Population Replacement In Pre-Columbian Columbia

UPDATE: I previously blogged this same paper closer to when it came out in 2025.

The "old world" is full of examples of hunter-gatherers being demographically replaced by farmers. The pre-Columbian New World was no different. The paper below explores a specific example of this happening in what is now the country of Columbia around 0 CE. In the "old world" this generally happened at the time that the Neolithic Revolution reached a region, and sometimes again when a civilization transitioned to the Bronze Age.

Also, to be clear, the extinct population is not outside the overall range of New World genetic diversity, it just doesn't correspond to any particular population that survived to the present that had been previously sampled. As the ancestry model chart below illustrates, it is within the range of South American specific ancestry.

Geographically, however, the location is notable. The modern DNA samples sometimes described as having Papuan affinity come from an area in the Amazon more or less due south of the highlands areas where the deceased subjects in this study, shown in the map below, were found. 

It is so geographically close, indeed, that the absence of any Papuan-like DNA in the hunter-gatherer samples in this study is itself notable, and tends to contradict the hypothesis that Papuan-like DNA seen in relict populations of living subjects nearby has a source older than the main New World founder population of ca. 14,000 years ago. I summed up a lot of the Paleo-Asian DNA in the New World discussion in a 2021 post, although I have made more posts since then on the subject.

Genetic studies on Native American populations have transformed our understanding of the demographic history of the Americas. However, a region that has not been investigated through ancient genomics so far is Colombia, the entry point into South America. Here, we report genome-wide data of 21 individuals from the Bogotá Altiplano in Colombia between 6000 and 500 years ago. 

We reveal that preceramic hunter-gatherers represent a previously unknown basal lineage that derives from the initial South American radiation. These hunter-gatherers do not carry differential affinity to ancient North American groups nor contribute genetically to ancient or present-day South American populations. 

By 2000 years ago, the local genetic ancestry is replaced by populations from Central America associated with the Herrera ceramic complex and survives through the Muisca period despite major cultural changes. These ancient Altiplano individuals show higher affinities to Chibchan speakers from the Isthmus of Panama than to Indigenous Colombians, suggesting a dilution of the Chibchan-related ancestry through subsequent dispersal events.

Krettek, K. L., Casas-Vargas, A., Mas-Sandoval, A., & Posth, C. "A 6000-year-long genomic transect from the Bogotá Altiplano reveals multiple genetic shifts in the demographic history of Colombia." 11(22) Science Advances (May 28, 2025) (open access). https://www.science.org/doi/10.1126/sciadv.ads6284

Razib Khan On Our Current Understanding Of Human Evolution

Razib Khan's latest piece on human evolution in his Unsupervised Learning series takes a step back and looks at how the big picture has changed with new discoveries made in the last several decades.

His main point is that archaic hominin introgression may have originally been a much higher percentage of ancestry, with most archaic hominin introgression expelled in the roughly 1,000 years after the initial introgression due to natural selection and incompatibilities between archaic hominin sourced genes and modern human genes. I suspect that the 10%-20% percentage that he cites is quite a bit too high, but surely this did happen to some extent.

As usual, he educated synthesis of the research and evidence is pretty solid, even if not every assertion he makes in laying out a single coherent narrative (like the Population A and Population B that hybridize to form modern humans, with Neanderthals, Denisovans, and "ghost African" populations all derived from Population A hypothesis in the diagram below) has reached the level of academic consensus yet, and even if there is some room to quibble over fine details.

Some highlights of his piece (but please, click on the link and read the whole thing) are quoted below:

A generation ago, we imagined that Homo sapiens, “thinking man,” emerged fully formed in Africa over 100,000 years ago and swept away all our monstrous kin before us through dint of our sheer genius. Today, it seems more likely that it was we who were the monsters out of the dark, the demons about which Neanderthal mothers would tell their little-ones.

In 2002’s The Dawn of Human Culture, Stanford paleoanthropologist Richard Klein presented what at that time was the standard model of the recent origins of humanity. Some time before 50,000 years ago, a new form of human arose through some sort of mutational jump. Klein posited that our genius, our superiority, was because of a macromutation that enabled us to generate fully articulate language. Before the emergence of this new species of human, there were many varieties of human, or, more precisely, hominin. Neanderthals in Europe and Central Asia, various “archaic” lineages in eastern Eurasia, and also descendants of other Homo forms in Africa. 

Ω humans, whom many popular slogans would refer to as “Africans,” rapidly swept away all these varieties of humanity after 50,000 years.

And so it was for a decade. There were dissents; in 2006 Jeffrey Wall and Michael Hammer published Archaic admixture in the human genome. This paper reflected suspicion among many evolutionary geneticists that the orthodoxy promulgated was too pat and simplistic (see also Magnus Nordborg’s 1998 On the Probability of Neanderthal Ancestry). But‌ despite an underground counter-consensus, very few evolutionary geneticists were vocal on this issue in public. . . . This all changed in 2010, when Svante Paabo and colleagues reported that Neanderthal whole genomes yielded strong evidence of several percent admixture into non-Africans, as well as the discovery of a new human lineage in eastern Eurasia, the Denisovans, who also contributed about 5% of the ancestry of Papuans.

Previous work had almost entirely been a matter of inference derived from contemporary populations. You looked at genetic variation in people alive today and worked backward to plausible models of how that variation could have arisen. In the 1980s, geneticists examined mitochondrial lineages, which represent the direct matrilineal genealogy. Geneticists noticed that all non-African populations nested within African genetic variation. They soon replicated this result with the Y chromosome, passed only through males, and the autosomes (markers on chromosomes 1 through 22) representing the whole genetic heritage. These results neatly dovetailed with the findings of paleoanthropologists like Chris Stringer of the British Museum of Natural History, who argued that modern human morphology, mostly exemplified by traits in human skulls, reflected continuity with African Homo, and not Neanderthals. Following the molecular genetic results, researchers applied similar phylogenetic methods to morphometric traits and discovered the same pattern of non-Africans nesting within African variation.

It was an immaculate and tidy story. . . . And that still seems to be much of the story. But not the entire story.

Over the last few years, geneticists have concluded that a much higher fraction of non-African DNA was originally Neanderthal. In an interview with Dwarkesh Patel Harvard’s David Reich asserted that as much as 10-20% of the overall heritage of early non-Africans, just as they were expanding out of the Near East 50,000 years ago, may have been Neanderthal. 

How then is that today we detect only about 2% Neanderthal genes outside of Africa? 

The genome rapidly sheds genetically incompatible segments within a few thousand years via purifying selection. Because Neanderthals diverged from our predominantly African ancestors 600 to 700,000 years ago, their overall genetic makeup exhibited much more striking incompatibilities with the expanding Africans than occurs when different branches of our own species mix (the deepest division in our own lineage dates to about 200,000 years, when Khoisan ancestors diverged from everyone else). No doubt the same phenomenon applied to Denisovan admixture, which today in some Oceanian populations, like those in New Guinea or the indigenous populations of the Philippines, approaches 5% or so.

What does this all mean? 

Because natural selection changes allele frequencies in ways that are out of step with the overall genome, the signatures that we get from modern and ancient DNA are deceptive as to the demographic dynamics of early anatomically modern humans and the Neanderthals (and Denisovans) whom they encountered. All the evidence, both ancient and modern, points to a tiny non-African ancestry population between 50 and 60,000 years ago, a few thousand individuals at most (some models posit a bottleneck of 200 breeding individuals!). If 10-20% of the ancestry of the early modern human expansion, also known as the Initial Upper Paleolithic (IUP), was Neanderthal, that implies the integration of hundreds of Neanderthals, as opposed to ten or twenty.

Did Archaic Ghost Hominins Admix With Humans In Africa?

This article supports the highly plausible theory that all humans share pre-Out of Africa admixture with "ghost" archaic hominin populations, but the methodology used is fairly new and untested.

Admixture between modern humans and extinct hominins has shaped the genomes of present-day individuals, but reconstructing this history has been constrained by the scarcity of archaic samples and unadmixed outgroup populations. 

We introduce TRACE, a reference- and outgroup-free approach that uses features of ancestral recombination graphs to identify archaic ancestry. Simulations show TRACE has high precision and low false discovery rates. 

Applied to 1000 Genomes, TRACE recovers known Neanderthal and Denisovan introgression and uncovers ghost admixture from uncharacterized hominins in both Africans and non-Africans. Ghost ancestry persists in Neanderthal and Denisovan ancestry deserts, challenging their interpretation as Homo sapiens–specific regions. In Oceanians, TRACE finds deep lineages are enriched in Denisovan compared to Neanderthal regions, supporting super-archaic introgression. TRACE enables mapping archaic introgression without archaic genomes.

Yulin Zhang, Arjun Biddanda, Sarah A. Johnson, Colm O’Dushlaine, and Priya Moorjani, "Recovering signatures of archaic hominin introgression using ancestral recombination graphs" Science (July 30, 2026) (open access) DOI: 10.1126/science.aef887

Denisovan Remains May Be Younger Than First Believed

Not long ago, we were finally able to find decent sized bones that proteins provided proteomic evidence (rather than DNA evidence which was not available) were able to match to Denisovans, which were found on the coast of the main island of Taiwan, finally putting a body together with the ghost population implied by DNA evidence. Two more leg bones were recently found.

