The genetics of the Tuatha Dé Danann

Newgrange

The power of ancient DNA in terms of human evolution at this point is to a large extent the ability to understand the arc of human cultural history as reflected in our genealogies. Archaeologists have long attempted to infer aspects of social and cultural practice from material remains. Now, geneticists are getting into this game, with mixed results.

Today the Bradley lab in Ireland published a paper about the genetics of Neolithic Ireland (i.e., before the arrival of Bell Beakers ~2,500 BC). The first author is Lara Cassidy, who I interviewed last year. There is a reason this paper is in Nature.

Let me quote the abstract first:

…The scale and sophistication of megalithic architecture along the Atlantic seaboard, culminating in the great passage tomb complexes, is particularly impressive…Although co-operative ideology has often been emphasized as a driver of megalith construction…the human expenditure required to erect the largest monuments has led some researchers to emphasize hierarchy…Here we present evidence that a social stratum of this type was established during the Neolithic period in Ireland. We sampled 44 whole genomes, among which we identify the adult son of a first-degree incestuous union from remains that were discovered within the most elaborate recess of the Newgrange passage tomb. Socially sanctioned matings of this nature are very rare, and are documented almost exclusively among politico-religious elites—specifically within polygynous and patrilineal royal families that are headed by god-king…We identify relatives of this individual within two other major complexes of passage tombs 150 km to the west of Newgrange, as well as dietary differences and fine-scale haplotypic structure (which is unprecedented in resolution for a prehistoric population) between passage tomb samples and the larger dataset, which together imply hierarchy. This elite emerged against a backdrop of rapid maritime colonization that displaced a unique Mesolithic isolate population, although we also detected rare Irish hunter-gatherer introgression within the Neolithic population.

There’s a lot of moving parts in this research, and the most interesting element isn’t the genetics, but the social structure that you can infer from the genetics. It seems entirely likely that the “Megalithic civilization” of Atlantic Europe was hierarchal. But this pretty much confirms it. As noted in the paper violations of first-order incest taboos as a cultural norm (as opposed to deviancy) are strongly associated with very stratified preliterate or semiliterate societies (with the possible exception of Zoroastrianism). Additionally, this research highlights that a set of individuals, likely paternally related, seem to be enriched in elite burials.

In a few circles, there are ideas that Neolithic Europeans were peaceful and matrilineal. The existence of stratification like this and the likelihood of ‘god-kings’ makes that very unlikely in Ireland. Though there was no doubt some variation in Neolithic Europe, the existence of “long-houses” in Germany from contemporary cultures is ominous. The matrilineal element is distinct. There are matrilineal societies that are quite warlike (e.g., the Nairs of Kerala or the Iroquois). But the possibility of common Y chromosomes suggests that this was a patrilineal society, which is, on the whole, more common anthropologically.

To me this is the most awesome part of the paper:

The Brú na Bóinne passage tombs appear in Medieval mythology that relates their construction to magical manipulations of the solar cycle by a tribe of gods, which has led to unresolved speculation about the durability of oral traditions across millennia…Although such longevity seems unlikely, our results strongly resonate with mythology that was first recorded in the eleventh century AD, in which a builder-king restarts the daily solar cycle by copulating with his sister…Fertae Chuile, a Middle Irish placename for the Dowth passage tomb (which neighbours Newgrange), is based on this lore, and can be translated as ‘Hill of Sin’ or ‘Hill of Incest’…

This is incredible. Unless you are set in your ways I think it is hard to deny that the medieval Irish were passing on a recollection in their myth from an encounter between Bell Beakers and the late descendants of the Newgrange people. In The Isles Norman Davies argues that the Irish, unlike the English and the British more generally (Brythonic), kept their own mythology, and so have a sense of their past in a way that is uncommon among Northern European peoples. The Irish legends imply that there were multiple waves of people, and it is assumed that the people who live in the great mounds are the Tuatha Dé Danann, who became ancient Irish demigods.

I suspect that the early Bell Beakers viewed the monuments of the Tuatha Dé Danann, the Newgrange people, like how some Americans view “Indian graveyards.” Even among modern people, there is superstition, so what can we expect from the ancients? The Greeks forgot their heritage and assumed that the cyclopean citadels of their ancestors were built by giants. No doubt agro-pastoralist Bell Beakers looked at the massive ruins, and perceived the work of the gods.

