Sub-Saharan admixture in West Eurasian groups (Moorjani et al. 2011)

Let me preface this by saying that I don't doubt that there exists some Sub-Saharan admixture in some West Eurasian (Caucasoid) groups, and I've quantified the different types of African admixture that can be found in many such groups, most recently here.

However, there are serious methodological flaws in a new paper by Moorjani et al. which render its estimates unreliable. This is unfortunate, as the authors assembled an important dataset, but they only consider a very simplistic model of 2-population admixture which is completely inappropriate for the problem they are studying.

Caucasoids on the Chinese-San axis of variation

Moorjani et al. motivate their study by projecting various West Eurasian groups from Europe and the Near East onto the first principal component of variation defined by CHB (Chinese) and San (Bushmen). The reasoning is the following:

To study the signal of African gene flow into West Eurasian populations, we began by computing principal components (PCs) using San Bushmen (HGDP-CEPH- San) and East Eurasians (HapMap3 Han Chinese- CHB), and plotted the mean values of the samples from each West Eurasian population onto the first PC, a procedure called ‘‘PCA projection’’ [17,18]. The choice of San and CHB, which are both diverged from the West Eurasian ancestral populations [19,20], ensures that the patterns in PCA are not affected by genetic drift in West Eurasians that has occurred since their common divergence from East Eurasians and South Africans.

This is indeed a good idea: if some Caucasoid group A has a common ancestral element with Sub-Saharans that is lacking in another Caucasoid group B, then A is expected to be shifted towards the San side of the first PC relative to B. Indeed, this is what the authors observe:

We observe that many Levantine, Southern European and Jewish populations are shifted towards San compared to Northern Europeans, consistent with African mixture, and motivating formal testing for the presence of African ancestry (Figure 1, Figure S2).

However, this is clearly a case of seeing the glass half full. The authors prefer the hypothesis that some Caucasoid groups have African ancestry, although the hypothesis that other Caucasoid groups have East Asian ancestry can equally well explain the observed pattern. Indeed, both hypotheses may explain the phenomenon they observe.

For example, African ancestry in Palestinians has been well-documented, so Palestinians are expected to be San-shifted relative to northern Europeans. On the other hand, East Eurasian ancestry has also been well-documented in HGDP Russians, so we expect them to be CHB-shifted relative to southern Europeans.

Things are not that clear for other Caucasoid populations, e.g., southern Europeans or northwestern Europeans. The authors assume that the different position of these two groups on the San-Chinese axis is due only to Sub-Saharan admixture in southern Europeans. This implicit assumption is the Achilles' heel of the paper.

Tests of population admixture

Because of genetic drift, two populations that diverged from a common ancestor will have different allele frequencies. However, imagine if we looked at these allele differences and saw that a population A not only had different frequencies than B, but also the difference in frequencies tended to be in the direction of a Sub-Saharan population. For example, at some locus f(A)=0.4, f(B)=0.3, and f(Sub-Saharan)=0.1. You can see that B's frequency deviates from A's in the direction of Sub-Saharans. This may occur due to random drift for one particular marker, but if it occurs systematically across the genome, then admixture is a likely explanation. This is the basis of the 3-population test used by the authors.

Another idea is to see whether frequency differences between A and B are correlated with frequency differences between Sub-Saharans and another Eurasian population unrelated to either A or B. Differences between Caucasoids and Sub-Saharans are (in part) due to divergence between Sub-Saharans and ancestral Eurasians. Suppose, for example, that we've identified a group (e.g., Papuans) unlikely to have admixed with Caucasoids. If B differs from A (over many markers) in the same direction that Sub-Saharans differ from Papuans, this is consistent with the notion that B has some Sub-Saharan admixture that A lacks. This is the basis of the 4-population test.

Note that because of symmetry, a highly negative value in their 4-population test (x, CEU, Papuan, YRI) indicates Sub-Saharan admixture, while a highly positive one would indicate "Papuan" admixture! The authors do observe positive values, suggesting that some northern European populations are Papuan-shifted even with respect to CEU, most notably Russia with a Z-score of 11.4. Thankfully, we are spared a paper on Papuan admixture in Russia.

Comparison to the Indian Cline work

These tests are an important statistical tool, and many of this paper's authors have used them before to study the Indian Cline of populations. However, the current paper has two important shortcomings in comparison to Reich et al. (2009).

In their study of the Indian Cline, Reich et al. (2009) excluded groups that were shifted towards CHB, thus ensuring that they were left with groups that could be modeled as a simple mix of two ancestral population elements.

Moreover, they used the Onge a relatively isolated population from the Indian Ocean as a control group that could be said to form a clade with Ancestral South Indians at the exclusion of West Eurasians. In the current paper it is simply assumed that northern Europeans have no African admixture.

Application of the test to each West Eurasian population (using A = YRI and B= CEU) finds little or no evidence of mixture in North Europeans but highly significant evidence in many Southern European, Levantine and Jewish groups (Table 1).

In other words: taking CEU (a northern European population) as the standard, northern Europeans have no evidence of African admixture.

Sardinians: an important test case

Sardinians are an important test case for the authors' model. Their 3-population test shows no evidence of admixture, while the 4-population test does. Moreover, their STRUCTURE analysis shows a trivial 0.2%, whereas the authors estimate their Sub-Saharan admixture as 2.9%.

Let's begin by performing a PCA analysis of Sardinians, CHB, and CEU, which is shown below.

(All PCA analyses are done in smartpca as implemented in EIGENSOFT 4.0 beta, withnumoutlieriter set to 0. All analyses are performed over datasets merged in PLINK with the --geno 0.001 flag, which effectively keeps only common markers and ensures a high quality dataset)

CEU is shifted towards CHB relative to Sardinian. This is made more visually obvious if we blow up the CEU/CHB portion of the above plot:

CEU is shifted towards CHB by 2.4% relative to Sardinians. This is quite close to the 2.5% East/South Asian K=3 admixture for Britons in my most recent analysis, done with a different East Asian reference and a different method (ADMIXTURE); the CEU sample of White Utahns has been repeatedly shown to be most similar to people from the British Isles or Northwestern Europe.

Now, let's look at Sardinians, CHB, and YRI:

and a blowup:



Sardinians are shifted 1.1% relative to CEU towards YRI. Again, this is close to the 0.9% K=3 Sub-Saharan ADMIXTURE result I recently obtained.

So, where does the 2.9% Sub-Saharan admixture in Sardinians come from? Moorjani et al. estimate this percentage under the assumption that Northern Europeans are not shifted towards Chinese, i.e., that East Eurasians are irrelevant. Clearly, as we have seen, this is wrong. As we shall see, this erroneous assumption leads to the erroneous admixture estimate.

2.9% Sub-Saharan admixture in Sardinians (?)

Now, I will demonstrate how the spurious 2.9% result can be obtained. By doing so, it will become obvious why Moorjani et al. obtained this result as a result of ignoring the eastern Asian shift of their northern European sample in their analysis.

Here is a PCA plot of Sardinians, CEU, CHB, YRI:



and the blowup:


When we run all four populations together, Sardinians are shifted towards YRI along Dimension 1, and CEU are shifted towards CHB along Dimension 2. Given that the eigenvalue for PC1 is approximately twice (50.15) that for PC2 (25.31), and doing a little high school geometry on the triangle (Sardinian, CEU, YRI), we project Sardinian onto the CEU-YRI line, intersecting at point X. We thus obtain the estimated "CEU" admixture as:

[distance(YRI,X)-distance(X,CEU)]/[distance(YRI,X)+distance(X,CEU)]

= [distance(YRI, Sardinian)^2-distance(CEU,Sardinian)^2] / distance(CEU,YRI)^2

which equals 0.971021, and so, "YRI" admixture is 2.9%!

