Refining Y-chromosome phylogeny with South African sequences

bioRxiv http://dx.doi.org/10.1101/034983

Refining the Y chromosome phylogeny with southern African sequences

Chiara Barbieri, Alexander Hübner, Enrico Macholdt, Shengyu Ni, Sebastian Lippold, Roland Schröder, Sununguko Wata Mpoloka, Josephine Purps, Lutz Roewer, Mark Stoneking, Brigitte Pakendorf

The recent availability of large-scale sequence data for the human Y chromosome has revolutionized analyses of and insights gained from this non-recombining, paternally inherited chromosome. However, the studies to date focus on Eurasian variation, and hence the diversity of early-diverging branches found in Africa has not been adequately documented. Here we analyze over 900 kb of Y chromosome sequence obtained from 547 individuals from southern African Khoisan and Bantu-speaking populations, identifying 232 new sequences from basal haplogroups A and B. We find new branches within haplogroups A2 and A3b1 and suggest that the prehistory of haplogroup B2a is more complex than previously suspected; this haplogroup is likely to have existed in Khoisan groups before the arrival of Bantu-speakers, who brought additional B2a lineages to southern Africa. Furthermore, we estimate older dates than obtained previously for both the A2-T node within the human Y chromosome phylogeny and for some individual haplogroups. Finally, there is pronounced variation in branch length between major haplogroups; haplogroups associated with Bantu-speakers have significantly longer branches. This likely reflects a combination of biases in the SNP calling process and demographic factors, such as an older average paternal age (hence a higher mutation rate), a higher effective population size, and/or a stronger effect of population expansion for Bantu-speakers than for Khoisan groups.

Link

Ancient mtDNA from southern Africa related to San

Genome Biol Evol (2014) doi: 10.1093/gbe/evu202

First Ancient Mitochondrial Human Genome from a Pre-Pastoralist Southern African

Alan G. Morris et al.

The oldest contemporary human mitochondrial lineages arose in Africa. The earliest divergent extant maternal offshoot, namely haplogroup L0d, is represented by click-speaking forager peoples of Southern Africa. Broadly defined as Khoesan, contemporary Khoesan are today largely restricted to the semi-desert regions of Namibia and Botswana, while archeological, historical and genetic evidence promotes a once broader southerly dispersal of click-speaking peoples including southward migrating pastoralists and indigenous marine-foragers. Today extinct, no genetic data has been recovered from the indigenous peoples that once sustained life along the southern coastal waters of Africa pre-pastoral arrival. In this study we generate a complete mitochondrial genome from a 2,330 year old male skeleton, confirmed via osteological and archeological analysis as practicing a marine-based forager existence. The ancient mtDNA represents a new L0d2c lineage (L0d2c1c) that is today, unlike its Khoe-language based sister-clades (L0d2c1a and L0d2c1b) most closely related to contemporary indigenous San-speakers (specifically Ju). Providing the first genomic evidence that pre-pastoral Southern African marine foragers carried the earliest diverged maternal modern human lineages, this study emphasizes the significance of Southern African archeological remains in defining early modern human origins.

Link

Admixture in Southern Africa (Petersen et al. 2013)

Related:

• The genetic prehistory of southern Africa 
• Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History

PLoS Genet 9(3): e1003309. doi:10.1371/journal.pgen.1003309

Complex Patterns of Genomic Admixture within Southern Africa

Desiree C. Petersen et al.

Within-population genetic diversity is greatest within Africa, while between-population genetic diversity is directly proportional to geographic distance. The most divergent contemporary human populations include the click-speaking forager peoples of southern Africa, broadly defined as Khoesan. Both intra- (Bantu expansion) and inter-continental migration (European-driven colonization) have resulted in complex patterns of admixture between ancient geographically isolated Khoesan and more recently diverged populations. Using gender-specific analysis and almost 1 million autosomal markers, we determine the significance of estimated ancestral contributions that have shaped five contemporary southern African populations in a cohort of 103 individuals. Limited by lack of available data for homogenous Khoesan representation, we identify the Ju/'hoan (n = 19) as a distinct early diverging human lineage with little to no significant non-Khoesan contribution. In contrast to the Ju/'hoan, we identify ancient signatures of Khoesan and Bantu unions resulting in significant Khoesan- and Bantu-derived contributions to the Southern Bantu amaXhosa (n = 15) and Khoesan !Xun (n = 14), respectively. Our data further suggests that contemporary !Xun represent distinct Khoesan prehistories. Khoesan assimilation with European settlement at the most southern tip of Africa resulted in significant ancestral Khoesan contributions to the Coloured (n = 25) and Baster (n = 30) populations. The latter populations were further impacted by 170 years of East Indian slave trade and intra-continental migrations resulting in a complex pattern of genetic variation (admixture). The populations of southern Africa provide a unique opportunity to investigate the genomic variability from some of the oldest human lineages to the implications of complex admixture patterns including ancient and recently diverged human lineages.

Link

Deep mtDNA substructure in southern Africa (Barbieri et al. 2013)

The Khoisan have been used in many different ways in reconstructions of human history.

Being probably the most genetically diverse modern human population, they are occasionally viewed as akin to the ur-humans, with everyone else shedding diversity via founder effects as they moved away from a south African modern human urheimat.

They are also sometimes viewed as a basal branch of the human family tree, and they probably are -if modern humans are made to fit a tree model. But, modern humans didn't really evolve tree-like (some African farmers have Khoisan-like admixture, and the Khoisan themselves have relatively "shallow" common ancestry with other Africans and many Eurasians on account of their possession of a respectable frequency of Y-haplogroup E).

I have sometimes noted that in the case of South African groups were are lucky that the Khoisan exist as a discrete set of populations, making it easier to discern the legacy of South African hunter-gatherers in the genomes of immigrant farmers and pastoralists who converged southwards over the last few thousand years. This can be contrasted with the presumable situation in places like West Africa (the cradle of Sub-Saharan African farming), in which any indigenous hunter-gatherer groups have ceased to exist as distinct entities a long time ago.

A new AJHG paper sample south African genomes extensively and arrives at a startling conclusion. In the words of the authors:

Overall, the results of this analysis indicate that it is very unlikely that the highly divergent L0k1b/L0k2 lineages were incorporated into the Bantu-speaking populations via gene flow from a population that was ancestral to a Khoisan population in our sample but subsequently lost from the Khoisan population via drift. Instead, these results support the hypothesis that the ancestors of the Bantu-speaking populations carrying the divergent L0k lineages (who now live mainly in Zambia) experienced gene flow from a pre-Bantu population that is nowadays extinct. Alternatively, it is possible that descendants from this pre-Bantu population do exist but have not yet been included in population genetic studies; however, our extensive sampling of populations from Botswana, Namibia, andWest Zambia (which includes representatives of nearly all known Khoisan groups) makes it highly unlikely that this pre-Bantu Khoisan population has not yet been sampled.

In other words, we must resist the tendency to think of the Khoisan as representatives of all pre-Bantu south Africans. The Khoisan are certainly descendants of old south Africans, and represent a part of the pre-Bantu genetic landscape that retained its cultural distinctiveness (and hence can be nowadays sampled as a distinct population). But, there were other, now submerged, peaks in that landscape that are no longer extant in distinct form, but only in absorbed form in the gene pool of south African farmers.

