Ancient DNA has revolutionized our understanding of human population history. However, its potential to examine how rapid cultural evolution to new lifestyles may have driven biological adaptation has not been met, largely due to limited sample sizes. We assembled genome-wide data from 1,291 individuals from Europe over 10,000 years, providing a dataset that is large enough to resolve the timing of selection into the Neolithic, Bronze Age, and Historical periods. We identified 25 genetic loci with rapid changes in frequency during these periods, a majority of which were previously undetected. Signals specific to the Neolithic transition are associated with body weight, diet, and lipid metabolism-related phenotypes. They also include immune phenotypes, most notably a locus that confers immunity to Salmonella infection at a time when ancient Salmonella genomes have been shown to adapt to human hosts, thus providing a possible example of human-pathogen co-evolution. In the Bronze Age, selection signals are enriched near genes involved in pigmentation and immune-related traits, including at a key human protein interactor of SARS-CoV-2. Only in the Historical period do the selection candidates we detect largely mirror previously-reported signals, highlighting how the statistical power of previous studies was limited to the last few millennia. The Historical period also has multiple signals associated with vitamin D binding, providing evidence that lactase persistence may have been part of an oligogenic adaptation for efficient calcium uptake and challenging the theory that its adaptive value lies only in facilitating caloric supplementation during times of scarcity. Finally, we detect selection on complex traits in all three periods, including selection favoring variants that reduce body weight in the Neolithic. In the Historical period, we detect selection favoring variants that increase risk for cardiovascular disease plausibly reflecting selection for a more active inflammatory response that would have been adaptive in the face of increased infectious disease exposure. Our results provide an evolutionary rationale for the high prevalence of these deadly diseases in modern societies today and highlight the unique power of ancient DNA in elucidating biological change that accompanied the profound cultural transformations of recent human history.
Sometimes statistics confirm what you can already intuitively discern. I’m an avid reader of the ancient DNA and pigmentation literature. It was immediately obvious to me that the Bronze Age Northern European samples were darker than modern populations in that region. There are massive sample sizes for modern Europeans, and it jumped out at me that the derived SNP at SLC45A2 was at a lower frequency two to four thousand years ago than it is today. This paper confirms that selection not only occurred during the Bronze Age, but has been happening in the historical period…
Note: The backstory on why I had my suspicions about this goes back to 2009. When the first Reich lab India paper came out I was pretty skeptical that the “Ancestral North Indians” were so similar to Northern Europeans. My rationale was straightforward: we should see way more blonde and blue-eyed people in Northern India and Pakistan. Nick Patterson pointed out the relevance of natural selection. Perhaps the Northern Indians got darker? There is a bit of evidence of this for some loci, but the Narasimhan et al. paper had a bunch of Sintashta, who are probably the best ancestral population proxy for the early Indo-Aryans, and they were clearly just not as lightly pigmented as related people on the Baltic today. The Sintashta were very similar to their relatives in Poland genetically, but they diverged from their Northern European relatives 4,500 years ago as the Fatyanovo population migrated eastward, and were probably in India when selection was changing the allele frequencies around SLC45A2.
The origin, development, and legacy of the enigmatic Etruscan civilization from the central region of the Italian peninsula known as Etruria have been debated for centuries. Here we report a genomic time transect of 82 individuals spanning almost two millennia (800 BCE to 1000 CE) across Etruria and southern Italy. During the Iron Age, we detect a component of Indo-European–associated steppe ancestry and the lack of recent Anatolian-related admixture among the putative non–Indo-European–speaking Etruscans. Despite comprising diverse individuals of central European, northern African, and Near Eastern ancestry, the local gene pool is largely maintained across the first millennium BCE. This drastically changes during the Roman Imperial period where we report an abrupt population-wide shift to ~50% admixture with eastern Mediterranean ancestry. Last, we identify northern European components appearing in central Italy during the Early Middle Ages, which thus formed the genetic landscape of present-day Italian populations.
By 1000 BC, on the eve of the Iron Age, a mixed ancestry derived from both Anatolian farmers and Indo-Europeans from the steppe was present all across continental Italy. Only on isolated islands such as Sardinia was the situation different, where Anatolian farmer societies continued unperturbed by Indo-European migrants, giving rise to the Nuragic civilization, with its massive fortifications. All the length of the Italian mainland, the ancestors of the Etruscans, Sabines, and Romans shared roughly the same genetic heritage, despite their ethno-linguistic differences.