Ashkenazi Jews

The example of the Sardinians showed how lack of controling for East Eurasian shift tended to overestimate the degree of Sub-Saharan admixture. Another test case is that of Ashkenazi Jews. The authors find no evidence of admixture with their 3-population test, but do find such evidence with their 4-population test, as well as with STRUCTURE.

On a PCA plot of CHB, Ashkenazi (Behar et al. 2011), and CEU, the Ashkenazi are shifted 3.3% towards CHB along eigenvector 1.

On a PCA plot of YRI, CEU, and Ashkenazi, the Ashkenazi are shifted by 5.3% towards YRI.

In the case of the Sardinians, their African-shift together with CEU's Asian-shift caused Sardinians/CEU to diverge on the African-Asian axis, and Moorjani et al. took the entirety of this divergence to represent African admixture in Sardinians.

In this case Ashkenazi are both Asian- and African-shifted relative to CEU. The two shifts partially cancel each other out: Ashkenazi are pulled towards Africans on the YRI-CHB axis because of their YRI-shift, and away from them because of their CHB-shift. Failing to account for these processes, the authors assume that only Sub-Saharan admixture in Ashkenazi can accont for the different position of CEU and Ashkenazi on the Asian-African axis, coming up with a 2.8-3.2% "Sub-Saharan admixture" in two different samples.

And, here is a second way of seeing how this spurious admixture estimate follows from the phenomenon I am describing. CEU are (in terms of Fst) 0.76 times distant from CHB as they are from YRI (Fst=0.17 and 0.129). In other words, Sub-Saharan admixture is more "potent" at shifting a population than East Eurasian ancestry is. Ashkenazi are YRI-shifted by 5.3%, and they are CHB-shifted by 3.3%. Multiplying the latter by 0.76 we obtain: 5.3-0.76*3.3 = 2.8%!

In other words, the 2.8% Sub-Saharan admixture in Ashkenazi Jews is a compromise between two different phenomena in a tug-of-war. It is not an accurate estimate of admixture.

Papuans

I have also carried an experiment with Sardinians, Ashkenazi Jews, CEU, and Papuans, instead of CHB, as Papuans are also used in the paper as an outgroup population.

and the blowup:

It is clear that the populations show differential shift towards Papuans that is concordant with their above-described shift towards the Chinese.

Luhya and Bilala

Failure to correct for differential shift towards Chinese/Papuans is problem enough, but the paper also fails to properly take into account non-West African populations. North African groups are conspicuous in their absence, while the HapMap3 Luhya (LWK) and a Bilala sample are used to represent East Africa.

Henn et al. (2011) contains Tuscan, Yoruba, Maasai, Bulala samples, so I ran the Tuscans as test data in a supervised ADMIXTURE 1.1 analysis together with these African groups, HGDP-CEPH North_Italian, and HapMap3 CEU. That is, I'm playing along -for the sake of argument- with the idea that East Eurasians are irrelevant, and Tuscans can be seen as a mixture of CEU "Europeans" and African groups.

The results are unambiguous: Tuscans/North Italians are found to be 2.1%/1.2% "Maasai" and 0% of all the other African groups. In other words whatever element there is in common between Tuscans and Africans is not particularly West African.

The inclusion in the paper of HapMap3 Luhya Bantu but not of HapMap3 Luhya Maasai is puzzling, and the choice of one group over the other is passed in silence.

In my own experiments, I distinguish between North, Sub-Saharan, and East African ancestral components.

Beyond a binary worldview

Much more can be said, but let's summarize: the model of Moorjani et al. (2011) fails because:

1. It does not account for the West-East Eurasian axis, folding everything onto the North European-Sub-Saharan African one
2. It undersamples African diversity by excluding both North African and East African populations

Perhaps I'll add more in the future, but I believe I've already said enough to cast serious doubt on this paper's conclusions.

PLoS Genet 7(4): e1001373. doi:10.1371/journal.pgen.1001373

The History of African Gene Flow into Southern Europeans, Levantines, and Jews

Priya Moorjani, Nick Patterson, Joel N. Hirschhorn, Alon Keinan, Li Hao, Gil Atzmon, Edward Burns, Harry Ostrer, Alkes L. Price, David Reich

Abstract

Previous genetic studies have suggested a history of sub-Saharan African gene flow into some West Eurasian populations after the initial dispersal out of Africa that occurred at least 45,000 years ago. However, there has been no accurate characterization of the proportion of mixture, or of its date. We analyze genome-wide polymorphism data from about 40 West Eurasian groups to show that almost all Southern Europeans have inherited 1%–3% African ancestry with an average mixture date of around 55 generations ago, consistent with North African gene flow at the end of the Roman Empire and subsequent Arab migrations. Levantine groups harbor 4%–15% African ancestry with an average mixture date of about 32 generations ago, consistent with close political, economic, and cultural links with Egypt in the late middle ages. We also detect 3%–5% sub-Saharan African ancestry in all eight of the diverse Jewish populations that we analyzed. For the Jewish admixture, we obtain an average estimated date of about 72 generations. This may reflect descent of these groups from a common ancestral population that already had some African ancestry prior to the Jewish Diasporas.

Link

Some ADMIXTURE estimates in Eurasia

(Last Update: Sep 29)

Continuing my exploration of ADMIXTURE, I turned to the HGDP data, which has 660,918 SNPs for a wide assortment of worldwide populations. After pruning 12,086 SNPs with more than 1% missing genotypes, I was still left with ~650k SNPs.

Here are some experiments on this dataset. First, a clustering with K=2 of Han Chinese, Russians, and Orcadians (left to right)

The emergence of 2 clusters (red=Mongoloid, blue=Caucasoid) is as expected, with Russians showing a small participation in the red cluster (7.2%). These northern Russians are believed to have a substantial Finno-Ugric genetic origin, so this is inline with a recent estimate for the eastern component in the westernmost Finno-Ugric speakers being less than 10% (but see below).

Notice a couple of Chinese individuals with a small Caucasoid component: as I've mentioned before Mongolians, and presumably northern Han have a small Caucasoid component from early movements of Iranian speakers from the west. That's an advantage of doing your own admixture analysis, that you can look at the data at a fine detail, and not rely on the published figures.

Next, a clustering of Orcadians, Uygur, and Han Chinese:
The variable admixture in Uygurs is evident (47.2-63.7%, mean: 54.2%)

Next, a clustering of Druze, Bedouin, and Bantu from Kenya.

Druze appear complete Caucasoid (red), Bantu completely Negroid (save for a couple of individuals), while Bedouins show a quite variable minor Negroid component. This variable African contribution (0-17.6%) makes an elongated cluster out of Bedouins in a recent analysis, pulling them away from other Middle Eastern populations in a Sub-Saharan direction.

Finally, I clustered European populations together with Mandenka and Han Chinese:

The populations are in the following order: Han, Mandenka, Orcadian, French Basque, French, North Italian, Tuscan, Sardinian, Russian.

Here are the admixture proportions:

Notice how the eastern component in Russians is now estimated as 10.9%. This probably reflects the inclusion of French Basque and Sardinians, i.e., populations which have historically no opportunity for eastern Eurasian admixture, rather than only Orcadians. This underscores the importance of having appropriate poles in inter-continental admixture estimates (see Appendix I).

Note also that the 100% value for the Han Chinese is not incompatible with the presence of the two aforementioned Caucasoid-admixed individuals, who are present here with an estimated 1.9% and 0.5% such admixture. However, this contributes little to the sample average of 40+ individuals.

The minor (0.1%) Sub-Saharan admixture in Tuscans and Sardinians is also interesting. As you can guess from the figure, this stems from a handful of individuals (green specks) with less than 1% admixture, which is, however more than the numerical low of 0.001% inferred for most Europeans by the software.

