Dienekes releases ancestry analysis tool

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

Advice for women and men

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

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

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

Ötzi (Tyrolean Iceman) genome coming "soon"

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

Irish DNA Atlas project launched

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

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

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

Svante Paabo to sequence Upper Paleolithic (early modern) Europeans

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

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

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

Neandertales y sapiens

-¿Qué motivo le ha traído a Cantabria?

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

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

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

-¿Y sus próximos retos?

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

-¿Qué teorías manejan al respecto?

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

Google translation below:

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

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

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

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

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

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

Some left response to latest Gould exposure

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

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

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

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

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

Gould’s analysis of Morton is widely read, frequently cited, and still commonly assigned in university courses (refs.). Morton has become a canonical example of scientific misconduct...

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

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

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

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

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

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

Some links

Ahnenkult: An Uyghur redhead

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

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

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

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

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

Light-skinned black women rated more attractive

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

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

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

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

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

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

Neolithic Y DNA from Southwestern France

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

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

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

Dienekes writes:

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

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

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

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

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

Who was the mother of Ingmar Bergman?

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

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

Racial differences in genetic load?

Another point of confusion in Kanazawa's deleted post:

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

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

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

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

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

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

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

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

Similarly, "An analysis of consanguineous marriages in Nigeria" finds:

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

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

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

Kanazawa explains:

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

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

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

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

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

23andMe sale Monday April 11

Details here.

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

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

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

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

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

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

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

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

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

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

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

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

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

Ethnic background of the British Royal family

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

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

A few links

The Unsilenced Science: The Racial Controversy of a Violent Gene

Viking ancestry explored on the Isle of Man by researchers

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

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

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

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

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

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

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

Open thread (6)

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