This is fairly interesting in itself, and certainly ought to change our belief about what Africa looked like pre-Bantu expansion. We ought to think of, perhaps, a cornucopia of groups: many of them may have gone extinct; some may have been completely absorbed into more successful ones, and perhaps only a handful survive as distinct entities. Such a view would agree with the conclusions of physical anthropology about the persistence of archaic-leaning groups in parts of Africa down to the Holocene boundary.

The American Journal of Human Genetics, 17 January 2013 doi:10.1016/j.ajhg.2012.12.010

Ancient Substructure in Early mtDNA Lineages of Southern Africa

Chiara Barbieri et al.


Among the deepest-rooting clades in the human mitochondrial DNA (mtDNA) phylogeny are the haplogroups defined as L0d and L0k, which are found primarily in southern Africa. These lineages are typically present at high frequency in the so-called Khoisan populations of hunter-gatherers and herders who speak non-Bantu languages, and the early divergence of these lineages led to the hypothesis of ancient genetic substructure in Africa. Here we update the phylogeny of the basal haplogroups L0d and L0k with 500 full mtDNA genome sequences from 45 southern African Khoisan and Bantu-speaking populations. We find previously unreported subhaplogroups and greatly extend the amount of variation and time-depth of most of the known subhaplogroups. Our major finding is the definition of two ancient sublineages of L0k (L0k1b and L0k2) that are present almost exclusively in Bantu-speaking populations from Zambia; the presence of such relic haplogroups in Bantu speakers is most probably due to contact with ancestral pre-Bantu populations that harbored different lineages than those found in extant Khoisan. We suggest that although these populations went extinct after the immigration of the Bantu-speaking populations, some traces of their haplogroup composition survived through incorporation into the gene pool of the immigrants. Our findings thus provide evidence for deep genetic substructure in southern Africa prior to the Bantu expansion that is not represented in extant Khoisan populations.


Link

71,000-year old South African microliths

Press release, Nature News, and podcast.

Nature (2012) doi:10.1038/nature11660

An early and enduring advanced technology originating 71,000 years ago in South Africa

Kyle S. Brown et al.

There is consensus that the modern human lineage appeared in Africa before 100,000 years ago1, 2. But there is debate as to when cultural and cognitive characteristics typical of modern humans first appeared, and the role that these had in the expansion of modern humans out of Africa3. Scientists rely on symbolically specific proxies, such as artistic expression, to document the origins of complex cognition. Advanced technologies with elaborate chains of production are also proxies, as these often demand high-fidelity transmission and thus language. Some argue that advanced technologies in Africa appear and disappear and thus do not indicate complex cognition exclusive to early modern humans in Africa3, 4. The origins of composite tools and advanced projectile weapons figure prominently in modern human evolution research, and the latter have been argued to have been in the exclusive possession of modern humans5, 6. Here we describe a previously unrecognized advanced stone tool technology from Pinnacle Point Site 5–6 on the south coast of South Africa, originating approximately 71,000 years ago. This technology is dominated by the production of small bladelets (microliths) primarily from heat-treated stone. There is agreement that microlithic technology was used to create composite tool components as part of advanced projectile weapons7, 8. Microliths were common worldwide by the mid-Holocene epoch, but have a patchy pattern of first appearance that is rarely earlier than 40,000 years ago9, 10, and were thought to appear briefly between 65,000 and 60,000 years ago in South Africa and then disappear. Our research extends this record to ~71,000 years, shows that microlithic technology originated early in South Africa, evolved over a vast time span (~11,000 years), and was typically coupled to complex heat treatment that persisted for nearly 100,000 years. Advanced technologies in Africa were early and enduring; a small sample of excavated sites in Africa is the best explanation for any perceived ‘flickering’ pattern.

Link

Complex origins and natural selection of the Khoe-San

The Khoe-San were recently made the object of a study by Pickrell et al. in a paper that was posted on arXiv and ought to appear in journal form in the near future. Good things come in pairs, so on the heels of that study, a new paper in Science by Schlebusch et al. deals with a similar set of populations. The former paper used the Affymetrix Human Origins Array which contains sets of SNPs ascertained in different individuals from around the world, and the dataset will be comparable to the HGDP set genotyped on the same chip. The current study uses the Illumina Omni 2.5, which would make its data to comparable to the 1000 Genomes data, as well as to a variety of other data genotyped on Illumina platforms. So, from the data perspective, I would say that the two nicely complement each other.

There is an abundance of good stuff in the 176 pages of supplementary material which are freely available in the Science website.

One important technical proposition in the paper is the use of a concordance ratio. As I understand it, this is based on the idea that when populations split, initially the signal that they did so is very weak, and becomes stronger with more time (and drift). So, by taking the ratio of concordant minus discordant alleles over concordant plus discordant ones, they can show support for a topology and estimate population split times.

Of course, Khoe-San populations cannot really be seen as having split from the rest of mankind at some particular time. Pickrell et al. argue for this on the basis of admixture LD in even the most "unadmixed" populations (such as HGDP San), but the most obvious reason why the simple split scenario cannot be true comes from the fact that the Khoe-San possess a substantial percentage of Y-haplogroup E, which links them to other Sub-Saharan Africans, and even Eurasians within a ~50ka framework at most, and probably much lower, since they carry derived sublineages within E that were founded much more recently.

Nonetheless, this admixture was probably not so great to destroy the evidence of isolation, and the authors give an estimate of ~100ka for the split:

This division forms the deepest divergence among extant humans (Fig. 2A, S32) and, assuming an effective population size (Ne) of 21,000 individuals (11, 12), the maximum likelihood divergence time is Ts = 0:083 × 2Ne generations (95% ML CI: 0.075-0.091) corresponding to ∼100,000 years ago (14), in agreement with previous estimates of 110,000-160,000 years ago (11, 12).

But, this estimate disagrees with the idea that Khoe-San split off 250-300 thousand years ago, which has been advanced on the basis of the slower autosomal mutation rate. Many of the news headlines on the paper talk about the paper showing that Khoe-San diverged before Out-of-Africa, but, actually, using the new slow mutation rate, a date of 100ka is actually around the time, or even after Out-of-Africa, which now appears to have taken place twice as early as previously thought.

Thankfully, Schlebusch et al. do not only give absolute age estimates, but also express their age estimates in terms of the effective population size. But, the effective population size is indirectly linked to the autosomal mutation rate, as I noted in my review of Gronau et al. and Veeramah et al., i.e. the two papers cited for the effective population size of 21,000 individuals. In order to generate the same amount of genetic divergence, a slower mutation rate requires a higher population size. Ergo, I don't think the estimates of Schlebusch et al. are discordant with those of Scally and Durbin, and, the two may harmonize once effective population sizes are re-calculated on the basis of the slow human autosomal mutation rate.