UPDATE I: Eurasian Cline

Below is a run for the following populations (left-to-right: French Basque, Russians, Uygur, Mongolians, Daur, Han Chinese). Notice that the Mongolic-speakers (Mongolian and Daur from HGDP have a small Caucasoid admixture, as I have mentioned before.

APPENDIX I: The importance of choosing poles

The choice of appropriate poles in the estimation of inter-continental admixture is extremely important.

If there is a racial admixture continuum between two major races, such as we observe in Eurasia, then we can express each intermediate population as a weighted sum of populations that live to the east and west of it.

For example, I will use a variable in interval [0, 1] to represent the position in the continuum, with 0: pure western, and 1: pure eastern.

A population at 0.4 can be expressed as the following weighted sum:

0.4 = 0.6*0 + 0.4*1

i.e., as an admixture of 60% western, and 40% eastern.

But, it can also be expressed as e.g.,

0.4 = 0.612*0.02 + 0.388*1

Notice that the choice of a slightly eastward-tilted "western pole" (at position 0.02 in the continuum) has resulted in a reduction of the inferred eastern component (from 40% to 38.8%).

This is exactly what happened in our example: Russian eastern admixture reduced when we used Orcadians, rather than French Basque as the western pole.

Note also, that this is all done automatically: no one told ADMIXTURE to identify these two poles: it was the presence of unlabeled individuals from different ends of the spectrum that influenced the admixture estimates for the rest.

APPENDIX II: Latent populations

Another important point that needs to be remembered has to do with the possible existence of latent ancestral populations.

For example, it is true that Eurasia (minus South Asia) is economically described as a continuum from the Caucasoids of the Atlantic coast to the Mongoloids of the Pacific, with a transition zone in Central Asia and Siberia, and spillovers on either side. But, we cannot exclude the prehistoric existence of other races in the Eurasian landmass that do not exist today in a relatively unadmixed form.

In Eurasia, the Proto-Uralic race was postulated as such a "third race" with features of its own and not reducible to simple Caucasoid-Mongoloid admixture. It is difficult to see whether these features are ancestral peculiarites (prior to admixture with Caucasoids and Mongoloids), or if they have arisen in a mixed Caucasoid-Mongoloid population.

It is also important to understand how such latent populations affect genetic continua:

First, if the latent population is equidistant from the two major races, then its admixture has no effect on an individual's position in the continuum between the two races. However, it is possible that the latent population was more related to one of the two major races. In that case, admixture with it will move a population towards that race.

So while the jury is still out about the existence of a Proto-Uralic race in Eurasia, its effects on admixed populations indicates that if it had existed it was genetically closer to Mongoloids than to Caucasoids.

Genetic Ancestry, Social Classification, and Racial Inequalities in Blood Pressure in Southeastern Puerto Rico (Gravlee et al. 2009)

I had posted when this appeared in AAPA 2008, and now the full paper has been published.

Figure 1 shows the relationship between "color" and genetic ancestry. As can be seen, the "color" categories overlap in terms of genetic ancestry, even though their averages are in the right order:

The paper is a powerful reminder that social race is not the same as genomic ancestry, and that racial disparities in an observable trait do not necessarily reflect differential genetic proclivities.

PLoS ONE 4(9): e6821. doi:10.1371/journal.pone.0006821

Genetic Ancestry, Social Classification, and Racial Inequalities in Blood Pressure in Southeastern Puerto Rico

Clarence C. Gravlee et al.

Abstract

Background

The role of race in human genetics and biomedical research is among the most contested issues in science. Much debate centers on the relative importance of genetic versus sociocultural factors in explaining racial inequalities in health. However, few studies integrate genetic and sociocultural data to test competing explanations directly.

Methodology/Principal Findings

We draw on ethnographic, epidemiologic, and genetic data collected in southeastern Puerto Rico to isolate two distinct variables for which race is often used as a proxy: genetic ancestry versus social classification. We show that color, an aspect of social classification based on the culturally defined meaning of race in Puerto Rico, better predicts blood pressure than does a genetic-based estimate of continental ancestry. We also find that incorporating sociocultural variables reveals a new and significant association between a candidate gene polymorphism for hypertension (α2C adrenergic receptor deletion) and blood pressure.

Conclusions/Significance

This study addresses the recognized need to measure both genetic and sociocultural factors in research on racial inequalities in health. Our preliminary results provide the most direct evidence to date that previously reported associations between genetic ancestry and health may be attributable to sociocultural factors related to race and racism, rather than to functional genetic differences between racially defined groups. Our results also imply that including sociocultural variables in future research may improve our ability to detect significant allele-phenotype associations. Thus, measuring sociocultural factors related to race may both empower future genetic association studies and help to clarify the biological consequences of social inequalities.

Link

Demographic history of African farmers and hunters (Cox et al. 2009)

From the paper:

Median times since the onset of population growth are 1,863 (513–6,625), 1,027 (97–6,656), and 901 (38–6,497) generations ago, for the San, Biaka and Mandenka, respectively. Given a generation interval of 28 years [21], these values correspond to chronological dates of 52, 29 and 25 thousand years ago (or 37, 21 and 18 kya if we assume a 20-year generation interval). We obtain similar results with our larger Yoruban dataset. We infer a growth rate of 1.7×10⁻⁴ per generation (4.3×10⁻⁶–6.6×10⁻²), and a time of onset of growth at 1,280 (28–6,780) generations ago (or 36 kya), and 5-fold growth from ancestral size (Table 2)

...

The data from the three surveyed non-African populations (French Basque, Chinese Han, and Melanesians) are inconsistent with the simple growth model, presumably because they reflect more complex demographic histories. In contrast, data from all four sub-Saharan African populations fit the two-phase growth model, and a range of onset times and growth rates is inferred for each population. Interestingly, both hunter-gatherers (San and Biaka) and food-producers (Mandenka and Yorubans) best fit models with population growth beginning in the Late Pleistocene.

I am very doubtful of low-level exponential growth sustained over hundreds of generations, very doubtful that modern-day human gene pools contain a strong enough signal of past demographic history, and very doubtful that the demography of Eurasians is more complex than that of Africans. The paper could probably be improved by taking into account admixture processes in Africa itself, i.e., the fact that both African farmers and hunter-gatherers are the result of fairly recent admixture events, with introgressing of "farmer" genes in both San and Pygmies being particularly important.

The observed difference in inferred demography for Eurasians and Africans certaintly means something, but it's hard to evaluate how strong the case is for the scenario proposed in this paper.

UPDATE: The authors consider a simple 2-way admixture model for either recent cryptic admixture, or the Bantu expansion (3kya):

In the presence of gene flow or admixture (or a combination of both), our inference methods would tend to overestimate the effects of population growth, thus leading us to infer slightly older and stronger growth than actually occurred.

But, what about more ancient admixture? The recent Tishkoff et al. paper suggests substantial structure and admixture in African populations that goes well beyond a simple Bantu+Hunter-gatherer model. Even clusters that appear to be homogeneous in that study may reflect stabilized blends of earlier admixture events. If Europeans came into contact with Africans after Pygmies and San had disappeared (as seems likely to happen eventually), we would not even know that such peoples ever existed. How many more small hunter groups were absorbed by expanding African populations (pre-Neolithic or Neolithic), leaving no trace today?

Unlike the authors, I think Eurasian demography is fairly simple in comparison to the African one. There is nothing metaphysical about this guess: Africa, being the cradle of Homo sapiens, is likely to have had the largest human populations, for the longest time. These populations did not sit idly for so long, waiting to be discovered by outsiders, but experienced growth, admixture, competition leading to extinction or absorption, etc.

