Razib Khan One-stop-shopping for all of my content

November 3, 2018

It’s raining selective sweeps

Filed under: Population genetics,Population genomics,Selection — Razib Khan @ 11:44 pm

A week ago a very cool new preprint came out, Identifying loci under positive selection in complex population histories. It’s something that you can’t even imagine just ten years ago. The authors basically figure out ways to identify deviations of markers from expected allele frequency given a null neutral evolutionary model. The method is put first, which I really like, before getting to results or discussion. Additionally, they did a lot of simulation ahead of time. The sort of simulation that is really not possible before the sort of computational resources we have now.

Here’s the abstract:

Detailed modeling of a species’ history is of prime importance for understanding how natural selection operates over time. Most methods designed to detect positive selection along sequenced genomes, however, use simplified representations of past histories as null models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the genome using arbitrarily complex admixture graphs, which are typically used to describe the history of past divergence and admixture events among any number of populations. The method – called Graph-aware Retrieval of Selective Sweeps (GRoSS) – has good power to detect loci in the genome with strong evidence for past selective sweeps and can also identify which branch of the graph was most affected by the sweep. As evidence of its utility, we apply the method to bovine, codfish and human population genomic data containing multiple population panels related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in under-studied human populations, as well as muscle mass, milk production and tameness in particular bovine breeds. We are also able to pinpoint the emergence of large regions of differentiation due to inversions in the history of Atlantic codfish.

On a related note in regards to selection, On the well-founded enthusiasm for soft sweeps in humans: a reply to Harris, Sackman, and Jensen. The authors are responding to a recent preprint criticizing their earlier work. The reason that it’s fascinating to me is that these sorts of arguments today are really concrete and not so theoretical. There’s a lot of data for analytic techinques to chew through, and computation has really transformed the possibilities.

A generation ago these sorts of debates would be a sequence of “you’re wrong!” vs. “no, you’re wrong!” Today the disputes involve a lot of data, and so have a reasonable chance of resolution.

The first preprint identifies the usual candidates in humans that you normally see, and expected targets in cattle and cod. Sure, that will given biologists more interested in mechanisms and pathways things to chew upon, but imagine once researchers have large numbers of genomes for thousands and thousands of species. Then they’ll be testing deviations from neutral allele frequencies across many trees, and getting a more general and abstract sense of the parameter that selection explores, conditional on particularities o evolutionary history.

This is why I’m excited about plans to sequence lots and lots of species.

October 6, 2018

The population genetic structure of China (through noninvasive prenatal testing)

Filed under: China genetics,Han genetics,Population genetics,Population genomics — Razib Khan @ 10:03 am


This week a big whole genome analysis of China was published in Cell, Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History. The abstract:

We analyze whole-genome sequencing data from 141,431 Chinese women generated for non-invasive prenatal testing (NIPT). We use these data to characterize the population genetic structure and to investigate genetic associations with maternal and infectious traits. We show that the present day distribution of alleles is a function of both ancient migration and very recent population movements. We reveal novel phenotype-genotype associations, including several replicated associations with height and BMI, an association between maternal age and EMB, and between twin pregnancy and NRG1. Finally, we identify a unique pattern of circulating viral DNA in plasma with high prevalence of hepatitis B and other clinically relevant maternal infections. A GWAS for viral infections identifies an exceptionally strong association between integrated herpesvirus 6 and MOV10L1, which affects piwi-interacting RNA (piRNA) processing and PIWI protein function. These findings demonstrate the great value and potential of accumulating NIPT data for worldwide medical and genetic analyses.

In The New York Times write-up there is an interesting detail, “This study served as proof-of-concept, he added. His team is moving forward on evaluating prenatal testing data from more than 3.5 million Chinese people.” So what he’s saying is that this study with >100,000 individuals is a “pilot study.” Let that sink in.

The PCA at the top of the post is a bit busy, so I want to highlight the salient aspect. These results confirm that 5-10% of the ancestry of the Hui, Chinese speaking Muslims, is West Eurasian. The Uygur and Kazakh are about ~40% on the left of the plot. The authors note that the Manchus overlapped almost perfectly with individuals sampled from Northern China. This is expected because by the end of the Ching dynasty most of the Manchus had been fully Sinicized, and in the 20th century fully assimilated. Recently due to an emphasis on “national minorities” and some privileges granted therein many people have identified as Manchu due to some ancestry who in all other ways simply northern Han (the Manchu language is moribund).

The sections on particular adaptations which vary by region are not surprising. In books like The Retreat of Elephants the slow, gradual, and inexorable expansion of the Chinese beyond the Yangzi basin is described in a way that makes it clear that southern diseases and climate were a major impediment. But through a process of acclimation, assimilation of local peoples, and adaptation, by 1000 AD the center of demographic gravity had shifted to the south.

There is a section of the text which I think will be falsified though:

After removing participants with 49bp read length and with sequencing error rate >0.00325, a principal component analysis of 45,387 self-reported Han Chinese from the 31 administrative divisions showed that the greatest differentiation of Han Chinese is along a latitudinal gradient (Figures S3E and S3F), consistent with previous studies (Chen et al., 2009, Xu et al., 2009). In contrast, there is, perhaps surprisingly, very little differentiation from East to West. This observation may be explained by the fact that a large proportion of the western Han populations in China are recent immigrants organized by the central government starting from 1949 when the People’s Republic of China was founded (Liang and White, 1996).

I don’t think there’s any need to make recourse to migration from 1949 and after. The argument in Guns, Germs, and Steel suffices: it’s just easier to move across latitudes than longitudes. The people of the north eat noodles made from wheat, and the people of the south eat rice. This is a big cultural transition for peasants to make, and so it didn’t happen as often as moving to the coast, or inland. We have documented instances of mass migrations from adjacent provinces due to famine and political instability. In the 17th century conflicts resulted in the depopulation of Sichuan and the arrival of large numbers of people from Hunan and Hubei to the east.

The plot below is one of the more interesting ones from the paper. From left to right, private alleles found in the HapMap Utah whites also found in all individuals in a given province, and then just Han, and then private alleles to ethnic Telugu Indians (from South India) found in all individuals in a given province, and then just Han.

Click to enlarge

The first thing to notice is that there is a correlation between the Han and non-Han. This shouldn’t be surprising. Plenty of ethnic groups have become Han through acculturation and become demographically absorbed. This is probably truer in parts of the south than in the north, but southern Chinese ethnic minorities are genetically and culturally much more like the Han in the first place.

Private alleles shared with Northern Europeans (CEU) almost certainly has to do with the interaction sphere of the steppe pastoralists, which extends from the Carpathians to Mongolia. The relatively high frequency of R1a, and to a lesser extent R1b, among many Turkic/Central Asian peoples is a pretty good sign of where this West Eurasian ancestry comes from.

The Indian affinity is perhaps more interesting. To be honest I was surprised at the high affinity in Yunnan and Hainan. Tibet has strong cultural connections to India through its form of Buddhism. But its interesting that Qinghai, where many Tibetans also live, does not have the affinity with India. What’s going on in the other provinces? I suspect that the aboriginal peoples assimilated by the Han and other groups in this region probably had some distant connections to the non-West Eurasian ancestry in South Asia.

September 23, 2018

Tracing the paths of Noah’s sons

Filed under: Population genomics — Razib Khan @ 10:40 pm

 
The above admixture graph is from a new preprint, Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry. To be honest, if you read the supplementary text there’s almost no point in reading the main preprint, as it is far more in depth when it comes to the methodology as well as spotlighting a variety of particular results. It’s hard to know where to begin with such a preprint so I want to highlight the “this is a simplified model” portion in the figure above. That’s actually the truth. Remember, no admixture graph is the Truth, it is an attempt by humans to capture concisely and informatively the major features of our species’ population history dynamics. The reality was never as clear and distinct as stylized graphical representations would have you think, and the researchers are aware of this.

In any case, if you want to really get at how they arrived at the conclusions they did, really read the supplementary section SI 2, “An admixture graph model of Upper Paleolithic West Eurasians.” The authors have so many potential combinations of ancestral populations that they can’t simply manually and intuitively posit admixtures. Rather, they have to explore a huge number of combinations (trees/graphs)…at which point they run into computational limits. This section explicitly lays out computationally efficient ways to automatically traverse the possibility space, and arrive at the best fitting set of models, within reason.

The title of the preprint says it all, but let me quote the abstract in full:

The earliest ancient DNA data of modern humans from Europe dates to ~40 thousand years ago, but that from the Caucasus and the Near East to only ~14 thousand years ago, from populations who lived long after the Last Glacial Maximum (LGM) ~26.5-19 thousand years ago. To address this imbalance and to better understand the relationship of Europeans and Near Easterners, we report genome-wide data from two ~26 thousand year old individuals from Dzudzuana Cave in Georgia in the Caucasus from around the beginning of the LGM. Surprisingly, the Dzudzuana population was more closely related to early agriculturalists from western Anatolia ~8 thousand years ago than to the hunter-gatherers of the Caucasus from the same region of western Georgia of ~13-10 thousand years ago. Most of the Dzudzuana population’s ancestry was deeply related to the post-glacial western European hunter-gatherers of the ‘Villabruna cluster’, but it also had ancestry from a lineage that had separated from the great majority of non-African populations before they separated from each other, proving that such ‘Basal Eurasians’ were present in West Eurasia twice as early as previously recorded. We document major population turnover in the Near East after the time of Dzudzuana, showing that the highly differentiated Holocene populations of the region were formed by ‘Ancient North Eurasian’ admixture into the Caucasus and Iran and North African admixture into the Natufians of the Levant. We finally show that the Dzudzuana population contributed the majority of the ancestry of post-Ice Age people in the Near East, North Africa, and even parts of Europe, thereby becoming the largest single contributor of ancestry of all present-day West Eurasians.

Shared drift with Dzudzuana

Longtime readers know that I hate the American racial term “Caucasians.” It’s pretentious when you could just say “white European,” because that’s what people really mean, judging by the fact that the real people from the Caucasus are marginally Caucasian in the eyes of many Americans. The genealogical origin of the term goes back to Johann Friedrich Blumenbach. And yet this paper takes these two samples, and finds that a lot of the ancestry of modern groups can be attributed to them! (also, a religion interpretation of the results is in the title of the post)

To be fair, they caution that these ancient Caucasian samples are representative of a particular thread of human heritage, not that the center of this thread was necessarily in the Caucasus. This does make me wonder about ascertainment bias in the Near East toward samples from mountainous areas which were colder. But, at the granularity they are attempting to understand human population history, it’s probably not that big of a deal. Ultimately, they conclude that this Paleo-Caucasian population contributes “~46-88% of the ancestry” of modern Europeans, Near Easterners, and North Africans. That’s kind of a big deal.

There are so many results in this preprint, so I think we need to back to the “beginning” of the non-African branch. The Paleo-Caucasian sample is of note in part because it is from before the Last Glacial Maximum, and, about halfway back to the massive diversification of most non-African populations around 55,000 years ago.  Using the Paleo-Caucasian samples’ affinities this preprint reinterprets results from last spring on ancient DNA from Northwest Africa. In that paper, the authors conclude that Paleolithic North Africans were a mix between an unspecific Sub-Saharan population and Natufians. Here though the authors suggest that the Natufians and Yoruba both received gene flow from Paleolithic North Africans. And, these Paleolithic North Africans were themselves mixed between something similar to the Paleo-Caucasians (a mix between an ancient West Eurasian ancestry and “Basal Eurasian”), and a “Deep” ancestry which diverged from other non-Sub-Saharan Africans before the Basal Eurasians did.

The reason that the Paleo-Caucasian sample is so important is that it allowed the researchers to see that the early Holocene Near East, where Anatolian and Iranian farmers, as well as Natufians in the Levant, were ancestral to many later groups, was subject to many genetic changes from before the Last Glacial Maximum. The Natufians seem to be well modeled as having ancestry from the Paleolithic North Africans as one of the major ways they are distinctive from the Paleo-Caucasians. This presents us with a reasonable model for the west to east movement of haplogroup E, and, the Afro-Asiatic languages. The gene flow of Paleolithic North African also explains the non-trivial level of Neanderthal admixture which is found in the Yoruba population. This is mediated through the presumed back migration of Paleo-Caucasians from the Near East at some point in the Pleistocene, contributing some Neanderthal ancestry to the genetic background of Paleolithic North Africans.

Additionally, the distinction between western (Anatolian/Levant) and eastern (Iran) farmers during the early Holocene can now be understood as a product of later admixture into eastern proto-farmers of basic Paleo-Caucasian stock. The relative closeness of Anatolian farmers to the Paleo-Caucasian samples is indicative of the fact that there was an “Ancestral North Eurasian” (ANE) admixture cline into the Near East during the Pleistocene, which meant that some populations to the east became rather different from the pre-LGM samples. Probably after the Last Glacial Maximum proto-Siberian ancestry became prominent in the zone between the Caucasus and Iran (additionally, some of the models imply there was eastern Eurasian ancestry). This is in keeping with the fact that ANE ancestry does seem to have been found in places like Khorasan before the expansion south of steppe populations after 2,000 BC.

As noted in the abstract, Paleo-Caucasians had Basal Eurasian ancestry ~30,000 years ago. This increases the likelihood that Basal Eurasians weren’t recent migrants from deep inside Africa. Additionally, for various reasons, the authors are now positing a Deep ancestry which diverged even further into the past. Both Basal Eurasians and Deep populations seem to lack Neanderthal admixture. The authors also repeatedly suggest that Basal Eurasians were part of the Out of Africa bottleneck event. In Who We Are and How We Got Here David Reich presents the model that this bottleneck population had a low effective population size for a long time. This seems plausible because the genetic homogeneity that you see in non-Africans is pretty striking vis-a-vis Sub-Saharan Africans. On the other hand, this work confirms earlier results that imply that Basal Eurasians did not admix with Neanderthals, and also indicates that the divergence has to be greater than 60,000 years before the present from other non-Africans, who diversified more recently.

In contrast, the Deep ancestry group, which nevertheless forms a clade with the new Eurasian lineages (Basal and non-Basal), does not clearly seem to have undergone the bottleneck event according to this preprint. It’s more a matter of what they don’t say, rather than what they say in this case.

The big picture needs to be integrated I think with the new “modern humans emerged through a multi-regional process” within Africa. If you think of modern humans as emerging across an African range which shifted in the Near East based on oscillating climatic conditions, the ancestors of the “non-African” lineages can be thought of as one of the main deeply rooted lineages, probably in the northeast of the continent. During the Pleistocene, the Sahara was even more brutal than today during many periods, so it is not implausible that some of these marginal populations on the edge of Africa were subject to long periods of very small effective population sizes. Most of them presumably went extinct. But one population was probably far enough north and east that it had a little more margin to play with. This population was probably connected along the Mediterranean littoral at some point with the Deep component in North Africa, which had higher effective population sizes because the mountainous terrain of the Atlas region was always going to remain more clement through dry phases.

At some point one a group of the bottlenecked population mixed with some Neanderthals, and began to break out of containment in southwest Asia. If I had to bet money, I suspect there were already other related groups, probably somewhat admixed with local hominin lineages, further east. That is, I believe the archaeological results in Southeast Asia, and think that those in Australia are credible. But these groups were probably small in number, and totally absorbed by the later migration wave.

Also, the timing of the separation of Africans and “non-Africans” is such that I wouldn’t be surprised Qafzeh-Skull people were somehow ancestral to, or closely related to, the ancestors of non-Africans.

Finally, let’s remember that the authors were focusing on North Africa and Western Eurasia in this preprint. Things will get more complicated as East Asia and Africa come “online” in terms of these analyses. Of course, we are going to be helped by the reality that human genetic variation is not arbitrarily and randomly distributed, but reflects real constraints in our evolutionary history and the forces of geography as well as contingency. The non-African story is made simpler in part because of the great bottleneck, and especially the common descent of most peoples from the population that mixed with Neanderthals. The modeling of effective population size changes over time in Sub-Saharan groups does not lead us to believe that it will be so simple in that continent.

Related papers: The genetic history of Ice Age Europe, Tales of Human Migration, Admixture, and Selection in Africa, and Genomic insights into the origin of farming in the ancient Near East.

September 22, 2018

The great human migrations (coming in waves)

Filed under: Migrations,Population genomics — Razib Khan @ 8:53 pm


The figure above is from a new paper, Estimating mobility using sparse data: Application to human genetic variation, which uses genomic data from late Pleistocene to the Iron Age in western Eurasia, and then infers migration rate considering both spatial distribution and the variable of time (remember that samples apart in time should also be genetically different, just as those apart in space often are).

The empirical results are shown above, but they validated their method first by running some simulations. Interestingly they modeled the migration as a Gaussian random walk. Which is fine. But I wonder how true this is for a lot of the Eurasian migrations of the last 10,000 years. Perhaps the the distribution of distances from the place of birth would turn out be multi-modal, with a minority of individuals tending to make “long jumps”?

With that out of the way, it’s fascinating that migration peaks around the Neolithic transition, the Bronze Age, and then the Iron Age. If you read a book like 1177 BC, you know that there was a major regression in the 13th century BC across the Near East, and for several centuries the region was in a “Dark Age.” In The Human Web William H. McNeill argues that one of the reasons for the length and depth of this Dark Age is that the network of complex societies exhibited less density and so less redundancy to failure.

The authors conclude:

We find that mobility among European Holocene farmers was significantly higher than among European hunter–gatherers both pre- and postdating the Last Glacial Maximum. We also infer that this Holocene rise in mobility occurred in at least three distinct stages: the first centering on the well-known population expansion at the beginning of the Neolithic, and the second and third centering on the beginning of the Bronze Age and the late Iron Age, respectively. These findings suggest a strong link between technological change and human mobility in Holocene Western Eurasia and demonstrate the utility of this framework for exploring changes in mobility through space and time.

Earlier they say:

We find strong support for a rise in mobility during the Neolithic transition in western Eurasia, likely corresponding to a well-established demic expansion of farmers, originating in the Middle East and resulting in the spread of farming technologies throughout most of Western Eurasia

One of the main findings of Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past is that oftentimes change is not gradual. Consider the transition to the Corded-Ware society in Northern Europe.

The “demic diffusion” model is an easy one because it relies on the mass-action of individuals and family-groups as they expand in space through high fertility rates. And yet one thing that I think it misses is the socio-political context of that demic diffusion. For prehistoric periods we don’t have writing, and so no socio-political context. This is why in War Before Civilization the author focused on ethnographies of historical societies which came into contact with literate cultures which recorded their organization and folkways. The short summation is that these societies were often very aggressive and well organized for war. Additionally, hunter-gatherers themselves were keen on expanding farmers, and it seems clear they too could mobilize for violence.

The upshot is we need to think of the rise and expansion of strong states and expansionist polities as the context for an increase in the rate of migration. The reality of low migration rates in Pleistocene Europe was pretty evident even before this formal analysis. The pairwise genetic difference due to drift, and therefore low migration rates, for some nearby populations in the Pleistocene and early Holocene indicates that small-scale societies tend to be quite insulated from each other. In contrast, the Iron Age has witnessed a great deal of admixture, as large states and polities, as well as meta-ethnic identities, have broken down genetic barriers.

A regression around 1000 BC correlates neatly with reduced migration, This was almost certainly due to the fact that without larger states much of West Eurasian society, such as in Greece, had disintegrated into smaller tribal units.

Future historians and geneticists will notice that in the period between 1500 and 2000 the distribution of the Y chromosome lineage R1b1a1a2 expanded far beyond Western Europe. They will also understand the political context for this expansion of the lineage…

May 20, 2018

Beyond “Out of Africa” within Africa

Filed under: Human Evolution,Population genomics,Uncategorized — Razib Khan @ 11:36 pm

It looks as if the vast majority (95% or more depending on the population) of the ancestry of non-African humans derives from a population expansion which began around ~60,000 years ago. Before this period some researchers argue there was a non-trivial period of isolation. The “long bottleneck” (David Reich alludes to this in Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past). For the vast majority of humans then the last 60,000 years is characterized by a branching process, some reticulation (e.g., South Asians merge West and East Eurasian lineages) between these branches from a common ancestor, as well as introgression from archaic lineages like Neanderthals and Denisovans.

Though I do accept that it seems that modern humans probably migrated out of Africa before 60,000 years ago, mostly due to the results from archaeology, I think the genetic evidence is strong that these groups contributed very little genetically to contemporary populations.

The situation within Africa is very different. Being conservative it seems likely that the Khoisan ancestral lineage diverged from some other Africans ~200,000 years ago. I say conservative because there are researchers who want to push the divergence much further back. Additionally, several different research groups are now converging in a result that West Africans are a mixture between eastern Sub-Saharan Africans (think the population ancestral to Mota in Ethiopia) and a lineage basal to all other humans. That means that the Khoisan are not the most basal, so even assuming the conservative 200,000 year divergence point for Khoisan, modern humans share a common ancestor earlier than 200,000 years ago.

The upshot here is that around 75 percent of the history of modern humans is within (greater)* Africa. The distinctive “Out of Africa” bottleneck and expansion defines most humans only in the last 25 percent of the history of our species. And, within Africa, the dynamics were very different. The biggest difference is that African populations are not defined by a large number of lineages emerging and diverging around the same period, because there wasn’t a massive and singular expansion within Africa analogous to what occurred outside of Africa (at least until the recent past, with the Bantu expansion). That’s why there’s deep structure within Africa today between groups as divergent as the Bantu, Mbuti, Hadza, and Khoisan.

The term “Basal Eurasian” kind of makes sense in the non-African context because of the singular importance of divergence between lineages in the first 10,000 years or so after the “Out of Africa” event. I’m not sure “Basal human” makes as much sense because there wasn’t a singular event within Africa that allowed for the emergence of modern humans. Rather, it was a process, and probably quite resembles something like multiregionalism.

* Some wiggle room here for the likelihood that modern humans were long present in the liminal Near East.

Beyond “Out of Africa” within Africa

Filed under: Human Evolution,Population genomics — Razib Khan @ 11:36 pm

It looks as if the vast majority (95% or more depending on the population) of the ancestry of non-African humans derives from a population expansion which began around ~60,000 years ago. Before this period some researchers argue there was a non-trivial period of isolation. The “long bottleneck” (David Reich alludes to this in Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past). For the vast majority of humans then the last 60,000 years is characterized by a branching process, some reticulation (e.g., South Asians merge West and East Eurasian lineages) between these branches from a common ancestor, as well as introgression from archaic lineages like Neanderthals and Denisovans.

Though I do accept that it seems that modern humans probably migrated out of Africa before 60,000 years ago, mostly due to the results from archaeology, I think the genetic evidence is strong that these groups contributed very little genetically to contemporary populations.

The situation within Africa is very different. Being conservative it seems likely that the Khoisan ancestral lineage diverged from some other Africans ~200,000 years ago. I say conservative because there are researchers who want to push the divergence much further back. Additionally, several different research groups are now converging in a result that West Africans are a mixture between eastern Sub-Saharan Africans (think the population ancestral to Mota in Ethiopia) and a lineage basal to all other humans. That means that the Khoisan are not the most basal, so even assuming the conservative 200,000 year divergence point for Khoisan, modern humans share a common ancestor earlier than 200,000 years ago.

The upshot here is that around 75 percent of the history of modern humans is within (greater)* Africa. The distinctive “Out of Africa” bottleneck and expansion defines most humans only in the last 25 percent of the history of our species. And, within Africa, the dynamics were very different. The biggest difference is that African populations are not defined by a large number of lineages emerging and diverging around the same period, because there wasn’t a massive and singular expansion within Africa analogous to what occurred outside of Africa (at least until the recent past, with the Bantu expansion). That’s why there’s deep structure within Africa today between groups as divergent as the Bantu, Mbuti, Hadza, and Khoisan.

The term “Basal Eurasian” kind of makes sense in the non-African context because of the singular importance of divergence between lineages in the first 10,000 years or so after the “Out of Africa” event. I’m not sure “Basal human” makes as much sense because there wasn’t a singular event within Africa that allowed for the emergence of modern humans. Rather, it was a process, and probably quite resembles something like multiregionalism.

* Some wiggle room here for the likelihood that modern humans were long present in the liminal Near East.

