Whole genomes of ancient farmers and hunter-gatherers

A new preprint uses about a dozen ancient genomes to create a model of the origins of Europeans and European farmers more precisely. The big deal here is that they aren’t relying on the same old SNP-array, but using the whole genome. This allows for some more explicit model-building and testing. I do think explicit model creation is something that needs to be done. A lot of the work today is data-first, and there needs to be more “theory”.

The mixed genetic origin of the first farmers of Europe:

While the Neolithic expansion in Europe is well described archaeologically, the genetic origins of European first farmers and their affinities with local hunter-gatherers (HGs) remain unclear. To infer the demographic history of these populations, the genomes of 15 ancient individuals located between Western Anatolia and Southern Germany were sequenced to high quality, allowing us to perform population genomics analyses formerly restricted to modern genomes. We find that all European and Anatolian early farmers descend from the merging of a European and a Near Eastern group of HGs, possibly in the Near East, shortly after the Last Glacial Maximum (LGM). Western and Southeastern European HG are shown to split during the LGM, and share signals of a very strong LGM bottleneck that drastically reduced their genetic diversity. Early Neolithic Central Anatolians seem only indirectly related to ancestors of European farmers, who probably originated in the Near East and dispersed later on from the Aegean along the Danubian corridor following a stepwise demic process with only limited (2-6%) but additive input from local HGs. Our analyses provide a time frame and resolve the genetic origins of early European farmers. They highlight the impact of Late Pleistocene climatic fluctuations that caused the fragmentation, merging and reexpansion of human populations in SW Asia and Europe, and eventually led to the world’s first agricultural populations.

The supplements are worth reading too. It’s all there.

No mention of Basal Eurasians. The last author told me on Twitter that they weren’t needed, but Iosif Lazaridis (also on Twitter) disagrees, naturally.

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They killed the daughter of the maryannu!


Human mobility at Tell Atchana (Alalakh) during the 2nd millennium BC: integration of isotopic and genomic evidence:

The Middle and Late Bronze Age Near East, a period roughly spanning the second millennium BC (ca. 2000-1200 BC), is frequently referred to as the first ‘international age’, characterized by intense and far-reaching contacts between different entities from the eastern Mediterranean to the Near East and beyond. In a large-scale tandem study of stable isotopes and ancient DNA of individuals excavated at Tell Atchana (Alalakh), situated in the northern Levant, we explore the role of mobility at the capital of a regional kingdom. We generated strontium isotope data for 53 individuals, oxygen isotope data for 77 individuals, and added ancient DNA data from 9 new individuals to a recently published dataset of 28 individuals. A dataset like this, from a single site in the Near East, is thus far unparalleled in terms of both its breadth and depth, providing the opportunity to simultaneously obtain an in-depth view of individual mobility and also broader demographic insights into the resident population. The DNA data reveals a very homogeneous gene pool, with only one outlier. This picture of an overwhelmingly local ancestry is consistent with the evidence of local upbringing in most of the individuals indicated by the isotopic data, where only five were found to be ‘non-local’. High levels of contact, trade, and exchange of ideas and goods in the Middle and Late Bronze Ages, therefore, seem not to have translated into high levels of individual mobility detectable at Tell Atchana.

From a DNA perspective two notable things about this preprint. First, it confirms that there was a massive pulse of Iranian/Caucasus ancestry into the western Fertile Crescent between 5000 and 2000 BC. We don’t have any idea what was going on here, but my own suspicion is that the Uruk period, 4000 to 3100 BC, has something to do with this genetic turnover and assimilation. We don’t know what happened during the Uruk period because there’s no real writing of narrative history (there is proto-cuneiform), but this is when city life really expanded in Mesopotamia. Additionally, there were replica copies of Mesopotamian style towns to the west, and even into Anatolia. The Uruk period was arguably the peak of Mesopotamian political power and influence before the rise of Assyria thousands of years later.

The end of the Uruk period was characterized by a massive collapse. Some archaeologists hypothesize that the catastrophe literature of the Sumerians may reflect memories of the end of the Uruk civilization. In some ways, the Akkadians and Sumerians may have lived in the shadows of their forebears.

The second issue is “the lady in the well”. This is a woman who seems to have been pushed into a well and fallen to her death. She is the major genetic outlier from this site: “Individual ALA019 – the Well Lady – takes up an extreme outlier position in the PCA closest to sampled individuals from Bronze Age Iran/Turkmenistan/Uzbekistan/Afghanistan.”

Her positioning is unambiguous. Unless we’re missing something this woman is of “steppe” heritage. Probably Indo-Iranian. But, the best guess from the isotope work is that she was raised in the region. The data they have indicate she lived between 1550-1600 BC. She was almost certainly from an Indo-Iranian group that had settled in the region. In fact, she was almost certainly associated with the Indo-European element in Mitanni.  But in this region of the world the Dasa in their walled cities overcame the free people and swallowed them up culturally and demographically.

The major lacunae in this paper, and all such papers, is Iraq. There is ancient DNA from Turkey, the Levant, but what about Iraq? I’m sure people are working on it, but this is a region that would give us a better sense of “donor” populations.

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A more nuanced model for the settling of the Americans

The genomic formation of First American ancestors in East and Northeast Asia:

Upward Sun River 1, an individual from a unique burial of the Denali tradition in Alaska (11500 calBP), is considered a type representative of Ancient Beringians who split from other First Americans 22000-18000 calBP in Beringia. Using a new admixture graph model-comparison approach resistant to overfitting, we show that Ancient Beringians do not form the deepest American lineage, but instead harbor ancestry from a lineage more closely related to northern North Americans than to southern North Americans. Ancient Beringians also harbor substantial admixture from a lineage that did not contribute to other Native Americans: Amur River Basin populations represented by a newly reported site in northeastern China. Relying on these results, we propose a new model for the genomic formation of First American ancestors in Asia.

Read the preprint. I’ll note three things

– The authors suggested that differentiation between American native lineages occurred in eastern Siberia, not Beringia. In other words, there’s a lot of ancient structure in the New World that dates to the Last Glacial Maximum

– Speaking of ancient structure, using the new methods in this paper they detect more pervasive “Australo-Melanesian” ancestry in lower quality ancient remains. It seems clear ta this point that this isn’t about Australo-Melanesian, as much as genetic variation in East Eurasia during the Pleistocene that we have a poor grasp of at this point

– In Europe ancient DNA quickly converged on the trihybrid model of Mesolithic hunter-gatherers, and early farmers, and steppe pastoralists. The tsunami of ancient DNA has fleshed out a lot of details, but the basic framework has been in place for five years. The situation in other parts of the world seems to be more unsettled and dynamic. More sophisticated models and more ancient DNA keeps returning surprise on the margin

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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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