The big novel find is that there is nontrivial Germanic ancestral shift after the fall of Rome. Some commenters have suggested this is actually just from rural Italians, who flooded back into the towns. This could probably be tested.
Modern humans appeared in Europe by at least 45,000 years ago but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago, and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bacho Kiro Cave, Bulgaria. They are the earliest Late Pleistocene modern humans known to have been recovered in Europe so far, and were found in association with an Initial Upper Palaeolithic artefact assemblage. Unlike two previously studied individuals of similar ages from Romania and Siberia who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations. This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia. Moreover, we find that all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common.
There are two primary points of interest:
More evidence of ubiquitous ‘admixture’ between Neanderthals and ‘modern humans’ who may have been in contact with them.
These earliest European modern humans in Southeast Europe seem to be more closely related to (possibly ancestral to?) people in East Asia than modern Europeans.
On the first point, twenty years ago there were some paleoanthropologists who were arguing there was no admixture between Neanderthals and modern humans. That is, no fertile offspring. To not pussyfoot around it, Neanderthals were barely acknowledged as human in the early years of this century by many scholars. This is evident in Richard Klein’s The Dawn of Human Culture, written in 2002. With hindsight much of this is ridiculous. It really didn’t make any sense that the Neanderthal and modern human lineage were not inter-fertile when you dug into the literature on mammalian hybridization. There just wasn’t that much time for them to be totally incompatible.
In 2010 when it was found that Neanderthal ancestry seems to be found in non-Africans, we updated many of our priors. I think it is clear on some level Neanderthal humanization is driven by the fact of Neanderthal admixture. Nevertheless, there was a plausible case this admixture was rare. Perhaps a single Neanderthal tribe was mixed into expanding modern humans? Perhaps a single Neanderthal? These were ideas that were mooted.
With what we know now I’m not sure this is tenable. There are two primary issues. First, there is variation in Neanderthal ancestry among non-African populations which does not seem to be due to African admixture. East Asians have more Neanderthal admixture (~25% more last I checked) than Europeans who have more than West Asians. South Asian Neanderthal admixture is proportional to their distance from East Asians. The less West Eurasian the South Asian, the more Neanderthal.
There are a few ways to understand this. A simple explanation is that there was a secondary admixture event that impacted people migrating to eastern Eurasia. Another hypothesis is that natural selection reduced the Neanderthal fraction over time, but East Eurasians were less impacted by this due to small effective population size. Then, there is the idea that a non-African population, “Basal Eurasians”, that did not have much Neanderthal admixture later mixed into West Asians and Europeans, reducing the original Neanderthal fraction.
Because of the small fractions and the paucity of ancient DNA more than 10,000 years old, there are still arguments around this. These results increase the probability that there were multiple Neanderthal admixture events. At least in my way of thinking.
The authors found that the Neanderthal fraction seems to have decreased from a higher level relatively early on. Rather than a gradual decrease, the authors found suggestions of strong effective selection in the first few generations. Though there is still room for the Basal Eurasian model, I’m not sure it’s quite as necessary now. Along with Oase, and the existence of a Neanderthal-Denisovan hybrid from Denisova cave, the likelihood of frequent admixture between ancient hominin lineages seems pretty high.
I believe the primary issue at this point is that the admixture event seems to be dated to a narrow time period, before the extinction of Neanderthals, but not too ancient (before 60,000 years ago), and the Neanderthal ancestry is quite similar. Perhaps there isn’t the power to detect multiple secondary admixtures at “around the same time.” From the perspective of today, 45,000 v. 50,000 years ago is “around the same time.” But the reality is 5,000 years is a long time.
In simulations, we find that estimates of the mean time of admixture are largely robust to details in gene flow models. In contrast, the duration of the gene flow is much more difficult to recover, except under ideal circumstances where gene flow is recent or the exact recombination rate is known. We conclude that gene flow from Neandertals into modern humans could have happened over hundreds of generations. Ancient genomes from the time around the admixture event are thus likely required to resolve the question when, where, and for how long humans and Neandertals interacted.
The second major finding of this paper is that the very first modern humans to settle in Europe are more genetically close to East Asians than to modern Europeans. This is in contrast to the Oase sample from Romania, just to the north, and a few thousand years later, that was no closer to East or West Eurasians. Or, a new 45,000-year-old sample from Czech Republic, which also shows no connection to any modern people.