And we shouldn’t underestimate the ability of oral tradition to recall events for premodern people. Mount Mazama blew 7,700 years ago, but native people in the area have legends of that explosion. Australian Aboriginals have myths that clearly outline and detail landmarks that are now underwater due to rising sea levels. The point is that it’s plausible that facts that are 3,000 years old could persist down to Christian Ireland, and be recorded by priests.

There are lots more I could say about this paper in the details. They found an infant with Down syndrome! They show recent introgression of hunter-gatherer ancestry into some Neolithic individuals. Also, they show hunter-gatherer substructure (Irish hunter-gatherers do not have ancestry from Magdelanian populations, only Villabruna). But the biggest aspect here is that this paper now sets a standard for how you can synthesize ancient DNA with archaeology and mythology.

Well done.

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Version alpha of trying to understand East Asian population history is now out!

We’ve been waiting for ancient DNA to answer some questions about eastern Eurasia for a while. I always thought Qiaomei Fu would spearhead it, but it doesn’t seem like it worked out that way. That’s because she’s not on a new preprint, The Genomic Formation of Human Populations in East Asia, which fills in a lot of gaps and confusing aspects of what has been reported from fragments of publications that came before (e.g., this clarifies a lot of things with Japan, see below). Since there has already been ancient DNA work on eastern Siberia and Southeast Asia, this is really focusing on the area in and around what is today the Peoples’ Republic of China. The first author has an affiliation with a university in Fujian, a province in southeast China.

Much of the analysis can be understood as organized around language families, and the demographics associated with them. In this way, it goes back to L. L. Cavalli-Sforza’s correlations between gene trees and language trees, as well as his later work on the agricultural Diasporas.

First, there isn’t something radically surprising here in their results. As I suggest above, the mass of ancient DNA in the preprint and model-building just snap together a lot of what you can see in other work, some going back decades.

Let’s start with the “Onge-like/related ancestry. ”

Below you see the strange pattern of Y chromosomal haplogroup D. It’s common in Tibet, Japan, and among the Andamanese.

In the preprint, the authors argue that there is a deep division among East Eurasian populations, going back further than 40,000 years, between a set of populations descended from groups related to Tianyuan man, and populations with affinities to the indigenous peoples of southeast Eurasia and Australia (“Ancestral Ancestral South Indians”, AASI, the Onge, the Negritos of Malaysia and the Phillippines, and Oceanians). Modern populations in East Asia can be thought of as a mix between these two groups, in various pulses and waves. The finding that some peoples in the Amazon had “Australo-Melanesian” affinity is very strange, but note that there’s no guarantee that the geographic distribution of the two clades was so skewed in the past in a north-south manner.

The Onge-related ancestry is apparently found as the deepest layer in the Tibetan plateau and contributes 45% of the ancestry to the Jomon of Japan. Among ancient proto-Austronesian peoples of Taiwan, it contributed 14% of the ancestry. Earlier work on Southeast Asia indicated that even before the expansion of Austro-Asiatic farmers out of southern China they mixed with a basal East Eurasian lineage related to the Onge.

Chinese annals record the presence of dark-skinned peoples in Yunnan nearly into historical periods. These could very well be legends or rumors, or, they could be the last relic populations that had not been fully absorbed into the Tianyuan-descended farmer expansion.

Moving more recently into the past, the preprint findings that of the Tianyuan descended populations in East Asia there is a northern and southern grouping. The northern grouping has been discussed before, it is the classic Amur-river valley population. It turns out that a sample from 5,000 years ago in northern Shaanxi, just to the north of the hearth of classical Chinese civilization in Henan, resembles these Amur-river valley populations. Though the authors don’t have samples from southern China, or even the Yangzi, they use modern samples from southern Chinese peoples, as well as ancient samples from Taiwan, to infer that it is likely that the Yangzi river valley was inhabited by a somewhat different group during prehistory than the modern Han Chinese.