PLoS ONE 4(7): e6366. doi:10.1371/journal.pone.0006366

Autosomal Resequence Data Reveal Late Stone Age Signals of Population Expansion in Sub-Saharan African Foraging and Farming Populations


Murray P. Cox et al.

Abstract

Background

A major unanswered question in the evolution of Homo sapiens is when anatomically modern human populations began to expand: was demographic growth associated with the invention of particular technologies or behavioral innovations by hunter-gatherers in the Late Pleistocene, or with the acquisition of farming in the Neolithic?

Methodology/Principal Findings

We investigate the timing of human population expansion by performing a multilocus analysis of≥20 unlinked autosomal noncoding regions, each consisting of ~6 kilobases, resequenced in ~184 individuals from 7 human populations. We test the hypothesis that the autosomal polymorphism data fit a simple two-phase growth model, and when the hypothesis is not rejected, we fit parameters of this model to our data using approximate Bayesian computation.

Conclusions/Significance

The data from the three surveyed non-African populations (French Basque, Chinese Han, and Melanesians) are inconsistent with the simple growth model, presumably because they reflect more complex demographic histories. In contrast, data from all four sub-Saharan African populations fit the two-phase growth model, and a range of onset times and growth rates is inferred for each population. Interestingly, both hunter-gatherers (San and Biaka) and food-producers (Mandenka and Yorubans) best fit models with population growth beginning in the Late Pleistocene. Moreover, our hunter-gatherer populations show a tendency towards slightly older and stronger growth (~41 thousand years ago, ~13-fold) than our food-producing populations (~31 thousand years ago, ~7-fold). These dates are concurrent with the appearance of the Late Stone Age in Africa, supporting the hypothesis that population growth played a significant role in the evolution of Late Pleistocene human cultures.

Link

Skeletal trauma before death in Cretans and South Africans

A a couple of days after I mentioned that levels of violence in populations could be studied by counting traumas, a new study does just that, albeit for much more recent populations.

International Journal of Osteoarchaeology doi:10.1002/oa.1096

Analysis of ante mortem trauma in three modern skeletal populations

M. Steyn et al.

Abstract

When archaeological skeletons are assessed, the prevalence (and patterns of bone involvement) of trauma is important. The number and pattern of fractures can be used to gain insight into the occurrence of interpersonal violence, workload and living conditions. However, the question remains as to how these results should be interpreted - such as what constitutes high or low levels of trauma? The aim of this study was to investigate the occurrence of trauma in a population of modern Greeks living in Crete, as well as South African (SA) whites and blacks in the Pretoria Bone and Raymond Dart collections. The sample comprised mostly of older individuals (n = 90-100 within a sex-population group). Each skeleton was studied for healed trauma. For the vertebrae, only spondylolysis was assessed. In the Greek sample, it was found that 42% of the males and 46% of females had at least one fracture, with corresponding figures of 63 and 44% for SA whites and 83 and 69% for SA blacks. Radius, rib and femur fractures were most common in Greeks, with skull, radius and ribs most common in SA whites and skull, ulna and ribs in SA blacks. These prevalences of trauma are high, but the composition of the samples (mostly of lower socio-economic origin) should be kept in mind. It may also be questioned whether these individuals reflect the society as a whole. It seems that the fractures in Greeks are mostly related to old age due to falls and accidents (radius and hip fractures), while the SA black sample reflects high prevalences of interpersonal violence (such as cranial vault and ulna fractures). The SA white sample follows a comparatively moderate pattern of trauma. These comparative figures may be useful when assessing trauma in other skeletal populations.

Link

Africans in Roman York, England

The authors used both anthroposcopy and FORDISC to assess ancestry. From the paper:

The results generated by the two different approaches for ancestral assessment were for the most part in accord. However, some individuals generated conflicting data (see Table 6). In these cases, it was the cranial vault rather than the facial characteristics that caused the discrepancy and this probably reflects a degree of intrapopulation variation, overlap, and genetic admixture (Howells, 1995). In addition, some crania showed little affinity with any of the FORDISC 3.0 reference populations (e.g., TDC472, TDC467, TDC317, and RE24, RE34, RE38) and may have originated from groups not represented in the dataset.

...

In the European groups, the crania showed the greatest affinity with the Northern European and American White reference samples. The diversity of the female crania from Trentholme Drive suggests a degree of heterogeneity, which contradicts Warwick’s (1962, p 110) assertion that the women from this site were indigenous. For the African groups, the crania demonstrated the greatest resemblance to the American Black reference samples of the nineteenth and twentieth centuries, perhaps reflecting a similar degree of genetic admixture in these populations. Individuals with a close affinity to the Egyptian skulls were also identified at both sites, and this is perhaps not surprising considering the Roman Empire included these areas of North Africa. What is also clear is that both males and females with affinities to African groups appear in both the high status Railway site and at Trentholme Drive.

American Journal of Physical Anthropology doi:10.1002/ajpa.21104 About DOI

Migration and diversity in Roman Britain: A multidisciplinary approach to the identification of immigrants in Roman York, England

Stephany Leach et al.

Abstract

Previous anthropological investigations at Trentholme Drive, in Roman York identified an unusual amount of cranial variation amongst the inhabitants, with some individuals suggested as having originated from the Middle East or North Africa. The current study investigates the validity of this assessment using modern anthropological methods to assess cranial variation in two groups: The Railway and Trentholme Drive. Strontium and oxygen isotope evidence derived from the dentition of 43 of these individuals was combined with the craniometric data to provide information on possible levels of migration and the range of homelands that may be represented. The results of the craniometric analysis indicated that the majority of the York population had European origins, but that 11% of the Trentholme Drive and 12% of The Railway study samples were likely of African decent. Oxygen analysis identified four incomers, three from areas warmer than the UK and one from a cooler or more continental climate. Although based on a relatively small sample of the overall population at York, this multidisciplinary approach made it possible to identify incomers, both men and women, from across the Empire. Evidence for possible second generation migrants was also suggested. The results confirm the presence of a heterogeneous population resident in York and highlight the diversity, rather than the uniformity, of the population in Roman Britain.

Link

Geometric morphometric quantification of Sub-Saharan cranial variation

American Journal of Human Biology doi:10.1002/ajhb.20908

A geometric morphometric approach to the quantification of population variation in sub-Saharan African crania

Daniel Franklin et al.

Abstract

We report here on new data examining cranial variation in 18 modern human sub-Saharan African populations. Previously, we investigated variation within southern Africa; we now extend our analyses to include a series of Central, East, and West African crania, to further knowledge of the relationships between, and variation and regional morphological patterning in, those populations. The sample comprises 377 male individuals; the three-dimensional coordinates of 96 landmarks are analyzed using Procrustes-based methods. Interpopulation variation is examined by calculating shape distances between groups, which are compared using resampling statistics and parametric tests. Phenotypic variance, as a proxy for genetic variance, is measured and compared across populations. Principal components and cluster analyses are employed to explore relationships between the populations. Shape differences are visualized using three-dimensional rendered models. Observed disparity patterns imply a mix of differences and similarities across populations, with no apparent support for genetic bottlenecks, which is likely a consequence of migrations that may have influenced differences in cranial form; supporting data are found in recent molecular studies. The Pygmy sample had the most distinctive cranial morphology; characteristically small in size with marked prognathism. These features characterized, although less strongly, the neighboring Bateke, and are possibly related to similar selective pressures in conjunction with interbreeding. Small cranial size is also involved in the considerable distinctiveness of the San and Khoikhoi. The statistical procedures applied in this study afford a powerful and robust means of quantifying and visualizing the magnitude and pattern of cranial variation between sub-Saharan African populations.