The authors do acknowledge the possibility of archaic admixture in Africa. In my opinion, the presence of this admixture can harmonize the evidence of shallow common ancestry with Eurasians and African farmers (e.g., in the form of Y-haplogroup E) with the deep autosomal divergence times.

I am also looking forward to getting the new data when it appears at the Jakobsson lab data page. Together with the HGDP San (on both Affymetrix and Illumina platforms), and the Henn et al. data, there will shortly be no shortage of data on the Khoe-San. And, together with the data from Pagani et al. on Ethiopia it may be a good idea to update my africa9 calculator when I find the time for it.

Science DOI: 10.1126/science.1227721

Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History

Carina M. Schlebusch et al.

The history of click-speaking Khoe-San, and African populations in general, remains poorly understood. We genotyped ~2.3 million SNPs in 220 southern Africans and found that the Khoe-San diverged from other populations >=100,000 years ago, but structure within the Khoe-San dated back to about 35,000 years ago. Genetic variation in various sub-Saharan populations did not localize the origin of modern humans to a single geographic region within Africa; instead, it indicated a history of admixture and stratification. We found evidence of adaptation targeting muscle function and immune response, potential adaptive introgression of UV-light protection, and selection predating modern human diversification involving skeletal and neurological development. These new findings illustrate the importance of African genomic diversity in understanding human evolutionary history.

Link

Redating of Later Stone Age brings it in line with Upper Paleolithic

Two new papers in PNAS document that the Later Stone Age (LSA), the period of African prehistory corresponding to the Upper Paleolithic in Europe, began earlier than previously thought (c. 44ka BP), and contained elements of the material culture of present-day San populations.

There really seems to have been a Big Bang of sorts during that time that has now been shown to have affected most of the world: early modern humans in Europe were replacing Neandertals and starting the Aurignacian, fishing in the open seas in East Timor, and, now it seems, hunting and living in a very modern way in South Africa.

Intriguingly, the evidence for archaic admixture in Africa (Lachance et al. 2012; Hammer et al. 2011) point to about the same time. And, the 37,000 year old Hofmeyr skull from South Africa is most similar to early Upper Paleolithic European specimens. Together with new evidence about the human Y-chromosome phylogeny, it seems inescapable that something very big was taking place all over the world around the same time, something quite akin to the spread of a new people and not only to a spread of a new technology or way of thinking.

While precursors to modern human behavior have been documented in earlier contexts in Southern Africa and even among European Neandertals, these pale in comparison to the MP/MSA to UP/LSA transition. Here, we have near-simultaneous appearance of fully modern human behavior all over the planet, the appearance of fully modern skull forms with unmistakeable long range links, the rooting of most major Y-chromosome haplogroups, evidence for archaic admixture/disappearance. It was a real quantum leap in both human creativity and in the spread of human physical presence around the globe.

I have previously expressed the opinon that the "trigger" for this remarkable phenomenon can be found a few thousand years earlier, when the Sahara-Arabia belt entered a dry phase that would have driven its population outwards. But, really, the near simultaneous appearance of the same phenomenon all over the planet makes it difficult to find its ultimate source. These are exciting times for human origins research!

Press releases: Later Stone Age got earlier start in South Africa than thought, Modern culture 44,000 years ago
Coverage elsewhere: NY Times.

UPDATE I: From d' Errico et al.:

Contrary to lithic technology, which shows at Border Cave agradual evolution toward the ELSA starting after 56 ka (21), organic artifacts unambiguously reminiscent of LSA and San materialculture emerge relatively abruptly, highlighting an apparent mismatch in rates of cultural change. Our results support the view that what we perceive today as modern behavior is the resultof nonlinear trajectories that may be better understood whendocumented at a regional scale (7, 12–14, 21, 54).

Villa et al. also have a section on whether or not the MSA persisted longer than the arrival of the LSA:

Did MSA Technology Survive Until 26–20 ka in South Africa? Several sites in South Africa Lesotho and Swaziland are dated to the interval between 40 and 20 ka and defined as MSA or transitional MSA–LSA (11–15, 63). However, many assemblages have uncertain stratigraphy or small and undiagnostic inventories or are poorly dated or unpublished. A few have only preliminary descriptions. 

At Rose Cottage three layers (DY, DC, and RU) dated between ca. 30.8 and 27 ka are defined as final MSA (64). They are described as having bladelets produced by the bipolar technique but also having “MSA” types of formal tools (11). 

Strathalan Cave B (Eastern Cape) has two main layers dated between 29 and 25.7 ka. Their inventory, defined as late MSA, includes single and multiplatform cores, some blades, many irregular flakes, and very few retouched blades and flakes (65). At Boomplas Cave (Western Cape) the uppermost MSA level (BP), dated to 34–32 BP, is unpublished. Layer LPC contains an assemblage classified as LSA, with two bone points and few bladelets, dated to ca. 21 ka (2, 14). Systematic technological analyses and more dates are needed to break the impasse (63). 

It does seem that part of the reason why the MSA/LSA transition was dated later was that it did not happen simultaneously overnight. There is also very good reason to think that if the simultaneous appearance of modern behavior around the world was related to the spread of modern humans, then the modern San are not simple direct descendants of the Border Cave population, since their divergence from Eurasians greatly exceeds 100,000 years. A simpler explanation might be that at 44kya there was a migration of behaviorally modern people (evidenced e.g., by links between Hofmeyr and Eurasians), but that in Africa this set of people admixed with more divergent African populations; there is evidence of deep links between South and East Africans, as well as of more recent links between South  and West African farmers and East African pastoralists. Clearly, things were going on in the region in the last 40,000 years, as they seem to have done elsewhere.

PNAS doi: 10.1073/pnas.1202629109

Border Cave and the beginning of the Later Stone Age in South Africa

Paola Villa et al.

The transition from the Middle Stone Age (MSA) to the Later Stone Age (LSA) in South Africa was not associated with the appearance of anatomically modern humans and the extinction of Neandertals, as in the Middle to Upper Paleolithic transition in Western Europe. It has therefore attracted less attention, yet it provides insights into patterns of technological evolution not associated with a new hominin. Data from Border Cave (KwaZulu-Natal) show a strong pattern of technological change at approximately 44–42 ka cal BP, marked by adoption of techniques and materials that were present but scarcely used in the previous MSA, and some novelties. The agent of change was neither a revolution nor the advent of a new species of human. Although most evident in personal ornaments and symbolic markings, the change from one way of living to another was not restricted to aesthetics. Our analysis shows that: (i) at Border Cave two assemblages, dated to 45–49 and >49 ka, show a gradual abandonment of the technology and tool types of the post-Howiesons Poort period and can be considered transitional industries; (ii) the 44–42 ka cal BP assemblages are based on an expedient technology dominated by bipolar knapping, with microliths hafted with pitch from Podocarpus bark, worked suid tusks, ostrich eggshell beads, bone arrowheads, engraved bones, bored stones, and digging sticks; (iii) these assemblages mark the beginning of the LSA in South Africa; (iv) the LSA emerged by internal evolution; and (v) the process of change began sometime after 56 ka.

Link

PNAS doi: 10.1073/pnas.1204213109

Early evidence of San material culture represented by organic artifacts from Border Cave, South Africa

Francesco d’Errico et al.