Earlier dating had suggested an age for the Taiwanese Denisovan remains of about 160,000 years ago, long before modern humans arrived in the region and overlapping with Homo erectus. Analysis of the new leg bones by a more reliable and credible method, however, reveals that they are actually just 45,000 years old, contemporaneous with a modern human presence in the region.

At one level this isn't a surprise. Modern humans in Southeast and East Asia and Oceania have genetic admixture from Denisovans, so they had to overlap at some point. But it is surprising that the two different dating methods differed from each other by a factor of four.

The chemical analysis also suggests that these Denisovans, like Neanderthals, had a diet heavy in meat from large mammals.

My link is to a blog post by John Hawks who cites his sources:

* Chang, Chun-Hsiang, et al., "The first archaic Homo from Taiwan." 6 Nature Communications 6037 (2015). doi:10.1038/ncomms7037

* Grün, R. & Stringer, C., "Direct dating of human fossils and the ever-changing story of human evolution." 322 Quaternary Science Reviews 108379 (2023). https://doi.org/10.1016/j.quascirev.2023.108379

* Kaifu, Y., Chang, et al., "Denisovan leg bones from Taiwan reveal large body size." bioRxiv (2026). https://doi.org/10.64898/2026.08.07.743438

* Tsutaya, et al., "A male Denisovan mandible from Pleistocene Taiwan." 388(6743) Science 176–180 (2025). https://doi.org/10.1126/science.ads3888

* Yoneda, et al., "Habitat and feeding ecology of a Denisovan from Late Pleistocene Taiwan." bioRxiv (2026). https://doi.org/10.64898/2026.08.07.743455

* Zhang, D., et al., "Denisovan DNA in Late Pleistocene sediments from Baishiya Karst Cave on the Tibetan Plateau." 370(6516) Science 584–587 (2020). https://doi.org/10.1126/science.abb6320

Davidski At Eurogenes On The Indo-European Homeland

Davidski at Eurogenese has provided some thoughts on the Indo-European homeland in a teaser post with an updated large data set of ancient and modern DNA from Europe. He states:

(Interactive version here)

- Yamnaya is almost certainly derived from Serednii Stih (aka Sredny Stog). I've been talking about this for years and you can probably pick it up without too much trouble in the PCA above. Finally, even Iosif Lazaridis, David Reich, Nick Patterson and friends are now on board with this idea as per their latest paper on the topic (see Lazaridis et al. 2025).

- However, I'm not convinced by the Lazaridis et al. hypothesis that the Caucasus–lower Volga (CLV) cline is intimately linked to the Indo-Anatolian and proto-Anatolian expansions. That's because the CLV cline is an artifact of isolation-by-distance working for thousands of years across a vast and highly diverse landscape, and it includes a wide range of populations that usually have nothing to do with each other.

- The question of who actually spoke Indo-Anatolian first will, in all likelihood, never be solved to everyone's satisfaction. But the number of true candidate groups is actually quite small, and I reckon they're almost certainly all highlighted in my PCA above. Wink, wink, nudge, nudge.

My longstanding hypothesis is that Indo-Europeans established themselves in Anatolia close in time to the first historical attestation of their presence in the 18th century BCE, and that the Indo-Anatolian languages are more divergent than other Indo-European languages due to a stronger substrate effect from the Hattic language and related pre-Indo-European languages from Anatolia, because the substrate culture that they conquered was a vital and functioning Copper Age culture rather than the nearly collapsed Neolithic cultures that other Indo-Europeans encountered as a substrate. I believe that conventional wisdom in the field of historical linguistics attributes too much of the divergence between the Anatolian languages and other Indo-European language to the time depth from their common ancestor dialect.

Medieval DNA From Russia

Medieval ancient DNA from Eastern Europe is consistent with the historical and linguistic narrative of the peoples who make up the Russian state.

The foundation of the first ancient Rus’ state occurred as a result of the consolidation of diverse communities inhabiting Eastern Europe during the second half of the first millennium CE. Historical sources imply that these communities mostly include East Slavs, whose settlement across a vast territory led to the emergence of the East Slavic/Rus’ culture within the Rus’ state. 

We generated genomic data for 200 medieval individuals from different locations to elucidate the origin and genetic structure of the Rus’ population during the early stages of the state formation. Our findings reveal a genetic continuum predominantly shaped by two key genetic groups: a broad Slavic-related continuity of different genetic subclusters of Rus’ occupying the enormous European Plain area, and a Fenno-Ugrian (Uralic)-related component in the Northern Rus’ region. Importantly, both groups have a shared genetic substrate inherited from preceding ancient Baltic region populations. 

To scale Scandinavian ("Viking") heritage, we traced minor Scandinavian genetic lineages that did not make up the dominating genetic stratum of the early Rus’ state. 

Our study presents the first comprehensive genomic image of the medieval Rus’, highlighting the intricate cultural and genetic interactions between Slavic, Fenno-Ugrian, and other groups that formed the first Rus’ state affecting Europe’s history.

Andreeva et al., Genetic history of Rus’, bioRxiv (December 30, 2025), doi: https://doi.org/10.64898/2025.12.30.695215 (Hat tip to Davidski at Eurogenes).

Historical Genetics in Albania and Greece

While not entirely static, Albania has more continuity from the late Bronze Age to the present than the rest of the Balkans. 

Most of Europe exhibits significant continuity with the late Bronze Age at a general level, but most of Europe has also seen that mix tweaked more in the subsequent 3200 years and the shuffling has been particularly great in the Balkans which saw migratory waves from Romans, Slavs, Germanic tribes, Huns, Avars, and Ottomans in the post-Bronze Age era, leaving the Balkans in their currently ethnically fragmented state.

The history of the Albanian people has long been debated, as they first appear in historical records in the eleventh century CE and their language is not closely related to any surviving Indo-European branches. Here, to reconstruct their history, we analysed over 6,000 ancient West Eurasian genomes and 74 newly sequenced present-day ethnic Albanians. Using a range of population genetics methods, including an enhanced protocol to detect identity-by-descent segments between ancient and present-day individuals, we detect continuity of West Balkan Late Bronze and Iron Age ancestry in Early Medieval Albania, to a greater degree than in neighbouring Balkan regions. 

We find that present-day Albanians predominantly descend from this remnant palaeo-Balkan group, which by at least 800–900 CE already exhibited a genetic profile suggesting that they are ancestral to many modern Albanians. In addition, we observe geographically structured admixture with Medieval East European-related groups, averaging 10–20% across present-day Albanians. Our findings provide insight into the demographic processes shaping Albanian ancestry and help locate the origin area of the Albanian language.

Davranoglou, LR., Lauka, A., Aristodemou, A. et al. "Ancient DNA evidence for the history of the Albanians." Nat Hum Behav (May 4, 2026) (pay per view). https://doi.org/10.1038/s41562-026-02462-z

Most of Greece has a gradient of Slavic ancestry dating to the middle ages that is largest in the north and smallest in the south. The Deep Maniots (a.k.a. Inner Mani) in southern mainland Greece are an exception to the rule on the paternal side. According to this Wikipedia link:

In the early modern period, Maniots gained a reputation as fierce and proudly independent warriors, who engaged in piracy and blood feuds. They lived mainly in fortified villages and "tower houses" built as defenses against "Frankish" (see Frankokratia) and Ottoman invaders.

The Maniots claim to be descendants of the ancient Spartans and heirs to their militaristic culture. Modern observers noted Maniots' self-identification as warriors ready to "preserve their liberty" with arms. Genetic studies have identified the Maniots of Inner Mani as a population isolate within mainland Greece, showing substantial parental genetic continuity from antiquity and limited influence from medieval population movements. 

. . .

In Outer Mani, family names end in -eas, while surnames of Inner Mani end in -akis, -akos, or—less frequently—-oggonas.

The Maniot dialect in Greece rejected sound chances found in other modern Greek dialects.

[It] shared with Tsakonian and with dialects spoken around Athens until the 19th century—is the divergent treatment of historical /y/ (written <υ>). Although this sound merged to /i/ everywhere else, these dialects have /u/ instead (e.g. [ˈksulo] versus standard [ˈksilo] 'wood'). These varieties are thought to be relic areas of a previously larger areal dialect group that used to share these features, and was later divided by the penetration of Arvanitika in much of its area, in the late Middle Ages. Other features of the Maniot dialect include the palatalization of velar consonants, i.e. the realization of /k, ɡ, x, ɣ/ as ([tɕ, dʑ] or [ɕ, ʑ] before /i, e, j/. This feature is shared with many southern dialects of Greek; especially Cretan.

The Mani can, in some respects, be seen as comparable to Appalachian populations in the U.S., which share its culture of honor, its tendency to be organized in clans, its reduced admixture with outside groups, and a conservative dialect of its language (the Appalachian dialect of English is the closest living dialect of England to the Elizabethan dialect spoken in Shakespeare's era).