Link

Facial anthropometry correlates with admixture proportions in African Americans

If you doubt that facial measurements can be used to determine racial makeup, feel free to use my old black-or-white calculator, which determines the chance that a given individual is Caucasoid or Negroid - rather than admixture proportions as in this study. I would be interested to hear of biracial individuals' results though, so send me an e-mail. Quite often, people don't take accurate measurements, though, so if you get an unexpected result, the odds are that you're measuring something wrong.

Mixed Population Provides Insights Into Human Genetic Makeup

The researchers looked at a combined sample of African Americans with West African and European ancestry whose genetic makeup was known through DNA testing. To make it simpler, anyone with Native American ancestry was eliminated so that only two genetic pools were represented -- West African and European. The researchers reported on a sample of 254 individuals using three-dimensional imaging and measured the distances between specific portions of the face. Each individual had provided a DNA sample.

...

From their DNA profiles, Shriver could determine the admixture percentages of each individual, how much of their genetic make up came from each group. He could then compare the genetically determined admixture to the facial feature differences and determine the relative differences from the parental populations.

...

Shriver found that there was a very strong statistical correlation between the amounts of admixture and the facial traits.

Common origin and differential admixture in Western Central African pygmies

The coverage of this at News at Nature is quite clear.

Current Biology doi:10.1016/j.cub.2008.12.049

Origins and Genetic Diversity of Pygmy Hunter-Gatherers from Western Central Africa

Paul Verdu et al.

Abstract

Central Africa is currently peopled by numerous sedentary agriculturalist populations neighboring the largest group of mobile hunter-gatherers, the Pygmies [1,2,3]. Although archeological remains attest to Homo sapiens' presence in the Congo Basin for at least 30,000 years, the demographic history of these groups, including divergence and admixture, remains widely unknown [4,5,6]. Moreover, it is still debated whether common history or convergent adaptation to a forest environment resulted in the short stature characterizing the pygmies [2,7]. We genotyped 604 individuals at 28 autosomal tetranucleotide microsatellite loci in 12 nonpygmy and 9 neighboring pygmy populations. We found a high level of genetic heterogeneity among Western Central African pygmies, as well as evidence of heterogeneous levels of asymmetrical gene flow from nonpygmies to pygmies, consistent with the variable sociocultural barriers against intermarriages. Using approximate Bayesian computation (ABC) methods [8], we compared several historical scenarios. The most likely points toward a unique ancestral pygmy population that diversified 2800 years ago, contemporarily with the Neolithic expansion of nonpygmy agriculturalists [9,10]. Our results show that recent isolation, genetic drift, and heterogeneous admixture enabled a rapid and substantial genetic differentiation among Western Central African pygmies. Such an admixture pattern is consistent with the various sociocultural behaviors related to intermariages between pygmies and nonpygmies.

Link

The Population Reference Sample (POPRES)

This sample was also used in the recent study of European variation. From the paper:

As expected, the first principal component (PC 1) distinguishes Africans from non-Africans. The next three principal components also characterize continental regions: PC 2 distinguishes East Asians from Africans and Europeans, with South Asians and Mexicans at intermediate values; PC 3 distinguishes South Asians from East Asians; and PC 4 distinguishes Mexicans from non-Mexicans. The subsequent principal components mark within-continent variation. PC 5 reveals a north-to-south cline within Europeans (Figure 3), consistent with existing studies of European substructure. [...] PC 6 distinguishes the African Americans from the HapMap Africans. [...] Principal component 7 (Figure 2D) separates the three East Asian populations: Japan (left), HapMap CHB (center right), and Taiwan (far right). [...] We do not show further results because PC 8 and subsequent PCs display substructure within Africans and African Americans, but do not correspond to any known geographic or population structure among individuals.

The American Journal of Human Genetics, doi:10.1016/j.ajhg.2008.08.005

The Population Reference Sample, POPRES: A Resource for Population, Disease, and Pharmacological Genetics Research

Matthew R. Nelson et al.

Abstract

Technological and scientific advances, stemming in large part from the Human Genome and HapMap projects, have made large-scale, genome-wide investigations feasible and cost effective. These advances have the potential to dramatically impact drug discovery and development by identifying genetic factors that contribute to variation in disease risk as well as drug pharmacokinetics, treatment efficacy, and adverse drug reactions. In spite of the technological advancements, successful application in biomedical research would be limited without access to suitable sample collections. To facilitate exploratory genetics research, we have assembled a DNA resource from a large number of subjects participating in multiple studies throughout the world. This growing resource was initially genotyped with a commercially available genome-wide 500,000 single-nucleotide polymorphism panel. This project includes nearly 6,000 subjects of African-American, East Asian, South Asian, Mexican, and European origin. Seven informative axes of variation identified via principal-component analysis (PCA) of these data confirm the overall integrity of the data and highlight important features of the genetic structure of diverse populations. The potential value of such extensively genotyped collections is illustrated by selection of genetically matched population controls in a genome-wide analysis of abacavir-associated hypersensitivity reaction. We find that matching based on country of origin, identity-by-state distance, and multidimensional PCA do similarly well to control the type I error rate. The genotype and demographic data from this reference sample are freely available through the NCBI database of Genotypes and Phenotypes (dbGaP).

Link

Nasal passage differences between Caucasoids and Negroids

American Journal of Physical Anthropology

Ecogeographic variation in human nasal passages

Todd R. Yokley

Abstract

Theoretically, individuals whose ancestors evolved in cold and/or dry climates should have greater nasal mucosal surface area relative to air volume of the nasal passages than individuals whose ancestors evolved in warm, humid climates. A high surface-area-to-volume (SA/V) ratio allows relatively more air to come in contact with the mucosa and facilitates more efficient heat and moisture exchange during inspiration and expiration, which would be adaptive in a cold, dry environment. Conversely, a low SA/V ratio is not as efficient at recapturing heat and moisture during expiration and allows for better heat dissipation, which would be adaptive in a warm, humid environment. To test this hypothesis, cross-sectional measurements of the nasal passages that reflect surface area and volume were collected from a sample of CT scans of patients of European and African ancestry. Results indicate that individuals of European descent do have higher SA/V ratios than individuals of African descent, but only when decongested. Otherwise, the two groups show little difference. This pattern of variation may be due to selection for different SA/V configurations during times of physical exertion, which has been shown to elicit decongestion. Relationships between linear measurements of the skeletal nasal aperture and cavity and cross-sectional dimensions were also examined. Contrary to predictions, the nasal index, the ratio of nasal breadth to nasal height, is not strongly correlated with internal dimensions. However, differences between the nasal indices of the two groups are highly significant. These results may be indicative of different adaptive solutions to the same problem.

Link

ESHG 2008 abstracts

The European Society of Human Genetics conference is coming up, and there are some very interesting abstracts.

Note: The ESHG site has updated with a notice that the abstracts are embargoed until their presentation time. Therefore, I have decided to remove the body of this post until then, although I think it is a bit weird to embargo something that one places on the public web. In any case, you can find the abstracts easily by going to the site above. (June 1): post restored.

The peopling of North Asia: Y and X perspectives

V. A. Stepanov, V. Kharkov, I. Khitrinskaya, O. Medvedeva, M. Spiridonova, A. Marusin, V. Puzyrev; Institute for Medical Genetics, Tomsk, Russian Federation.

Presentation Number: P07.056

To reconstruct the origin and evolution of human populations in North Asia we investigated the genetic diversity in 50 population samples (about 2000 individuals totally) using Y and X chromosome lineages. Y-chromosomal haplotypes were constructed with unique event polymorphisms (UEP) and STR markers according to Y Chromosome consortium (YCC) classification. SNP markers in a single 60 kb linkage disequilibrium region of ZFX gene was used to trace the X chromosomal population history. The genetic diversity of Y haplogroups was quite high (0.70 - 0.95) in most populations except few very isolated groups. The proportion of inter-population differences in the total genetic variability measured by Fst statistics is 17% for binary haplogroups and 19% for YSTR. Multidimensional scaling and principal component analysis revealed four major components in North Asian Y gene pool, reflecting the presence of Paleoasiatic (Q), Proto-Uralic (N3, N2), Eastern Asian (O, C), and Western Eurasian (R1, I, J) lineages. X-chromosomal haplotypes in North Asia are less divers (gene diversity within populations 0.65 - 0.80) and less differentiated (Fst = 4%) compared to Y lineages. The population clustering by X and Y gives, to a first approximation, a similar picture, and matrixes of genetic distances between populations for X and Y haplotypes significantly correlates. The age of genetic diversity generation and time of population differentiation demonstrates the Upper Paleolithic origin of major Y and X lineages and post-glacial population expansions. This work is supported by RFBR grants ##06-04-48274 and 07-04-01629.

The following seems to be a very important study; in particular the notion that particular Y chromosome/mtDNA haplogroups may be associated with higher or lower fertility may have implications about their distribution.

UPDATE (May 21): I did a quick and dirty analysis of the Y-haplogroup and mtDNA-haplogroup data from Bosch et al. (2006) (Ann Hum Genet. 2006 Jul;70(Pt 4):459-87.), and there is a -0.43 correlation between Y-haplogroup I and mtDNA-haplogroup H and a +0.46 correlation between Y-haplogroup R1 and mtDNA-haplogroup H. While not significant (with only 10 populations), this is definitely in the right direction for a selection effect for/against specific Y-DNA/mtDNA combinations.

... on the other hand, another quick and dirty analysis of 23 populations from Rootsi's survey on Y-haplogroup I and mtDNA frequencies from AJHG Volume 80, Issue 4, April 2007, Pages 759-768 didn't turn up any correlation. Perhaps, someone can look at possible correlations between Y-chromosome and mtDNA haplogroups in Europe to see if anything interesting turns up.

Male infertility induced by mtDNA/Y unfavorable combination? An association study on human mitochondrial DNA

S. C. Gomes1, S. Fernandes2, R. Gonçalves1, A. T. Fernandes1, A. Barros3, H. Geada4, A. Brehm1; 1Human Genetics Laboratory, University of Madeira, Funchal, Portugal, 2Genetics Department, Faculty of Medicine, University of Porto, Porto, Portugal, 3Centre of Reproductive Genetics A Barros, Porto, Portugal, 4Faculty of Medicine, University of Lisbon, Lisboa, Portugal.

Presentation Number: P07.084

There is growing evidence that certain mtDNA haplogroups determine a genetic susceptibility to various disorders bringing out the interest in the possible role of mtDNA background on the phenotype expression of mitochondrial genetic disorders. An association between haplogroup T and asthenospermia has been reported and several sublineages of haplogroup U were associated with differences in sperm motility and vitality. The deletion of some DAZ copies gene in 10-15% of azoospermic and oligospermic patients has been reported but also present in fertile men belonging to certain Y-haplogroups. The findings of one study have rarely been replicated by studies in other populations and conflicting associations have been reported. Our focus in this case-control study is to investigate the existence of other influences, besides a weak mtDNA background, promoting male infertility. The occurrence of a specific mtDNA variant associated to a certain Y-chromosome haplogroup could represent a vital link that will compromise the sperm function and be responsible for male infertility. A group of 99 infertile men and other one composed by 90 subjects with proven fertility were selected and analysed. The frequency of the combination mtDNA-haplogroup H (especially with the CRS sequence) and Y-haplogroup R was higher in fertile than in infertile men seemingly to be favorable to fertility. On the other hand, a considerable number of infertile men belonging to mtDNA-haplogroup H (CRS) and to Y-haplogroup I, associated to a specific DAZ gene deletion pattern- 2+4d, suggests a non favorable combination to male fertility.

The Bayash Roma: phylogenetic dissection of Eurasian paternal genetic elements

I. Martinovic Klaric, M. Pericic Salihovic, L. Barac Lauc, B. Janicijevic; Institute for Anthropological Research, Zagreb, Croatia.

Presentation Number: P07.110

The Bayash consist of numerous and small Romani groups speaking different dialects of the Romanian language and living dispersedly in Croatia, Hungary, Bosnia and Herzegovina, Serbia, Romania, Bulgaria, and to the lesser extent in Macedonia, Greece, Ukraine, Slovakia and Slovenia. Larger Bayash groups migrated to Croatia most likely during the 19th century, after abolition of slavery in Romania. Molecular architecture and the origin of the Croatian Bayash paternal gene pool was addressed by analysing 151 Bayash Y chromosomes from two Croatian regions, 332 Y chromosomes from Romani populations across Europe, 814 Y-chromosomes from non-Romani host populations living in Southeastern, Southern and Eastern Europe as well as with 1680 Y-chromosomes from South Asian populations. The Bayash in Croatia represent one population of largely shared paternal genetic history characterized by substantial percentage (44%) of common H1-M82 and E3b1-M78 lineages. Relatively ancient expansion signals and limited diversity of Indian specific H1-M82 lineages imply descent from closely related paternal ancestors who could have been settled in the Indian subcontinent between 7th and 9th centuries AD. Minimal time divergence of the Bayash subpopulations is consistent with their putative migratory split within Romania towards Wallachia and Transilvania. Substantial percentage of E3b1 lineages and high associated microsatellite variance in the Bayash men is a reflection of significant admixture with majority populations from the Vardar-Morava-Danube catchment basin - possibly a common paternal signature of Romani populations in Southeastern Europe. Additional traces of admixture are evident in the modest presence of typical European haplogroups.

Are the Moravian Valachs of Czech Republic the Aromuns of Central Europe? Model population for isolation and admixture

E. Ehler1,2, V. Vančata2; 1Department of Anthropology and Human Genetics, Charles University in Prague, Faculty of Science, Prague, Czech Republic, 2Department of Biology and Ecological Education, Charles University in Prague, Faculty of Education, Prague, Czech Republic.

Presentation Number: P07.129

Moravian Valachs of Czech Republic are one of the most distinct ethnic groups from Central Europe. Related to similar populations in Poland and Slovakia, they emerge at the end of 15th century, as the north-westernmost prominence of migration that started 250 years earlier in northern Romania. Being predominately highland sheep herders and of putative Romanian origin, they represent a Central European analogue of Balkan Aromanian populations. We have gathered Y-chromosomal, linguistic, ethnographic and historical data for this population and compared them with surrounding as well as with east European populations. Linguistic data show specific parts of shared vocabulary of Romanian origin between several pastoral groups in Central and Eastern Europe. Comparing genetic and linguistic pairwise distance matrices (Mantel test) in these populations did not revealed any significant correlation. Thus we confirmed that plain geographical distance still plays the major role in genetic distances between populations in Europe. From our further analysis it is clear, that the Moravian Valachs, after at least five centuries of admixture, are not overly genetically different from surrounding populations. On the other hand, from the point of view of intra-population diversity, they are much more similar to isolated Balkan populations (e.g. Aromuns) than to Central European populations.

Phylogeography of the human Y chromosome haplogroup E3a

F. Cruciani1, B. Trombetta1, D. Sellitto2, C. Nodale1, R. Scozzari1; 1Sapienza Università di Roma, Rome, Italy, 2Consiglio Nazionale delle Ricerche, Rome, Italy.