In the preprint, the argument is made that Austronesian, Tai-Kadai, and Austro-Asiatic all emerged out of the Yangzi valley and its rice cultures. As noted above, other papers have already outlined the peopling of Southeast Asia using ancient DNA, so I will ignore that. But, note that for Austro-Asiatic populations, ~1/3 of the ancestry is Onge-related. Some of this was mixed in while in southern China, but some of it probably accrued later on in Southeast Asia.

Modern Austro-Asiatic populations can then be thought of as a compound of Tianyuan, and various  Onge-related groups.

China:  

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Ten individuals give you the history of whole populations – yes they do!

In the recent paper on the genetics of Philistines they had good quality DNA from 10 individuals. Some archaeologists have criticized over-generalizing from such a small dataset. Naively I think this is a good caution. But we have many many ancient DNA results from humans now, and I think this naive objection needs to be tamped down some. Additionally, 10 samples in a genomic sense have a lot more information than that “10” might imply.

Genome-wide data is such that you can take one individual, and infer their ancestral lineage and so capture the history of many upstream in the genealogy. Additionally, when it comes to f-4 statistics and what not they used 20,000 markers.

Also, we’ve got some experience now with the “first” individual from given populations, and how representative and informative they were as more data came in. The Loschbour sample was the first of what we later called “Western Hunter-Gatherers” (WHG). Later WHG are all pretty similar to this individual, with only minor differences (the late Pleistocene “Villabruna cluster” prefigured it). The reason that the Loschbour sample worked so well is that human metapopulation dynamics seem to be characterized by rapid range expansions and population turnovers, especially in some regions of northern Eurasia. The genetics of “Cheddar Man” was surprising to no one within the field (actually it would have been a bigger publication if he was not so WHG).

Think of what Ma’lta and the first Neolithic farmers in Europe have taught us, and how little further samples from these cultures told us.

One of the things biologists like to say about humans is that we’re a young species that went through a bottleneck. In fact, there have been serial bottlenecks. That means there’s a lot of homogeneity in many groups across geographies. This doesn’t even take into account endogamy. Representativeness still matters…but the reality is that humans across a huge region don’t vary that much.

The main exceptions seem to be due to cultural barriers. Endogmany in South Asia, religious differences in the Near East, and variance in mode-of-production in Africa can mean that who you sample matters a great deal. The last was clearly operative early in the Holocene (early farmers often did not intermarry with hunter-gatherers), but I doubt the first two were particularly important until very complex literate polities emerged.

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The sons of Japeth divide the world between them


Most “old hands” in the discipline of historical population genetics remember when grand narratives were constructed out of Y chromosomal haplogroup distributions. One of the most distinctive ones is that of haplogroup R1b, which exhibits very high frequencies in the west of Europe, as high as more than 80% among the Basques. Because the Basques are the only non-Indo-European population which exists today in Western Europe, it was presumed that they are more ancient than other groups. And, their high frequency of R1b (along with other peculiarities such as a high frequency of Rh-), was taken to indicate that they reflected the genetics of Europe’s aboriginal hunter-gatherers when farming arrived.

This turned out to be wrong in a lot of details. Genetically the Basques are quite like the European farmers from Anatolia who replaced the original hunter-gatherers. Less so than the Sardinians, as they have more hunter-gatherer ancestry. But instead of being the language of European hunter-gatherers, it seems plausible that the Basque language descends from that of the Cardial culture.

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Cave bears live on in brown bears, and were vegetarians (what!?!?!)


Unless you’ve been asleep you are aware of another megafauna ancient DNA discover, Partial genomic survival of cave bears in living brown bears:

Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species.

A sad thing about this publication is that brought to my attention that these ancient cave bears were mostly herbivores. It makes me view The Clan of the Cave Bear differently!

I assume most readers of this weblog are not surprised. We know that various extant and extinct members of the elephant lineage have mixed. By a strange coincidence (or perhaps not?) the fraction of cave bear DNA in modern brown bears seems very similar to the fractions of Neanderthal DNA we seen in modern lineages. The authors infer that the gene flow may also have been bidirectional, so various bear lineages had multiple and complex interactions over hundreds of thousands of years. Something notable is that the divergence between cave and brown bears is considerably deeper than that between Neanderthals and modern humans. If the latter can be dated to around 750,000 years ago, with large intervals on either side, the bears apparently separated into separate species 1.2 to 1.4 million years ago.