Notably, the founder effects seen are contemporaneous with the influx of Slavic migration into Greece (and Slavic expansion more generally), and may have been associated with a conscious resistance to and rejection of Slavic migration in the several centuries after the fall of the Western Roman Empire. Per Wikipedia:

A 2017 study found they are genetically different from other groups in the Peloponnese region. Maniot individuals share a significant amount of their genome with each other, indicating a high degree of relatedness. They are also genetically isolated from other Greek populations, though they show some overlap with people from Sicily and southern Italy. This is attributed to the Maniots having the lowest levels of Slavic genetic ancestry in the Peloponnese. Maniots from East Mani have very little Slavic ancestry (0.7–1.6%), while those from West and Lower Mani have higher, but still relatively low, amounts (4.9–10.9%). The rest of the Peloponnesian population has a higher percentage of Slavic ancestry (4.8–14.4%). 

This genetic isolation suggests that the Maniots may be descended from the ancient Dorians.

The paper and its abstract are as follows: 

The Deep Maniots, an isolated population at the southernmost tip of mainland Greece, have drawn scholarly interest for their unique dialect, culture, and patrilineal clan structure. Geographically shielded by the Mani Peninsula, they are thought to have been minimally affected by 6th-century CE migrations that transformed Balkan demography. 

To investigate their genetic origins, we analysed Y-DNA and mtDNA from 102 Deep Maniots using next-generation sequencing. Paternally, Deep Maniots exhibit an exceptional prevalence (~80%) of West Asian haplogroup J-M172 (J2a), with subclade J-L930 accounting for ~50% of lineages. 

We identify Bronze Age Greek ancestry in Y-haplogroups nearly absent elsewhere, highlighting their longstanding genetic isolation. The absence of northeast European-related paternal lineages, common in other mainland Greeks, suggests preservation of southern Greece’s pre-Medieval genetic landscape. 

Y-haplogroup phylogeny reveals strong founder effects dated to ~380–670 CE, while the emergence of clan-based social structure is estimated around 1350 CE, centuries earlier than previously thought. 

In contrast, maternal lineages display greater heterogeneity, primarily originating from ancient Balkan, Levantine, and West Eurasian sources. These results align with historical and anthropological accounts, showcasing Deep Maniots as a genetic snapshot of pre-Medieval southern Greece, offering new perspectives on population continuity and mobility in the Late Antique eastern Mediterranean.

Davranoglou, LR., Kofinakos, A.P., Mariolis, A.D. et al. "Uniparental analysis of Deep Maniot Greeks reveals genetic continuity from the pre-Medieval era." 9 Commun Biol 157 (2026) (open access). https://doi.org/10.1038/s42003-026-09597-9

Ancient Tooth Proteins Tell Tales

An analysis of six ancient Homo erectus tooth proteins from three locations in China, a Denisovan tooth protein, and some modern human and animal tooth proteins reveal some notable insights. Bernard's Blog has the story. Proteins in teeth are easier to recover than ancient DNA and can serve as a proxy for it in cases like these.

Interestingly, it implies that a tooth enamel protein found in 1% of humans in or near the former Denisovan range, and Denisovans have a tooth enamel protein also found in Chinese Homo erectus, probably due to introgression from Homo erectus to Denisovans and then from Denisovans to modern humans, in the view of the researchers.

John Hawk has a discussion of the paper, however, that interprets the data differently:

All six teeth share two derived amino acid changes, both in the sequence of an enamel matrix protein known as ameloblastin, or AMBN. One of these hasn’t before been seen in hominins: a change from alanine to glycine at position 253 of the sequence, or A253G. The other is 20 positions downstream, swapping in valine for the ancestral methionine, M273V. The DNA mutation encoding this change is shared by both the Denisova 3 and Denisova 25 genomes. The M273V amino acid change itself is in the Harbin and Penghu 1 dental proteomes—part of why they align with Denisovans. A number of genomes from modern people also share this change, possibly from Denisovan ancestors.

The hypothesis presented by Fu and coworkers is that Homo erectus was the source of M273V, and its presence in Denisovans is a result of introgression. In support of this idea of introgression, they note earlier research on the Denisova 3 and Denisova 25 genomes that suggests a contribution from a “superarchaic” source population. Many—including me—have speculated that this superarchaic ancestry came from H. erectus. Fu’s team may have just proved it.

But I don’t think these teeth are Homo erectus.

Their estimated ages, all around 400,000 years ago, are prime Denisovan time. Fu and coworkers find that all the teeth share a derived link with later Denisovan genomes. For me, the most likely hypothesis is that these teeth come from a population within the Denisovan branch of humanity.

This situation is basically the same as the Sima de los Huesos fossils. Those remains are around 430,000 years old. Those fossils look like Neanderthals in some subtle ways, but until DNA was recovered from them, many researchers considered them to be part of a different group, often called Homo heidelbergensis. DNA revised both the timeline and their identification.

It may seem heretical, but I think protein data may be about to do the same for fossils from East Asia.

South American Genetic History

I remain skeptical that the Australasian ancestry is as ancient as claimed. It is much less than 2%, maybe a hundred times less, and the regional variation in its frequency is far too great for it to be ancient. I suspect an origin in Polynesian sea farers that may be obscured by natural selection against some signature Polynesian genes. 

I have not yet seen any really solid evidence that it has been present for 10,000+ years, or any explanation for the extremely varied frequency of these genes in the populations where they are found, indicating a very recent dispersal to these populations that hasn't had time for these frequencies to harmonize. 

South American ancient DNA samples are few and far between at that time depth, and this paper has some of them, but a lot of the references supporting this analysis are in supplementary materials and extended data, or references to other papers, and the nature of the ancient DNA sample is one I haven't been able to look at closely yet. As I've only had time to cut, paste, and highlight, rather than enough to do a proper critical analysis of this claim. 

I'll add more analysis in an update in this post, if time permits, which may or may not happen (I'm busy preparing for an upcoming jury trial).

[A] study published today in Nature reveals these migrations were anything but simple. Examining ancient and modern genomes collected from across South America and beyond, the team found that genetically diverse groups populated the continent in at least three separate pulses. And some people or communities carried with them possibly advantageous genes acquired from long-ago Australasian ancestors. . . .

His team published a complementary study today in Current Biology, finding evidence of unexpected genetic diversity and otherwise invisible migrations in 52 ancient genomes from Argentina and Uruguay.

In the Nature study, Tábita Hünemeier, a geneticist at the University of São Paulo and the Institute of Evolutionary Biology, collaborated with researchers and Indigenous communities across Latin America to sequence 128 whole genomes from living people from north Mexico to southern Argentina. The team then analyzed them alongside existing databases and previously published ancient genomes.

Previous work had identified the first two waves of settlement in South America, the earliest of which included people related to the Anzik child, who was buried in Montana 12,700 years ago. A second dispersal followed about 9000 years ago and ultimately contributed more to the genomes of most ancient and modern South Americas, including those Posth studied.

Hünemeier and her team found evidence of a third dispersal, whose genetic signature first appears in their data about 1300 years ago and then spreads widely across the continent and even into the Caribbean. The newcomers show hints of being related to Mesoamericans from Mexico and Central America, but so far, researchers don’t know exactly where they came from or who were their closest relatives. “Without the source population and more direct evidence [of a third pulse] from ancient DNA, it’s hard to really wrap our heads around” how and when a third migration might have happened, Posth says.

The study also digs deeper into a mystery that has bedeviled the genetic history of the Americas for over a decade: How did traces of Australasian ancestry end up in some ancient and modern South American genomes? Genetic variants from this lineage make up only about 2% of ancestry in the people who carry it, but that proportion has stayed remarkably consistent over the past 10,000 years. “This signal is found again and again and again,” Posth says. “It must mean something.”

Hünemeier suspects people carrying this ancestry were among several distinct populations that lived for thousands of years in Beringia, the now-drowned landmass that connected eastern Siberia to Alaska, and that it eventually spread southward into the Americas from there. (This Australasian ancestry, sometimes known as Population Y or the Ypykuéra signal after the Tupi word for “ancestor,” is different from the genetic sequences some Polynesian populations share with South American ones. Scientists continue to debate how that more recent gene flow happened—for example, whether Polynesian voyagers may have reached western South America about 800 years ago—but the findings from the Nature paper have no bearing on that mystery.)

From Science.

Both of these papers are open access.

The Nature article and its abstract:

Indigenous peoples of America represent the last principal expansion of humans across the globe, yet their genetic history remains one of the least explored. Although these populations have inhabited the continent for thousands of years, their evolutionary history remains largely unresolved, owing to the limited availability of genomic data. 

Here we present data on 128 high-coverage Indigenous American genomes and show they harbour extensive and previously uncharacterized genetic diversity, reflecting at least three dispersals into South America, followed by regional differentiation and long-term continuity. 

We identified widespread natural selection signals in genes associated with immunity, metabolism, reproduction and development, which were shaped by adaptation to diverse environmental conditions. 