If you read the first paper, you know that years ago the GoyetQ116-1 sample from Belgium that dates to 35,000 years before the present, and which seems to have some ancestral connection to the later Magdalenian people of Pleistocene Europe, had an East Eurasian affinity. Additionally, earlier mtDNA work showed eastern affinities in some Pleistocene Europeans. The authors above make the connection between these eastern-affinity early Europeans and the “Initial Upper Paleolithic” (IUP), which seems to have expanded across a broad swath of Eurasian, from Europe all the way to western Mongolia.
The implication then is that some of the ancestry of East Eurasians comes from a migration that took a route through Europe, and around the Black Sea littoral. This is a bit more complicated than a pure “southern route”, but it’s not crazy, and has long been proposed.
I think at this point we need to take a step back, and acknowledge that the period between 40 and 60 thousand years ago is important, but we look through the glass darkly. Something happened, as all the ancient Eurasian hominin lineages were absorbed by the “Out of Africa” population (which may not have been expanding out of Africa!), and the phylogenetic relationships of some of these people do not make sense in light of the phylogeography of the present.
It is entirely feasible to me that the ancient non-African or proto-non-African populations had already started to develop some internal structure. The putative Basal Eurasian v. “the rest” is one key bifurcation, but there may already have been divisions between the western and eastern branches of Eurasians in northeast Africa or the Near East. We just don’t know yet. Basically, ancient substructure that is getting “blown up” with rapid radiation.
In 2014 when BEu was created as a construct to explain the greater affinities of Mesolithic European hunter-gatherers with East Eurasians than modern Europeans*, I probably would have been a little surprised that a mostly BEu individual had still not been discovered in the ancient DNA. After all, we had seen Ma’lta boy answer the question of who the mysterious “Siberians” were that left an imprint all over West Eurasia. Ma’lta was part of an ancient Paleo-Siberian group, the Ancient North Eurasians (ANE), who no longer exist in “pure” form, but contributed ancestry (or more precisely were related to groups that did so) to hunter-gatherers in Eastern Europe and the ancestors of New World populations.
No such luck with BEu. In fact, BEu as a construct is so vaguely understood that research groups can estimate that populations are 10% BEu, or 40% BEu, contingent upon various specifications in their model. In the middle 2010’s one of the scientists involved in the groups working in this space and using BEu as a construct even told me that this population may never have existed in pure form anyhow (not Iosif Lazaridis to be clear).
Basically, there is still not a lot of clarity. BEu seems to have diverged before Neanderthal admixture into the non-African lineage ~55,000 years ago. It also seems to have been subject to the long bottleneck of all non-Africans. A very plausible model that BEu occupied the southern Middle East, while non-basal Eurasians occupied the northern Middle East, seem to be the highest probability to me. The authors of this preprint argue that the Basal Eurasian ur-heimat might be in and around the Persian Gulf. I laughed when I read that because it reminds me of the early 20th century “Lost Civilization Underwater” motif. But it could be true.
I would hazard to guess dates, but I think the separation and later (early) admixture of BEu and non-BEu people in the Near East is probably strongly conditional on the paleoclimate data, which I am not fluent in.
* BEu ancestry came into Europe with Neolithic farmers, so affinities between Mesolithic hunter-gatherers and East Asians is higher than between modern Europeans and East Asians.
Several people have asked me about the new study on ancient DNA in the Caribbean, A genetic history of the pre-contact Caribbean. There is a lot to this paper, some of which is outside of my purview (e.g., I don’t know anything about the archaeology of this region so can’t interpret the genetic results well). One of the major things they did was establish patterns of relatedness. This seems like a major step forward in terms of future applicability to ancient DNA.
But the biggest thing that jumped out at me had to do with effective population size. Carl Zimmer’s write-up highlights this issue:
The genetic variations also allowed Dr. Reich and his colleague to estimate the size of the Caribbean society before European contact. Christopher Columbus’s brother Bartholomew sent letters back to Spain putting the figure in the millions. The DNA suggests that was an exaggeration: the genetic variations imply that the total population was as low as the tens of thousands.
This matters because it starts to change our sense of revisionism (now orthodox?) in books such as 1491: New Revelations of the Americas Before Columbus. To reconcile the small numbers of indigenous people by the 16th century in the Caribbean the hypothesis that there were mass die-offs due to disease, or, the Spanish were inordinately cruel (“The Black Legend”). These results suggest that the scale of the pandemic shock was less of an issue since the baseline number of native peoples is lower in the area.
What does this imply for the rest of the New World? I don’t know. But perhaps the huge census sizes argued for by some scholars won’t hold? It probably depends on the region. But with enough ancient DNA, the same sort of analyses could be replicated.
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”.
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.
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.
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
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.
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.