April 15, 2018

Rainforest hunter-gatherers are not primitive or primal

Filed under: Population genomics — Razib Khan @ 8:18 pm

Recently I had a discussion with a friend that I suspect the “tropical pygmy” phenotype you see Central Africa and Southeast Asia is a pretty recent development. So this sort of assertion, “The Sentinelese tribe have remained on their North Sentinel Island, almost completely uncontacted for nearly 60,000 years…” is probably wrong. First, the Sentinelese probably arrived with other Andaman peoples during the Pleistocene from mainland Southeast Asia when the archipelago may have been connected to the mainland due to low sea levels.

Second, the small size of many tropical hunter-gatherer populations may simply be due to the difficulty of surviving in this environment. Though rainforests are lush, humans can’t access a lot of it, and small animals tend to require more energy to catch than is justified by how much meat they provide.

Genomics is now on the case: Polygenic adaptation and convergent evolution across both growth and cardiac genetic pathways in African and Asian rainforest hunter-gatherers:

Different human populations facing similar environmental challenges have sometimes evolved convergent biological adaptations, for example hypoxia resistance at high altitudes and depigmented skin in northern latitudes on separate continents. The pygmy phenotype (small adult body size), a characteristic of hunter-gatherer populations inhabiting both African and Asian tropical rainforests, is often highlighted as another case of convergent adaptation in humans. However, the degree to which phenotypic convergence in this polygenic trait is due to convergent vs. population-specific genetic changes is unknown. To address this question, we analyzed high-coverage sequence data from the protein-coding portion of the genomes (exomes) of two pairs of populations, Batwa rainforest hunter-gatherers and neighboring Bakiga agriculturalists from Uganda, and Andamanese rainforest hunter-gatherers (Jarawa and Onge) and Brahmin agriculturalists from India. We observed signatures of convergent positive selection between the Batwa and Andamanese rainforest hunter-gatherers across the set of genes with annotated ‘growth factor binding’ functions (p<0.001). Unexpectedly, for the rainforest groups we also observed convergent and population-specific signatures of positive selection in pathways related to cardiac development (e.g. 'cardiac muscle tissue development'; p=0.003). We hypothesize that the growth hormone sub-responsiveness likely underlying the pygmy phenotype may have led to compensatory changes in cardiac pathways, in which this hormone also plays an essential role. Importantly, we did not observe similar patterns of positive selection on sets of genes associated with either growth or cardiac development in the agriculturalist populations, indicating that our results most likely reflect a history of convergent adaptation to the similar ecology of rainforest hunter-gatherers rather than a more common or general evolutionary pattern for human populations.

A minor note: there is some ethnographic data that the isolated Sentinelese are not as small as the other Andaman Islanders. Some of their small size may simply be due to exposure to diseases and the stress of settlers from the mainland.

February 6, 2018

The genome of “Cheddar Man” is about to be published

If you are American you have probably heard about “Cheddar Man” in Bryan Sykes’ Seven Daughters of Eve. If you don’t know, Cheddar Man is a Mesolithic individual from prehistoric Britain, dating to 9,150 years before the present. Sykes’ DNA analysis concluded that he was mtDNA haplogroup U5, which is found in ~10% of modern Europeans, and which ancient DNA has found to be overwhelmingly dominant among European hunter-gatherers. But for years there has been controversy as to whether this result was contamination (after all, if it’s found in ~10% of modern Europeans it wouldn’t be surprising if the DNA was contaminated).

Today that is a moot point. On February 18th Channel 4 in the UK will premier a documentary that seems to indicate genomic analysis of Cheddar Man’s remains have been performed, and he turns out to be exactly what we would have expected. That is, he’s a “Western Hunter-Gatherer” (WHG) with affinities to the remains from Belgium, Spain, and Central Europe. These WHG populations were themselves relatively recent arrivals in Pleistocene Europe, with connections to some populations in the Near East, and with unexplored minor genetic admixture from an East Asian population. Their total contribution to the ancestry of modern Europeans varies, with lower fractions in the south of the continent, and the highest in the northeast.

Overall, the consensus seems to be that in Western Europe the genuine descent from indigenous hunter-gatherers passed down through admixture with Neolithic farmers, and then the Corded Ware and Bell Beaker groups, is around ~10%. This is the number that shows up in the press write-ups. But, there are some researchers who contend it is far less than 10%, and that that fraction is misattribution due to early admixture with relatives of these hunter-gatherers as steppe and farmer peoples were expanding.

Phylogenetics aside, one of the major headline aspects of the Cheddar Man is that reconstructions are now of a very dark-skinned and blue-eyed individual. Some of the more sensationalist press is declaring that the “first Britons were black!” As far as the depiction goes, this is literally true. The reconstruction is of a black-skinned individual in the sense we’d describe black-skinned.

But on one level it is entirely expected that this is what Cheddar Man would look like. The hunter-gatherers of Mesolithic Western Europe were genetically homogenous. They seem to derive from a small founder population. And, on the pigmentation loci which make modern Europeans very distinctive vis-a-vis other populations, SLC24A5, SLC45A2 and HERC2-OCA2, they were quite different from anything we’ve encountered before. First, these peoples seem to have had a frequency for the genetic variants strongly implicated in blue eyes in modern Europeans close to what you find in the Baltic region. The overwhelming majority carried the derived variant, perhaps even in regions such as Spain, which today are mostly brown-eyed because of the frequency of the ancestral variant. Second, these European hunter-gatherers tended to lack the genetic variants at SLC24A5 and SLC45A2 correlated with lighter skin, which today in European is found at frequencies of ~100% and 95% to 80% respectively.

The reason that one of the scientists being interviewed stated that there was a “76 percent probability that Cheddar Man had blue eyes” is that they used something like IrisPlex. They put in the genetic variants and popped out a probability. The problem is that the training set here is modern groups, which may have a very different genetic architecture than ancient populations. Recent work on Africans and East Asians indicate that the focus on European populations when it comes to pigmentation genetics has left huge lacunae in our understanding of common variants which affect variation in outcome.

East Asians, for example, lack both the derived variants of SLC24A5 and SLC45A2 common in Europeans but are often quite light-skinned. A deeper analysis of the pigmentation architecture of WHG might lead us to conclude that they were an olive or light brown-skinned people. This is my suspicion because modern Arctic peoples are neither pale white nor dark brown, but of various shades of olive.