Recent archaeological discoveries have revealed that pigment use, beads, engravings, and sophisticated stone and bone tools were already present in southern Africa 75,000 y ago. Many of these artifacts disappeared by 60,000 y ago, suggesting that modern behavior appeared in the past and was subsequently lost before becoming firmly established. Most archaeologists think that San hunter–gatherer cultural adaptation emerged 20,000 y ago. However, reanalysis of organic artifacts from Border Cave, South Africa, shows that the Early Later Stone Age inhabitants of this cave used notched bones for notational purposes, wooden digging sticks, bone awls, and bone points similar to those used by San as arrowheads. A point is decorated with a spiral groove filled with red ochre, which closely parallels similar marks that San make to identify their arrowheads when hunting. A mixture of beeswax, Euphorbia resin, and possibly egg, wrapped in vegetal fibers, dated to ~40,000 BP, may have been used for hafting. Ornaments include marine shell beads and ostrich eggshell beads, directly dated to ~42,000 BP. A digging stick, dated to ~39,000 BP, is made of Flueggea virosa. A wooden poison applicator, dated to ~24,000 BP, retains residues with ricinoleic acid, derived from poisonous castor beans. Reappraisal of radiocarbon age estimates through Bayesian modeling, and the identification of key elements of San material culture at Border Cave, places the emergence of modern hunter–gatherer adaptation, as we know it, to ~44,000 y ago.

Link

Khoisan genetic prehistory (Pickrell et al. 2012)

This appears to be the first paper using the specialized Affymetrix chip, which was announced some time ago, and used in some of my previous experiments. The new array has been dubbed "Affymetrix Human Origins array" and has been composed by intersecting panels of SNPs ascertained in individuals from several world populations.

It is of course great to see that this paper has appeared as a preprint in arXiv, and hopefully this is a trend that will continue; biology should be like physics, with papers appearing immediately online for commenting, and not hidden away in authors', editors', and reviewers' drawers for months if not years before they become available to all.

I will highlight some points of particular interest to me:

Some caveats of interpretation here are warranted. First, all the Khoisan populations have some level of admixture with non-Khoisan populations. There is thus no single \split time" in their history, and any method (like the one used here) that estimates a single such time will actually be estimating a composite of several signals. Second, we have made the modeling assumption that history involves populations splitting in two with no gene  ow after the split. More complex demographies are quite plausible, but render the interpretation of a split time nearly meaningless (if populations continue to exchange migrants after \splitting", they arguably have not split at all). We thus consider strong interpretations of split times estimated from genetic data to be impossible, but we nonetheless and the estimates to be useful in constraining the set of historical hypotheses that are consistent with the data. 

This echoes (somewhat) my sentiments about split times being a tug-of-war in the presence of admixture. Another interesting bit from the paper:

Interestingly, a few of the Khoe-speaking populations have slightly positive f4 statistics in this com- parison, and in the Shua the f4 statistic is significantly greater than zero. We speculate that some of the Khoe-speaking populations have a low level of east African ancestry, and that the relevant east African population was itself admixed with a western Eurasian population. The Shua also show a detectable signal of admixture LD, though we estimate the admixture date as much older (44 generations). This signal of east African ancestry specifically in Khoe-speaking populations is of particular interest in the light of the hypoth esis that the Khoe-Kwadi languages were brought to southern Africa by a pre-Bantu pastoralist immigration from eastern Africa [Guldemann, 2008] 

The authors also announce an improvement on TreeMix:

In the original TreeMix algorithm, one first builds the best-tting tree of populations. However, this approach is not ideal if there are many admixed populations (as in our application here, where all of the Khoisan populations are admixed). To get around this, we allow for known admixture events to be incorpo- rated into this tree-building step. Imagine that there are several populations that we think a priori might be unadmixed (in our applications, these are the Chimpanzee, Yoruba, Dinka, Europeans, and East Asians). We  first build the best tree of these unadmixed populations using the standard TreeMix algorithm. Now assume we have an independent estimate of the admixture level of each Khoisan population, and imagine we know the source population for the mixture. 

I don't think that Sub-Saharan African populations can any longer be considered unadmixed. When one used SNPs ascertained in Eurasian individuals, many Sub-Saharan populations appear symmetrically related to Eurasians, because they lack variation at sites where new polymorphism appeared outside Africa. 

This is not, however, the case when one uses SNPs ascertained in African individuals, and a clear pattern of differential affiliation with West Eurasians across the continent is evident. As I have said before, I strongly suspect that this is due to fairly late back-migration of Eurasians into Africa, carrying Y-haplogroup DE chromosomes. Within haplogroup CT, both its major subclades CF and DE are represented in Eurasia, and both D,E, and DE* as well. In Africa, as far as we know, only DE* and E are native. On balance, the weight of the evidence would suggest a Eurasian origin of the DE-YAP haplogroup.

(I would perhaps be as bold as to extend this into the even more basal clades of the phylogeny which turn up with surprising regularity in Eurasian datasets, and are usually discounted as the result of recent admixture. I'm not so sure; if recent admixture was at fault, then the African signal in Eurasia would be absolutely dominated by E-related lineages: but the A's and B's turn up in quite unexpected places. Are they really all recent Africans, or could they share a much deeper common ancestry? If I had deep pockets, I'd surely invest in genome sequencing the collection of such Eurasian erratics)

As a parting thought, I hope that the data used in this paper will become publicly available in time, perhaps when the article appears in journal form. True open science depends not only in the public availability of research results, but also of the data that produced them.

UPDATE: Here is the ADMIXTURE analysis from the paper (Figure 7):

It would have been nice if the Fst values between ancestral populations were reported in the paper; also, if an East Eurasian group was added in the analysis. In any case, there does appear a pattern of differential affiliation with the French population (K=2). At K=3 the main Sub-Saharan (blue) component emerges, and a few populations continue to exhibit an excess of West Eurasian affiliation.

arXiv:1207.5552v1 [q-bio.PE]
The genetic prehistory of southern Africa

Joseph K. Pickrell et al.

The hunter-gatherer populations of southern and eastern Africa are known to harbor some of the most ancient human lineages, but their historical relationships are poorly understood. We report data from 22 populations analyzed at over half a million single nucleotide polymorphisms (SNPs), using a genome-wide array designed for studies of history. The southern Africans-here called Khoisan-fall into two groups, loosely corresponding to the northwestern and southeastern Kalahari, which we show separated within the last 30,000 years. All individuals derive at least a few percent of their genomes from admixture with non-Khoisan populations that began 1,200 years ago. In addition, the Hadza, an east African hunter-gatherer population that speaks a language with click consonants, derive about a quarter of their ancestry from admixture with a population related to the Khoisan, implying an ancient genetic link between southern and eastern Africa.

Link

AAPA 2012 abstracts (Part 3)

Continuing from Part 2.


An analysis of the Klasies River hominins using a hybrid model.
LILY MALEKFAR. Anthropology, Northern Illinois University.

