloid characteristics. Iuzefovich considered these to be of Tujue (Turkish) origin (Keith, A., 1929; Hjortsjo, C.H. and A. Walander, 1942; Iusefovich, A.N., 1949). [. . .]

Chinese scientists have conducted systematic excavations in this region since 1940. I have studied all the skeletal material housed at the Institute of Archeology of Xinjiang and analyzed the physical and racial characteristics of these human bones. The materials included about 274 skulls which were collected from nine ancient cemeteries in Xinjiang. The cemeteries range in age from about 1800 B.C.E. to 300 C.E.

Ancient French megalithic mtDNA

Sample size is three:

We reproducibly retrieved partial HVR-I sequences (nps 16,165 to 16,390) from three human remains (Prisse´ 1, 2, and 4, Table 1), one adult and two children deposited during different stages of use of the burial chamber. Corresponding sequences could be unambiguously assigned to haplogroups X2, U5b, and N1a

Marie-France Deguilloux et al. News from the west: Ancient DNA from a French megalithic burial chamber. American Journal of Physical Anthropology DOI: 10.1002/ajpa.21376.

Recent paleogenetic studies have confirmed that the spread of the Neolithic across Europe was neither genetically nor geographically uniform. To extend existing knowledge of the mitochondrial European Neolithic gene pool, we examined six samples of human skeletal material from a French megalithic long mound (c.4200 cal BC). We retrieved HVR-I sequences from three individuals and demonstrated that in the Neolithic period the mtDNA haplogroup N1a, previously only known in central Europe, was as widely distributed as western France. Alternative scenarios are discussed in seeking to explain this result, including Mesolithic ancestry, Neolithic demic diffusion, and long-distance matrimonial exchanges. In light of the limited Neolithic ancient DNA (aDNA) data currently available, we observe that all three scenarios appear equally consistent with paleogenetic and archaeological data. In consequence, we advocate caution in interpreting aDNA in the context of the Neolithic transition in Europe. Nevertheless, our results strengthen conclusions demonstrating genetic discontinuity between modern and ancient Europeans whether through migration, demographic or selection processes, or social practices.

Ezra Pound: racial preservationist

From one of his World War 2 radio speeches:

I am not arguing, I am just telling you. One of these days you will have to start thinking about the problem of race, BREED, preservation.

I do NOT like to think of my race as going toward total extinction, NOR into absolute bondage.

The Cincinnati etc. erred from snobbery. They did not in George Washington’s time organize on racial basis. No one thought of it, no one could have then thought of it. There WAS a racially homogeneous population in the newly freed colonies. Certain privileges were dear to the privileged. Snobbism is NOT conservative. Fashion is not conservative. La Mode, etc. is a ramp.

[#51 (July 2, 1942) U.S.(B65) DISBURSEMENT OF WISDOM]

Incidentally, Ezra Pound is another person with more New England ancestry than George Gilder. (Four of Pound's great-grandparents were born in Massachusetts; one was born in New Hampshire; one was born in New York, with ancestry entirely tracing back to Connecticut; one was a Quaker from New Jersey; and one was from Ireland.) Update: More from Pound below.

Intelligence and pigmentation in Hirsch's sample

Additional results from Nathaniel Hirsch's 1926 study of children of immigrants -- this table further subdividing the sample by degree of hair and eye pigmentation.

In this section of the study, Hirsch is opposing some straw man version of Nordicism:

The Racialists maintain not only that the Nordics are long-headed, tall people with blue eyes and light hair, but more importantly it is claimed that they are mentally superior to all non-Nordic races.

And the results satisfy him:

that intellectual differences although (1) significant, (2) innate and (3) relatively permanent are Natio-Racial in character rather than Racial.

Which definitely shows "the Racialists". I did find the differences between pigmentation morphotypes within some national groups interesting (though I don't put undue weight on these results), considering light hair and light eyes have apparently been reported elsewhere as correlates of IQ. You can read the entire monograph (which includes more information on the tests used and answers to some criticisms) online at Harvard's open collection on immigration.

Reference: Hirsch, Nathaniel D. M. A study of natio-racial mental differences. Worcester, Mass. : Clark University, c1926.

"Social Darwinism" in Anglophone academic journals

GEOFFREY M. HODGSON. Social Darwinism in Anglophone Academic Journals. Journal of Historical Sociology, 17(4), December 2004, pp. 428-63. (pdf)

This essay is a partial history of the term ‘Social Darwinism’. Using large electronic databases, it is shown that the use of the term in leading Anglophone academic journals was rare up to the 1940s. Citations of the term were generally disapproving of the racist or imperialist ideologies with which it was associated. Neither Herbert Spencer nor William Graham Sumner were described as Social Darwinists in this early literature. Talcott Parsons (1932, 1934, 1937) extended the meaning of the term to describe any extensive use of ideas from biology in the social sciences. Subsequently, Richard Hofstadter (1944) gave the use of the term a huge boost, in the context of a global anti-fascist war.

Hodgson mentions:

A massive 1934 fresco by Diego Rivera in Mexico City is entitled ‘Man at the Crossroads’. To the colorful right of the picture are Diego’s chosen symbols of liberation, including Karl Marx, Vladimir Illych Lenin, Leon Trotsky, several young female athletes and the massed proletariat. To the darker left of the mural are sinister battalions of marching gas-masked soldiers, the ancient statue of a fearsome god, and the seated figure of a bearded Charles Darwin. These conceptions of good and evil, progress and regress, and light and shade, were prominent in much of Western social science for the next fifty years.

Diego Rivera attributed his politics to his Jewish ancestry:

"My Jewishness is the dominant element in my life," Rivera wrote in 1935. "From this has come my sympathy with the downtrodden masses which motivates all my work."

Coincidentally (I'm sure), Hofstadter was also a Jewish-identified half-Jew. More excerpts within: