Ancestry of Cubans

PLoS Genet 10(7): e1004488. doi:10.1371/journal.pgen.1004488

Cuba: Exploring the History of Admixture and the Genetic Basis of Pigmentation Using Autosomal and Uniparental Markers

Beatriz Marcheco-Teruel et al.

We carried out an admixture analysis of a sample comprising 1,019 individuals from all the provinces of Cuba. We used a panel of 128 autosomal Ancestry Informative Markers (AIMs) to estimate the admixture proportions. We also characterized a number of haplogroup diagnostic markers in the mtDNA and Y-chromosome in order to evaluate admixture using uniparental markers. Finally, we analyzed the association of 16 single nucleotide polymorphisms (SNPs) with quantitative estimates of skin pigmentation. In the total sample, the average European, African and Native American contributions as estimated from autosomal AIMs were 72%, 20% and 8%, respectively. The Eastern provinces of Cuba showed relatively higher African and Native American contributions than the Western provinces. In particular, the highest proportion of African ancestry was observed in the provinces of Guantánamo (40%) and Santiago de Cuba (39%), and the highest proportion of Native American ancestry in Granma (15%), Holguín (12%) and Las Tunas (12%). We found evidence of substantial population stratification in the current Cuban population, emphasizing the need to control for the effects of population stratification in association studies including individuals from Cuba. The results of the analyses of uniparental markers were concordant with those observed in the autosomes. These geographic patterns in admixture proportions are fully consistent with historical and archaeological information. Additionally, we identified a sex-biased pattern in the process of gene flow, with a substantially higher European contribution from the paternal side, and higher Native American and African contributions from the maternal side. This sex-biased contribution was particularly evident for Native American ancestry. Finally, we observed that SNPs located in the genes SLC24A5 and SLC45A2 are strongly associated with melanin levels in the sample.

Link

A nuanced reading of Earnest Hooton

AJPA DOI: 10.1002/ajpa.22162

Two faces of Earnest A. Hooton

Eugene Giles

The American Anthropological Association's multimedia project, “Race: Are We So Different?” alleges that Earnest A. Hooton (1887–1954) of Harvard University was a racist eugenicist who “perhaps more than any other scientist of his time… did more to establish racial stereotypes…” and infers racism from his having sat on a National Research Council Committee on the Negro in the 1920s. I take issue with this perspective to argue against Hooton as a racist by exploring Hooton's relationship with African American students, particularly Caroline Bond Day, and with the National Association for the Advancement of Colored People when it awarded a medal to Charles R. Drew, M.D. In the heyday of eugenics, Hooton was an atypical eugenicist in espousing a resolutely nonracial view of the woes of humankind perpetuated by what he considered the biologically unfit. As eugenics and Nazism became conflated in the late 1930s, Hooton hewed to a path that was more antiracist than many of his anthropological colleagues and publicly disputed Nazi racial ideology. Am J Phys Anthropol 2012. © 2012 Wiley Periodicals, Inc.

Link

ADMIXTURE analysis of Schlebusch et al. (2012) data

The ADMIXTURE analysis of Schlebusch et al. (2012) did not include Eurasian references, but thanks to the fact that the authors have made their data publicly available, anyone can carry out additional analyses on it. I am sure that this data will be very useful in the future. The list of included populations, with sample sizes are:

• ColouredColesberg_Sch 20
• ColouredWellington_Sch 20
• Khomani_Sch 39
• Karretjie_Sch 20
• Khwe_Sch 17
• GuiGhanaKgal_Sch 15
• Juhoansi_Sch 18
• Nama_Sch 20
• Xun_Sch 19
• SEBantu_Sch 20
• SWBantu_Sch 12

As is my convention, the _Sch ending denotes that these populations are from the Schlebusch et al. paper

As always with a new dataset, after processing it, I ran a quick test to make sure everything seemed to be alright. This time, I included the 220 individuals in the released datasets together with 28 HGDP Sardinians and 10 HGDP Dai, and ran a quick K=4 ADMIXTURE analysis:

These appear to make sense. The "green" Dai-like element in the Coloured samples is probably a stand-in for Indian ancestry in that population. The plot of individuals shows considerable variation within several populations:

Out-of-Asia and Into-Africa (?)

The publication of version 2 of the Pickrell et al. paper on South Africa is as good an opportunity as any to discuss something anew something that I've been hinting at for some time now.

First things first: Pickrell et al. find West Eurasian admixture in the Hadza and Sandawe:

Both of these are consistent with west Eurasian (either European or, more likely, Arabian), gene  ow into these populations. To further examine this, we turned to ROLLOFF. We used Dinka and French as representatives of the mixing populations (since date estimates are robust to improperly speci ed reference populations). The results are shown in Supplementary Figure S22. Both populations show a detectable curve, though the signal is much stronger in the Sandawe than in the Hadza. The implied dates are 89 generations ( 2500 years) ago for the Hadza and 66 generations ( 2000 years) ago for the Sandawe. These are qualitatively similar signals to those seen by Pagani et al. [65] in Ethiopian populations.

The presence of West Eurasian ancestry in the Hadza and Sandawe was anticipated in my world9 calculator, where both these populations were shown to possess Caucasoid admixture entirely of the "Southern" component. This component peaks in Arabia, and is unaccompanied by any other type of Caucasoid element really only there. So, it is very likely that there was indeed such a migration into East Africa. What Pickrell et al. have added to our knowledge is that this migration is fairly recent.

Razib repeats one of his favorite analogies about events taking place in Africa after the pyramids were rising in Egypt. I will use a Greek epic analogy, by pointing out that at the time that Memnon the Ethiopian led his contingent to the aid of Troy, these events had not yet taken place.

Depictions of Memnon changed during classical antiquity, from a Caucasoid norm, as in the red-figure kylix on the left, to a more stereotypically African form by Roman times. This is sometimes taken as simply a consequence of the fact that the ancient Greeks were unfamiliar with African phenotypes, and changed their portraiture of Ethiopians as they became more familiar with them during Hellenistic and Roman times.

But, the very name of Aithiopes first attested in Homer (8th c. BC) attests to the fact that the Greeks were aware of what Ethiopians looked like, at least in terms of their dark pigmentation. And, there are depictions of Africans in classical art, as well as a famous quote in Herodotus which makes abundantly clear that he was aware of the physical characteristics of what we would call "Sub-Saharan Africans".

We don't only need to look at Ethiopia for evidence of the strange events that were taking place in Africa during classical antiquity. A great punch-in-the-face reminder of these events comes from the much later Greek author Pausanias who records that a statue of Athena he observed in Attica had blue eyes which he ascribed to the Libyan origin of her myth. How strange it seems to us that one would look to Africa for an explanation for the blue-eyed goddess.

Libya was of course, the ancient name for Africa, and especially Africa west of Egypt, what we might call Berber-land. Egypt was often reckoned by the ancient as part of Asia. In any case, Pausanias' strange assertion finds support in the Egyptian monuments that really do depict the ancient Libyans (=Berbers) as Caucasoid, and often lighter than Middle Eastern people. This would also accord with Coon's famous discovery of "Irish-like" Berbers among the Riffians; I often dismissed such assertions, but in a landscape of human prehistory that is getting stranger by the month, it is worth digging for gold nuggets in old texts.

A recent study claimed that there was back-to-Africa gene flow into Eurasia more than 12,000 years ago. On the other hand, both HAPMIX and StepPCO estimate the admixture in Mozabite Berbers as taking place ~120 generations ago, or, about 3.5kya assuming a generation length of 29 years as Patterson et al. (2012) do. I have observed that rolloff produces generally lower dates than these two methods, so I would not be surprised if that is the case here as well.

It seems that as recently as a few thousand years ago, West Eurasian populations were moving into Africa from both north and east. As Pickrell et al. have discovered, their eastern branch also contributed to South Africans, tagging along the dispersal of pastoralists from East-to-South Africa.

The big question is: did West and Central Africa escape this population movement?

I seriously suspect that it did not. I base that assertion on several arguments, of varying strength:

1. Why would they? If they inundated East and North Africa, why would they not venture further?
2. Living Sub-Saharan African farmers are not symmetrically related to West and East Eurasians: they are closer to the former. West Eurasian back-migration would explain this phenomenon.
3. The Great Event in Sub-Saharan Africa was doubtlessly the Bantu explosion, and it is a curious coincidence that this took place precisely close to the time of these events
4. The Iwo Eleru crania from Nigeria are of late Pleistocene age, archaic in character, and unlike modern West Africans. Something did happen in West Africa over the course of, say, the last 10,000 years

And, I always try to remind myself of the Kiffians and Tenerians. I have not seen any follow-up work on them, but if anyone has an ancient DNA lab, I'd think they would be prime candidates for a study.

Speaking of ancient DNA, this unexpected archaeogenetic study from the University of Khartoum, hints at important changes in Africa:

The area known today as Sudan may have been the scene of pivotal human evolutionary events, both as a corridor for ancient and modern migrations, as well as the venue of crucial past cultural evolution. Several questions pertaining to the pattern of succession of the different groups in early Sudan have been raised. To shed light on these aspects, ancient DNA (aDNA) and present DNA collection were made and studied using Y-chromosome markers for aDNA, and Y-chromosome and mtDNA markers for present DNA. Bone samples from different skeletal elements of burial sites from Neolithic, Meroitic, Post-Meroitic and Christian periods in Sudan were collected from Sudan National Museum. aDNA extraction was successful in 35 out of 76 samples, PCR was performed for sex determination using Amelogenin marker. Fourteen samples were females and 19 were males. To generate Y-chromosome specific haplogroups A-M13, B-M60, F-M89 and Y Alu Polymorphism (YAP) markers, which define the deep ancestral haplotypes in the phylogenetic tree of Y-chromosome were used. Haplogroups A-M13 was found at high frequencies among Neolithic samples. Haplogroup F-M89 and YAP appeared to be more frequent among Meroitic, Post-Meroitic and Christian periods. Haplogroup B-M60 was not observed in the sample analyzed.

I was reminded of it recently when this curious abstract came up, which I still believe is missing a zero somewhere, but these days you never know.

Evidence that Sub-Saharan Africans too have experienced gene flow from West Eurasians occasionally comes up, but formal tests of admixture, e.g., f3(Yoruba; San, French) usually do not achieve significance. But, we must be cautious: South Africans do appear admixed between San and East Africans, but this is a consequence of the fact that admixture is recent, leaving a trail of populations of varying East African ancestry, and the San still exist and can serve as one pole in a comparison of admixture.

David Reich has hinted at dual origins for West Africans. I am looking forward to learning what he means by it, but I would not be surprised if it involves admixture between a Eurasian-like population with a Palaeoafrican population of indigenous West African hunter-gatherers.

In any case, ex Africa semper aliquid novi even today. But, interdum, aliquid novum in Africam.

UPDATE: Pickrell and co-authors discuss their paper here.

Clusters Galore analysis of East Africans

I have included the new data from Pagani et al. (2012) together with various other East African datasets available to me, including various East African Dodecad Project participants.

The first four PCA dimensions can be seen below:

Project participants can find their co-ordinates in the first four dimensions below:

I have also run MCLUST over the first 4 dimensions, which resulted in 12 clusters inferred:

All Project participants fall in the expected clusters, so there is no need to report any individual clustering results.

Ethiopian origins (Pagani et al. 2012)

The study attempts to answer four questions:

Our current study is motivated by four questions. First, where do the Ethiopians stand in the African genetic landscape? Second, what is the extent of recent gene flow from outside Africa into Ethiopia, when did it occur, and is there evidence of selection effects? Third, do genomic data support a route for out-of-Africa migration of modern humans across the mouth of the Red Sea? Fourth, assuming temporal stability of current populations, what are the estimated ages of Ethiopian populations relative to other African groups?

Link to press release. Link the supplemental data.

The authors reiterate that modern humans left Africa 50-70kya, a hypothesis that seems to me pretty much dead in the light of recent archaeological evidence.

The lack of antiquity in the Ethiopian population, even in only the African component thereof argues against that population being ancestral to modern humans. Note that if the Out-of-East Africa hypothesis is correct, then skulls like Omo I represent ancestral modern humans and they are followed much later by modern humans anywhere else. So, while anatomical modernity may have emerged in East Africa --or maybe not; let's not forget that we have early modern skulls from the region in part because of the excellent preservation conditions and excess of scholarly interest-- there is no evidence that they spread from there.

I have little doubt that my own theory about substantial back-migration of Eurasians into Africa will eventually win the day. Of course, I am not referring to the recent (in the last 3,000 years) admixture with West Eurasians that the Ethiopian population has undergone, but rather to the more ancient migration that was probably associated with Y-haplogroup DE-YAP.

The fact that the African component of diverse African populations is more closely related to West than to East Eurasians is one piece of evidence among many for that scenario. Hopefully, it can be tested soon using whole genome data which may have enough density to detect much older admixture events.

UPDATE I: Since the dates in the paper are based on ROLLOFF, a piece of software that is not publicly available more than a year after its announcement, and which contradicts other software released by the same authors, I will take the Queen of Sheba stories circulated in the media with a huge grain of salt.

The American Journal of Human Genetics, 21 June 2012 doi:10.1016/j.ajhg.2012.05.015

Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool

Luca Pagani et al.

Humans and their ancestors have traversed the Ethiopian landscape for millions of years, and present-day Ethiopians show great cultural, linguistic, and historical diversity, which makes them essential for understanding African variability and human origins. We genotyped 235 individuals from ten Ethiopian and two neighboring (South Sudanese and Somali) populations on an Illumina Omni 1M chip. Genotypes were compared with published data from several African and non-African populations. Principal-component and STRUCTURE-like analyses confirmed substantial genetic diversity both within and between populations, and revealed a match between genetic data and linguistic affiliation. Using comparisons with African and non-African reference samples in 40-SNP genomic windows, we identified “African” and “non-African” haplotypic components for each Ethiopian individual. The non-African component, which includes the SLC24A5 allele associated with light skin pigmentation in Europeans, may represent gene flow into Africa, which we estimate to have occurred ∼3 thousand years ago (kya). The African component was found to be more similar to populations inhabiting the Levant rather than the Arabian Peninsula, but the principal route for the expansion out of Africa ∼60 kya remains unresolved. Linkage-disequilibrium decay with genomic distance was less rapid in both the whole genome and the African component than in southern African samples, suggesting a less ancient history for Ethiopian populations.

Link

Looking at faces of other races (Fu et al. 2012)

PLoS ONE 7(6): e37688. doi:10.1371/journal.pone.0037688

Adults Scan Own- and Other-Race Faces Differently

Genyue Fu et al.

It is well established that individuals show an other-race effect (ORE) in face recognition: they recognize own-race faces better than other-race faces. The present study tested the hypothesis that individuals would also scan own- and other-race faces differently. We asked Chinese participants to remember Chinese and Caucasian faces and we tested their memory of the faces over five testing blocks. The participants' eye movements were recorded with the use of an eye tracker. The data were analyzed with an Area of Interest approach using the key AOIs of a face (eyes, nose, and mouth). Also, we used the iMap toolbox to analyze the raw data of participants' fixation on each pixel of the entire face. Results from both types of analyses strongly supported the hypothesis. When viewing target Chinese or Caucasian faces, Chinese participants spent a significantly greater proportion of fixation time on the eyes of other-race Caucasian faces than the eyes of own-race Chinese faces. In contrast, they spent a significantly greater proportion of fixation time on the nose and mouth of Chinese faces than the nose and mouth of Caucasian faces. This pattern of differential fixation, for own- and other-race eyes and nose in particular, was consistent even as participants became increasingly familiar with the target faces of both races. The results could not be explained by the perceptual salience of the Chinese nose or Caucasian eyes because these features were not differentially salient across the races. Our results are discussed in terms of the facial morphological differences between Chinese and Caucasian faces and the enculturation of mutual gaze norms in East Asian cultures.

Link

Spatial Ancestry Analysis (Yang et al. 2012)

Link to SPA software.

Nature Genetics 44, 725–731 (2012) doi:10.1038/ng.2285

A model-based approach for analysis of spatial structure in genetic data

Wen-Yun Yang et al.

Characterizing genetic diversity within and between populations has broad applications in studies of human disease and evolution. We propose a new approach, spatial ancestry analysis, for the modeling of genotypes in two- or three-dimensional space. In spatial ancestry analysis (SPA), we explicitly model the spatial distribution of each SNP by assigning an allele frequency as a continuous function in geographic space. We show that the explicit modeling of the allele frequency allows individuals to be localized on the map on the basis of their genetic information alone. We apply our SPA method to a European and a worldwide population genetic variation data set and identify SNPs showing large gradients in allele frequency, and we suggest these as candidate regions under selection. These regions include SNPs in the well-characterized LCT region, as well as at loci including FOXP2, OCA2 and LRP1B.

Link

Population structure of US Hispanics

Just a quick observation: the "Native American" components at K=4 and K=5 are probably partially Caucasoid. For example, at K=3, Puerto Ricans are 62% Caucasian, and this becomes 18% at K=5. This is due to the fact that the three "Native American" components at K=5 are actually mixes of a Caucasoid with a local Amerindian component.

As I explain here, ADMIXTURE increases the proportion of the "native" component in the absence of pure-blooded representatives of the indigenous inhabitants. Since the Taino are extinct, the "Native American 3" component is actually a hybrid of the Taino aborigines and Europeans.


PLoS Genet 8(4): e1002640. doi:10.1371/journal.pgen.1002640

Population Structure of Hispanics in the United States: The Multi-Ethnic Study of Atherosclerosis

Ani Manichaikul et al.

Using ~60,000 SNPs selected for minimal linkage disequilibrium, we perform population structure analysis of 1,374 unrelated Hispanic individuals from the Multi-Ethnic Study of Atherosclerosis (MESA), with self-identification corresponding to Central America (n = 93), Cuba (n = 50), the Dominican Republic (n = 203), Mexico (n = 708), Puerto Rico (n = 192), and South America (n = 111). By projection of principal components (PCs) of ancestry to samples from the HapMap phase III and the Human Genome Diversity Panel (HGDP), we show the first two PCs quantify the Caucasian, African, and Native American origins, while the third and fourth PCs bring out an axis that aligns with known South-to-North geographic location of HGDP Native American samples and further separates MESA Mexican versus Central/South American samples along the same axis. Using k-means clustering computed from the first four PCs, we define four subgroups of the MESA Hispanic cohort that show close agreement with self-identification, labeling the clusters as primarily Dominican/Cuban, Mexican, Central/South American, and Puerto Rican. To demonstrate our recommendations for genetic analysis in the MESA Hispanic cohort, we present pooled and stratified association analysis of triglycerides for selected SNPs in the LPL and TRIB1 gene regions, previously reported in GWAS of triglycerides in Caucasians but as yet unconfirmed in Hispanic populations. We report statistically significant evidence for genetic association in both genes, and we further demonstrate the importance of considering population substructure and genetic heterogeneity in genetic association studies performed in the United States Hispanic population.

Link

Admixture in different regions of Argentina

99 AIMs are probably not good enough to obtain accurate admixture estimates, but they are probably sufficient to highlight real differences in the origins of different Argentinean sub-populations.

PLoS ONE 7(4): e34695. doi:10.1371/journal.pone.0034695

Heterogeneity in Genetic Admixture across Different Regions of Argentina

Sergio Avena et al.

The population of Argentina is the result of the intermixing between several groups, including Indigenous American, European and African populations. Despite the commonly held idea that the population of Argentina is of mostly European origin, multiple studies have shown that this process of admixture had an impact in the entire Argentine population. In the present study we characterized the distribution of Indigenous American, European and African ancestry among individuals from different regions of Argentina and evaluated the level of discrepancy between self-reported grandparental origin and genetic ancestry estimates. A set of 99 autosomal ancestry informative markers (AIMs) was genotyped in a sample of 441 Argentine individuals to estimate genetic ancestry. We used non-parametric tests to evaluate statistical significance. The average ancestry for the Argentine sample overall was 65% European (95%CI: 63–68%), 31% Indigenous American (28–33%) and 4% African (3–4%). We observed statistically significant differences in European ancestry across Argentine regions [Buenos Aires province (BA) 76%, 95%CI: 73–79%; Northeast (NEA) 54%, 95%CI: 49–58%; Northwest (NWA) 33%, 95%CI: 21–41%; South 54%, 95%CI: 49–59%; p less than 0.0001] as well as between the capital and immediate suburbs of Buenos Aires city compared to more distant suburbs [80% (95%CI: 75–86%) versus 68% (95%CI: 58–77%), p = 0.01]. European ancestry among individuals that declared all grandparents born in Europe was 91% (95%CI: 88–94%) compared to 54% (95%CI: 51–57%) among those with no European grandparents (p less than 0.001). Our results demonstrate the range of variation in genetic ancestry among Argentine individuals from different regions in the country, highlighting the importance of taking this variation into account in genetic association and admixture mapping studies in this population.

Link

African American athletes have more European mtDNA than the general AA population

Does anyone have a theory why this is the case?

American Journal of Physical Anthropology DOI: 10.1111/j.1600-0838.2010.01289.x

Importance of mitochondrial haplotypes and maternal lineage in sprint performance among individuals of West African ancestry

M. Deason et al.

Mitochondrial DNA (mtDNA) is inherited solely along the matriline, giving insight into both ancestry and prehistory. Individuals of sub-Saharan ancestry are overrepresented in sprint athletics, suggesting a genetic advantage. 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 less than 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.

Link

Projecting Sub-Saharan Africans on the European-East Asian axis

Continuing my exploration of Sub-Saharan origins, I projected African populations onto the Principal Components created by a set of European and East Asian populations. The set of SNPs was ascertained on a San individual, as before, and 112 European/110 East Asian individuals were used to avoid sample size issues.

Note that projecting populations onto PCs generated by other populations tends to make the projected populations regress to the mean somewhat. Overall, it appears that African populations are strongly shifted to the European side of the fist principal component.

There is a dearth of haplogroups of Sub-Saharan origin in Europe. Most of them occur as outliers, and in small percentages. Hence, the very strong shift of African populations towards Europeans cannot be ascribed to occasional African admixture in Europe.

Y-haplogroup E is the only major link between Africa and Europe, which is not also shared by Africa and East Asia. But, this haplogroup occurs at very small frequencies in all the included European populations, and at quite variable frequencies overall. As McEvoy et al. correctly observed, even Y-haplogroup E devoid European populations exhibit a closeness with Africans not shared by East Asians.

If admixture with Y-haplogroup E bearing males in Europe cannot account for the relative closeness of Africans to Europeans, what does? As I have mentioned in my review of McEvoy et al., there are two possibilities:

• An Asian component not shared by Eurafricans is actually pulling East Asians away from Europeans and Africans. With the discovery of Denisovans and archaic-leaning Red Deer Cave people, this is a possibility that must be seriously entertained.
• Y-haplogroup E bearers were originally closer to West than to East Eurasians. This is also quite likely, since the origins of haplogroup E are traced to East Africa from DE-bearing ancestors who may have well lived in Eurasia; Asia possesses both sister clades E and D, as well as both sister clades DE and CF one level-up. But, even if DE originated in East Africa itself, we must remember that the population there was originally different than many of the current inhabitants of the region, and may very well have been genetically closest to the emerging Proto-Caucasoids of the adjacent regions of Asia, rather than to the more distant human populations that would ultimately evolve into the East Asians of today.

I tend toward the second explanation -because of the relatively shallow divergence times between East Asians and Europeans, and the lack of any archaic Y-chromosomes/mtDNA. It is hard to imagine such a strong divergence being explained by a little archaic admixture in East Asia.

Dual origins of Sub-Saharan Africans?

A reader quotes from Coon's The Living Races of Man (1965):

''Meanwhile we may note that a detailed analysis of 571 modern Negro crania, made by advanced mathematical techniques, has shown that these crania gravitate between two poles, a Mediterranean Caucasoid and a Pygmy one. The former type is again divisible into an ordinary Mediterranean and a Western Asian type, which suggests more than a single northern point of origin for the Caucasoid element. As we shall in greater detail in Chapter 8 and 9, the Negroes resemble Caucasoids closely a number of genetic traits that are inherited in a simple fashion. Examples of these are fingerprints, types of earwax, and the major blood groups. The Negroes also have some of the same local, predominantly African, blood types as the Pymies. 

This evidence suggests that the Negroes are not a primary sub-species but rather a product of mixture between invading Caucasoids and Pygmies who lived on the edges of the forest, which at the end of the Pleistocene extended farther north and east than it does now.''

Since I'm not one to reject old theories just because they're old, I decided to test this particular idea. I used the San ascertainment panel of the Harvard HGDP dataset, and plotted all African populations, together with West and East Eurasian ones in a PCA plot:

African populations fall along a cline towards West Eurasian populations, with the most isolated Mbuti Pygmies on one end, and a tight blob of West Eurasian populations on the other. Hence, there is evidence for variable affiliation of Sub-Saharans with West Eurasians, but no real evidence for variable affiliation of West Eurasians with Sub-Saharans, except for the Mozabites and HGDP Arabs, with their well-known African admixture.

Nor can the results be explained in terms of more recent common ancestry of African farmers with Eurasians in general, because African populations fall in a clear cline towards West Eurasian populations.