Current research indicates that modern Homo sapiens originated in East Africa and then migrated across Africa as well as out of Africa, where they encountered archaic hominins. The Klasies River Main site (KRM) in South Africa is one location where there is evidence that modern and archaic Homo sapiens may have interacted. As Smith and other researchers have suggested, the KRM mandibular sample, in particular, exhibits significant size and morphological variability, which counters claims that the KRM specimens are fully modern.
The null hypothesis predicts that KRM’s range of variation does not significantly differ from the ranges of variation indicated in the comparative samples, including Sima de los Huesos, Krapina, Skhul, Qafzeh, and the Northern Illinois University (NIU) Collection, the latter containing specimens classified as modern Homo sapiens from India. If the null hypothesis is rejected, this would be tentative support that the KRM sample may possibly be a hybrid sample. This study examines first and second mandibular molar lengths and widths as well as mandibular corpus height and breadth in adult hominins and compares patterns of variation using the coefficient of variation.
The results demonstrate that the KRM sample is markedly more variable than any of the comparative samples, which rejects the null hypothesis and is one possible indicator of an admixed sample at KRM. This study is limited by small sample sizes for KRM. This and the fact that KRM spans several thousand years may impact these results.

The origins of dental modernity.

SHARA E. BAILEY1,2 and JEAN-JACQUES HUBLIN2.
Research over the past decade has established that the study of dental morphological characters is a useful and important tool for interpreting the later stages of human evolution. A good deal of this research has focused on identifying dental characters that are relevant specifically to the distinction between Neandertals and H. sapiens, and more broadly to the question of modern human origins. However, while the dental patterns of certain recent H. sapiens populations have been described as primitive (e.g., Sub-Saharan Africans) or derived (Northeast Asians) relative to other groups, no study to date has proposed a dental pattern that characterizes H. sapiens as a species. To this end, this study investigates (1) whether or not there is a unique dental pattern in H. sapiens; (2) if so, which traits comprise this pattern; and (3) when, during the course of human evolution, these traits emerge. Our results show that size notwithstanding, H. sapiens has few uniquely derived dental traits that distinguish them from other hominins. These include the U-shaped fissure pattern of the lower P4, relatively flat, featureless upper incisors that are buccolingually narrow, lower molars lacking a hypoconulid and lower molars lacking any form of trigonid crest on enamel and dentine surfaces. Early H. sapiens from Qafzeh, Klasies River Mouth and Jebel Irhoud possess some of these characters. Interestingly, none of the recently discovered teeth from Qesem Cave, Israel exhibit any derived H. sapiens non-metric traits, while the molars of H. floresiensis are derived toward the H. sapiens condition.

Endocranial shape in early modern humans.

SIMON NEUBAUER, PHILIPP GUNZ and JEAN-JACQUES HUBLIN.
Humans have more globular brains and therefore endocasts than our extant and extinct relatives: chimpanzees and Neanderthals both have anterioposteriorly elongated endocasts. Based on an ontogenetic series of recent modern humans, we have previously shown that this modern human globular shape develops directly after birth during an ontogenetic phase that is absent in chimpanzees and Neanderthals. However, it is unclear at which point in the evolution of our species this unique pattern of brain development appeared.
Here, we aim to trace its evolutionary origin. Based on the shape of fossil adult humans, we investigate the morphological evolution of Homo sapiens endocasts using geometric morphometrics. Investigating representatives of H. sapiens from different time periods (comprising samples from Jebel Irhoud, Qafzeh, Skhul, Mladec, Cro-Magnon) makes it possible to assess when and how (gradually or rapidly) this developmental phase appeared in the course of recent human evolution. As several relevant fossils are fragmentary and partly deformed, they require reconstruction before they can be analyzed. To this end, we generate and reconstruct virtual endocasts based on CT scans. We first use mirror-imaging and segmentation techniques, and then the thin-plate-spline interpolation function for reference-based reconstruction. Generating multiple reconstructions based on landmarks of 60 recent human endocasts, we keep track of the reconstruction uncertainty throughout the shape analysis. We document temporal trends of endocranial shape within anatomically modern humans during the Late Pleistocene and discuss potential implications for the evolution of the modern human brain.

AAPA 2012 abstracts (part 1)

Here are some interesting abstracts from the 81st Annual Meeting of the American Association of Physical Anthropologists.


Maternal marks of admixture in Cape Coloreds of South Africa.
KRISTINE G. BEATY1, DELISA L. PHILLIPS1, MACIEJ HENNEBERG2 and MICHAEL H. CRAWFORD1.

Previous studies of genetic diversity have suggested that the Cape Coloureds of South Africa are a highly admixed population with genetic roots from indigenous African groups including Khoisans, and the later arrival of Bantu speaking Xhosa farmers. Further genetic contributions came during European colonization of South Africa, which added to the inclusion of largely male European markers to the gene pool. Slaves from Indonesia, Malaysia, Madagascar and India are also thought to have contributed to the genetic makeup of this ethnic group. This study examines the maternal contribution of each of these groups to the genetic diversity of the Cape Coloreds through sequencing of the hypervariable region I of the mitochondrial DNA and through restriction fragment length polymorphism.
A total of 123 individuals were examined for this study. High frequencies of haplogroups L1 and L2 were found at 81.3 percent in this group (100 of the 123 individuals), which indicates that this group has a large African contribution to its mitochondrial makeup. Restrictions of the major European haplogroups identified nine individuals, 7.3 percent of the sample, belonged to haplogroups I and J. Five individuals (4.1 percent of the sample) belonged to the superhaplogroup M, indicating that Asian slaves did contribute to the maternal gene pool. The majority of maternal lineages in this Cape Coloured sample are African in origin, with some European influence and a small contribution from Asian maternal lineages.

Ancient DNA reveals the population origin of the Eastern Xinjiang.
SHIZHU GAO2, HONGJIE LI1, CHUNXIANG LI1 and HUI ZHOU1,3.

Connecting with the Turpan Basin, the Eurasia steppe and the Gansu Corridor, the Eastern region of Xinjiang has played a significant role in the history of human migration, cultural developments, and communications between the East and the West. The population origin, migration and integration of this region have attracted extensive interest among scientists.
In order to research the population origin and movement of the Eastern Xinjiang, genetic polymorphisms studies of the Hami population were conducted. The Hami site is located in the East of Tian-Moutain in Xinjiang, dating back to the Bronze-early Iron Age. Archaeological studies showed that the culture of the Hami site possessed features from both the East and the West. Ancient mtDNA analysis showed that A, C, D, F, G, Z and M7 of the Eastern maternal lines, and W, U2e, U4, and U5aof the Western maternal lines were identified. Tajimas’D test and mismatch distribution analysis show that the Hami population had experienced population expansion in recent time. The demographic analysis of haplogroups suggests that the populations of the Northwest China, Siberia and the Central Asia have contributed to the mtDNA gene pool of the Hami population.
Our study reveals the genetic structure of the early population in Eastern Xinjiang, and its relationships with other Eurasian populations. The results will provide valuable genetic information to further explore the population origin and migration of Xinjiang and Central Asia.

Analysis of Chuvash mtDNA points to Finno-Ugric origin.
ORION M. GRAF1, STEPHEN M. JOHNSON1, JOHN MITCHELL2, STEPHEN WILCOX3, GREGORY LIVSHITS4 and MICHAEL H. CRAWFORD1.

A sample of 92 unrelated individuals from Chuvashia, Russia was sequenced for hypervariable region-I (HVR-I) of the mtDNA molecule. These data have been verified using RFLP analysis of the control region, revealing that the majority exhibit haplogroups H (31%), U (22%), and K (11%), which occur in high frequencies in western and northern Europe, but are virtually absent in Altaic or Mongolian populations. Multidimensional scaling (MDS) was used to examine distances between the Chuvash and reference populations from the literature. Neutrality tests (Tajima’s D (-1.43365) p<0.05, Fu’s FS (-25.50518) p<0.001) and mismatch analysis, which illustrates unimodal distribution, all suggest an expanding population.
The Chuvash speak a Turkic language that is not mutually intelligible to other extant Turkish groups, and their genetics are distinct from Turkic-speaking Altaic groups. Some scholars have suggested that they are remnants of the Golden Horde, while others have advocated that they are the products of admixture between Turkic and Finno-Ugric speakers who came into contact during the 13th century. Earlier genetic research using autosomal DNA markers indicated a Finno-Ugric origin for the Chuvash. This study examines uniparental mitochondrial DNA markers to better elucidate their origins. Results from this study maintain that the Chuvash are not related to Altaic or Mongolian populations along their maternal line, thus supporting the “Elite” hypothesis that their language was imposed by a conquering group —leaving Chuvash mtDNA largely of Eurasian origin. Their maternal markers appear to most closely resemble Finno-Ugric speakers rather than Turkic speakers.

An ancient DNA perspective on the Iron Age “princely burials” from Baden-Wurttemberg, Germany.
ESTHER J. LEE1, CHRISTOPH STEFFEN1, MELANIE HARDER1, BEN KRAUSE-KYORA1, NICOLE VON WURMB-SCHWARK2 and ALMUT NEBEL3.

During the Iron Age in Europe, fundamental social principles such as age, gender, status, and kinship were thought to have played an important role in the social structure of Late Hallstatt and Early Latene societies. In order to address the question of kinship relations represented in the Iron Age “princely burials” that are characterized by their rich material culture, we carried out genetic analysis of individuals associated with the Late Hallstatt culture from Baden-Wurttemberg, Germany. Bone specimens of thirty-eight skeletal remains were collected from five sites including Asperg Grafenbuhl, Muhlacker Heidenwaldle, Hirschlanden, Ludwigsburg, and Schodeingen. Specimens were subjected to DNA extraction and amplification under strict criteria for ancient DNA analysis. We successfully obtained mitochondrial DNA (mtDNA) control region sequences from seventeen individuals that showed different haplotypes, which were assigned to nine haplogroups including haplogroups H, I, K, U5, U7, W, and X2b. Despite the lack of information from nuclear DNA to infer familial relations, information from the mtDNA suggests an intriguing genetic composition of the Late Hallstatt burials. In particular, twelve distinct haplotypes from Asperg Grafenbuhl suggest a heterogeneous composition of maternal lineages represented in the “princely burials”. The results from this study provide clues to the social structure reflected in the burial patterns of the Late Hallstatt culture and implications on the genetic landscape during the Iron Age in Europe.

Genetic snapshot from ancient nomads of Xinjiang.
HONGJIE LI1, SHIZHU GAO2, CHUNXIANG LI1, YE ZHANG1, WEN ZENG3, DONG WEI3 and HUI ZHOU1,3.

Nomads of the Eurasian steppes are known to have played an important role in the transfer commodities and culture among East Asia, Central Asia, and Europe. However, the organization of nomadic societies and initial population genetic composition of nomads were still poorly understood because of few archaeological materials and written history.
In this study, the genetic snapshot of nomads was emerged by examining mitochondrial DNA and Y-chromosome DNA of 30 human remains from Heigouliang (HGL) site in the eastern of Xinjiang, which dated 2000 years ago and associated to the nomadic culture by archaeological studies. Mitochondrial DNA analysis showed that the HGL population included both East Eurasian haplogroups (A, C, D, G, F and Z) and West Eurasian haplogroups (H, K, J, M5 and H). The component of Eastern haplogroups is dominant. The distribution frequency and Fst values of Eastern haplogroups indicated the HGL population presented close genetic affinity to the nearby region modern populations of Gansu and Qinghai, while those of western haplogroups showed similar with Mongolia and Siberia populations. The results implied various maternal lineages were introduced into the HGL population. Regarding the Y chromosomal DNA analysis, nearly all samples belonged to haplogroup Q which is thought to be the mark of the Northern Asian nomads. We identified paternal kinship among three individuals at the same tomb by Y-STR marker.
Combined with archaeological and anthropological investigations, we inferred that the gene flow from the neighboring regions was possibly associated with the expansion of Xiongnu Empire.

Vikings, merchants and pirates at the top of the world: Y-chromosomal signatures of recent and ancient migrations in the Faroe Islands.
ALLISON E. MANN1, EYDFINN MAGNUSSEN2 and CHRISTOPHER R. TILLQUIST1.

The Faroe Islands are a small archipelago in the North Atlantic Ocean. With a current population of approximately 48,000 individuals and evidence of high levels of genetic drift, the Faroese are thought to have remained highly homogeneous since the islands were settled by Vikings around 900CE. Despite their geographic isolation, however, there is historical evidence that the Faroese experienced sporadic contact with other populations since the time of founding. Contact with Barbary pirates in the seventeenth century is documented in the Faroes; there is also the possibility of modern migrations to work in the highly productive fishery. This study set out to distinguish the signal of the original founders from later migrants. Eleven Y-chromosomal STR markers were scored for 139 Faroese males from three geographically dispersed islands. Haplotypes were analyzed using Athey's method to infer haplogroup. Median-joining networks within haplogroups were constructed to determine the phylogenetic relationships within the Faroese and between likely parental populations—Danish, Irish, and Norwegians. Dispersal patterns of individuals around Faroese haplogroups suggest different times of haplotype introduction to the islands. The most common haplogroup, R1a, consists of a large node with a tight network of neighbor haplotypes, such that 68% of individuals are one or two mutational steps away. This pattern may represent the early founder event of R1a in the Faroes. Other distributions, especially of non-Scandinavian haplotypes, document more recent introductions to the islands. The overall pattern is one of a strong founder effect followed by minor instances of later migrations.

Date estimates for major mitochondrial haplogroups in Yemen.
DEVEN N. VYAS1, VIKTOR ČERNÝ2, ALI AL-MEERI3 and CONNIE J. MULLIGAN1.