Notably, several genomic regions exhibit a remarkable allele sharing with Australasian populations, probably originating from an ancient admixture event and partly maintained by selection for more than 10,000 years. 

We also detected distinct contributions from archaic humans with adaptive introgression affecting key biological functions. The limited overlap between the regions of Australasian affinity and archaic ancestry indicates independent evolutionary origins of these signals. These findings challenge simplified models of continental settlements and show a more dynamic and complex evolutionary history for the Indigenous peoples in America.

Castro e Silva, M.A., Nunes, K., Ribeiro, M.R. et al. :The evolutionary history and unique genetic diversity of Indigenous Americans." Nature (April 22, 2026). https://doi.org/10.1038/s41586-026-10406-w

The section on archaic and Australasian ancestry in the body text of the Nature article states (with citations omitted):

Affinity with Australasians and archaics

Some Indigenous American populations show elevated genetic affinity to present-day Australasians relative to other groups contradicting a single non-Arctic Indigenous American clade. This affinity is best explained by admixture between the ancestors of Indigenous Americans and an unsampled ancient Asian population, termed Ypykuéra (here referred to as Ypykuéra ancestry), partially related to a sister clade of present-day Australasians.

We assessed genetic affinity between ancient and modern Indigenous Americans and present-day Australasians, the closest living proxies for Ypykuéra ancestry. We applied F-statistics to modern Indigenous American pairwise comparisons and to comparisons including ancient individuals.

Several Indigenous groups, including the Awajún, Ayoreo, Guarani, Karitiana, Sirionó, Suruí and Tsimané, show significant excess genetic affinity to Australasians relative to other present-day populations (Z > 3). These groups span eastern and western South America and the Chaco, with the strongest enrichment in the southwestern Amazon, where five of these seven populations are located.

A second analysis detected at least one individual with significant affinity in all examined clusters, except Arctic and northern North American groups, which were excluded from this analysis because of partial or complete ancestry from independent Siberian dispersals. The earliest signal occurs in the 10,400-year-old Sumidouro individual. Signals persist from the Early Holocene to the present, increasing in frequency during the Late Holocene, especially in the Andes, Pacific Coast and western South America. The partially discontinuous spatiotemporal pattern probably reflects variation in prevalence within and among populations. Taken together, these findings indicate that this ancestry was present during the initial peopling of America and that it may have contributed more strongly to Late Holocene and present-day genetic diversity.

We tested whether Ypykuéra-related ancestry in Indigenous Americans reflects shared ancestry with Australasians by means of archaic hominins (Neanderthals and/or Denisovans). We compared D(Mbuti, Onge; Mixe, X) with D(Mbuti, Neanderthal or Denisova; Mixe, X), where X denotes Indigenous American groups. Mixe served as a Mesoamerican reference to match earlier studies reporting Australasian affinity. No correlation was detected between Australasian and Neanderthal (Spearman’s r = −0.006, P = 0.971) or Denisovan affinity (r = −0.1002, P = 0.5372). By contrast, Neanderthal and Denisovan affinities were strongly correlated (r = 0.6572, P = 7.2 × 10^−6), consistent with homogeneous archaic ancestry in the founding populations.

An alternative hypothesis proposes that Australasian affinity reflects retention of the Ypykuéra component in isolated groups with high internal genetic similarity. Such populations and genomic regions, characterized by elevated ROH, would be less affected by admixture that could dilute signals of ancient Population Y ancestry. This hypothesis is not supported by our data, which show no correlation between Australasian affinity and inbreeding (FROH) (Spearman’s r = 0.2503; P = 0.1192). Moreover, ROH hotspots, defined as regions with ROH density greater than three standard deviations above the mean, show little overlap with loci of Australasian affinity, with only about 6% of such positions coinciding.

We tested whether Indigenous American affinity to present-day Australasians also includes ancient Hòabìnhian individuals, proposed ancestors of mainland Southeast Asian hunter-gatherers, including the Onge Using D(Mbuti, Y; Mixe, X), with Y as Onge or Hòabìnhian individuals (La368, La364) and X as Indigenous American populations, we evaluated correlations in affinity to Onge and Hòabìnhian individuals. La368 forms a sister branch to Onge, whereas La364 is modelled as Australasian-related plus Austronesian ancestry, sister to Ami. We observed significant correlations for La368 (Spearman’s r = 0.6444; P = 1.1856 × 10^−5) and La364 (Spearman’s r = 0.6208; P = 2.8848 × 10^−5). These results support a shared ancestry component between Indigenous Americans and Australasians that extends deep into the past.

The Current Biology article and its abstract:

• Expansion of ancestry into the Pampas, Uruguay, and Patagonia from the Middle Holocene

• Repeated mobility from southern Andean and southern Patagonian-related populations

• Genetic differentiation between the Upper and Lower Paraná River Delta ∼600 years ago

• Coastal dispersal from southern Brazil to eastern Uruguay via mound-builder societies

The Southern Cone represents the southernmost region of South America settled by humans. Although ancient genomes from southern Patagonia have been sequenced, genomes from the central Southern Cone (CSC) remain temporally and spatially sparse. Archaeology documents major cultural transformations during the Middle and Late Holocene, yet their relationship with demographic processes has been debated. 

We present genome-wide data from 52 individuals spanning 6,000 years, originating from four regions of the CSC in present-day Argentina and Uruguay: the central and southern Pampas, Northwest Patagonia, the Paraná River Delta and Lower Uruguay River, and the eastern lowlands of Uruguay. 

Genomic evidence from the Pampas reveals the presence of at least three distinct ancestries during the Middle Holocene. Although genetic contacts with southern Patagonian groups were sporadic, we identified the expansion of an ancestry of unknown geographic origin by 5,500 years ago (ya), which increased during the Late Holocene. This ancestry arrived in Northwest Patagonia by at least 600 ya and co-existed locally with a southern Andean genetic profile until colonial times. 

Genetic structure differentiates populations along the Paraná River Delta and Lower Uruguay River by 1,500 ya. 

Individuals from the eastern lowlands of Uruguay show genetic links with Sambaqui-associated populations from the southern coast of Brazil, suggesting the role of human dispersals in connecting tropical lowland cultural traditions. 

Our work documents the diffusion of genetically distinct groups across all studied regions and provides compelling evidence that large-scale human movements contributed to the remarkable cultural diversity of CSC populations during the Middle and Late Holocene.

Kim-Louise Krettek, et al., "The shared genomic history of Middle- to Late-Holocene populations from the Southern Cone of South America" Current Biology (April 22, 2026).

Population Discontinuity At The End Of The Neolithic In Paris, France

Bernard's blog, Généalogie génétique, lives. (I had removed it from the blogroll when technical difficulties at the site made it look dead. I'll reinstate it when I have time.)

His latest post examines an ancient DNA paper looks at ancient DNA from a graveyard in Paris, part of which dates to around 3000 BCE in the megalithic Neolithic era, and part of which comes a century later after a long gap in burials there, when the previous megalithic Neolithic civilization there had collapse: forests had regrown, megalithic construction had ceased, and infectious diseases including the black plague had ravaged the population. 

The post-collapse social organization was different too, with the earlier burials reflecting a large extended family/clan social structure of related people, and the later burials reflecting a smaller nuclear family with multiple generations of related people but only a few people in each generation.

In this case, there was population discontinuity in which the prior Neolithic population was replaced by another Neolithic population from the South with a different social organization that moved in after the original megalithic Neolithic culture in Paris collapsed. Both the original group (in brown on the PCA plot below) and the subsequent one (in green) cluster together as European Neolithic populations, distinct from prior European hunter-gather peoples and the later Bronze Age steppe peoples, despite being distinct enough to indicate a population replacement.

This graveyard pins down the timing of this collapse fairly precisely to a single century.

This also makes clear that Neolithic collapse in Western Europe happened before the arrival of Bronze Age people with steppe ancestry. It also illustrates the civilizational vacuum that those Bronze Age people swept into a few centuries later, replacing much of the first farmer wave of people in this part of Europe, in a dynamic distinct from the conquest of a vibrant Neolithic civilization.

The abstract and citation appears below:

At the transition between the third and the fourth millennium BC, there is evidence for a population decline concurrent with the end of megalith building across continental northwestern Europe. In Scandinavia this ‘Neolithic decline’ is followed by a massive population turnover, as farming communities disappeared and were replaced by people with steppe ancestry. In western Europe, however, ancestry associated with Neolithic farmers persisted beyond the Neolithic decline, and it remains unclear whether a similar demographic replacement occurred.

To investigate the population dynamics around the Neolithic decline in present-day France, we sequenced 132 ancient genomes from the allée sépulcrale at Bury. Located in the Paris area, Bury spans two burial phases separated by a hiatus with no burial activity: one phase directly preceding the Neolithic decline in the late fourth millennium BC, ending around 3000 BC, and a later phase some time after the Neolithic decline in the early- to mid-third millennium BC.

Our analysis revealed that the two burial phases at Bury represented largely discontinuous genetic groups of a markedly different social organization as inferred from three large pedigrees. We show that the difference between the two burial phases can be linked to a northwards movement of Neolithic ancestry from the south, which only spread into the Paris Basin after the Neolithic decline, at around 2900 BC. 

Together with genetic evidence of various infectious diseases in the dataset, such as Yersinia pestis and Borrelia recurrentis, as well as evidence for forest regrowth between the two phases, these findings detail a population turnover at the end of the fourth millennium BC, offering a possible explanation for the cessation of megalith building.

Frederik Seersholm, et al, "Population discontinuity in the Paris Basin linked to evidence of the Neolithic decline" Nature Ecology and Evolution (April 3, 2026).

Steppe ancestry starts to appear in Southern France ca. 2650 BCE, with Bell Beaker artifacts found in the Lower Rhine ca. 2600 BCE. This is about 250-300 years after population replacement in the Paris basin.

Notably, however, the source of the Southern France Neolithic migrants to the Paris basin ca. 2900 BCE is, geographically, one of the earliest places of the Bell Beaker phenomena in France and is the geographic source of the French Bell Beaker people. Indeed, southern France is the first place that the Bell Beaker phenomena arose after Iberia (it arose originally in the Tagus River basin in Portugal). 

Also notably, the very first Bell Beaker people had Neolithic, rather than Steppe ancestry, which only came two or three centuries later.

It is thus conceivable that the Southern French replacement population in Paris ca. 2900 BCE may be from the same population that was the source of the pre-Steppe Bell Beaker progenitors.

Palau Is An Oceania Outlier

This is a further refinement of an already pretty well worked out story of Oceanian origins. 

The ultimate source of Oceanian and Austronesian seafaring people was one of the indigenous tribes of what is now called Taiwan (we have identified which of them it was based upon linguistic evidence), via island Southeast Asia.  

Before expanding very far east, however, these Formosan origin Lapita people admixed with Papuan people (in an encounter that amounted to a hostile conquest).

This "graphical abstract" really sums up a new paper on the topic. 

Note that the dates in this image are "before present", i.e. before 1950 by archeological convention, and not BCE. The initial settlement of Palau was roughly contemporaneous with the Greek "dark ages" after Bronze Age collapse, for example, while the admixture of the people who settled Palau was contemporaneous with the Late Bronze Age in Europe.

An educated layman's explanation of the paper explains: 

About 3200 years ago, Southeast Asian seafarers known as the Lapita pushed east into the tropical islands of the Pacific Ocean, hitting nearly every habitable isle in that corner of the globe from New Guinea to Fiji and Tonga. As they did so, they left behind artifacts of their culture, including pottery stamped with distinctive geometric patterns.

But on Palau, there’s not a single shard of Lapita pottery—and the island’s inhabitants speak a language that’s distinct from the tongues spoken on other Pacific islands. So who were the first Palauans, and where did they come from?

A new study published last week in Cell suggests an answer. Genetic evidence confirms Palau’s first settlers descended from Southeast Asians who had intermingled with the Papuans, Indigenous peoples who settled the island of New Guinea some 50,000 years ago.

“It’s lovely to see a piece of Pacific history—which we’ve traditionally been at a bit of a loss to explain—finally start to come together into a more understandable story,” says Murray Cox, a computational biologist at Massey University of New Zealand who wasn’t involved in the new work.

The discovery builds on previous ancient DNA research into the origins of the Lapita themselves. That work, led by evolutionary biologist David Reich at Harvard University and his colleagues, showed that Lapita were essentially pure Southeast Asians of Taiwanese roots—but that modern populations on Pacific islands showed Papuan ancestry, too. The studies suggested this Papuan ancestry came in about 2500 years ago, as Papuans began to join the same canoe voyages that had earlier carried Lapita settlers into the region.

From Science.

The underlying paper in Cell is as follows:

Highlights

• Ancient DNA of 21 individuals from Palau spans around 2,400 years

• Papuan-East Asian admixture in Palauans predates initial settlement

• Over 2,900 years of genetic continuity in Palau

• Shared East Asian-Papuan admixture in Palau and eastern Indonesia 

Summary 

The first people reached Remote Oceania 3,000 years before present (BP), arriving roughly simultaneously in the southwest Pacific, the Marianas Archipelago, and Palau. However, no genome-wide ancient DNA data have been available from Palau, a gap we address by reporting 21 individuals from four archaeological sites dating between 2,900 and 500 BP. 

All had approximately 60% ancestry related to East Asians and 40% to Papuans, similar to present-day Palauans, the longest stretch of population continuity anywhere in Remote Oceania. The lengths of contiguous Papuan ancestry segments in the oldest individuals show that major admixture between Papuans and East Asians in the ancestors of all sampled Palauans began prior to first settlement. This differs from the pattern in the southwest Pacific, where sampled individuals of the Lapita archaeological culture from three different islands had almost entirely East Asian ancestry, with large amounts of Papuan admixture observed only hundreds of years later. 

Yue-Chen Liu, et al., "Papuan admixture predated the settlement of Palau" (March 10, 2026).

Gender And Neanderthal-Modern Human Interbreeding

The New York Times and other general audience media outlets are reporting on a new genetics study in the Journal Science, examining the gender dynamics of Neanderthal admixture. The editor's summary and abstract and citation are:

Editor’s summary

Although a low level of Neanderthal ancestry is present in most humans, these regions are not uniformly distributed. A handful of regions in the autosome are entirely devoid of such ancestry in essentially all living humans, and the X chromosome is strongly depleted across its sequence. Platt et al. modeled the possible demographic processes and selection that could have produced this pattern. They found that these patterns are most consistent with Neanderthal contributions to human populations being heavily male biased. The concurrent additional depletion in functional regions on the X chromosome suggests that the effects of this skew may have been strengthened by negative selection on Neanderthal variants. —Corinne Simonti

Abstract

Sex biases in admixture and other demographic processes are recurrent features throughout human evolution. For admixture between Neanderthals and anatomically modern humans (AMHs), sex bias has been proposed as an explanation for the relative lack of Neanderthal ancestry in modern human X chromosomes compared with that in modern human autosomes. By observing a 62% relative excess of AMH ancestry in Neanderthal X chromosomes, we characterized the interbreeding between the two groups as predominantly male Neanderthals with female AMHs. Analytic and numerical modeling presents mate preference as a more parsimonious cause of the sex bias than purely demographic processes with differential patterns of male and female migration.

Alexander Platt, Daniel N. Harris, and Sarah A. Tishkoff, "Interbreeding between Neanderthals and modern humans was strongly sex biased", 391 (6788) Science 922-925 (February 26, 2026).

While I don't dispute the genetic data that the study discloses and bases its narrative upon, I don't think that the narrative that the general audience presentation and even the study itself have chosen a narrative that is anything close to being the most plausible one.

I've previously discussed the narrative that I think is closer to the truth, using just the Y-DNA, mtDNA, and overall autosomal genetic data previously available, without the X chromosome specific data from both admixed modern humans and admixture in Neanderthal ancient DNA  that this study brings to the table. 

In a nutshell, my prior analysis was that admixed Neanderthal-modern human hybrid children ended up in the communities to which their mothers belonged, and that Haldane's rule (which provides as relevant to this context, that cross-species hybrids are disproportionately female, perhaps sometimes sterile males, and only rarely fertile males) was also a key factor in why there are no modern humans with Neanderthal Y-DNA, there is no Neanderthal ancient DNA with modern human Y-DNA, why there are no modern humans with Neanderthal mtDNA, and why there is no Neanderthal ancient DNA with modern human mtDNA.

I also suggests that hybrid children may have often been the product of rape or episodic hookups, rather than long term marriage-like relationships embedded in a modern human or a Neanderthal tribe.

While the X chromosome data may require some fine tuning of that analysis, I don't think that it justifies a wholesale paradigm shift from it. I think that the new study's narrative gives insufficient consideration of these priors from that data when evaluating when kind of narrative makes the most sense to interpret its X chromosome based data, and focusing on a sexual selection and attraction based narrative instead.

The default assumption of the simple, uniparental DNA driven paradigm with Haldane's law paradigm is that the X chromosome would have the same proportions of Neanderthal and modern human DNA as other chromosomes, since almost all of the fertile hybrid children would have one Neanderthal X chromosome and one modern human X chromosome.

Admixture in X chromosomes could be reduced in early modern human communities if they had an influx of "basal" modern human populations (i.e. introgression from modern humans with no Neanderthal admixture) and that introgression was female biased because the Neanderthal admixed population was usually (at least with its own species pairing in marriage-like ways) patrilocal and recruited brides from outside its tribe in a way that had a significant basal modern human component. This kind of marriage pattern was common in the Neolithic Age, the Bronze Age and the Iron Age, including in herder populations who were culturally more similar to ancestral modern human hunter-gatherer societies, so it is quite plausible.

The lack of modern human mtDNA in Neanderthal ancient DNA strongly constrains the extent to which the mothers of hybrid individuals in Neanderthal communities were modern humans, although the fact that Neanderthal effective populations were falling at the time of Neanderthal-modern human contact means that it would be easier to lose low frequency modern human mtDNA variants in Neanderthal communities than it would be to lose low frequency Neanderthal mtDNA variants in human communities.