As far as blue eyes go, it is reasonable that these individuals had that eye color because that trait seems somewhat less polygenic than skin color. There are darker complected people with light eyes, from the famous “Afghan girl” to the first black American Miss America, Vanessa Williams. The homozygote of the derived HERC-OCA2 variant seems relatively penetrant. From what I recall the literature indicates many people with blue eyes are not homozygotes on this locus for the derived haplotypes, but those who are homozygotes for the derived haplotypes invariably have blue eyes.

Addendum: It isn’t clear in the press pieces, but it looks like they got a high coverage genome sequence out of Cheddar Man. They refer to sequencing, and, they seem to have hit all the major pigmentation loci. This indicates reasonable coverage of the genome.

January 17, 2018

Runs of homozygosity are not good for your functioning

Filed under: Population genomics,Runs of Homozygosity — Razib Khan @ 8:20 pm


A must read review in Nature Reviews Genetics, Runs of homozygosity: windows into population history and trait architecture. Because it’s a paper on runs of homozygosity, James F. Wilson is on the apper.

If you are the product of a first cousin marriage, you have lots of runs of homozygosity. That’s because some of you will have large sections of the genome where both of the homologous chromosomes come from the same individual and are identical. In populations with small populations, this occurs not through recent inbreeding, as much as the reduced genetic diversity cranking up the frequency of some haplotypes over and above others.

The review covers all the bases, from distributions of runs of homozygosity in modern populations to ancient ones, as well as their functional consequences.

To the left, the plot shows that some populations, such as the Makrani of Pakistan, have fewer numbers of runs of homozygosity, but long ones when they have them. The populations on this part of the diagram are part of the “inbreeding belt.” In contrast, there are other populations with lots of runs of homozygosity, but they’re shorter. These are usually part of the “bottleneck belt,” where bottlenecks and small long-term effective populations have produced greater levels of homozygosity even on the genotype scale.

Perhaps the most interesting point though is that runs of homozygosity strongly correlate with changes in the values of a complex trait. In general, inbreeding is not too good, because recessively expressing deleterious alleles get exposed, and runs of homozygosity are a proxy for that.* This is why more exogamy in the Middle East and India may be such a social good.

* There may be confounds here. More educated and smarter people may marry those more distant from them geographically due to mobility.

December 20, 2017

Natural selection in humans (OK, 375,000 British people)

Filed under: Natural Selection,Population genetics,Population genomics,Selection — Razib Khan @ 10:41 pm

 


The above figure is from Evidence of directional and stabilizing selection in contemporary humans. I’ll be entirely honest with you: I don’t read every UK Biobank paper, but I do read those where Peter Visscher is a co-author. It’s in PNAS, and a draft which is not open access. But it’s a pretty interesting read. Nothing too revolutionary, but confirms some intuitions one might have.

The abstract:

Modern molecular genetic datasets, primarily collected to study the biology of human health and disease, can be used to directly measure the action of natural selection and reveal important features of contemporary human evolution. Here we leverage the UK Biobank data to test for the presence of linear and nonlinear natural selection in a contemporary population of the United Kingdom. We obtain phenotypic and genetic evidence consistent with the action of linear/directional selection. Phenotypic evidence suggests that stabilizing selection, which acts to reduce variance in the population without necessarily modifying the population mean, is widespread and relatively weak in comparison with estimates from other species.

The stabilizing selection part is probably the most interesting part for me. But let’s hold up for a moment, and review some of the major findings. The authors focused on ~375,000 which matched their sample criteria (white British individuals old enough that they are well past their reproductive peak), and the genotyping platforms had 500,000 markers. The dependent variable they’re focusing on is reproductive fitness. In this case specifically, “rRLS”, or relative reproductive lifetime success.

With these huge data sets and the large number of measured phenotypes they first used the classical Lande and Arnold method, which leveraged regression to measure directional and stabilizing selection. Basically, how does change in the phenotype impact reproductive fitness? So, it is notable that shorter women have higher reproductive fitness than taller women (shorter than the median). This seems like a robust result.

The results using phenotypic correlations for direction (β) and stabilizing (γ) selection are shown below. The abbreviations are the same as above.

 

There are many cases where directional selection seems to operate in females, but not in males. But they note that that is often due to near zero non-significant results in males, not because there were opposing directions in selection. Height was the exception, with regression coefficients in opposite directions. For stabilizing selection there was no antagonistic trait.

A major finding was that compared to other organisms stabilizing selection was very weak in humans. There’s just not that that much pressure against extreme phenotypes. This isn’t entirely surprising. First, you have the issue of the weirdness of a lot of studies in animal models, with inbred lines, or wild populations selected for their salience. Second, prior theory suggests that a trait with lots of heritable quantitative variation, like height, shouldn’t be subject to that much selection. If it had, the genetic variation which was the raw material of the trait’s distribution wouldn’t be there.

Using more complex regression methods that take into account confounds, they pruned the list of significant hits. But, it is important to note that even at ~375,000, this sample size might be underpowered to detect really subtle dynamics. Additionally, the beauty of this study is that it added modern genomic analysis to the mix. Detecting selection through phenotypic analysis goes back decades, but interrogating the genetic basis of complex traits and their evolutionary dynamics is new.

To a first approximation, the results were broadly consonant across the two methods. But, there are interesting details where they differ. There is selection on height in females, but not in males. This implies that though empirically you see taller males with higher rLSR, the genetic variance that is affecting height isn’t correlated with rLSR, so selection isn’t occurring.

~375,000 may seem like a lot, but from talking to people who work in polygenic selection there is still statistical power to be gained by going into the millions (perhaps tens of millions?). These sorts of results are very preliminary but show the power of synthesizing classical quantitative genetic models and ways of thinking with modern genomics. And, it does have me wondering about how these methods will align with the sort of stuff I wrote about last year which detects recent selection on time depths of a few thousand years. The SDS method for example seems to be detecting selection for increasing height the world over…which I wonder is some artifact, because there’s a robust pattern of shorter women having higher fertilty in studies going back decades.

December 10, 2017

Visualizing intra-European phylogenetic distances

Filed under: Europe,European genetics,Population genetics,Population genomics — Razib Khan @ 4:53 pm
Neighbor-joining tree of genetic distances between populations

 

In L. L. Cavalli-Sforza’s The History and Geography of Human Genes he used between population group genetic distances, as measured in FST values, to generate a series of visualizations, which then allowed him to infer historical processes. Basically the way it works is that you look at genetic variation, and see how much of it can be allocated to between groups. If none of it can be allocated to between groups, then in a population genetic sense it doesn’t make much sense to speak of distinctive groups, they’re basically one breeding population. The higher the FST statistic is, the more of the variation is partitioned between the groups.

