Very interesting abstract at the ASHG meeting of a plenary presentation,Novel loci associated with skin pigmentation identified in African populations. This is clearly the work that one of the comments on this weblog alluded to last summer during SMBE. There I was talking about the likely introduction of the derived SLC24A5 variant to the Khoisan peoples and its positive selection in peoples in southern Africa.
Below is the abstract in full. Those who follow the literature on this see the usual suspects in relation to genes, but also new ones:
Despite the wide range of variation in skin pigmentation in Africans, little is known about its genetic basis. To investigate this question we performed a GWAS on pigmentation in 1,593 Africans from populations in Ethiopia, Tanzania, and Botswana. We identify significantly associated loci in or near SLC24A5, MFSD12, TMEM138…OCA2 and HERC2. Allele frequencies at these loci in global populations are strongly correlated with UV exposure. At SLC24A5 we find that a non-synonymous mutation associated with depigmentation in non-Africans was introduced into East Africa by gene flow, and subsequently rose to high frequency. At MFSD12, we identify novel variants that are strongly correlated with dark pigmentation in populations with Nilo-Saharan ancestry. Functional assays reveal that MFSD12 codes for a lysosomal protein that influences pigmentation in cultured melanocytes, zebrafish and mice. CRISPR knockouts of murine Mfsd12 display reduced pheomelanin pigmentation similar to the grizzled mouse mutant (gr/gr). Exome sequencing of gr/gr mice identified a 9 bp in-frame deletion in exon two of Mfsd12. Thus, using human GWAS data we were able to map a classic mouse pigmentation mutant. At TMEM138…we identify mutations in melanocyte-specific regulatory regions associated with expression of UV response genes. Variants associated with light pigmentation at this locus show evidence of a selective sweep in Eurasians. At OCA2 and HERC2 we identify novel variants associated with pigmentation and at OCA2, the oculocutaneous albinism II gene, we find evidence for balancing selection maintaining alleles associated with both light and dark skin pigmentation. We observe at all loci that variants associated with dark pigmentation in African populations are identical by descent in southern Asian and Australo-Melanesian populations and did not arise due to convergent evolution. Further, the alleles associated with skin pigmentation at all loci but SLC24A5 are ancient, predating the origin of modern humans. The ancestral alleles at the majority of predicted causal SNPs are associated with light skin, raising the possibility that the ancestors of modern humans could have had relatively light skin color, as is observed in the San population today. This study sheds new light on the evolutionary history of pigmentation in humans.
Much of this is not surprising. Looking at patterns of variation around pigmentation loci researchers suggested years ago that Melanesians and Africans exhibited evidence of similarity and functional constraint. That is, the dark skin alleles date back to Africa and did not deviate from their state due to selection pressures. In contrast, light skin alleles in places like eastern and western Eurasia are quite different.
Nyakim Gatwech
This abstract also confirms something I said in a comment on the same thread, that Nilotic peoples are the ones likely to have been subject to selection for dark skin in the last 10,000 years. You see above that variants on MFSD12 are correlated with dark complexion. In particular, in Nilo-Saharan groups. The model Nyakim Gatwech is of South Sudanese nationality and has a social media account famous for spotlighting her dark skin. In comparison to the Gatwech and the San Bushman child above are so different in color that I think it would be clear these two individuals come from very distinct populations.
The fascinating element of this abstract is the finding that most of the alleles which are correlated with lighter skin are very ancient and that they are the ancestral alleles more often than the derived! We’ll have to wait until the paper comes out. My assumption is that after the presentation Science will put it on their website. But until then here are some comments:
There is obviously a bias in the studies of pigmentation toward those which highlight European variability.
The theory of balancing selection makes sense to me because ancient DNA is showing OCA2 “blue eye” alleles which are not ancestral in places outside of Western Europe. And in East Asia there their own variants.
Lots of variance in pigmentation not accounted for in mixed populations (again, lots of the early genomic studies focused on populations which were highly diverged and had nearly fixed differences). Presumably, African research will pick a lot of this up.
This also should make us skeptical of the idea that Western Europeans were necessarily very dark skinned, as now we know that human pigmentation architecture is complex enough that sampling modern populations expand our understanding a great deal.
Finally, it’s long been assumed that at some stage early on humans were light skinned on most of their body because we had fur. When we lost our fur is when we would need to have developed dark skin. This abstract is not clear at how far long ago light and dark alleles coalesce to common ancestors.
When I first got my father’s 23andMe results the Y and mtDNA were an interesting contrast. He, and therefore myself, carried Y lineage R1a1a, the lord of the paternal lineages. That was not that great a surprise. In the 1000 Genomes results for the Bangladeshi sample 20% of the men were direct paternal descendants of the R1a1a progenitor.