Yemen occupies a key location as the first stop for anatomically modern humans on a theoretical southern migration route out of Africa. If modern humans did pass through Yemen during the first migrations out of Africa and if they left modern-day descendants, we would expect to see deep divergences in the Yemeni mitochondrial gene tree. Alternatively, if modern humans passed through Yemen but did not leave modern-day descendants or if Yemen was not on the path of these ancient migrations, we would expect more recent dates to be associated with Yemeni mitochondrial haplogroups.
Using 44 previously sequenced mitochondrial genomes as well as 24 newly sequenced mitochondrial genomes from samples collected throughout Yemen, several methods were used to estimate divergence dates of major Yemeni haplogroups including L2, M, R0a and HV. Specifically, phylogenetic trees were generated using MrBayes and maximum likelihood methods. Bayesian and ρ statistic based methods were used to estimate dates of Yemeni haplogroups and these dates were compared with each other, previously published dates for these haplogroups, approximate dates of climatic change that might be expected to correlate with population expansions, and estimates based on archaeological and paleontological evidence for the first migrations out of Africa. These comparisons are intended to cover the range of possible haplogroup divergence dates with respect to the history of early modern humans in southern Arabia.

Australopithecus sediba in Science

From the press release.

Researchers have confirmed the age of possibly our oldest direct human ancestor at 1.98 million years old.

The discovery was made after researchers conducted further dating of the early human fossils, Australopithecus sediba, found in South Africa last year.

A series of studies carried out on newly exposed cave sediments at the Malapa Cave site in South Africa, where the fossils were found, has assisted researchers to determine their more precise age at 1.98 million years old, making the Malapa site one of the best dated early human sites in the world.

...

"Knowing the age of the fossils is critical to placing them in our family tree, and this new age means that Australopithecus sediba is the current best candidate for our most distant human ancestor."

"The results of these studies present arguably the most precise dates ever achieved for any early human fossils," she said.

It appears the fossils were deposited in the Malapa Cave during a 3,000-year period around 1.98 million years when the Earth's magnetic field reversed itself by 180 degrees and back again.

List of papers in Science. Judging by the list of co-authors, I would hazard a guess that this research was funded and supported (directly or not) by public money from institutions across several continents. This may have been money well-spent in advancing science, but it is Science that will now profit from it, for nothing more than providing a glorified web-hosting service. The public must pay once more, either directly to Science or by inconveniencing itself with a trip to a Science-subscribing library, if there is one nearby.

This is as good a place as any to plu the open science Malapa Soft Tissue Project.

Y-chromosomes of South Africans

Investigative Genetics 2010, 1:6

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

Thijessen Naidoo et al.

Abstract

Background: The ability of the Y chromosome to retain a record of its evolution has seen it become an essentialtool of molecular anthropology. In the last few years, however, it has also found use in forensic genetics, providinginformation on the geographic origin of individuals. This has been aided by the development of efficient screeningmethods and an increased knowledge of geographic distribution. In this study, we describe the development ofsingle base extension assays used to resolve 61 Y chromosome haplogroups, mainly within haplogroups A, B andE, found in Africa.

Results: Seven multiplex assays, which incorporated 60 Y chromosome markers, were developed. These resolved Ychromosomes to 61 terminal branches of the major African haplogroups A, B and E, while also including a fewEurasian haplogroups found occasionally in African males. Following its validation, the assays were used to screen683 individuals from Southern Africa, including south eastern Bantu speakers (BAN), Khoe-San (KS) and SouthAfrican Whites (SAW). Of the 61 haplogroups that the assays collectively resolved, 26 were found in the 683samples. While haplogroup sharing was common between the BAN and KS, the frequencies of these haplogroupsvaried appreciably. Both groups showed low levels of assimilation of Eurasian haplogroups and only two individuals in the SAW clearly had Y chromosomes of African ancestry.

Conclusions: The use of these single base extension assays in screening increased haplogroup resolution andsampling throughput, while saving time and DNA. Their use, together with the screening of short tandem repeatmarkers would considerably improve resolution, thus refining the geographic ancestry of individuals.

Link (pdf)

Genome-wide structure of West Cape Coloured population (de Wit et al. 2010)

On the left Figure S5: Proportion of each individual’s ancestry derived using the linkage model in STRUCTURE for the optimal number of ancestral populations (K = 4) (TIFF 102 kb)

Related:

• Genetic ancestry of Coloured South Africans
• Origin of South African Couloured population

Human Genetics doi:10.1007/s00439-010-0836-1

Genome-wide analysis of the structure of the South African Coloured Population in the Western Cape

Erika de Wit et al.

Admixed populations present unique opportunities to discover the genetic factors underlying many multifactorial diseases. The geographical position and complex history of South Africa has led to the establishment of the unique admixed population known as the South African Coloured. Not much is known about the genetic make-up of this population, and the historical record is patchy. We genotyped 959 individuals from the Western Cape area, self-identified as belonging to this population, using the Affymetrix 500k genotyping platform. This resulted in nearly 75,000 autosomal SNPs that could be compared with populations represented in the International HapMap Project and the Human Genome Diversity Project. Analysis by means of both the admixture and linkage models in STRUCTURE revealed that the major ancestral components of this population are predominantly Khoesan (32–43%), Bantu-speaking Africans (20–36%), European (21–28%) and a smaller Asian contribution (9–11%), depending on the model used. This is consistent with historical data. While of great historical and genealogical interest, this information is also essential for future admixture mapping of disease genes in this population.

Link

Origin of South African Couloured population

Photo from Wikipedia article.

AJHG doi:10.1016/j.ajhg.2010.02.014

Strong Maternal Khoisan Contribution to the South African Coloured Population: A Case of Gender-Biased Admixture

Lluis Quintana-Murci et al.

Abstract

The study of recently admixed populations provides unique tools for understanding recent population dynamics, socio-cultural factors associated with the founding of emerging populations, and the genetic basis of disease by means of admixture mapping. Historical records and recent autosomal data indicate that the South African Coloured population forms a unique highly admixed population, resulting from the encounter of different peoples from Africa, Europe, and Asia. However, little is known about the mode by which this admixed population was recently founded. Here we show, through detailed phylogeographic analyses of mitochondrial DNA and Y-chromosome variation in a large sample of South African Coloured individuals, that this population derives from at least five different parental populations (Khoisan, Bantus, Europeans, Indians, and Southeast Asians), who have differently contributed to the foundation of the South African Coloured. In addition, our analyses reveal extraordinarily unbalanced gender-specific contributions of the various population genetic components, the most striking being the massive maternal contribution of Khoisan peoples (more than 60%) and the almost negligible maternal contribution of Europeans with respect to their paternal counterparts. The overall picture of gender-biased admixture depicted in this study indicates that the modern South African Coloured population results mainly from the early encounter of European and African males with autochthonous Khoisan females of the Cape of Good Hope around 350 years ago.

Link

Complete Khoisan and Bantu genomes

The number of published complete genomes is starting to grow exponentially it seems. Pretty soon, I'm guessing, once most major groups are covered by at least one individual, they will cease to be paper-worthy, and we will move on to the era of full-genome population studies.

One of the published individuals is Desmond Tutu, so I am adding this to the Famous DNA label as well.

From the paper:

In the 117 megabases (Mb) of sequenced exome-containing intervals, the average rate of nucleotide differences between a pair of the Bushmen was 1.2 per kilobase, compared to an average of 1.0 per kilobase differing between a European and Asian individual.