But, one still has to explain the new data point that there is an excess of modern human DNA in the ancient DNA of admixed Neanderthal X chromosomes. But that data still has to be reconciled with the lack of modern human mtDNA in any Neanderthal ancient DNA.

Since the Neanderthal ancient DNA sample, unlike the modern human DNA sample, is a small one, the statistical significance of this excess also needs to be examined as well as possible selective genetic fitness based explanations for some of the modern human X chromosome excesses relative to Neanderthal genes at those loci. But the number of genes per chromosome is great enough and 62% is a significant enough excess, that statistical flukes probably don't explain that much of the excess.

The first possible explanation that comes to mind for the excess modern human genes in admixed Neanderthal ancient DNA is that the effective population size of Neanderthals in that era was much smaller than the effective population size of modern humans in that era. In other words, the Neanderthals were more inbred.

This would make children in Neanderthal communities with pure Neanderthal source X chromosomes more vulnerable to harmful X chromosome based recessive diseases than hybrid Neanderthal children who would enjoy hybrid fitness. Over time, at multiple generations and not just the first one, this would favor individuals in Neanderthal communities with hybrid ancestry over those with pure Neanderthal ancestry. And the effect would be strong on the X chromosome than on the other autosomal chromosomes, because Neanderthal boys would not be at risk of suffering from harmful X chromosome based recessive diseases, while unadmixed Neanderthal girls would be at risk of suffering from these diseases.

This factor alone, depending on the prevalence of X chromosome based recessive diseases in much more inbred Neanderthal gene pools, might very well have been enough to explain the excess of modern human X chromosomes in the ancient DNA of admixed Neanderthals, without requiring modern human woman who have hybrid children to frequently live in and raise their children in Neanderthal communities (leaving us with the problem of explaining why there is no modern human mtDNA in these admixed Neanderthal individuals in Neanderthal communities).

I'll update this post with more analysis as time permits, after I've had more time to read the paper and consider its analysis.

A New 200,000 Year Old Denisovan Genome

Bernard's blog does a good job of reviewing the recent publication of a 200,000 year old Denisovan genome. 

This Denisovan's life predates the emergence of modern humans from Africa, but overlaps with the existence of the earliest modern humans within Africa.

In a nutshell, the preprint is: Stéphane Peyrégne, et al., "A high-coverage genome from a 200,000-year-old Denisovan" bioRxiv (October 20, 2025). According to Bernard (via Google translate from French):

They sequenced the genome of molar Denisova 25. Initial results showed that the individual was male. Furthermore, the mitochondrial and Y chromosome haplogroups both belong to the Denisovan population.

The Hunter-Gather To Bronze Age Transition In Kazakhstan

Bernard discusses a paper on ancient DNA from Kazakstan. It revealed that the hunter-gatherer population that persisted there until the late Neolithic era in Europe was roughly 95% replaced by Bronze Age early Indo-Europeans herders similar to the Sintashta and Andronovo cultures genetically. The paper is Haechan Gill, et al., "Ancient genomes from eastern Kazakhstan reveal dynamic genetic legacy of Inner Eurasian hunter-gatherers" (2025).

The paper also has many other secondary insights.

The samples from the current study are in yellow, with the Bronze age samples on the left, and in the MLBA clines, and the Neolithic samples in the Steppe HG cline on the right.

The Population Genetics Of Egypt Have Been Stable For A Long Time

An ancient DNA sample from ca. 2500 BCE in Egypt reveals a great deal of continuity in the population genetics of Egypt then and the population genetics of Egypt today. 

I didn't have a lot of time to look carefully at this study, but prior studies have shown a modest increase in sub-Saharan African admixture since then, due to the trans-Saharan slave trade in more recent time periods.

The Huns Were Paleo-Siberian, Not Linguistically Turkic (Also Slavic Origins)

A new paper makes a strong case that the Huns, a group of "barbarians" (in the eyes of Roman historians) who made multiple attempts to invade the Roman empire, spoke a Paleo-Siberian language (to which the Na-Dene languages of North America, such as Navajo, are distantly related), rather than a Turkic language, as conventional wisdom in historical linguistics prior to this paper had wrongly believed.

The Xiōng-nú were a tribal confederation who dominated Inner Asia from the third century BC to the second century AD. Xiōng-nú descendants later constituted the ethnic core of the European Huns. It has been argued that the Xiōng-nú spoke an Iranian, Turkic, Mongolic or Yeniseian language, but the linguistic affiliation of the Xiōng-nú and the Huns is still debated. 

Here, we show that linguistic evidence from four independent domains does indeed suggest that the Xiōng-nú and the Huns spoke the same Paleo-Siberian language and that this was an early form of Arin, a member of the Yeniseian language family. This identification augments and confirms genetic and archaeological studies and inspires new interdisciplinary research on Eurasian population history.

Svenja Bonmann et al, "Linguistic Evidence Suggests that Xiōng‐nú and Huns Spoke the Same Paleo‐Siberian Language," Transactions of the Philological Society (June 16, 2025). DOI: 10.1111/1467-968X.12321

A news report about the paper spells it out this hypothesis at greater length:

New linguistic findings show that the European Huns had Paleo-Siberian ancestors and do not, as previously assumed, originate from Turkic-speaking groups. The joint study was conducted by Dr. Svenja Bonmann at the University of Cologne's Department of Linguistics and Dr. Simon Fries at the Faculty of Classics and the Faculty of Linguistics, Philology and Phonetics at the University of Oxford.

The results of the research, "Linguistic evidence suggests that Xiōng-nú and Huns spoke the same Paleo-Siberian language," have been published in the journal Transactions of the Philological Society.

On the basis of various linguistic sources, the researchers reconstructed that the ethnic core of the Huns—including Attila and his European ruling dynasty—and their Asian ancestors, the so-called Xiongnu, shared a common language. This language belongs to the Yeniseian language family, a subgroup of the so-called Paleo-Siberian languages. These languages were spoken in Siberia before the invasion of Uralic, Turkic and Tungusic ethnic groups. Even today, small groups who speak a Yeniseian language still reside along the banks of the Yenisei River in Russia.

From the 3rd century BCE to the 2nd century CE, the Xiongnu formed a loose tribal confederation in Inner Asia. A few years ago, during archaeological excavations in Mongolia, a city was discovered that is believed to be Long Cheng, the capital of the Xiongnu empire. The Huns, in turn, established a relatively short-lived but influential multi-ethnic empire in southeastern Europe from the 4th to 5th centuries CE.

Research has shown that they came from Inner Asia, but their ethnic and linguistic origins have been disputed until now, as no written documents in their own language have survived. A great deal of what we know about the Huns and the Xiongnu is therefore based on written documents about them in other languages; for example, the term "Xiōng-nú' derives from Chinese. 

 

[Based on the "World Topographic Map" by Esri. Sources: Esri, HERE, Garmin, Intermap, INCREMENT P, GEBCO, USGS, FAO, NPS, NRCAN, GeoBase, IGN, Kadaster NL, Ordnance Survey, Esri Japan, METI, Esri China (Hong Kong), OpenStreetMap contributors, GIS User Community, Simon Fries. Created with QGIS 3.36.]. Credit: Transactions of the Philological Society (2025). DOI: 10.1111/1467-968X.12321

From the 7th century CE, Turkic peoples expanded westwards. It was therefore assumed that the Xiongnu and the ethnic core of the Huns, whose own westward expansion dates back to the 4th century CE, also spoke a Turkic language. However, Bonmann and Fries have found various linguistic indications that these groups spoke an early form of Arin, a Yeniseian language, in Inner Asia around the turn of the millennium.

"This was long before the Turkic peoples migrated to Inner Asia and even before the splitting of Old Turkic into several daughter languages. This ancient Arin language even influenced the early Turkic languages and enjoyed a certain prestige in Inner Asia. This implies that Old Arin was probably the native language of the Xiongnu ruling dynasty," says Bonmann.

Bonmann and Fries analyzed linguistic data based on loan words, glosses in Chinese texts, proper names of the Hun dynasty as well as place and water names. Taken by itself, the data on each of these aspects would have comparatively little significance, but taken together it is hard to argue with the conclusion that both the ruling dynasty of the Xiongnu and the ethnic core of the Huns spoke Old Arin.

The findings of the study also made it possible for the first time to reconstruct how the Huns came to settle in Europe: For the two researchers, place and water names still prove today that an Arin-speaking population once left its mark on Inner Asia and migrated westwards from the Altai-Sayan region. Attila the Hun probably also bears an ancient Arin name: Until now, "Attila" was thought to be a Germanic nickname ("little father"), but according to the new study, "Attila" could also be interpreted as a Yeniseian epithet, which roughly translates as "swift-ish, quick-ish."

The new linguistic findings support earlier genetic and archaeological findings that the European Huns are descendants of the Xiongnu. "Our study shows that alongside archaeology and genetics, comparative philology plays an essential role in the exploration of human history. We hope that our findings will inspire further research into the history of lesser-known languages and thereby contribute further to our understanding of the linguistic evolution of mankind," concludes Fries.