The mtDNA was a surprise. It was G1a2. This was curious to me since Bangladesh has some of the highest frequencies in the world of haplogroups M, the subhaplogroups in question being mostly restricted to South Asia. I wasn’t surprised that I was R1a1a, but I was even more confident that my maternal lineage was going to be an M, as would my father’s (my own mtDNA is U2b, not common, but not so surprising). As you can see from the map 23andMe places my father’s maternal lineage somewhere in Northeast Asia. The only information I could get about the geography was for G1a, “G1a has been found in samples from China (Daur, Hui, Kazakh, Korean, Manchu, and a sample of the general population of the city of Shenyang), Japan, Korea, Vietnam, and Siberia (Yakut).”
The biggest sample of mtDNA results from Bangladesh I could find at N = 240 does not find any G at all, let alone G1a2. So this is clearly it is a rare haplogroup in the region. But, the authors do classify 13% of the Bangladeshis as carrying an “East Eurasian” haplogroup. Haplogroup A is found among Southeast Asians and Southern China, though not among Austronesians. Haplogroup F seems to have a similar distribution, as does D, B. The other haplogroups also seem “correctly” assigned in terms of modal distribution. They are all mostly East Asian.
Looking at the Y chromosome haplogroups in the 1000 Genomes there are two of O2 and O3, and one of C3, which are clearly of Southeast Asian origin. With N =5 out of 44 samples that is ~10%. O2 is interesting because it is found at very high frequencies among the Austro-Asiatic populations in South Asia, whether it be the Khasi, or Munda groups (general O2a). O3 seems associated with Tibeto-Burman populations, and C3 with East Asia more generally.
Martin Meredith’s The Fortunes of Africa glosses very quickly over one of the major reasons that the “great scramble” for the continent occurred in the late 19th century, the discovery of the usefulness of quinine as an anti-malarial agent. Perhaps because I’ve read Plagues and Peoples and The Retreat of the Elephants: An Environmental History of China, I have always been conscious of the role of disease in discouraging conquest and migration (malaria in Italy was also a way to limit the extent of long-term occupation).
The coastal regions of Africa had been subject to the trade and depredations of European actors for nearly 400 years when the Berlin Conference partitioned the continent amongst European powers. Despite the fact that much of the interior was not charted, there had long been a colonial presence. Accra, the modern capital of Ghana, was originally a 16th-century Portuguese fort, but for several centuries between the 17th and 19th centuries, it was actually a possession of Scandinavian powers, Sweden and Denmark! (before passing on to the British)
For all these centuries the heart of Africa was unknown to Europeans, in part because there were native powers blocking their way, but also because the mortality rates were so high for outsiders, as indicated above. It is no surprise that the main European settlement in Africa which was more than a simple trading fort was at the southern tip of the continent, where the climate was Mediterranean and so the disease burden low.
But once quinine, and machine guns, came into the equation the interior was accessible. It all happened rather quickly in a few decades, though in some cases European ‘colonialism’ involved little more than nominal allegiance of tribal chieftains.
It was only two years ago that researchers found the first ancient human genome in Africa: a skeleton in a cave in Ethiopia yielded DNA that turned out to be 4,500 years old.
On Thursday, an international team of scientists reported that they had recovered far older genes from bone fragments in Malawi dating back 8,100 years. The researchers also retrieved DNA from 15 other ancient people in eastern and southern Africa, and compared the genes to those of living Africans.
The general results of the paper, Skoglund et.al’s Reconstructing Prehistoric African Population Structure, were presented at the SMBE meeting this summer. So in broad sketches I was not surprised, though the details require some digging into.
The Bantu Expansion repatterned the population structure of Africa
Between 1000 BC and 500 AD the expansion of iron wielding agriculturalists from the environs of modern day southern Cameroon reshaped the cultural and genetic landscape of Sub-Saharan Africa. The relatively late date of this expansion should give us a general sense of how careful we need to be about making assertions about “prehistoric Africa.” When Egypt’s New Kingdom was expanding southward along the Nile and into the Levant, Sub-Saharan Africa was qualitatively very different from what we see today in both culture and genetic structure. The continent’s contemporary human geography does not have a deep time depth.
In any case, anyone who has worked with genetic data from Africa is struck by how similar Bantu-speaking populations are genetically. So these results are not world-shaking. South African Zulus occupy positions far closer to Kenyans and Congolese than they do to Khoisan peoples to the west of them facing the Kalahari. The Xhosa people on the cultural frontier of the Bantus in South Africa exhibit substantial admixture from Khoisan (to the point where they have even integrated clicks into their language!), but even they are preponderantly non-Khoisan.
By sampling ancient genomes across a geographical transect which runs up the Rift Valley to Ethiopia, Skoglund et al. show that before the Bantu Expansion there was a north-south genetic relatedness cline. When this result was presented at SMBE a few friends were quite excited that they were being presented a cline, as some researchers have felt that this particular lab group has a tendency to model everything as pulse admixtures between distinct ancestral populations. But the reasonably deep time transect in Malawi exhibited no variance in admixture fractions, which is indicative of the likelihood that its “mixed” status at a particular K cluster is simply an artifact (see this post for what’s going on).
One particular aspect of the results from Malawi is that they found no continuity between contemporary populations, Bantu agriculturalists, and these ancient hunter-gatherers. That is, hunter-gatherers were replaced in toto. This is not entirely surprising, as many researchers who have worked with European ancient DNA believe that hunter-gatherers in many areas left no descendants at all as well (the “hunter-gatherer” fractions in modern groups in a particular region are believed to be due to migration of mixed populations who obtained “hunter-gatherer” ancestry at another locale).
But the Bantus were not the first “intrusive” population
These results also have some moderate surprises. A Tanzanian sample from 1100 BC from a pastoralist context exhibits an ancestral mix which is Sub-Saharan African and West Eurasian/North African. More precisely, about 38 percent of this individual’s ancestry resembles that of the Pre-Pottery Neolithic culture of the Levant, and the rest of the genome most resembles a 4500 year old sample from Ethiopia.
This date is before the initiation of the Bantu Expansion. The genetic results in this work, and earlier publications, strongly points to the likelihood that this population(s) mediated the spread of pastoralism to the south and west. In particular, all Khoisan groups of southern Africa seem to have admixture from this group, more (Khoi) or less (San).
But a curious aspect of this result is that these early pastoralists do not carry any evidence of admixture from ancient eastern farmers from the Zagros region. That is, the West Eurasian gene flow into the Tanzanian pastoralists predates the great exchange/admixture in the Middle East between western and eastern lineages. Since that reciprocal gene flow seems to have occurred at least 2,000 years before the Tanzanian pastoralist’s time, it suggests that this West Eurasian element was in Africa for thousands of years.
The second important point to emphasize is that the Iranian-like component is found among Cushitic speaking Somali and Afar samples, at 15-20% clips. Looking at the supporting tables a wide range of East African populations have the Tanzanian pastoralist ancestry but do not show evidence of the Iranian-like ancestry, which is now ubiquitous in the Middle East, and presumably in the highlands of Ethiopia as well (which usually show somewhat higher levels of Eurasian ancestry than is the case on the coast, especially among Semitic language speakers).
This fact is important because many of the Nilotic peoples are reputed to have absorbed Cushitic groups relatively recently in the past. This is also true for Bantu speaking groups according to these and other data. Finally, the Sandawe, who speak a language with clicks, and so may have some affinity to Khoisan, are often stated to have Cushitic affinities (looking at the data they clearly have West Eurasian ancestry). But their Eurasian ancestry seems to lack the Iranian-like component as well.
None of the populations with putative Cushitic ancestry, but who lack Iranian-like ancestry, speak a Cushitic language (most speak Nilotic languages, but East African Bantus have mixed with these Nilotic groups, so they have the same ancestry). Therefore I wonder if these pastoralists spoke an Afro-Asiatic language in the first place.
A patchy landscape
The phylogenetic tree illustrates the relationships of various African populations without much recent Eurasian ancestry. In The New York Times article David Reich indicates that the Hadza people of Tanzania are the closest Sub-Saharan Africans to the lineage ancestral to non-Africans. This is actually a simplification of what you see in the paper, and is illustrated in the tree to the left. The 4500 year old Ethiopian sample, which does not have Eurasian ancestry, nevertheless is the closest of all Sub-Saharan groups to Eurasians. The Hadza have the highest fraction of this ancestral component of all Sub-Saharan Africans in their data set, but many other populations also carry this ancestry (the Tanzanian pastoralist combined the PPN ancestry with this element).
This was a patchy landscape of inhabitation, because though the Tanzanian pastoralist ancestry, a combination of PPN and proto-Ethiopian, spread all the way to the Cape, there were populations, such as the Hadza and a 400 year old individual sampled from the Kenya island of Pemba, which lacked this genetic variation. Indeed, they are also not on the north-south (proto-Ethiopian to Khoisan) cline that featured so prominently above.
The sampling of ancient individuals is not very dense yet, so we can’t say much. But I think it does indicate we need to be cautious about assumpting gene flow dynamics as-the-crow-flies, simply a function of distance. Ecological suitability no doubt plays a strong role in how populations expand. The Bantus, for example, were stopped in South Africa by the fact that their agricultural toolkit was not suitable for the western half of the country. So when Europeans arrived in the 16th century the residents of the Cape where Khoi pastoralists.
The presence of the Hadza in Tanzania, or an individual of unmixed proto-Ethiopian ancestry on Pemba 400 years ago, indicates that the ethnic geography of East Africa has long been fluid and dynamic. There is no reason to suppose that the Hadza are not themselves migrants from further north, perhaps easily explaining why they are not on the north-south cline so evident from the ancient DNA.