Roughly this is used to correlate with genetic distance as well as evolutionary divergence. The longer two populations have been separated, the more and more genetic differences they’ll accumulate, inflating the FST value. There are a lot of subtleties that I’m eliding here (see Estimating and interpreting FST: the impact of rare variants for a survey of the recent literature on the topic and pathways forward), but for a long time, FST was the go-to statistic for making phylogenetic inferences on a within-species scale.

Today we have other techniques, Structure, Treemix, fineStructure, and various local ancestry packages.

But FST is still useful to give one a Gestalt sense of population genetic differences. Cavalli-Sforza admits in The History and Geography of Human Genes that European populations had very low pairwise FST, but because of the importance of Europe for sociocultural reasons a detailed analysis of the region was still provided in the text. Additionally, they had lots of European samples (non-European Caucasoids were thrown into one category for macro-group comparisons because there wasn’t that many samples).

Using results from the 2015 paper Massive migration from the steppe was a source for Indo-European languages in Europe, I visualized pairwise genetic distances for European populations, ancient and modern (Han Chinese as an outgroup), on a tree. What the results illustrate is that

  1. Ancient populations were very distinct in Europe from modern ones.
  2. Many modern groups are clustered close together.

The bulk of the population genetic structure in modern Europe seems to have been established in the period between 3000 BCE and 2000 BCE. This is not that much time for a lot of distinctiveness to develop, especially on the geographically open North European plain. I suspect with more and more Mesolithic and early to middle Neolithic DNA we’ll see that some of the modern population structure is a ghost of ancient substrate absorption.

Many of the ethno-national categories that are very significant in recent history, and impact the cultural memories of modern people and their genealogies, have very shallow roots. This does not mean they are not “real” (I don’t know what that’s supposed to mean at all), just that many of the identities which seem so salient to us today may be relatively recent in terms of their significance to large groups of humans….

Visualizing intra-European phylogenetic distances

Filed under: Europe,European genetics,Population genetics,Population genomics — Razib Khan @ 4:53 pm
Neighbor-joining tree of genetic distances between populations

 

In L. L. Cavalli-Sforza’s The History and Geography of Human Genes he used between population group genetic distances, as measured in FST values, to generate a series of visualizations, which then allowed him to infer historical processes. Basically the way it works is that you look at genetic variation, and see how much of it can be allocated to between groups. If none of it can be allocated to between groups, then in a population genetic sense it doesn’t make much sense to speak of distinctive groups, they’re basically one breeding population. The higher the FST statistic is, the more of the variation is partitioned between the groups.

Roughly this is used to correlate with genetic distance as well as evolutionary divergence. The longer two populations have been separated, the more and more genetic differences they’ll accumulate, inflating the FST value. There are a lot of subtleties that I’m eliding here (see Estimating and interpreting FST: the impact of rare variants for a survey of the recent literature on the topic and pathways forward), but for a long time, FST was the go-to statistic for making phylogenetic inferences on a within-species scale.

Today we have other techniques, Structure, Treemix, fineStructure, and various local ancestry packages.

But FST is still useful to give one a Gestalt sense of population genetic differences. Cavalli-Sforza admits in The History and Geography of Human Genes that European populations had very low pairwise FST, but because of the importance of Europe for sociocultural reasons a detailed analysis of the region was still provided in the text. Additionally, they had lots of European samples (non-European Caucasoids were thrown into one category for macro-group comparisons because there wasn’t that many samples).

Using results from the 2015 paper Massive migration from the steppe was a source for Indo-European languages in Europe, I visualized pairwise genetic distances for European populations, ancient and modern (Han Chinese as an outgroup), on a tree. What the results illustrate is that

  1. Ancient populations were very distinct in Europe from modern ones.
  2. Many modern groups are clustered close together.

The bulk of the population genetic structure in modern Europe seems to have been established in the period between 3000 BCE and 2000 BCE. This is not that much time for a lot of distinctiveness to develop, especially on the geographically open North European plain. I suspect with more and more Mesolithic and early to middle Neolithic DNA we’ll see that some of the modern population structure is a ghost of ancient substrate absorption.

Many of the ethno-national categories that are very significant in recent history, and impact the cultural memories of modern people and their genealogies, have very shallow roots. This does not mean they are not “real” (I don’t know what that’s supposed to mean at all), just that many of the identities which seem so salient to us today may be relatively recent in terms of their significance to large groups of humans….

November 27, 2017

Understanding prehistory through genetic inference and ancient DNA

Filed under: Ancient DNA,Population genomics — Razib Khan @ 8:23 pm

Before David Reich’s book, Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past, I highly recommend a new preprint from Pontus Skoglund and Iain Mathieson*, Ancient genomics: a new view into human prehistory and evolution.

It’s basically at the sweet spot for a lot of readers: doesn’t overemphasize methods or archaeological minutiae that’s hard to follow. That being said I do think you would benefit if you read two things which would complement in those directions, First Farmers: The Origins of Agricultural Societies, and Ancient Admixture in Human History.

* I have to say, I consider Iain a friend, but am I the only one a bit perplexed by how a British person can have such a difficult to spell version of his name? I always have to look it up!

November 24, 2017

Soft selection for gentleness in Puerto Rican African Honeybees

Filed under: Population genetics,Population genomics,Soft Selection,Soft Sweep — Razib Khan @ 3:07 pm


When I was a kid “killer bees” were a major pop culture thing. There were movies about the bees, and we would get updates about their march northward in the news. They were a cautionary tale of our species’ hubris.

Today we have a little bit more perspective. These bees were actually just African honeybees, the ancestral population to European honeybees, which were introduced to the New World with Europeans centuries earlier than the African honeybees. African honeybees were not that different from European honeybees, but they were more aggressive and tended to outcompete European honeybee colonies. They are a major problem for the beekeeping industry, but not a major threat to human life.

Today the African and European populations in the United States seem to have stabilized in their ranges, with a hybrid zone between them. African bee’s migratory behavior makes them less competitive with European bees in colder climates.