In the body text, a section of the paper explores the previous conventional wisdom and its difficulties:

Although direct evidence is lacking, Iranian, Turkic and Mongolic languages have all been proposed as the language of the ruling dynasty of the Xiōng-nú (cf. e.g. Shiratori 1900; Benzing 1959; Pritsak 1982; Bailey 1985; Dybo 2007; Janhunen 2010; Beckwith 2018; Beckwith 2022) and of the Huns (cf. e.g. Doerfer 1973; Pritsak 1982; Savelyev 2020; Savelyev & Jeong 2020), because in the 1st millennium AD languages from these three families were spoken in Inner Asia. Inscriptions dating between the 4th and 9th century AD demonstrate that Iranian languages (Sogdian, early 4th to 6th century AD, Sims-Williams 2011; Vovin 2018) and Mongolic ones (Khüis Tolgoi and Bugut inscriptions of the 5th–6th centuries AD, Vovin 2018) as well as, much later, Turkic languages (isolated Turkish phrases in Bactrian manuscripts of the 7th century AD, Orkhon and Yenisei Kirgiz inscriptions between the early 8th and 9th century AD, Erdal 2004: 4–8) were spoken in the territory between the Yenisei River in the West, the Tian Shan range in the South and Mongolia in the East. Other Indo-European languages were spoken in oasis cities along the northern and southern ridges of the Takla Makan desert in the 1st millennium AD including Indo-Iranian (Iranian Khotanese and Tumshuqese Saka, Bactrian, Indo-Aryan Prakrit, Sanskrit) and ‘Tocharian’ languages (Agnean and Kuchean).

However, this linguistic situation of a coexistence of Iranian, Turkic and Mongolic in Inner Asia can only be reliably established as such for the late 1st millennium AD. Hypotheses on an Iranian, Mongolic or Turkic identity of the Xiōng-nú primarily rest on written sources post-dating the Xiōng-nú era. 

While the theoretical possibility of a Mongolic or Turkic presence in Inner Asia already at the beginning of the common era cannot be ruled out a priori, it is important to note that there is, on the other hand, also no robust evidence – especially from textual sources – that could directly imply or prove a Turko-Mongolic presence in this area at such an early date. 

The earliest sources from the Tarim Basin and the territories alongside the Oxus River/Amu Darya (Chorasmia, Sogdia, Bactria) only document Indo-European languages from the Indo-Iranian and ‘Tocharian’ branches (to which might be added, as a cultural import, also Ancient Greek in Macedonian colonies). Judging by more indirect evidence – especially loanwords in other languages, toponyms, etc. – other Iranian languages, namely different Sakan varieties (Tremblay 2005) and ‘Old Steppe Iranian’ (Bernard 2023), must have been spoken in the steppe corridor from the Kazakh steppe to Dzungaria, and perhaps even to Gansu (see Beckwith 2022). It is only centuries later, namely in the Migration Period of the 5th–6th centuries AD, that a (Para-)Mongolic language might be attested in Inner Asia (Vovin 2018), and fragments of this (Para-)Mongolic language, in turn, are still much earlier documented than the earliest secure Turkic words dating from the 7th century AD.

There is thus neither direct nor indirect evidence supporting the claim of a Mongolic or Turkic presence in Inner Asia between the 3rd century BC and the 2nd century AD, and the hypothesis of a Mongolic or Turkic identity of the ethnic core of the Xiōng-nú (as proposed by Benzing 1959, Pritsak 1982; Tenišev 1997; Dybo 2007; Janhunen 2010; Savelyev 2020) is thus rather unlikely from the outset, as is the hypothesis of a completely unknown or unclassifiable language without any living descendants (as proposed by Doerfer 1973). The same applies to the Huns: there is a complete lack of evidence supporting claims of a Turkic presence among the Huns.1 On the other hand, an Iranian component in the Xiōng-nú Empire is possible, and indeed quite likely, although, as we intend to point out with the present study, such Indo-European ethnicity must not necessarily have been shared by the ruling dynasty or ethnic core of the Xiōng-nú (pace Bailey 1985; Beckwith 2022) or the Huns.

Concerning such an Iranian component, (Beckwith 2018, 2022) has argued recently that Xiōng-nú words preserved in Chinese texts are indicative of an Iranian language, which he calls ‘East Scythian’. However, his interpretation depends on a reconstruction of the Old and Middle Chinese pronunciation of Chinese signs which significantly differs from established reconstructions such as the classic one of Pulleyblank, and which has also been criticised by Vovin et al. (2016: 129–30). In addition to this, his Iranian etymologies must be met with serious doubts. For instance, the ethnonym ‘Aryan’, which is amply attested in many Indo-Iranian languages, is given by Beckwith with a word-initial laryngeal sound (discussion in Beckwith 2022: 183–86, cf. particularly p. 186): ‘East Scythian *ḥarya [ɣa.rya] “noble, royal; Scythian” → Old Chinese *ḥaryá 夏/*ḥâryá 華 “royal; Chinese, China”’. This would indeed be a remarkable Iranian word form, because no Indo-Iranian language points to an initial laryngeal (†Hā̆ri̯a- vel sim.): A word-initial laryngeal should have left direct traces in Persianide languages (see Kümmel 2018), but Old Persian <ariy-> /ariya-/ or inscriptional Middle Persian ēr ‘Iranian’ do not preserve such a sound. The hypothetical (East) Scythian would be the only Iranian language to preserve it, and independent evidence for this is entirely lacking. Other etymologies equally rest upon highly questionable ad hoc assumptions on Iranian historical phonology and must accordingly be dismissed (e. g. the etymology of Old Turkic täŋri ‘heaven’ that Beckwith 2022: 195, 203 wants to derive from an East Scythian *tagri through the application of an alleged Scythian syllable contact law of nasalization completely unheard of in the specialist literature and remaining without any reliable parallel; on this word rather cf. Georg 2001).

It must therefore be conceded that, while it is a priori likely that Iranian tribes were one factor among others in the ethnolinguistic melting pot of the eastern Eurasian steppe some 2000 years ago (the Sakan languages would be a good starting point for further research in this direction), the evidence adduced by scholars in favour of a dominant role of Iranian groups and their languages in the Xiōng-nú empire so far does not follow the rigorous methodological standards of Historical-Comparative Linguistics and is therefore insufficient to allow for any reliable inferences.

Etymological analyses of Xiōng-nú glosses in Chinese sources (collected by Pulleyblank 1962, criticised and reanalysed by Dybo 2007), complemented by the interpretation of the so-called Jié couplet, the only short text preserved in the Xiōng-nú language,2 have led to a more promising alternative hypothesis. This hypothesis acknowledges both the multi-ethnic composition of the Xiōng-nú empire as such and the presence of Indo-European and specifically Iranian languages in Inner Asia at the beginning of the common era, yet adds to the complexity the idea that the native language of the ruling dynasty of the Xiōng-nú empire might have been a Yeniseian one (Ligeti 1950; Pulleyblank 1962; Dul'zon 1966; Dul'zon 1968; Vovin 2000; Vovin 2003; Vovin 2007; Werner 2014; Vovin 2020). Yeniseian languages are usually considered remnants or survivors of the original linguistic diversity of Siberia, historically spoken in retreat areas as the result of several waves of superimposition or displacement by expanding Uralic/Samoyedic, Turkic and Tungusic languages. Therefore, Yeniseian languages are also known as Paleo-Siberian languages.3 Several different Yeniseian languages were spoken in the 18th century AD alongside the middle reaches of the Yenisei River and some of its tributaries, yet this probably reflects a northward migration from a point of departure further south, around the headwaters of the Yenisey, the Ob and the Irtyš rivers (see Dul'zon 1959a; Dul'zon 1959b; Dul'zon 1964; Maloletko 1992; Maloletko 2000; Vajda 2019: 194–95; cf. also Janhunen 2020: 167). From the six historically attested Yeniseian languages Ket, Yugh, Kott, Assan, Arin and Pumpokol, it has so far been suggested that Ket/Yugh (Ligeti 1950; Pulleyblank 1962) or Pumpokol (Vovin 2000, 2003, 2007, 2020; Vovin et al. 2016) may have been the native language of the Xiōng-nú ruling dynasty.

Adding value to this hypothesis is the fact that the northward migration of Yeniseian-speaking groups, as reflected in toponyms, from the Altai-Sayan area would well agree with detailed historical studies considering Indic, Iranian and Chinese written sources (de la Vaissière 2005; de la Vaissière 2014). These studies indicate that, following the eventual demise of their steppe empire, remnants of the Xiōng-nú migrated to the north of the Altai-Sayan Mountain ranges in the mid-2nd century AD and that this retreat area was the starting point of a secondary expansion of Xiōng-nú descendants roughly two hundred years later, between ca. 350–370 AD. This expansion occurred in three directions: One migratory trajectory led northward and left traces in the form of toponyms. This population movement downstream of the major rivers Yenisey, Ob and Irtyš perfectly explains the linguistic situation as documented for the first time in the 18th century and provides a direct link between Yeniseian languages and the Xiōng-nú. Another migratory route led to southern Asia and involved groups known from Iranian and Indic sources as Chionites, Kidarites, Hephthalites, Alchons as well as the so-called Huṇa (cf. Pfisterer 2013). A third migratory trajectory led westward, into Europe and involved the Huns who appeared in Eastern Europe in 370 and posed a threat to Roman hegemony until Attila's death in 453, the Battle of Nedao shortly afterwards and the ensuing disintegration of their confederation (cf. e.g. Heather 1996; Bóna 2002; Halsall 2007; Schmauder 2009; Maas 2014; Pohl 2022).