The rise of Basal Humans
Several years ago researchers discovered that the first farmers of Europe, who descended from an Anatolian population, were in part derived from a group which split off very early from other Eurasian populations. This group was termed “Basal Eurasian” (BEu) because it was an outgroup to all other Eurasians, including European hunter-gatherers, East Asians, Oceanians, and the natives of the New World. Subsequent work has shown that the early Neolithic farmers of the Near East, whether they’re from the Levant or the Zagros, had about half their ancestry from this population.
No ancient genomes which are predominantly BEu have been discovered yet. The fact that populations on the cusp of the Holocene seem to have Basal Eurasian ancestry across the Middle East suggests that the admixture with hunter-gatherers related to those of Europe must have occurred during the Pleistocene. But Basal Eurasian is arguably the most parsimonious explanation of the shared drift patterns that we see.
Skoglund et al. suggest that there may be the necessity of a similar construct in Africa. They are not the first, Schlebusch et al. also suggested the necessity of this lineage in the supplements of their preprint on ancient South Africans. Within Skoglund et al. the authors see variation between the far West African Mende and the eastern West African Yoruba, where the latter exhibits closer affinity to East African populations than the former (this includes those such as the proto-Ethiopian with no Eurasian admixture). Additionally, the authors found that Khoisan groups share more alleles with populations in East Africa than they do with those in West Africa even when you account for admixture.
One model that can explain this variation is long range gene flow, so that there would be connections between various regions as a function of their distance. Another explanation is that West African populations are the product of a Basal Human (BHu) population which separated first, before the bifurcation of Khoisan from other human populations. This would reorder our understanding of who the most basal humans are. Additionally, it would align with long-standing work on deep lineages within Africa contributing a minor component of the continent’s ancestry.
As should be clear due to the tree above, BHu postdates the separation of African humans from Neanderthals. One does wonder about the relevance of the Moroccan “modern” human to these models.
Understanding culture from genetics and genetics from culture
The spread of the Bantus over 1500 years from one end of the continent to the other is perhaps one of the most important dynamics we can use to understand the spread of farming more generally. The linguistic unity of the Bantus, or at least their affinity, suggests to us that the first farmers of Europe, who spread across much of the continent in 2500 years, probably exhibited the same pattern. The low levels of gene flow between hunter-gatherers and farmers, despite living in the same regions for thousands of years, can be illustrated with African examples (e.g., the Hadza vs. their Bantu neighbors).
We are rather in the early phase of understanding these dynamics. There are more remains to be found, perhaps in the dry fastness of the Sahara or Sahel? (though unfortunately political considerations may prevent excavation due to danger to archaeologists) The genetics will give us a general idea about the nature of genetic variation and how it arose, but robust cultural models also need to be developed which illustrate how these genetic patterns arose.
The above tweet is in response to a article which reports on the finding past month in PNAS, Early history of Neanderthals and Denisovans. It’s open access, you should read it. I don’t think I’ve reviewed it because I haven’t dug through the supplements. To be frank this is a paper where you pretty much have to read the supplements because they’re introducing a somewhat different model here than is the norm.
I talked to Alan Rogers at SMBE about this paper. Broadly, I think there might be something to it, and it’s because of what David says above. It is simply hard to imagine that Neanderthals could be extremely successful with such low genetic diversity as we see, and spread so thin. Now, the Quanta Magazine tries to emphasize that the effective population is not the true census population, but I wish it would have explained it more clearly. Basically, the size that is relevant for breeding is obviously not going to the same as a head count. And, because effective populations are highly sensitive to bottlenecks you can get really small numbers even when the extant population at any given time may be large.
The PNAS paper makes some novel inferences, and I’ll set that to the side until I read the supplements. But I don’t think it’s crazy that population structure within Neanderthals could be leading to lower total genetic diversity.
We construct genomic predictors for heritable and extremely complex human quantitative traits (height, heel bone density, and educational attainment) using modern methods in high dimensional statistics (i.e., machine learning). Replication tests show that these predictors capture, respectively, ~40, 20, and 9 percent of total variance for the three traits. For example, predicted heights correlate ~0.65 with actual height; actual heights of most individuals in validation samples are within a few cm of the prediction. The variance captured for height is comparable to the estimated SNP heritability from GCTA (GREML) analysis, and seems to be close to its asymptotic value (i.e., as sample size goes to infinity), suggesting that we have captured most of the heritability for the SNPs used. Thus, our results resolve the common SNP portion of the “missing heritability” problem – i.e., the gap between prediction R-squared and SNP heritability. The ~20k activated SNPs in our height predictor reveal the genetic architecture of human height, at least for common SNPs. Our primary dataset is the UK Biobank cohort, comprised of almost 500k individual genotypes with multiple phenotypes. We also use other datasets and SNPs found in earlier GWAS for out-of-sample validation of our results.
A scatter-plot is worth a thousand derivations.
You know what better than 500,000 samples? One billion samples! A nerd can dream….