It's striking that two Bushmen are more different from each other than a European and an Asian are. This is in agreement with the idea that Bushmen have a substantial Palaeoafrican genomic component, while Eurasians and most other Africans emerged from a younger population flowering within the species, which I have termed "Afrasian". Eurasians are descended from these (presumably East African "Afrasians"), as are most Africans, but with varying degrees of intermixture with other (non-"Afrasian") groups of humans that lived in the continent from times immemorial at the time of the Out-of-Africa (and "Deeper-into-Africa") expansions.

From the paper, number of SNPs shared:

On the right we see some interesting facts for three individuals (Bushman, KB1; Chinese: YH; European-American: J.C. Venter). 2-way sharing between individuals is roughly in the order of ~500. The Bushman has twice as many "private" variation as the Eurasians, consistent with the ancient basal position in the human family.

From the paper:

The large number of novel SNPs raises concerns regarding the ability of current genotyping arrays to capture effectively the true extent of genetic diversity and haplotype structure represented in southern Africa. Assessing percentage heterozygosity for 1,105,569 autosomal SNPs using current-content Illumina arrays, we were surprised to find lower heterozygosity in KB1 compared to a region-matched European control (Supplementary Data and Supplementary Fig. 3a, b), because it is well known that genetic diversity is highest in Africa. However, analysis of whole-genome sequencing data for KB1 and ABT revealed high percentages of heterozygous SNPs (59% and 60%, respectively), as expected. This discrepancy underscores the inadequacy of current SNP arrays for analysing southern African populations.

This is not very surprising: SNPs used in microarrays have not been discovered in Bushmen, so by testing for heterozygosity in Bushmen using them, you actually underestimate it. By not including Bushmen in the SNP-discovery process you implicitly assume non-variability (hence "no SNP") at sites where Bushmen (but not other humans) are variable.

With whole-genome sequencing we are able to see that Bushmen are indeed highly heterozygous. This should serve as a warning for making too much of patterns of heterozygosity from microarray genotype data, even the latest ~1M ones.

The PCA is also interesting as it points out the familiar differentiation between Europeans-African farmers-Bushmen at the top and Bushmen-West-South Africans at the bottom):

NB: The paper is freely available to non-subscribers, so you can go ahead and read it in full.

Nature doi:10.1038/nature08795

Complete Khoisan and Bantu genomes from southern Africa

Stephan C. Schuster et al.

Abstract

The genetic structure of the indigenous hunter-gatherer peoples of southern Africa, the oldest known lineage of modern human, is important for understanding human diversity. Studies based on mitochondrial1 and small sets of nuclear markers2 have shown that these hunter-gatherers, known as Khoisan, San, or Bushmen, are genetically divergent from other humans1, 3. However, until now, fully sequenced human genomes have been limited to recently diverged populations4, 5, 6, 7, 8. Here we present the complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and a Bantu from southern Africa, as well as protein-coding regions from an additional three hunter-gatherers from disparate regions of the Kalahari. We characterize the extent of whole-genome and exome diversity among the five men, reporting 1.3 million novel DNA differences genome-wide, including 13,146 novel amino acid variants. In terms of nucleotide substitutions, the Bushmen seem to be, on average, more different from each other than, for example, a European and an Asian. Observed genomic differences between the hunter-gatherers and others may help to pinpoint genetic adaptations to an agricultural lifestyle. Adding the described variants to current databases will facilitate inclusion of southern Africans in medical research efforts, particularly when family and medical histories can be correlated with genome-wide data.

Link

Genetic ancestry of Coloured South Africans

Hum Mol Genet. 2009

Genetic structure of a unique admixed population: implications for medical research.

Patterson N, Petersen DC, van der Ross RE, Sudoyo H, Glashoff RH, Marzuki S, Reich D, Hayes VM.

Understanding human genetic structure has fundamental implications for understanding the evolution and impact of human diseases. In this study we describe the complex genetic substructure of a unique and recently admixed population arising approximately 350 years ago as a direct result of European settlement in South Africa. Analysis was performed using over 900,000 genome-wide single nucleotide polymorphisms in 20 unrelated ancestry-informative marker selected Coloured individuals and made comparisons with historically predicted founder populations. We show that there is substantial genetic contribution from at least four distinct population groups: Europeans, South Asians, Indonesians, and a population genetically close to the isiXhosa sub-Saharan Bantu. This is in good accord with the historical record. We briefly examine the implications of determining the genetic diversity of this population, not only for furthering understanding of human evolution out of Africa, but also for genome-wide association studies using admixture mapping. In conclusion, we define the genetic structure of a uniquely admixed population that holds great potential to advance genetic-based medical research.

Link

72 thousand year old heat-treated tools from South Africa

Elsewhere:

• Early toolmakers were 'engineers'
• Early Humans Used Heat-Treated Stone for Tools

Science doi:10.1126/science.1175028

Fire As an Engineering Tool of Early Modern Humans

Kyle S. Brown et al.

Abstract

The controlled use of fire was a breakthrough adaptation in human evolution. It first provided heat and light and later allowed the physical properties of materials to be manipulated for the production of ceramics and metals. The analysis of tools at multiple sites shows that the source stone materials were systematically manipulated with fire to improve their flaking properties. Heat treatment predominates among silcrete tools at ~72 thousand years ago (ka) and appears as early as 164 ka at Pinnacle Point, on the south coast of South Africa. Heat treatment demands a sophisticated knowledge of fire and an elevated cognitive ability and appears at roughly the same time as widespread evidence for symbolic behavior.

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

Later Stone Age South African Hunter gatherers and Herders as a single population

Related regarding a pastoralist migration to South Africa: Y-chromosomal evidence of a pastoralist migration through Tanzania to southern Africa.

Journal of Archeological Science doi: 10.1016/j.jas.2008.11.001

Craniometric evidence for South African Later Stone Age herders and hunter-gatherers being a single biological population

Deano D. Stynder

Abstract

Later Stone Age (LSA) hunter-gatherers and herders co-existed in South Africa during the last 2,000 years. In spite of being the focus of intensive research over the years, the biological status and origins of the herders are still unclear. Did they represent a genetically distinct immigrant population who remained separate from the indigenous hunter-gatherers, or where they indigenous hunter-gatherers who took up herding after contact with herders, probably in northern Botswana? Here, this issue is investigated using craniometric data collected on a large sample of individually dated human crania from coastal LSA context. Mahalanobis distances (D), calculated from the raw metric data, show that there was a small increase in inter-individual craniofacial variation after the introduction of herding at c. 2,000 BP. Here it is argued that this small increase in variation is neither consistent with a largescale immigration of genetically distinct herders into South Africa, or the long-term coexistence of two genetically distinct populations. Two alternative explanations fit the data better: (1) herding entered South Africa via the small-scale immigration of genetically distinct herders; and (2) local hunter-gatherer populations adopted herding after coming in contact with herders in northern Botswana. While small-scale immigration would not have had a major influence on the local gene pool, it would have increased variation to some extent as immigrants mixed with local populations. If small-scale external gene flow was not a factor in the introduction of herding, secular issues related to the introduction of herding could explain the increased variation in post-2,000 BP populations.

Link