Several nomadic groups of late Antiquity that originated in Inner Asia and migrated to the southern and western peripheries of the Eurasian landmass apparently used the same ethnonymic constituent (Chion-ites – Al-chon – Huṇa – Huns; cf. de la Vaissière 2005; de la Vaissière 2014, but see Atwood 2012), and the traditional hypothesis of a link between the ethnic core of the European Huns of the 4th–5th centuries AD and the Inner Asian Xiōng-nú of the 3rd century BC–2nd century AD, first proposed by the French scholar Joseph de Guignes in the 18th century, has, strictly speaking, never been falsified (de la Vaissière 2005: 15). 

A genetic connection between the Xiōng-nú and the Huns is usually considered unlikely in modern archaeological and historical scholarship (e.g. Beckwith 2009: 72; Savelyev & Jeong 2020; Pohl 2022; Maenchen-Helfen 1944–1945; Maenchen-Helfen 1955; Maenchen-Helfen 1973; Schmauder 2009), partly because of the large chronological gap between the dissolution of the Xiōng-nú empire in the 2nd century AD and the appearance of the Huns in the 4th century AD, and partly because only two archaeological features render a connection likely: large bronze cauldrons of a certain type and artificially deformed or elongated skulls (Pohl 2022: 147).

Despite the prevailing scepticism of historians and archaeologists, the hypothesis of a connection between the Xiōng-nú and the Huns has been corroborated recently by previously unknown and unavailable genetic data analysed by Gnecchi-Ruscone et al. (2025): ‘(…) long-shared genomic tracts provide compelling evidence of genetic lineages directly connecting some individuals of the highest Xiongnu-period elite with 5th to 6th century AD Carpathian Basin individuals, showing that some European Huns descended from them’. 

On the provision that there was indeed some continuation between the ethnic core of the European Huns and the former Xiōng-nú, the ruling classes of both multi-ethnic confederations may have spoken the same language in two different diachronic stages (an older form and a younger one), implying that the identification of the linguistic affiliation of one of these groups probably also means identifying the native language of the other group. 

In the following, we will discuss previously unknown linguistic evidence from four domains independently supporting such a connection and thus corroborating the recent archaeological and genetic findings: (1) loanwords, (2) glosses, (3) anthroponyms and (4) toponyms/hydronyms.

This analysis, which moves the Turkic and Tungistic migrations several centuries later in history than previously believed, is also relevant to the Altaic linguistic hypothesis and our understanding of these ethnic mass migrations more generally.

Close in time and space: Slavic ethnogenesis

The Slavic people emerged around the same time as the fall of the Roman Empire and the demise of the short lived Hunnic Kingdom in the Balkans, but before the Magyar conquest of what is now called Hungary and before the appearance of Gypsies in Europe. This period was traditionally called the "Dark Ages" in Europe. There are some historical roots, however, which suggest Slavic origins several centuries earlier (from the Wikipedia link at the start of this paragraph):

Ancient Roman sources refer to the Early Slavic peoples as "Veneti", who dwelt in a region of central Europe east of the Germanic tribe of Suebi and west of the Iranian Sarmatians in the 1st and 2nd centuries AD, between the upper Vistula and Dnieper rivers. Slavs – called Antes and Sclaveni – first appear in Byzantine records in the early 6th century AD. Byzantine historiographers of the era of the emperor Justinian I (r. 527–565), such as Procopius of Caesarea, Jordanes and Theophylact Simocatta, describe tribes of these names emerging from the area of the Carpathian Mountains, the lower Danube and the Black Sea to invade the Danubian provinces of the Eastern Empire.

Jordanes, in his work Getica (written in 551 AD), describes the Veneti as a "populous nation" whose dwellings begin at the sources of the Vistula and occupy "a great expanse of land". He also describes the Veneti as the ancestors of Antes and Slaveni, two early Slavic tribes, who appeared on the Byzantine frontier in the early-6th century.

Procopius wrote in 545 that "the Sclaveni and the Antae actually had a single name in the remote past; for they were both called Sporoi in olden times". The name Sporoi derives from Greek σπείρω ("to sow"). He described them as barbarians, who lived under democracy and believed in one god, "the maker of lightning" (Perun), to whom they made sacrifice. They lived in scattered housing and constantly changed settlement. In war, they were mainly foot soldiers with shields, spears, bows, and little armour, which was reserved mainly for chiefs and their inner circle of warriors. Their language is "barbarous" (that is, not Greek), and the two tribes are alike in appearance, being tall and robust, "while their bodies and hair are neither very fair or blond, nor indeed do they incline entirely to the dark type, but they are all slightly ruddy in color. And they live a hard life, giving no heed to bodily comforts..."

Jordanes describes the Sclaveni as having swamps and forests for their cities. Another 6th-century source refers to them living among nearly-impenetrable forests, rivers, lakes, and marshes.

Menander Protector mentions Daurentius (r. c. 577 – 579) who slew an Avar envoy of Khagan Bayan I for asking the Slavs to accept the suzerainty of the Avars; Daurentius declined and is reported as saying: "Others do not conquer our land, we conquer theirs – so it shall always be for us as long as there are wars and weapons".

The Slavic languages are a relatively recent offshoot of the Indo-European Baltic languages, which in turn may be the most direct descendants of the language(s) of the Corded Ware culture (ca. 3000 BCE to 2350 BCE).

Eurogenes reports on new ancient DNA driven discoveries drawn from the earliest ancient Slavic DNA at his blog.

A paper dealing with the origin of Slavic speakers, titled Ancient DNA connects large-scale migration with the spread of Slavs, was just published at Nature by Gretzinger et al. (see here).

The dataset from the paper includes ten fascinating ancient samples from Gródek upon the Bug River in Southeastern Poland. These individuals are dated to the so called Tribal Period (8th – 9th centuries), and, as far as I know, they represent the earliest Slavic speakers in the ancient DNA record.

The really interesting thing about these early Slavs is that they already show some Germanic and other Western European-related ancestries. Nine of the samples made it into my G25 analysis (see here). In the Principal Component Analysis (PCA) plots . . . five of them cluster near present-day Ukrainians, while the rest are shifted towards present-day Northwestern and Western Europeans. . . .  GRK015, a female belonging to Western European-specific mtDNA haplogroup H1c, shows Scandinavian ancestry. On the other hand, GRK014, a female belonging to the West Asian-specific mtDNA haplogroup U3b, probably has Southern European ancestry.

These results aren't exactly shocking, because the people who preceded the early Slavs in the Gródek region were Scandinavian-like and associated with the Wielbark archeological culture. In other words, they were probably Goths who also had significant contacts with the Roman Empire.

However, it's not a given that the ancestors of the Tribal Period Slavs mixed with local Goths. It's also possible that they brought the western admixture, or at least some of it, from the Slavic homeland, wherever that may have been.

That's because the early Slavs who migrated deep into what is now Russia also showed Western European-related admixture. This is what Gretzinger et al. say on page 74 of their supplementary info (emphasis is mine):

The only deviation from this pattern is observed for ancient samples from the Russian Volga-Oka region, where we measure higher genetic affinity between present-day Southern/Western Europeans and the SP population compared to the pre-SP population (Fig. S17). This agrees with the pattern observed in PCA and ADMIXTURE that, in contrast to the Northwestern Balkan, Eastern Germany, and Poland-Northwestern Ukraine, the arrival of Slavic-associated culture in Northwestern Russia was associated with a shift in PCA space to the West, a decrease of BAL [Baltic] ancestry, and the introduction of Western European ancestries such as CNE [Continental North European] and CWE [Continental Western European].

Thus, it's highly plausible that the Tribal Period Slavs from Gródek were very similar, perhaps even practically identical, to the proto-Slavs who lived in the original Slavic homeland. Hopefully we won't have to wait too long to discover whether that's true or not. More Migration period and Slavic period samples from the border regions of Belarus, Poland and Ukraine are needed to sort that out.

Eurogenes goes on to criticize a suggestion in the supplemental materials to the Slavic ancient DNA paper that suggests that 

Sycthian groups from Ukraine show varying fractions of South Asian ancestry (between 5% and 12%), a component present in many ancient individuals from Moldova, Ukraine, Western Russia, and the Caucasus, but (nearly) absent in the SP genomes from Central and East-Central Europe (<5%). [Ed. references to specific samples showing this omitted.]

Eurogenes, rightly, explains that the data are really showing European introgression into South Asia arising from the Indo-Aryan invasion of the region in the Bronze Age, and before that from Iran.