I wasn’t paying close attention because of course human evolution is still happening actively. From a genetic perspective, evolution is just change in allele frequencies. Populations aren’t infinite, so even if there wasn’t any selection stochastic forces would shift allele frequencies. But of course selection is probably happening. For adaptation by natural selection to occur you need heritable variation on a trait where there are fitness differences as a function of variation within the population. It seems implausible that these conditions don’t still apply. There’s plenty of fitness variation in the population, and it’s unlikely to be random as a function of heritable variation.
But the devil is in the details. And last year Field et al. used the modern genomic tools available to detect selection occurring over the past 2,000 years. It is not credible that it would have magically stopped a few centuries ago.
So why is this new paper such a big deal? (note that it’s in PLOS BIOLOGY, not PLOS GENETICS) Because the method they use is ingenious and simple. Basically, they’re looking at changes in allele frequencies as a function of age in huge populations. It’s a little more complicated than that, they used a logistic regression to control for some of the other variables. But they found some biologically plausible hits with their data set of 50,000-150,000. And, they replicated their hits from a European sample to a non-European one.
This does bring me back to a discussion I observed a while back. An evolutionary geneticist who works with Drosophila mentioned offhand that in his field there really wasn’t that much of a need for more data. They could spend all their time to doing analysis. A prominent human geneticist whose work focused on biomedicine piped up that that wasn’t true at all for their field. There are some differences in the scientific questions, but there are also differences in terms of what you can do with humans as a model organism.
In the paper they look forward to the day of increasing sample sizes an order of magnitude beyond where it is now. At some point in the near future, large fractions of entire nations will be sequenced at medical grade level (30x coverage).
What does “strong genetic structure” mean? Basically Fst is showing the proportion of genetic variation which is partitioned between groups. Intuitively it is easy to understand, in that if ~1% of the genetic variation is partitioned between groups in one case, and ~10% in another, then it is reasonable to suppose that the genetic distance between groups in the second case is larger than in the first case. On a continental scale Fst between populations is often on the order of ~0.10. That is the value for example when you pool the variation amongst Northern Europeans and Chinese, and assess how much of it can be apportioned in a manner which differentiates populations (so it’s about ~10% of the variation).
This is why ancient DNA results which reported that Mesolithic hunter-gatherers and Neolithic farmers in Central Europe who coexisted in rough proximity for thousands of years exhibited differences on the order of ~0.10 elicited surprise. These are values we are now expecting from continental-scale comparisons. Perhaps an appropriate analogy might be the coexistence of Pygmy groups and Bantu agriculturalists? Though there is some gene flow, the two populations exist in symbiosis and exhibit local ecological segregation.
In PNG continental scale Fst values are also seen among indigenous people. The differences between the peoples who live in the highlands and lowlands of PNG are equivalent to those between huge regions of Eurasia. This is not entirely surprising because there has been non-trivial gene flow into lowland populations from Austronesian groups, such as the Lapita culture. Many lowland groups even speak Austronesian languages today.
Using standard ADMIXTURE analysis the paper shows that many lowland groups have significant East Asian ancestry (red), while none of the highland groups do (some individuals with East Asian admixture seem to be due to very recent gene flow). But even within the highlands the genetic differences are striking. The Fst values between Finns and Southern European groups such as Spaniards are very high in a European context (due to Finnish Siberian ancestry as well as drift through a bottleneck), but most comparisons within the highland groups in PNG still exceeds this.
The paper also argues that genetic differences between Papuans and the natives of Australia pre-date the rising sea levels at the beginning of the Holocene, when Sahul divided between its various constituents. This is not entirely surprising considering that the ecology of the highlands during the Pleistocene would have been considerably different from Australia to the south, resulting in sharp differences in the hunter-gatherer lifestyles. Additionally, there does not seem to have been a genetic cline. Papuans are symmetrically related to all Australian groups they had samples from.
Using coalescence-based genomic methods they inferred that separation between highlands and some lowland groups occurred ~10-20,000 years ago. That is, after the Last Glacial Maximum. For the highlands, the differences seem to date to within the last 10,000 years. The Holocene. Additionally, they see population increases in the highlands, correlating with the shift to agriculture (cultivation of taro).
None of the above is entirely surprising, though I would take the date inferences with a grain of salt. The key is to observe that large genetic differences, as well as cultural differences, accrued in the highlands of PNG during the Holocene. In the paper they have a social and cultural explanation for what’s going on:
Fst values in PNG fall between those of hunter-gatherers and present-day populations of west Eurasia, suggesting that a transition to cultivation alone does not necessarily lead to genetic homogenization.
A key difference might be that PNG had no Bronze Age, which in west Eurasia was driven by an expansion of herders and led to massive population replacement, admixture, and cultural and linguistic change (7, 8), or Iron Age such as that linked to the expansion of Bantu-speaking farmers in Africa (24). Such cultural events have resulted in rapid Y-chromosome lineage expansions due to increased male reproductive variance (25), but we consistently find no evidence for this in PNG (fig. S13). Thus, in PNG, wemay be seeing the genetic, linguistic, and cultural diversity that sedentary human societies can achieve in the absence of massive technology-driven expansions.
