Adaptive introgression of Denisovan HLA alleles across Asia?

John Hawks:

If it turns out that we have widespread adaptive introgression in Asia today from Denisovans, that will change the game of studying the origins of these populations. Based on the genome-wide comparison, it looks like the genetic interaction that led to the habitation of Asia did not involve Denisovans, who contributed only to populations at the most eastern extreme of habitation in island Southeast Asia. But the only Denisovans we know about lived near the geographic center of the Asian landmass, not at the extreme southeastern extreme.

The HLA pattern may suggest a more widespread pattern of mixture across Asia, which was later overwritten by population movements of people who didn't have Denisovan ancestry. That means that the habitation of Asia was a process of successive migrations and replacements, which imperfectly covered up the evidence of archaic intermixture. The genes that remain as signs of this intermixture are those that had selective advantages in later populations.

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

Deary / Visscher IQ paper

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

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

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

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

The study uses SNPs across the genome to measure this relatedness and then shows it correlates with phenotypic similarity – i.e., the trait is heritable. We knew that already.

What they claim is that you can break down this effect by chromosome or by subregion. When they use the SNPs along longer chromosomes they seem to get a bigger effect – “explaining more of the phenotypic variance”. The inference is that thousands of SNPs, scattered across the whole genome, contribute to the trait or, more specifically to variance in the trait across the population (the implication is that they contribute to the value of the trait in individuals).

There is an alternative explanation for this effect, however, which is that using more SNPs simply gives a better estimate of genetic relatedness. So, the SNPs on chromosomes 1 (the longest) give a better estimate than those on chromosome 21 (the shortest) – they index relatedness with more precision. As a result, they correlate better with phenotypic similarity – this looks like you have “explained more of the variance”. In fact, getting such a signal from SNPs on chromosome 1 does not mean that any of the causal variants are actually on chromosome 1. Nor does the fact that such signals can be derived from anywhere in the genome mean that there are thousands of variants across the genome affecting the trait.

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

What is the evidence that population structure is not causing the observed effects?

We took several steps to avoid population structure inflating the estimate of the variance explained by the SNPs. We excluded one individual from any pair that had an estimated relationship > 0.025 (approximately equivalent to between 3rd and 4th cousins). We fitted the first 20 principal components from the relationship matrix in the statistical model so that any population substructure that they picked up was excluded from the variance explained by the SNPs. Critically, we then estimated the correlation between the relationship matrices estimated from different chromosomes and did not find significant correlation. We tested a set of SNPs that are ancestry-informative in Europe for association with height and did not observe inflation of the test-statistics.

For the purpose of this paper, we performed an additional simulation experiment (inspired by comments from Dan Stram) by assuming that the causal variants were all carried on one set of chromosomes (odd numbers) and another set of chromosomes (even numbers) carried SNPs from which we estimated relatedness. If there is structure in the population then this would imply that a pair of individuals that are closely related on odd chromosomes will also be closely related on even chromosomes. We used the observed genotype data of 3,925 individuals and 295K SNPs as the basis of the simulation, and simulated 1,000 causal variants on the odd chromosomes with a total heritability of 80%. Then we performed a restricted maximum likelihood (REML) analysis of the simulated phenotypes on the genetic relationship matrix estimated from the SNPs on the even chromosomes. The estimates and standard errors (SEs) from 10 simulation replicates are shown in Table 1. Since REML estimates of variance are always positive, if the true variance explained is zero, we expect half the replicates to return an estimate of 0.0 and half to return an estimate with mean value 0.8 times the standard error. This is exactly what happened. Therefore we conclude (again) that there is no structure in the data that would inflate the estimate of the variance explained by the SNPs.

Steve Hsu correctly points out:

If I understand correctly, you want to claim that the observed population variation could be due to a few rare variants of large effect. But then it would be surprising for this study to have found .5 of the total variation to be associated with SNPs — compare to earlier studies using twins/adoptions/siblings that found narrow sense heritability of about .6 or so. I would not expect the rare alleles you hypothesize to be in good LD with SNPs (which are designed to tag common variants), so we would expect to lose a big chunk of the .6 additive heritability.