The greater time depth is of interest to the authors. From The New York Times:

“We did not expect to find this at all because they’re really quite diverse in terms of their evolution,” Dr. Barlow said.

The team was also able to determine that the genes flowed both ways between species, with the cave bears also carrying some brown bear DNA. The most recent transfer of genes came from the cave bear to the brown, the study found.

Brown bears are more closely related to polar bears than they were to cave bears from whom they diverged more than a million years ago, he said. Cave bears were largely herbivores, while brown bears are meat-eaters and about 20 percent smaller than cave bears, with more delicate bones. A brown bear would probably have looked “wimpy” next to a cave bear, he said.

The expectation here is conditional on the idea that bears which occupy different ecological niches probably won’t hybridize even if they overlap in range.

All that being said, when Greg Cochran started talking about archaic admixture into modern lineages in 2005 I read up on the mammalian hybridization literature and came to the conclusion that a priori there was no reason why Neanderthals and modern (African) humans couldn’t have produced fertile offspring. Big mammals tend to occupy a lot of territory, and different big mammal lineages overlap. It seems rather common for gene flow to occur between them. There is evidence of jackal and coyote introgression into Eurasian wolves, for example.

So I  guess I’m not that surprised. And David Quammen’s new book, The Tangled Tree, presents a rather non-revolutionary message from where I stand. Though perhaps it hasn’t gotten out to the “public.” The complexity and multi-textured reality of the “species problem” is pretty clear to any biologist who work’s on population-level data.

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Understanding prehistory through genetic inference and ancient DNA

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!

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Another great-great-great…great-uncle in Asia


The paper which surveys the relationship of the 40,000 year old Tianyuan sample is finally out in Current Biology, 40,000-Year-Old Individual from Asia Provides Insight into Early Population Structure in Eurasia. There isn’t anything too surprising here. Here is the part of the abstract that presents new finding:

…we generated genome-wide data from a 40,000-year-old individual from Tianyuan Cave, China…We find that he is more related to present-day and ancient Asians than he is to Europeans, but he shares more alleles with a 35,000-year-old European individual than he shares with other ancient Europeans, indicating that the separation between early Europeans and early Asians was not a single population split. We also find that the Tianyuan individual shares more alleles with some Native American groups in South America than with Native Americans elsewhere, providing further support for population substructure in Asia [8] and suggesting that this persisted from 40,000 years ago until the colonization of the Americas. Our study of the Tianyuan individual highlights the complex migration and subdivision of early human populations in Eurasia.

The Tianyuan sample lived about ~40,000 years ago in China, and it does not seem to have been the direct ancestor of modern East Eurasians. It also seems to have had some relationship to the Australo-Melanesian affiliated population which contributed ancestry to the indigenous peoples of South America. Additionally, it also shares ancestry above what you’d expect with a 35,000 year old Paleolithic European, the GoyetQ116-1 sample, which is found in an Aurignacian context.

There are some direct conclusions that one can infer from this paper. First, as known beforehand the divergence between East Eurasians and West Eurasians has to predate 40,000 years before the present since this sample already shares drift with East Eurasians far more than West Eurasians. In the paper, the authors give an interval of 40,000 to 80,000 years before the present, which seems advised. Remember that “Basal Eurasians” separated before the divergence of East and West Eurasians.

Second, “ghost” populations were common. There are at minimum two ancient Eurasian populations, represented by the Oase1 sample in Romania from 40,000 years ago, and the 45,000 year old Ust’-Ishim from Siberia, who were not closely related to any populations which left descendants today.

Third, the human “family tree” looks more like a human “family bramble.” One of the interesting points in this paper is that Tianyuan shares drift with Goyet, but does not share drift with El-Miron, which seems to be descended in large from a population like Goyet. The key here is to note that Goyet is the closest proxy to some of the ancestors of El-Miron, but it may not be the ancestor at all. So if Goyet-like populations were heterogeneous in relation to East Eurasian, then El-Miron may descend from a group which never mixed with East Eurasians.

This is clear when you read many of these ancient DNA papers closely. The Mal’ta boy was representative of a population which contributed to both Northern Europeans (via Eastern Hunter-Gatherers) and Amerindians, but the deeper results also indicated that the common contributor to these populations was not the Mal’ta population, but related to them. That is, there is no expectation that the sparse sampling of ancient DNA in many regions and epochs will find the ancestral populations, as opposed to groups related to the ancestral populations.

This is a looking-through-the-glass-darkly situation. The true pattern of population relationships of the past needed to be inferred from a finite set of individuals randomly drawn from those populations. If most of those populations left no descendants due to common and repeated local extinction events, then it may be that most of the time we’re going to have to triangulate to the “true” ancestral groups, who left descendants simply due to luck.

Finally, this should really put the nail in the coffin of the idea that we can think of ancient populations are algebraic recombinations of modern populations. Modern groups almost certainly sample only a small part of the distribution of ancient populations.

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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, 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.

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

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Origin of modern humanity pushed back 260,000 years BP (?)


The above figure is from a preprint, Ancient genomes from southern Africa pushes modern human divergence beyond 260,000 years ago. The title and abstract are pretty clear:

Southern Africa is consistently placed as one of the potential regions for the evolution of Homo sapiens. To examine the region’s human prehistory prior to the arrival of migrants from East and West Africa or Eurasia in the last 1,700 years, we generated and analyzed genome sequence data from seven ancient individuals from KwaZulu-Natal, South Africa. Three Stone Age hunter-gatherers date to ~2,000 years ago, and we show that they were related to current-day southern San groups such as the Karretjie People. Four Iron Age farmers (300-500 years old) have genetic signatures similar to present day Bantu-speakers. The genome sequence (13x coverage) of a juvenile boy from Ballito Bay, who lived ~2,000 years ago, demonstrates that southern African Stone Age hunter-gatherers were not impacted by recent admixture; however, we estimate that all modern-day Khoekhoe and San groups have been influenced by 9-22% genetic admixture from East African/Eurasian pastoralist groups arriving >1,000 years ago, including the Ju|’hoansi San, previously thought to have very low levels of admixture. Using traditional and new approaches, we estimate the population divergence time between the Ballito Bay boy and other groups to beyond 260,000 years ago. These estimates dramatically increases the deepest divergence amongst modern humans, coincide with the onset of the Middle Stone Age in sub-Saharan Africa, and coincide with anatomical developments of archaic humans into modern humans as represented in the local fossil record. Cumulatively, cross-disciplinary records increasingly point to southern Africa as a potential (not necessarily exclusive) ‘hot spot’ for the evolution of our species.

These results in the outlines were actually presented at a conference. I saw it on Twitter and don’t remember which conference anymore. But this is not entirely surprising.

First, much respect to Mattias Jakobsson’s group for breaking through the Reich-Willerslev duopoly. Hopefully this presages some democratization of the ancient DNA field as expenses are going down.

Second, notice how in most cases ancient DNA shows that modern reference populations turn out to be admixed. This was the problem with much of Eurasia, and why using modern genetic variation to make inferences about the past totally failed.

I am entirely convinced that the genome from Ballito Bay dating to ~2,000 years does not carry the Eurasian inflected East African admixture. The Mota genome implies that Eurasian admixture did not come to eastern Africa much before 4,500 years ago. There needs to be a much deeper big picture analysis of the archaeology of Africa and the genetic information we have to get a sense of what happened back then…but, it seems likely that the Bantu migration has over-written much of the earlier genetic variation.

The fact that ancient genomes always show that our current populations are admixed makes me wonder if the Ballito Bay sample itself is admixed from more ancient populations. That is, if we found a genome from 20,000 years ago, would it be very different from the Ballito Bay samples? The relatively thick time transect from Europe indicates that turnover happens every 10,000 years or so. Australian Aborigines seem to have been resident in their current locations for ~50,000 years, but this seems the exception, not the rule. Do we really think that the ancestors of the Bushmen were living in southern Africa for five times as long as Australian Aborigines?

Another curious aspect of this paper is that it suggests the effective population size of Bushmen is smaller than we might have thought, and they’re somewhat less diverse than we’d thought. That’s because East African (with Eurasian ancestry) gene flow increased heterozygosity, as well as inferred effective population sizes. I’ve mentioned this effect on statistics before. Unless you have a true model of population history (or close to it) your assumptions might distort the numbers you get.

There is another aspect to this preprint mentioned glancingly in the text, and a bit more in the supplements: they seem to only be able to model Yoruba well if you assume that they themselves are a mix of “Basal Humans” (BH) and other African population which gave rise to East Africans and “Out of Africa” populations. Note that the BH seem to diverge from other human populations before the ancestors of Southern Africans like the Ballito Bay sample. That is, BH could push the diversification of the ancestors of modern humans considerably before 260,000 years before the present.

The possibility of deep structure in the Yoruba is pretty notable because they’ve been the gold standard in many human population genetic data sets as a reference population. But this is not result of deep structure is not entirely surprising. For years researchers have been hinting at confusing results in relation to the possibility of Eurasian back-migration. Perhaps the deep structure was confounding inferences?

The authors themselves are quite cautious about their dating of the divergence. It’s sensitive to many assumptions, and in particular the mutation rate being known and constant over time. But I think it’s hard to deny that this is pushing back the emergence of modern humans beyond what we know today. The earliest anatomically modern humans are found in Ethiopia 195,000 years ago from what I know. As I said, I’m convinced that the ancient genome has shown that modern “pristine” populations have some serious admixture. But I’m not as convinced about any specific point estimate, because that’s sensitive to a lot of assumptions which might not hold.

Finally, first a quick shout out to the blogger Dienekes. As early as ten years ago he anticipated the basic outlines of these sorts of results in the generality, if not the details. We really have come a long way from popular science declaring that all humans descend from a small group of East Africans who lived 50,000 to 100,000 years ago. The real picture was much more complex.

Also, I have to admit I considered titling this blogspot “Wolpoff’s revenge.” As in Milford Wolpoff. The reason being that we’re getting quite close to territory familiar to the much maligned multi-regionalist model of modern human origins.

Note: These findings should make us less surprised perhaps by a “modern” human migration before the primary one out of Africa.

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The Canaanites walk among us: ancient DNA edition

Ancient DNA from here to there:

Ancient DNA has illuminated many things, but there is a logic as to what topics and questions it tackles. The focus on northern Eurasia is clearly a function of the probability of preservation, though techniques of extraction are getting better and better. I can’t imagine how we’d ever get a sample out of a moist tropical environment, but I won’t be surprised if something is obtained from a cave in southern Africa or high in the Tibesti in the near future.

But another parameter is time since the demographic events in question. Too ancient, and the probability of success is too low(ok, time is a parameter in much of science!). It seems plausible that in idealized circumstances we’re going to push beyond the one million year barrier. And yet too recent is also a problem (or not a problem!). For humans and even non-humans we have lots of corroboration about questions we might ask about the recent past. You could use “ancient DNA” to trace the migration of Mormons across the Intermontane West, but why would you?

So you see the earliest ancient DNA work on humans was biased toward testing models about gene flow and ancestry tens of thousands of years in the past, between modern humans and archaic lineages. Obviously we don’t have oral history or written texts from this period, and archaeology will only get us so far.

More recently the time depth has been getting shallower and shallower. Both David Reich and Eske Willerslev’s work on European prehistory is liminally historical. By this, I mean that what is prehistory in Europe is a historical period in the Near East. We may not have written records from the Corded Ware or Bell Beaker cultures, but we do have plenty of them from contemporaneous Near Eastern groups.

The Cauldron of Peoples:

There are still questions to be asked about European prehistory, but the gaps are getting narrower and narrower. Scholars are finally devoting resources to other regions of the world. Last year Iosif Lazaridis’ The genetic structure of the world’s first farmers finally opened up the box that was the prehistory of the Near East. This was important, because much of prehistory and history began in the Near East. Farmers from this region seem to have moved into Europe, South Asia, Central Eurasia, and Africa. To understand the population histories of these areas one needs to understand the population history of the Near East.