Peter Turchin in books like Ultrasociety has aruged that one of the theses in Steven Pinker’s The Better Angels of Our Nature is incorrect: that violence has not decreased monotonically, but peaked in less complex agricultural societies. PNG is clearly a case of this, as endemic warfare was a feature of highland societies when they encountered Europeans. Lawrence Keeley’s War Before Civilization: The Myth of the Peaceful Savage gives so much attention to highland PNG because it is a contemporary illustration of a Neolithic society which until recently had not developed state-level institutions.
What papers like these are showing is that cultural and anthropological dynamics strongly shape the nature of genetic variation among humans. Simple models which assume as a null hypothesis that gene flow occurs through diffusion processes across a landscape where only geographic obstacles are relevant simply do not capture enough of the dynamic. Human cultures strongly shape the nature of interactions, and therefore the genetic variation we see around us.
I didn’t figure I would have to say much about 9/11 really that others could not say (aside from perhaps you should read Marc Sageman’s Understanding Terror Networks if you want an ethnography of the Salafi jihadist movement which lead to al-Qaeda). But The Daily Best has a profile of one of Osama bin Laden’s sons:
Moreover, by this time, bin Laden already had two wives. But Najwa, the first of them, encouraged him to pursue Khairia, believing that having someone with her training permanently on hand would help her son Saad and his brothers and sisters, some of whom also suffered from developmental disorders.
Osama bin Laden had two dozen some children (approximately). But it was strange to me to see mention of several children with developmental disorders. Inbreeding is a major burden for Arab Muslim societies. And sure enough, Osama bin Laden’s first wife was his first cousin. She gave birth to around 10 children. Her father was Osama bin Laden’s mother’s brother. With the possibility of several generations of cousin marriage their relatedness may have been closer than normal half-siblings.
Note: Osama bin Laden’s father was from Yemen and his mother from Syria. So he was most certainly not inbred.
A few years ago I suggested to the paleoanthropologist Chris Stringer that the first modern humans who arrived in Europe did not contribute appreciable ancestry to modern populations in the continent (appreciable as in 1% or more of the genome).* It seems I may have been right according to results from a 2016 paper, The genetic history of Ice Age Europe. The very oldest European ancient genome samples “failed to contribute appreciably to the current European gene pool.”
Why did I make this claim? Two reasons:
1) 40,000 years is a long time, and there was already substantial evidence of major population turnovers across northern Eurasia by this point. You go far enough into the future and it’s not likely that a local population leaves any descendants. So just work that logic backward.
2) There was already evidence of low population sizes and high isolation levels between groups in Pleistocene and Mesolithic/Neolithic Europe. This would again argue in favor of a high likelihood of local extinctions give enough time.
This does not only apply to just modern humans, descendants of southern, likely African, populations. Neanderthals themselves show evidence of high homogeneity, and expansions through bottlenecks over the ~600,000 years of their flourishing.
The reason that these dynamics characterized modern humans and earlier hominins in northern Eurasia is what ecologists would term an abiotic factor: the Ice Age. Obviously humans could make a go of it on the margins of the tundra (the Neanderthals seem less adept at penetrating the very coldest of terrain in comparison to their modern human successors; they likely frequented the wooded fringes, see The Humans Who Went Extinct). We have the evidence of several million years of continuous habitation by our lineage. But many of the ancient genomes from these areas, whether they be Denisovan, Neanderthal, or Mesolithic European hunter-gatherer, show indications of being characterized by very low effective population sizes. Things only change with the arrival of farming and agro-pastoralism.
For two obvious reasons we happen to have many ancient European genomes. First, many of the researchers are located in Europe, and the continent has a well developed archaeological profession which can provide well preserved samples with provenance and dates. And second, Europe is cool enough that degradation rates are going to be lower than if the climate was warmer. But if Europe, as part of northern Eurasia, is subject to peculiar exceptional demographic dynamics we need to be cautious about generalizing in terms of the inferences we make about human population genetic history. Remember that ancient Middle Eastern farmers already show evidence of having notably larger effective population sizes than European hunter-gatherers.
Two new preprints confirm the long term population dynamics typical of European hunter-gatherers, Assessing the relationship of ancient and modern populations and Genomics of Mesolithic Scandinavia reveal colonization routes and high-latitude adaptation. The first preprint is rather methods heavy, and seems more of a pathfinder toward new ways to extract more analytic juice from ancient DNA results. Those who have worked with population genomic data are probably not surprised at the emphasis on collecting numbers of individuals as opposed to single genome quality. That is, for the questions population geneticists are interested in “two samples sequenced to 0.5x coverage provide better resolution than a single sample sequenced to 2x coverage.”
I encourage readers (and “peer reviewers”) to dig into the appendix of Assessing the relationship of ancient and modern populations. I won’t pretend I have (yet). Rather, I want to highlight an interesting empirical finding when the method was applied to extant ancient genomic samples: “we found that no ancient samples represent direct ancestors of modern Europeans.”