For example, in the Visscher paper on height they had to hand wave about imperfect LD to recover the full .8 or so of heritability. In this case the global fit comes out very close to .6, which suggests common rather than rare variants (at least, they are well tagged by SNPs). But if they are common variants their individual effect sizes must be small and there are a lot of them. Let me know if I am missing something.

Mitchell:

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

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

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

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

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

Y haplogroup R1b and light hair in Italy

Via Italian Wikipedia.

 

Update addressing some questions/comments:

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

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

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

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

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

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

Variance of R-P312 lineages highest in eastern Europe

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

Recently-revealed structure in Y haplogroup R1a

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

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

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

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

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

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

Swedish McDonald's

Open thread (7)

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

Editorial and preliminary paper on People of the British Isles project

Both freely accessible.

A British approach to sampling:

The acronym ‘PoBI’ may not yet be familiar to human geneticists in the way that ‘HGDP’, ‘WTCCC’ or ‘HapMap’ are, but a paper in this issue of EJHG1 that introduces the ‘People of the British Isles’ project to the scientific community aims to change this. The PoBI project will collect up to 5000 DNA samples from diverse regions of the British Isles, taking great care to sample individuals with several generations of ancestry in rural locations. These samples are intended to serve as controls for future medical genetic studies, and to provide insights into the peopling of the British Isles over the last few millennia. [. . .] Although readers will have to wait for future publications to discover the insights from these large-scale genetic analyses, the current paper describes the sampling strategy and initial 3865 samples in some detail, outlines an approach to investigating fine-scale population structure using surnames, and presents some preliminary genetic analyses of a handful of chosen loci. [. . .]

In addition to collecting blood, the project recorded surnames. Using data from a census performed in 1881, these were classified as ‘local’ or ‘non-local’, and the two classes examined separately. The authors then modelled a population such as that from central England as a mixture between south-western (taken to represent Ancient Britons) and eastern (Anglo Saxon) populations, and estimated the contribution of each population to the central England autosomal genotypes. These contributions differed between the local surname class (mostly eastern) and the non-local class (half and half), which the authors take as evidence of subtle population structure. Published genetic analyses using much larger numbers of markers have already detected low, but significant levels of genetic structure within Britain in more straightforward ways,4, 5 even with less stringently ascertained samples (Figure 1): Europe-wide south-east to north-west gradients extend into the British Isles. We can look forward to deeper insights into genetic differentiation and its causes when large-scale genetic analyses of the PoBI samples are available.

[. . .] anthropological and evolutionary geneticists should rejoice in the assembly of this resource, the foresight of The Wellcome Trust in funding the project over a decade or so, and hope that resources are available for establishing more cell lines and performing more genome-wide sequencing, so that both the full set of samples and their sequences can be made widely available.

It is obvious why British people interested in their ancestry, and medical geneticists working with British subjects should welcome PoBI, but why should others pay attention? PoBI will not provide information about global genetic diversity in the way that HGDP7 and HapMap8 do, but its microcosmic survey of genetic variation in a set of small islands off the western coast of the Eurasian continent is revealing the level of differentiation that builds up over millennia via events well documented by archaeology and history, so these alternative data sets can be compared to address questions about the initial peopling of the area, and its subsequent reshaping by internal and external forces. And if the characteristics of the British – politeness, eccentricity, or drunken loutishness, according to your viewpoint and experience – have any genetic basis, perhaps PoBI can provide a starting point for identifying it! 

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

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

Swedish population structure

Via Dienekes, The Genetic Structure of the Swedish Population:

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

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

Few of whites' best friends are black

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

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

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

More evidence of Sephardic ancestry in some new world Hispanic groups

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

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

Sorbs autosomally distinct from Germans

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

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

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

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

Dienekes releases ancestry analysis tool

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