While I would hesitate to say that the above results prove the correctness of Coon's theory, they're certainly quite consistent with it. It may very well be that Y-haplogroup E1b1 bearers from East Africa, descended from Y-haplogroup DE-YAP from Eurasia are ultimately responsible for the introduction of the Caucasoid component into Africa.

Panel for admixture inference in Americas

This is based on only a few hundred AIMs, but nonetheless is quite useful because it reports new data for a variety of South American populations.

PLoS Genet 8(3): e1002554. doi:10.1371/journal.pgen.1002554

Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the Americas

Joshua Mark Galanter et al.

Most individuals throughout the Americas are admixed descendants of Native American, European, and African ancestors. Complex historical factors have resulted in varying proportions of ancestral contributions between individuals within and among ethnic groups. We developed a panel of 446 ancestry informative markers (AIMs) optimized to estimate ancestral proportions in individuals and populations throughout Latin America. We used genome-wide data from 953 individuals from diverse African, European, and Native American populations to select AIMs optimized for each of the three main continental populations that form the basis of modern Latin American populations. We selected markers on the basis of locus-specific branch length to be informative, well distributed throughout the genome, capable of being genotyped on widely available commercial platforms, and applicable throughout the Americas by minimizing within-continent heterogeneity. We then validated the panel in samples from four admixed populations by comparing ancestry estimates based on the AIMs panel to estimates based on genome-wide association study (GWAS) data. The panel provided balanced discriminatory power among the three ancestral populations and accurate estimates of individual ancestry proportions (R2>0.9 for ancestral components with significant between-subject variance). Finally, we genotyped samples from 18 populations from Latin America using the AIMs panel and estimated variability in ancestry within and between these populations. This panel and its reference genotype information will be useful resources to explore population history of admixture in Latin America and to correct for the potential effects of population stratification in admixed samples in the region.

Link

Facial attractiveness and interracial marriage

The data:

From the paper:

The results of the experiment demonstrated that there are robust differences in the relative perceived attractiveness of different racial groups. Further, these differences are affected by the gender of the person being rated. Among males, Black faces were rated as the most attractive followed by White faces and then Asian faces. For the females, Asian faces were seen as the most attractive followed by White and then Black faces. The same pattern was found regardless of the ethnicity of the person doing the ratings.

Whatever the perceptions of attractiveness, it seems that people still tend to marry within their own races. For example, in the UK 0.24% of white females marry black males, and the corresponding percentage for the US is 0.56%. Since blacks make up roughly 1/10 of the population in the US, then if race was not an issue, we'd expect white females to marry black males about 10% of the time; the empirical figure is about ~20 times lower.

So, what this study shows is that while intra-racial marriage is still the norm, black males have an easier time overcoming the racial barrier compared to black females, and Asian females compared to Asian males.

The paper does not seem to present any facial attractiveness data, although it does present an analysis to discount an alternative hypothesis based on stature differences. According to that hypothesis, Asian females outmarry more easily than Asian males because Asians are shorter, and women tend to marry taller men than themselves.

PLoS ONE 7(2): e31703. doi:10.1371/journal.pone.0031703


A Facial Attractiveness Account of Gender Asymmetries in Interracial Marriage

Michael B. Lewis


Abstract 
Background
In the US and UK, more Black men are married to White women than vice versa and there are more White men married to Asian women than vice versa. Models of interracial marriage, based on the exchange of racial status for other capital, cannot explain these asymmetries. A new explanation is offered based on the relative perceived facial attractiveness of the different race-by-gender groups.

Method and Findings
This explanation was tested using a survey of perceived facial attractiveness. This found that Black males are perceived as more attractive than White or East Asian males whereas among females, it is the East Asians that are perceived as most attractive on average.

Conclusions
Incorporating these attractiveness patterns into the model of marriage decisions produces asymmetries in interracial marriage similar to those in the observed data in terms of direction and relative size. This model does not require differences in status between races nor different strategies based on gender. Predictions are also generated regarding the relative attractiveness of those engaging in interracial marriage.

Link

Back to (North) Africa (Henn et al. 2012)

A great new paper has just appeared, presenting new data, new conclusions about African prehistory, and new methodologies. I'll have to read it before I comment on it, but since it's open access you can read it for yourselves.

UPDATE I:


The new data are publicly available here, with information about samples here.
The new PCADMIX software is also available.

PLoS Genet 8(1): e1002397. doi:10.1371/journal.pgen.1002397 

Genomic Ancestry of North Africans Supports Back-to-Africa Migrations 

Brenna Henn et al.

 North African populations are distinct from sub-Saharan Africans based on cultural, linguistic, and phenotypic attributes; however, the time and the extent of genetic divergence between populations north and south of the Sahara remain poorly understood. Here, we interrogate the multilayered history of North Africa by characterizing the effect of hypothesized migrations from the Near East, Europe, and sub-Saharan Africa on current genetic diversity. We present dense, genome-wide SNP genotyping array data (730,000 sites) from seven North African populations, spanning from Egypt to Morocco, and one Spanish population. We identify a gradient of likely autochthonous Maghrebi ancestry that increases from east to west across northern Africa; this ancestry is likely derived from “back-to-Africa” gene flow more than 12,000 years ago (ya), prior to the Holocene. The indigenous North African ancestry is more frequent in populations with historical Berber ethnicity. In most North African populations we also see substantial shared ancestry with the Near East, and to a lesser extent sub-Saharan Africa and Europe. To estimate the time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method based on the distribution of migrant tracts. In order to first identify migrant tracts, we assign local ancestry to haplotypes using a novel, principal component-based analysis of three ancestral populations. We estimate that a migration of western African origin into Morocco began about 40 generations ago (approximately 1,200 ya); a migration of individuals with Nilotic ancestry into Egypt occurred about 25 generations ago (approximately 750 ya). Our genomic data reveal an extraordinarily complex history of migrations, involving at least five ancestral populations, into North Africa.