This is not surprising. The ‘hunter-gatherer’ resurgence of the Middle Neolithic notwithstanding, Northern Europe was subject to two major population replacements, while Southern Europe was subject to one, but of a substantial nature. Recall that the Bell Beaker paper found that “spread of the Beaker Complex to Britain was mediated by migration from the continent that replaced >90% of Britain’s Neolithic gene pool within a few hundred years.” This means that less than 10% of modern Britons’ ancestry are a combination of hunter-gatherers and Neolithic farmers.
And yet if you look at various forms of model-based admixture analyses it seems as if modern Europeans have substantial dollops of hunter-gatherer ancestry (and hunter-gatherer U5 mtDNA and Y chromosomal lineage I1 and I2, associated with Pleistocene Europeans, is found at ~10% frequency in modern Europe in the aggregate; though I suspect this is a floor). What gives? Let’s look at the second preprint, which is more focused on new empirical results from ancient Scandinavian genomes, Genomics of Mesolithic Scandinavia reveal colonization routes and high-latitude adaptation. From early on in the preprint:
Based on SF12’s high-coverage and high-quality genome, we estimate the number of single nucleotide polymorphisms (SNPs) hitherto unknown (that are not recorded in dbSNP (v142)) to be c. 10,600. This is almost twice the number of unique variants (c. 6,000) per Finnish individual (Supplementary Information 3) and close to the median per European individual in the 1000 Genomes Project (23) (c. 11,400, Supplementary Information 3). At least 17% of these SNPs that are not found in modern-day individuals, were in fact common among the Mesolithic Scandinavians (seen in the low coverage data conditional on the observation in SF12), suggesting that a substantial fraction of human variation has been lost in the past 9,000 years (Supplementary Information 3). In other words, the SHGs (as well as WHGs and EHGs) have no direct descendants, or a population that show direct continuity with the Mesolithic populations (Supplementary Information 6) (13–17). Thus, many genetic variants found in Mesolithic individuals have not been carried over to modern-day groups.
The gist of the paper in terms of archaeology and demographic history is that Scandinavian hunter-gatherers were a compound population. One component of their ancestry is what we term “Western hunter-gatherers” (WHG), who descended from the late Pleistocene Villabruna cluster (see paper mentioned earlier). Samples from Belgium, Switzerland, and Spain all belong to this cluster. The second element are “Eastern hunter-gatherers” (EHG). These samples derive from the Karelia region, to the east of modern Finland, bound by the White Sea to the north. EHG populations exhibit affinities to both WHG as well as Siberian populations who contributed ancestry to Amerindians, the “Ancestral North Eurasians” (ANE). There is a question at this point whether EHG are the product of a pulse admixture between an ANE and WHG population, or whether there was a long existent ANE-WHG east-west cline which the EHG were situated upon. That is neither here nor there (the Tartu group has a paper addressing this leaning toward isolation-by-distance from what I recall).
Explicitly testing models to the genetic data the authors conclude that there was a migration of EHG populations with a specific archaeological culture around the north fringe of Scandinavia, down the Norwegian coast. Conversely, a WHG population presumably migrated up from the south and somewhat to the east (from the Norwegian perspective).
And yet the distinctiveness of the very high quality genome as inferred from unique SNPs they have suggests to them that very little of the ancestry of modern Scandinavians (and Finns to be sure) derives from these ancient populations. Very little does not mean all. There is a lot of functional analysis in the paper and supplements which I will not discuss in this post, and one aspect is that it seems some adaptive alleles for high latitudes might persist down to the present in Nordic populations as a gift from these ancient forebears. This is no surprise, not all regions of the genome are created equal (a more extreme case is the Denisovan derived high altitude adaptation haplotype in modern Tibetans).
Nevertheless, there was a great disruption. First, the arrival of farmers whose ultimate origins were Anatolia ~6,000 years ago to the southern third of Scandinavia introduced a new element which came in force (agriculture spread over the south in a few centuries). A bit over a thousand years later the Corded Ware people, who were likely Indo-European speakers, arrived. These Indo-European speakers brought with them a substantial proportion of ancestry related to the hunter-gatherers because they descended in major fraction from the EHG (and later accrued more European hunter-gatherer ancestry from both the early farmers and likely some residual hunter-gatherer populations who switched to agro-pastoralism**).
For several years I’ve had discussions with researchers whose daily bread & butter are the ancient DNA data sets of Europe. I’ve gotten some impressions implicitly, and also from things they’ve said directly. It strikes me that the Bantu expansion may not be a bad analogy in regards to the expansion of farming in Europe (and later agro-pastoralism). Though the expanding farmers initial mixed with hunter-gatherers on the frontier, once they got a head of steam they likely replaced small hunter-gatherer groups in totality, except in areas like Scandinavia and along the maritime fringe where ecological conditions were such hunter-gatherers were at advantage (War Before Civilization seems to describe a massive farmer vs. coastal forager war on the North Sea).