What Lazaridis et al. found this that there were at least two major groups of very genetically distinct Near Eastern farmers at the dawn of agriculture. Once group faced the eastern Mediterranean, while the other seems to have flourished on the slopes of the Zagros. Western and eastern farmers respectively. It is important to note that these two groups were very genetically distinct. If we sampled these two groups of farmers, who faced each other across northern Mesopotamia, in any modern population survey we’d assume that the genetic distance meant that they were sampled from different continents or very distant regions of Eurasia.

This finding suggest that the clinal patterns of variation in much of today’s world may be a consequence of massive population admixture between groups which had heretofore exhibited deep population structure. Why such deep structure existed and persisted is an interesting question, but at this point it is important to note descriptively that the past 10,000 years have seen a massive reduction of this structure due to gene flow between populations.

In the Near East Lazaridis et al. found that there was significant reciprocal gene flow between the western and eastern regions of the Near East after the emergence of farming, down to the historical period. This is one reason that estimates of “farmer” ancestry in modern Europeans always gave very low estimates: the reference populations no longer existed in unmixed form in the Near East. The peoples who brought agriculture to Southern Europe were related exclusively to the western farmers of the Near East, a population which no longer exists in unmixed form in that region of the world (ergo, among modern groups Sardinians are the closest proxies we have).

The Age of Bronze:

But there is much that occurred after prehistory in the Near East. We know this because we have extensive records going back 4,500 years, and even earlier. And though put into written form in the first millennium before Christ, the Hebrew Bible also records the deeds and names of people who have come and gone well before the Classical Age.

A new preprint on biorxiv sheds some light on a critical transitory period, Continuity and admixture in the last five millennia of Levantine history from ancient Canaanite and present-day Lebanese genome sequences:

The Canaanites inhabited the Levant region during the Bronze Age and established a culture which became influential in the Near East and beyond. However, the Canaanites, unlike most other ancient Near Easterners of this period, left few surviving textual records and thus their origin and relationship to ancient and present-day populations remain unclear. In this study, we sequenced five whole-genomes from ~3,700-year-old individuals from the city of Sidon, a major Canaanite city-state on the Eastern Mediterranean coast. We also sequenced the genomes of 99 individuals from present-day Lebanon to catalogue modern Levantine genetic diversity. We find that a Bronze Age Canaanite-related ancestry was widespread in the region, shared among urban populations inhabiting the coast (Sidon) and inland populations (Jordan) who likely lived in farming societies or were pastoral nomads. This Canaanite-related ancestry derived from mixture between local Neolithic populations and eastern migrants genetically related to Chalcolithic Iranians. We estimate, using linkage-disequilibrium decay patterns, that admixture occurred 6,600-3,550 years ago, coinciding with massive population movements in the mid-Holocene triggered by aridification ~4,200 years ago. We show that present-day Lebanese derive most of their ancestry from a Canaanite-related population, which therefore implies substantial genetic continuity in the Levant since at least the Bronze Age. In addition, we find Eurasian ancestry in the Lebanese not present in Bronze Age or earlier Levantines. We estimate this Eurasian ancestry arrived in the Levant around 3,750-2,170 years ago during a period of successive conquests by distant populations such as the Persians and Macedonians.

The period between 1700 and 1800 BCE in the Near East saw many changes and was a sort of nexus. Sumer had fallen, the Hittites had not emerged as a superpower, while Egypt was not heavily involve in the game of kings as of yet. The system of international relationships described in Brotherhood of Kings had not crystallized. That was for the late Bronze Age.

But some of the pieces we were to recognize were already in place. An Amorite Babylon under Hammurabi established the contours of the culture and polity we’d recognize down to the Persian conquest. In Egypt the Middle Kingdom was going into decline, and the Hyksos interregnum would give rise to the New Kingdom, which would become a major player in the Levant (and probably is the model for much of the Egypt we see described in the Bible).

The admixture plot above reflects the five individuals from Sidon dating to about ~1750 BCE. They are about a 50:50 mix of western and eastern farmer. Though they seem to be genetically rather similar to modern Lebanese (the authors sampled Lebanese Christians in particular), there have been some changes between the Bronze Age and the modern period. In particular, a genetic component that seems to be related to the Eurasian steppe is present in modern Lebanese. Explicit admixture estimates give a range of 5-10% mixing into a ~90-95% Bronze Age ancestral background.