Link

Mega-study on Mexican admixture

There have been other studies on Mexican admixture patterns before, but this one breaks new ground, by determining the more specific origin of the three major components of the Mexican population. From the paper:

In addition to the HapMap CEU, who are mostly of Northern European ancestry, we used individuals recruited from Dublin, (Ireland), Warsaw (Poland), Rome (Italy) and Porto (Portugal) to provide references for different areas within Europe. The first two PCs provide good separation of these reference populations, and correspond roughly to North-South and West-East gradients (Figure 3A). Both the MEX1EUR and MEX2EUR virtual genomes are most closely related to intact genomes from Porto, which we interpret as a surrogate for populations from the Iberian Peninsula, [3], consistent with the historical record that the first European migrants to Mexico were Spaniards.

The paper is also methodologically interesting:

Continental-level admixture proportions were estimated two ways: (1) a model-based clustering algorithm implemented in frappe [35], and (2) average locus-specific ancestries across all markers. Locus-specific ancestry was estimated with SABER+, an extension of a previously described approach, SABER, that uses a Markov-Hidden Markov Model [12]. SABER+ differs from SABER in implementation of a new algorithm, an Autoregressive Hidden Markov Model (ARHMM), in which haplotype structure within the ancestral populations is adaptively constructed using a binary decision tree based on as many as 15 markers, and which therefore does not require a priori knowledge of genome-wide ancestry proportions (Johnson et al., in preparation). In simulation studies, the ARHMM achieves accuracy comparable to HapMix [36] but is more flexible in modeling the three-way admixture in the Mexican population and does not require information about the recombination rate.

PLoS Genet 7(12): e1002410. doi:10.1371/journal.pgen.1002410

Ancestral Components of Admixed Genomes in a Mexican Cohort

Nicholas A. Johnson et al.

For most of the world, human genome structure at a population level is shaped by interplay between ancient geographic isolation and more recent demographic shifts, factors that are captured by the concepts of biogeographic ancestry and admixture, respectively. The ancestry of non-admixed individuals can often be traced to a specific population in a precise region, but current approaches for studying admixed individuals generally yield coarse information in which genome ancestry proportions are identified according to continent of origin. Here we introduce a new analytic strategy for this problem that allows fine-grained characterization of admixed individuals with respect to both geographic and genomic coordinates. Ancestry segments from different continents, identified with a probabilistic model, are used to construct and study “virtual genomes” of admixed individuals. We apply this approach to a cohort of 492 parent–offspring trios from Mexico City. The relative contributions from the three continental-level ancestral populations—Africa, Europe, and America—vary substantially between individuals, and the distribution of haplotype block length suggests an admixing time of 10–15 generations. The European and Indigenous American virtual genomes of each Mexican individual can be traced to precise regions within each continent, and they reveal a gradient of Amerindian ancestry between indigenous people of southwestern Mexico and Mayans of the Yucatan Peninsula. This contrasts sharply with the African roots of African Americans, which have been characterized by a uniform mixing of multiple West African populations. We also use the virtual European and Indigenous American genomes to search for the signatures of selection in the ancestral populations, and we identify previously known targets of selection in other populations, as well as new candidate loci. The ability to infer precise ancestral components of admixed genomes will facilitate studies of disease-related phenotypes and will allow new insight into the adaptive and demographic history of indigenous people.

Link

Natural selection in African Americans pre- and post-admixture

I have mentioned before that African Americans should not be used to generalize about Africa, not only because of their ~20% European admixture, but also because they live in an environment completely different from the one their African ancestors adapted to: different climate, different set/intensity of pathogens, different social position, different physical requirements and workloads. It is nice to see a paper which attempts to quantify pre- and post-admixture signals of selection in this population; I think this may be a fertile area of future research, and it may also illuminate some of the specificities of the AA population.

Genome Research doi:10.1101/gr.124784.111

Genome-wide detection of natural selection in African Americans pre-and post-admixture

Wenfei Jin et al.

It is particularly meaningful to investigate natural selection in African Americans (AfA) due to the high mortality their African ancestry has experienced in history. In this study, we examined 491,526 autosomal SNPs genotyped in 5,210 individuals and conducted a genome-wide search for selection signals in 1,890 AfA. Several genomic regions showing excess of African or European ancestry, which were thought as the footprints of selection since population admixture, were detected based on a commonly used approach. However, we also developed a new strategy to detect natural selection both pre-and post-admixture by reconstructing an ancestral African population (AAF) from inferred African components of ancestry in AfA and comparing it with indigenous African populations (IAF). Interestingly, many selection-candidate genes identified by the new approach were associated with AfA specific high-risk diseases such as prostate cancer and hypertension, suggesting an important role these disease-related genes might have played in adapting to new environment. CD36 and HBB, whose mutations confer a degree of protection against malaria, were also located in the highly differentiated regions between AAF and IAF. Further analysis showed that the frequencies of alleles protecting against malaria in AAF were lower than that in IAF, which consists with the relaxed selection pressure of malaria in the New World. There is no overlap between the top candidate genes detected by the two approaches, indicating the different environmental pressures AfA experienced pre-and post-population-admixture. We suggest that the new approach is reasonably powerful and can also be applied to other admixed populations such as Latinos and Uyghurs.