But this is not the end of the story for Norden. At SMBE I saw some ancient genome analysis from Finland on a poster. Combined with ancient genomic analysis from the Baltic, along with deeper analysis of modern Finnish mtDNA, it seems likely that the expansion of Finno-Samic languages occurred on the order of ~2,000 years ago. After the initial expansion of Corded Ware agro-pastoralists.
The Sami in particular seem to have followed the same path along the northern fringe of Scandinavia that the EHG blazed. Though they herd reindeer, they were also Europe’s last indigenous hunter-gatherers. Genetically they exhibit the same minority eastern affinities in their ancestry that the Finns do, though to a greater extent. But their mtDNA harbors some distinctive lineages, which might be evidence of absorption of ancient Scandinavian substate.
I’ll leave it to someone else to explain how and why the Finns and Sami came to occupy the areas where they currently dominate (note that historically Sami were present much further south in Norway and Sweden than they are today). But note that in Latvia and Lithuania the N1c Y chromosomal lineage is very common, despite no language shift, indicating that there was a great deal of reciprocal mixing on the Baltic.
Overall the story is of both population and cultural turnover. This should not surprise when one considers that northern Eurasia is on the frontier of the human range. And perhaps it should temper the inferences we make about other areas of the world.
* You may notice that this threshold is lower than the Neanderthal admixture proportions in the non-African genome. Why is this old admixture still detectable while modern human lineages go extinct? Because it seems to have occurred with non-African humans had a very small effective population, and was mixed thoroughly. Because of the even genomic distribution this ancestry has not been lost in any of the daughter populations.
** Haplogroup I1, which descends from European late Pleistocene populations, exhibits a star phylogeny of similar time depth as R1b and R1a.
Is India’s caste system the remnant of ancient India’s social practices or the result of the historical relationship between India and British colonial rule? Dirks (history and anthropology, Columbia Univ.) elects to support the latter view. Adhering to the school of Orientalist thought promulgated by Edward Said and Bernard Cohn, Dirks argues that British colonial control of India for 200 years pivoted on its manipulation of the caste system. He hypothesizes that caste was used to organize India’s diverse social groups for the benefit of British control. His thesis embraces substantial and powerfully argued evidence. It suffers, however, from its restricted focus to mainly southern India and its near polemic and obsessive assertions. Authors with differing views on India’s ethnology suffer near-peremptory dismissal. Nevertheless, this groundbreaking work of interpretation demands a careful scholarly reading and response.
The condensation is too reductive. Dirks does not assert that caste structures (and jati) date to the British period, but the thrust of the book clearly leaves the impression that this particular identity’s formative shape on the modern landscape derives from the colonial experience. The British did not invent caste, but the modern relevance seems to date to the British period.
This is in keeping with a mode of thought flourishing today under the rubric of postcolonialism, with roots back to Edward Said’s Orientalism. As a scholar of literature Said’s historical analysis suffered from the lack of deep knowledge. A cursory reading of Orientalism picks up all sorts of errors of fact. But compared to his heirs Said was actually a paragon of analytical rigor. I say this after reading some contemporary postcolonial works, and going back and re-reading Orientalism.
To not put too fine a point on it postcolonialism is more about a rhetorical posture which aims to destroy what it perceives as Western hegemonic culture. In the process it transforms the modern West into the causal root of almost all social and cultural phenomenon, especially those that are not egalitarian. Anyone with a casual grasp of world history can see this, which basically means very few can, since so few actually care about details of fact.
Castes of Mind is an interesting book, and a denser piece of scholarship than Orientalism. Its perspective is clear, and though it is not without qualification, many people read it to mean that caste was socially constructed by the British.
This seems false. It has become quite evident that even the classical varna categories seem to correlate with genome-wide patterns of relatedness. And the Indian jatis have been endogamous for on the order of two thousand years. From The New York Times, In South Asian Social Castes, a Living Lab for Genetic Disease:
The Vysya may have other medical predispositions that have yet to be characterized — as may hundreds of other subpopulations across South Asia, according to a study published in Nature Genetics on Monday. The researchers suspect that many such medical conditions are related to how these groups have stayed genetically separate while living side by side for thousands of years.
Unfortunately though science is not well known in any depth among the general public. The ascendency of social constructionism is such that a garbled and debased view that “caste was invented by the British” will continue to be the “smart” and fashionable view among many intellectual elites.
Much of this is not surprising. Looking at patterns of variation around pigmentation loci researchers suggested years ago that Melanesians and Africans exhibited evidence of similarity and functional constraint. That is, the dark skin alleles date back to Africa and did not deviate from their state due to selection pressures. In contrast, light skin alleles in places like eastern and western Eurasia are quite different.
The biggest sample of mtDNA results from Bangladesh I could find at 