This seems to establish basic continuity between the Bronze Age and the modern period. Totally unsurprising. Remember that Italy exhibits deep population structure that dates back to at least 2,000 years ago, and probably earlier. It is likely that much of the same applies to the Near East. Though looking at Muslim populations one can see minor and non-trivial contributions of populations which moved in after Islam (Sub-Saharan and East Asia segments are clear signs of slavery impacting Muslims that would not apply to ethno-religious minorities), most of the ancestry broadly is deeply rooted back to antiquity.

Because of sampling issues one can’t estimate admixture between eastern and western farmers just from looking at ancient DNA transects. We don’t have the density that we have in Europe (yet). So the authors used a more classic inference technique looking at decays of linkage disequilibrium in the genome. In short you can see how many generations that a pulse admixture between two populations occurred by looking at correlations of variants across the genome. The authors arrive at the intervals above, and in particular focus on the period that seems to overlap with the rise and fall of the empire of Sargon of Akkad and correlated with a climatic disruption.

I suspect they are wrong here. First, it seems pretty clear to me that LD based admixtures assuming a pulse event have a bias toward underestimating values. There are theoretical reasons for this. So usually I pad the mid-point value across the interval on these estimates.

One thing that ancient DNA has told us is that often the less complex the society, the more demographic turnover you have. All things equal then we would expect turnover to be an older event, as simple societies are succeeded by complex ones. The succession of complex societies by other complex societies is often less disruptive for the masses because this transformation is more a matter of elite replacement.

By ~2200 BCE the Near East was already quite complex. I believe that the massive western-eastern farmer admixture occurred between 3600 and 3100 BCE, during the Uruk Expansion. The evidence of lower Mesopotamian influence and demographic settlement in places as far afield as Anatolia, the Caucasus, and Syria, are well attested from the archaeology of this period. This was was a time when a very complex and sophisticated civilization emerged almost de novo across much of the Near East. I believe that a prehistoric expansion of Sumerian civilization mediated the merging of eastern and western farmers, though some of the mixing pre-dates and post-dates the Uruk Expansion and collapse (e.g., the movement of western farmer ancestry into Mesopotamia seems certain to have occurred through the arrival of groups like the Amorites).

Additionally, buried in this preprint is evidence of major Y chromosomal turnover. We’ve seen this  before. The prominence of haplogroup J in Bronze Age and modern Levantines seems to be due to eastern farmer migration. In fact, adding haplogroup J and R together we get the inference that more than half the paternal lineages of Lebanese today are not from western farmers native to the area.

Beyond the Bronze Age:

What about the second ancestral component? Drilling down on the Y chromosomes of the Levant, R1b seems to far outnumber R1a, though the R1a clades are all of the Asian/Scythian Z-93 branch which is dominant in Central Asia and the Levant. The R1a may have come with the Persians, but in region of the western Levant for several hundred years after the period of the Bronze Age Sidon samples there was a state, the Mitanni, which clearly had an Indo-Aryan ruling class.

An Aegean influence occurred multiple times. First, at the end of the Bronze Age many of the “Sea Peoples” were clearly of Aegean origin, and so may have brought steppe-like ancestry. Second, there was the long period under Hellenistic and Roman rule, when Greek and non-Greek ethnic identity existed side by side, and movement occurred in both directions. I think only ancient DNA will answer this question, and it may be that there were multiple post-Bronze Age inputs of genes which shaped modern Levantines.

After Babel:

The curious thing that many of these studies are telling us is two-fold:

  1. Most of the population genetic structure we see around us dates to the Bronze Age, on the borderlands between history and prehistory. I think we can start to set this as a strong prior. It holds true for the Near East, Africa, South Asia, Japan and Southeast Asia. We’ll see about core East Asia, but I think probably it is true there too.
  2. Selection has continued, so that alleles for lactose tolerance and lighter skin have changed in frequency even since that period. The derived allele for SLC45A2 is found at about 2/3 frequency in modern Lebanon, but was absent in these five Sidonians. Though the sample size is small, this was somewhat surprising, and suggests that they were a swarthier people than modern Lebanese.

Addendum: I have said little here about Afro-Asiatic languages, as I don’t know enough about this topic.

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