Link

The Taíno are extinct

Nature corrects itself for stating that the Taíno, pre-Columbian inhabitants of the Caribbean were extinct:

This article originally stated that the Taíno were extinct, which is incorrect. Nature apologizes for the offence caused, and has corrected the text to better explain the research project described.

This is, of course, nonsense. How timorous has the modern scientific culture become, that it is willing to acquiesce so easily, lest one be perceived as not having sufficient "sensitivity" in matters ethnic?

When we say that the Taíno are extinct, we are, in fact claiming that a population group is extinct. We do not say that pieces of DNA are extinct, or that words in a language are extinct. There are pieces of Taíno DNA in modern Puerto Ricans, and there are Taíno words in the Spanish spoken there. But the Taíno group is extinct.

For example, you will not found any aurochsen (Bos primigenius) in Europe today, even though they did pass on some of their genes to modern European cattle. The aurochsen are extinct, even though some of their genes persist. You can say that modern European cattle are just Bos taurus influenced by Bos primigenius in Europe, but you can't say that B. primigenius is in existence today.

Similarly, there are Etruscan words and genes floating around in Europe today, but there are no longer any Etruscans. The Etruscans are extinct. There were, there are not => they are extinct.

A group is defined by a set of common genetic (and, in some animals, cultural) features. The survival of a few of these features is not the same as the survival of the group. The fact that some modern humans have preserved bits of Neandertal immunogenetics does not reverse the fact of Neandertal extinction, because Neandertals were not reducible to bits of their immune systems.

It is well-known that Egyptian pyramids have been used for building materials since the demise of ancient Egyptian civilization. If the building blocks of the pyramids had all found themselves in Cairo buildings, we would be justified in saying that "the pyramids are gone", because the arrangement of parts called "pyramids" was no longer in existence, even though their parts remain.

It is somewhat ironic that the same crowd of "ethnically sensitive" people can simultaneously propose that differences between races and ethnic groups have no biological basis, and, at the same time, affirm the non-extinction of an ethnic group precisely on account of its having preserved a few bits of distinctive DNA.

Let us suppose, for the sake of argument, that five hundred years into the future, there is a United Europe, with English as its common language. Further suppose, that in a province of that United Europe, say Finland, the population's gene pool is composed of 10% current Finnish DNA and 90% other European/non-European DNA. Would we be justified in saying that the Finns were extinct?

Bits of our DNA have reached us from the remotest depths of time, joined, more recently, by bits of our culture. They aggregate, for a time, into distinctive biocultural packages, such as the Taíno, they are transformed, and then they are dissolved: some dying out, some latching onto new units. The Taíno are extinct, but parts of them remain.

First aboriginal Australian genome published

Aboriginal Australians (AA) have been somewhat of a black hole in population genetics research. So, it's great news that after today's Reich et al. paper on Denisova admixture, there is another new paper that presents the first full genome sequence of an aboriginal Australian.

I don't know why it has been so difficult to study AAs so far; my guess is that some type of politics has prevented it, similar to those that have hindered population genetics research in some Amerindian groups. Unfortunately, the current publication does not seem to represent the beginning of a new era in AA research, as the genome does not belong to a living AA, but rather to a 100-year old hair sample.

On one hand this makes sense: old DNA is preferable to fresh one when one deals with populations that have undergone admixture in recent times. I don't know how many AA have European admixture, but my guess is that, surely, pure-blooded living AA still exist, so, one could in principle obtain DNA from them.

Nonetheless, we should be thankful for the new data which provide a much needed new data point of mankind's diversity. Also, given recent developments, even a single genome may prove to be invaluable.

The supplementary material (pdf) has, as usual, most of the interesting details of the paper.

Coverage in the Australian.

(to be continued)

UPDATE: I will take the age estimates in the paper with a grain of salt, because they are not independent estimates, but rely on a calibration of the European-East Asian split (fixed at 2,000 generations), and the Out-of-Africa event (fixed at 3,500 generations). Hence, from the supplement:

Based on how our model was set up, the European-Aboriginal Australian and African-Aboriginal Australian split times that we presented above could be no less than 2,000 and 3,500 generations ago, respectively.

So, at most the data shows that Europeans are closer related to East Asians than either of them is to Australian aboriginals. The actual ages in years are conditioned on the timing of the aforementioned events, which, in turn, have been estimated in the past using various assumptions (see my recent post on Gronau et al. 2011).

Science DOI: 10.1126/science.1211177

An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia

Morten Rasmussen et al.

ABSTRACT

We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow between populations of the two dispersal waves prior to the divergence of Native Americans from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.

Link