A friend of mine once mentioned to me that if he had to do it all over again he would do research on the evolutionary genomics of Hymenoptera, and in particular bees. People care about bees. So it ‘s no surprise that I noticed this paper out in Nature Communications, A soft selective sweep during rapid evolution of gentle behavior in an Africanized honeybee:

Highly aggressive Africanized honeybees (AHB) invaded Puerto Rico (PR) in 1994, displacing gentle European honeybees (EHB) in many locations. Gentle AHB (gAHB), unknown anywhere else in the world, subsequently evolved on the island within a few generations. Here we sequence whole genomes from gAHB and EHB populations, as well as a North American AHB population, a likely source of the founder AHB on PR. We show that gAHB retains high levels of genetic diversity after evolution of gentle behaviour, despite selection on standing variation. We observe multiple genomic loci with significant signatures of selection. Rapid evolution during colonization of novel habitats can generate major changes to characteristics such as morphological or colouration traits, usually controlled by one or more major genetic loci. Here we describe a soft selective sweep, acting at multiple loci across the genome, that occurred during, and may have mediated, the rapid evolution of a behavioural trait.

Come for the bees, but stay for the soft selection! If you talk to anyone in evolutionary and population genomics you know that the future is in understanding patterns of soft selection and polygenic selection from standing variation. Though these are related phenomena which are associated with each other, all are all distinct.

Standing variation just refers to the diversity which is segregating in the population at any given time. At any given moment many loci exhibit polymorphism. This polymorphism can be a target of natural selection if it is correlated with heritable variation and differentials in fitness. Though soft selection can be quite wooly it’s inverse, hard selection, is clear: in genetic terms hard selection can be seen in allele frequency changes at a single variant in a locus, going from the point where it is a novel mutation to nearly fixed in the population. In Haldane’s original conception hard selection involved excess deaths, and imposed a limit on the rate of evolution as well as the amount variation you could expect within a given population. This model was convenient in the pre-genomic and early genomic era because empirical selection tests had to focus on large allele frequency changes around singular loci. Researchers didn’t have large numbers of whole-genome samples available (nor the computational ability to analyze them).

Today this is not a limitation. In the analysis above the authors had 30 individuals of the 3 populations sequenced at high quality (20x). They ended up with millions of genetic variants they could analyze.

The plot to the left shows that “gentle African honeybees” (gAHB) tend to be closer to the African honeybee populations (AHB) overall (though with some hybridization with European honeybees, EHB). This is not surprising.

But the key observation was that over 12 generations the African honeybees of Puerto Rico became progressively less aggressive, despite maintaining overall morphological similarities to the mainland Mexican African bees from which they likely derive. Though buried in the discussion, there is a rationale for why this morphological change may have occurred: the Puerto Rican bees are subject to a lot of negative selection against aggression because of the density of the island, as well as the reality that aside from humans there aren’t other many species where their aggressive tendencies are beneficial. Basically, if you are an aggressive colony, it’s harder to make a go in densely settled areas (the implication here then is that there are probably “gentle” African honeybee populations across Latin America, they just are never disaggregated from the broader meta-population).

Credit: Phillip Messer and Nandita Garud

It’s the genomics where the real evolutionary insight comes in: they found that there were multiple soft sweep events around genetic regions implicated in behavior. In their overall genome the gAHB of Puerto Rico resembled mainland AHB, but in this subset of genetic loci they resembled EHB. Many of these loci had also been known to be targets of selection when the original European bee population diverged from the ancestral African population. Basically this is a genomic illustration of convergent evolution.

Regular readers of this blog will recognize the ways they detected selection. They used a modified form of EHH, which is reasonable since the selection event was recent enough to have been associated with distinct haplotype blocks. Also, standard Fst analysis showed that these were outliers in relation to the broader genetic pattern of relatedness (these loci were more like EHB than AHB, while most loci were more like AHB than EHB).

So this a form of polygenic selection. Remember, natural selection only knows genes through the phenotype (with intra-genomic selection being an exception). A behavior like aggression is probably subject to the fourth law of behavior genetics. That is, variation won’t be defined around a single genetic locus. Rather, variation across the genome will be correlated with variation in the phenotype. As selection favors a particular value of the phenotype across the distribution the allele frequencies across many genetic loci will shift, but they will not necessarily fix. Polygenic selection operates on the dispersed standing genetic variation which explains much of the variation of the phenotype in question. Instead of total sweeps to fixation due to large fitness differences between a given allele and its alternative form, the selection impact is distributed and diffused across the genome.

Though most of the genetic variants seem to recapitulate the evolution of the less aggressive phenotype that occurred with the original migration north of African honeybees, some of the selection signatures were novel. This points to the reality that when you have soft selection on standing variation you may have similar phenotypes which evolve via different means. Additionally, the authors noted that these results were in contrast to controlled breeding experiments in mammals where selection for gentility (“domestication”) often targeted a few loci and exhibited strong pleiotropic effects (due to the genetic correlation). These results point to the limitations of inferences made from human-directed selection.

Soft selection is probably ubiquitous. Consider the evolution of skin color in humans. There are lots of variants and lots of variation, and most of the variation seems to be ancestral. Only at the locus SLC24A5 do you have a perfect illustration of a hard selective sweep, probably from a de novo mutation that emerged around the Last Glacial Maximum.

From a geneticists’ perspective evolution is basically conceived of as changes in allele frequencies over time. Much of this is due to natural selection. Now that the world of soft selection is opening up, I suspect that we’ll understand a lot more of what we see around us, at least in the generality.

Citation: A soft selective sweep during rapid evolution of gentle behaviour in an Africanized honeybee.

September 23, 2017

Africa, the churning continent

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.

Now A new paper in Cell may herald the beginning of a great genomic scramble to understand the history of Africa. Carl Zimmer in The New York Times has a piece up, Clues to Africa’s Mysterious Past Found in Ancient Skeletons. It begins:

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, was presented at the SMBE meeting this summer. So in broad sketches I was not surprised at the results, 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 surprising. 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 from South Africa 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 groups. 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 (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 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 of 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 understanding 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.

Citation: Reconstructing Prehistoric African Population Structure, Skoglund, Pontus et al. Cell , Volume 171 , Issue 1 , 59 – 71.e21

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