Presentation Number: P07.134

The Y chromosome specific biallelic marker DYS271 defines the most common haplogroup (E3a) currently found in sub-Saharan Africa. A sister clade, E3b (E-M215), is rare in sub-Saharan Africa, but very common in northern and eastern Africa. On the whole, these two clades represent more than 70% of the Y chromosomes of the African continent. A third clade belonging to E3 (E3c or E-M329) has been recently reported to be present only in eastern Africa, at low frequencies. In this study we analyzed more than 1,600 Y chromosomes from 55 African populations, using both new and previously described biallelic markers, in order to refine the phylogeny and the geographic distribution of the E3a haplogroup. The most common E-DYS271 sub-clades (E-DYS271*, E-M191, E-U209) showed a non uniform distribution across sub-Saharan Africa. Most of the E-DYS271 chromosomes found in northern and western Africa belong to the paragroup E-DYS271*, which is rare in central and southern Africa. In these latter regions, haplogroups E-M191 and E-U209 show similar frequency distributions and coalescence ages (13 and 11 kyr, respectively), suggesting their involvement in the same migratory event/s. By the use of two new phylogenetically equivalent markers (V38 and V89), the earlier tripartite structure of E3 haplogroup was resolved in favor of a common ancestor for haplogroups E-DYS271 (formerly E3a) and E-M329 (formerly E3c). The new topology of the E3 haplogroup is suggestive of a relatively recent eastern African origin for the majority of the chromosomes presently found in sub-Saharan Africa.

Y-chromosome lineages in Xhosa and Zulu Bantu speaking populations

R. P. A. Gonçalves, H. Spínola, A. Brehm; Human Genetics Laboratory, Funchal, Portugal.

Presentation Number: P07.137

Y-chromosome Single Nucleotide Polymorphisms have been analysed in Zulu and Xhosa, two southern Africa Bantu speaking populations. These two ethnic groups have their origin on the farmer’s Bantu expansion from Niger-Congo border towards sub-Sahel regions on the southern tip of the continent, during the past 3000 years. Seven different Y-chromosome haplogroups were found in Zulu contrasting with only two in Xhosa. E3a, a common haplogroup among West sub-Saharans associated to Bantu migration was the most prevalent in both populations (56.9% in Zulu and 90% in Xhosa). The second most common haplogroup was E2 (29.3% in Zulu and 10% in Xhosa), present both in West and East African populations. The present-day Zulu and Xhosa paternal legacy is essentially of West sub-Saharan origin. Zulu population shows a most diverse genetic influence comparing to Xhosa, revealing some pre-Bantu expansion markers and East African influences. Zulu presents 8.6% Y-chromosome haplogroups (A, B, J1) of non-Bantu influence that could indicate gene flow from other populations, particularly Khoisan.

Human genetic population structure: Patterns and underlying processes

Presentation Time: Tuesday, 9:15 a.m. - 9:45 a.m.

G. Barbujani; University of Ferrara, Department of Biology and Evolution, Ferrara, Italy.

Presentation Number: S15.2

Classical studies of genetic diversity in humans consistently showed that the largest proportion of human diversity occurs among members of the same population. On average, differences among different populations in the same continent represent 5% of the global human variance, and differences among continents another 10%. Genetic variation is largely discordant across the genome, meaning that different loci show different spatial patterns, and implying that a good description of population structure can only be based on the analysis of multiple loci. Studies of single loci are also unlikely to reasonably identify an individual’s place of origin. A general decline of genetic of genetic diversity with distance from Africa, and a parallel increase in linkage disequilibrium, can be accounted for by the effects of a series of founder effects accompanying the spread of anatomically-modern humans from Africa. Recent DNA analyses at the global level show that most allelic variants are cosmopolitan and only a small percentage are continent-specific, whereas a clearer continental structure emerges when considering composite haplotypes. This suggests that, at the global level, gene flow has had a strong impact on genetic diversity, through both directional dispersal and successive short-range migratory exchanges. At the local level, several factors have contributed to genetic differentiation, and, in particular, language barriers have been shown to be associated with small but non-negligible increases of the genetic differences between neighboring populations.

Hierarchical analysis of 28 Y-chromosome SNP’s in the population of the Republic of Macedonia

P. Noveski, S. Trivodalieva, G. D. Efremov, D. Plaseska-Karanfilska;
Macedonian Academy of Sciences and Arts, Research Centre for Genetic Engineering and Biotechnology, Skopje, Macedonia, The Former Yugoslav Republic of.

Presentation Number: P05.211

Analysis of Y-chromosome haplogroups, defined by single nucleotide polymorphisms (SNP’s), has become a standard approach for studying the origin of human populations and measuring the variability among them. Furthermore, Y-SNP’s represent a new forensic tool, because their population specificity may allow to determine the origin of any male sample of interest for forensic purposes. The aim of this study was to develop a strategy for rapid, simple and inexpensive Y-chromosome SNP’s typing in the population of R. Macedonia. We have studied a total of 343 DNA male samples; 211 Macedonians, 111 Albanians and 21 of other ethnic origin (Roma, Serbs and Turks). Methodology included multiplex PCR and single nucleotide extension reaction by SNaPshot multiplex kit. The set of 28 markers has been grouped in 5 multiplexes in order to determine the most frequent haplogroups using only 1 or 2 multiplexes. Twenty different Y haplogroups were determined among 343 male DNA samples. The finding that five haplogroups (E3b1, I1b1, J2b1a, R1a and R1b) comprise more than 70% of the Y chromosomes is consistent with the typical European Y chromosome gene pool. The distribution of the Y-haplogroups differs between Macedonians and Albanians. The most common Y haplogroup among Macedonians is I1b1 (27.5%), followed by three haplogroups present with similar frequencies E3b1 (15.6%), R1a (14.2%) and R1b (11.4%). Among Albanians the most frequent Y haplogroup is E3b1 (28.8%), followed by R1b (18.0%), J2b1a (13.5%) and R1a (12.6%).

The following paper (probably) refers to a recent study, according to which:

One of the most elevated values of 35delG prevalence corresponds to Greece (1/28); the pattern of various 35delG prevalences is interpretated in the present meta-analysis as the result of Ancient Greek colonizations of the "Magna Grecia" in historical times.

Strong linkage disequilibrium for the frequent GJB2 35delG mutation in the Greek population
H. Kokotas¹, L. Van Laer², M. Grigoriadou¹, V. Iliadou³, J. Economides⁴, S. Pomoni¹, A. Pampanos¹, N. Eleftheriades⁵, E. Ferekidou⁶, S. Korres⁶, A. Giannoulia-Karantana⁷, G. Van Camp², M. B. Petersen¹;
¹Institute of Child Health, Athens, Greece, ²University of Antwerp, Antwerp, Belgium, ³AHEPA Hospital, Thessaloniki, Greece, ⁴‘Aghia Sophia’ Children’s Hospital, Athens, Greece, ⁵St. Loukas Hospital, Thessaloniki, Greece, ⁶Athens University, Athens, Greece, ⁷Athens University Medical School, Athens, Greece.

Presentation Number: P06.080

Approximately one in 1,000 children is affected by severe or profound hearing loss at birth or during early childhood (prelingual deafness). Up to forty percent of autosomal recessive, congenital, severe to profound hearing impairment cases result from mutations in a single gene, GJB2. The 35delG mutation accounts for the majority of GJB2 mutations detected in Caucasian populations and represents one of the most frequent disease mutations identified so far. Some previous studies have assumed that the high frequency of the 35delG mutation reflects the presence of a mutational hot spot, whilst other studies support the theory of a common founder. Greece is amongst the countries presenting high frequency of the 35delG mutation (3.5%), and a recent study raised the hypothesis of the origin of this mutation in ancient Greece. We genotyped 60 Greek deafness patients homozygous for the 35delG mutation for six single nucleotide polymorphisms (SNPs) and two microsatellite markers, mapping within or flanking the GJB2 gene, as compared to 60 Greek hearing controls. A strong linkage disequilibrium was found between the 35delG mutation and markers inside or flanking the GJB2 gene, at distances of 34 kb on the centromeric and 90 kb on the telomeric side of the gene, respectively. Our study supports the hypothesis of a founder effect and we further propose that ethnic groups of Greek ancestry could have propagated the 35delG mutation, as evidenced by historical data beginning from the 15^th century BC.

Skin color evolution in Europeans and Social skin color vs Disease in Puerto Ricans

Science last year (thanks commenter!) had a news story about the evolution of European skin color:

Researchers have disagreed for decades about an issue that is only skin-deep: How quickly did the first modern humans who swept into Europe acquire pale skin? Now a new report on the evolution of a gene for skin color suggests that Europeans lightened up quite recently, perhaps only 6000 to 12,000 years ago. This contradicts a long-standing hypothesis that modern humans in Europe grew paler about 40,000 years ago, as soon as they migrated into northern latitudes. Under darker skies, pale skin absorbs more sunlight than dark skin, allowing ultraviolet rays to produce more vitamin D for bone growth and calcium absorption. "The [evolution of] light skin occurred long after the arrival of modern humans in Europe," molecular anthropologist Heather Norton of the University of Arizona, Tucson, said in her talk.

This seems to be in agreement with accelerating recent selection in the human genome. The Science story is referring to the AAPA 2007 meeting. More from the Science story regarding the SLC24A5 gene:

The genetic origin of the spectrum of human skin colors has been one of the big puzzles of biology. Researchers made a major breakthrough in 2005 by discovering a gene, SLC24A5, that apparently causes pale skin in many Europeans, but not in Asians. A team led by geneticist Keith Cheng of Pennsylvania State University (PSU) College of Medicine in Hershey found two variants of the gene that differed by just one amino acid. Nearly all Africans and East Asians had one allele, whereas 98% of the 120 Europeans they studied had the other (Science, 28 October 2005, p. 601).

This is a wonderful confirmation of Cavalli-Sforza's prediction about recent selection for skin color:

Either way, the implication is that our European ancestors were brown-skinned for tens of thousands of years--a suggestion made 30 years ago by Stanford University geneticist L. Luca Cavalli-Sforza. He argued that the early immigrants to Europe, who were hunter-gatherers, herders, and fishers, survived on ready-made sources of vitamin D in their diet. But when farming spread in the past 6000 years, he argued, Europeans had fewer sources of vitamin D in their food and needed to absorb more sunlight to produce the vitamin in their skin. Cultural factors such as heavier clothing might also have favored increased absorption of sunlight on the few exposed areas of skin, such as hands and faces, says paleoanthropologist Nina Jablonski of PSU in State College.

Perhaps it was the larger population sizes made possible by farming that made it possible for the adaptive mutation to arise in one individual, or the mutation pre-existed in early agriculturalists.

I was looking through the book of abstracts (pdf) of this year's AAPA 2008, and another skin color-related abstract caught my attention:

Social classification, skin color, and genetic ancestry: a bio-cultural analysis of health disparities.

A.L. Non, C.C. Gravlee, C.J. Mulligan. Dept. of Anthropology, University of Florida.

Consistent disparities in health are well documented across racially defined groups for many complex diseases. Researchers have proposed both genetic and socio-cultural hypotheses to explain these disparities, but few studies combine both genetic and sociocultural data to test competing hypotheses directly. Here we address this problem in the context of debate about hypertension in populations of African descent. Some researchers suggest that people of greater African ancestry are genetically predisposed to develop high blood pressure. In support of this hypothesis, some researchers point to preliminary evidence of a modest association between blood pressure and genetic estimates of African ancestry. However, the association between ancestry and disease phenotypes may be due to residual confounding with environmental stressors such as discrimination and poverty. Our study, based on fieldwork in southeastern Puerto Rico, is the first to test these alternatives. We incorporate genetic measures of ancestry, genotyping of candidate genes, and an ethnographically derived measure of social classification that estimates how individuals’ color is perceived in everyday social interactions. We find that social classification of color, but not genetic ancestry, is associated with both systolic and diastolic blood pressure through an interaction with socioeconomic status. These findings emphasize the importance of gathering bociocultural data in studies on health and disease, rather than relying on skin color or genetic ancestry as a proxy for potential disease status.

Remember that while skin color is correlated with ancestry, the correlation is not perfect, i.e., a person with more Caucasoid than Negroid ancestry could in fact be darker than a person with more Negroid than Caucasoid ancestry (*). On top of that, the social perception of skin color may blur the picture even more, since skin color is not value-neutral in most multiracial societies. Thus, "social skin color" is two levels removed from "ancestry". What this abstract suggests is that "social skin color", rather than "ancestry" is the culprit for the disease discrepancies. Hopefully a paper on this will follow.

(*) "More" within reason, e.g., a 100% Caucasoid will be almost always lighter than a 100% Negroid.

Origins of African mtDNA in Slavs

See also Origins of Mongoloid mtDNA in Slavs. and Sub-Saharan African mtDNA admixture in several West Eurasian (Caucasoid) populations.

European Journal of Human Genetics advance online publication 9 April 2008; doi: 10.1038/ejhg.2008.70

Reconstructing the phylogeny of African mitochondrial DNA lineages in Slavs.

Malyarchuk BA, Derenko M, Perkova M, Grzybowski T, Vanecek T, Lazur J.

To elucidate the origin of African-specific mtDNA lineages, revealed previously in Slavonic populations (at frequency of about 0.4%), we completely sequenced eight African genomes belonging to haplogroups L1b, L2a, L3b, L3d and M1 gathered from Russians, Czechs, Slovaks and Poles. Results of phylogeographic analysis suggest that at least part of the African mtDNA lineages found in Slavs (such as L1b, L3b1, L3d) appears to be of West African origin, testifying to an opportunity of their occurrence as a result of migrations to Eastern Europe through Iberia. However, a prehistoric introgression of African mtDNA lineages into Eastern Europe (approximately 10 000 years ago) seems to be probable only for European-specific subclade L2a1a, defined by coding region mutations at positions 6722 and 12903 and detected in Czechs and Slovaks. Further studies of the nature of African admixture in gene pools of Europeans require the essential enlargement of databases of African complete mitochondrial genomes.

Link

Maternal common ancestry between pygmies and farmers in Central Africa

This is an Open Access article in PNAS.

PNAS 10.1073/pnas.0711467105

Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter–gatherers and Bantu-speaking farmers

Lluís Quintana-Murci et al.

Abstract

Two groups of populations with completely different lifestyles—the Pygmy hunter–gatherers and the Bantu-speaking farmers—coexist in Central Africa. We investigated the origins of these two groups and the interactions between them, by analyzing mtDNA variation in 1,404 individuals from 20 farming populations and 9 Pygmy populations from Central Africa, with the aim of shedding light on one of the most fascinating cultural transitions in human evolution (the transition from hunting and gathering to agriculture). Our data indicate that this region was colonized gradually, with an initial L1c-rich ancestral population ultimately giving rise to current-day farmers, who display various L1c clades, and to Pygmies, in whom L1c1a is the only surviving clade. Detailed phylogenetic analysis of complete mtDNA sequences for L1c1a showed this clade to be autochthonous to Central Africa, with its most recent branches shared between farmers and Pygmies. Coalescence analyses revealed that these two groups arose through a complex evolutionary process characterized by (i) initial divergence of the ancestors of contemporary Pygmies from an ancestral Central African population no more than {approx}70,000 years ago, (ii) a period of isolation between the two groups, accounting for their phenotypic differences, (iii) long-standing asymmetric maternal gene flow from Pygmies to the ancestors of the farming populations, beginning no more than {approx}40,000 years ago and persisting until a few thousand years ago, and (iv) enrichment of the maternal gene pool of the ancestors of the farming populations by the arrival and/or subsequent demographic expansion of L0a, L2, and L3 carriers.

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