The Linguistic Golden Age

The most notable findings of the study are that the number of languages in the world was already starting to decline five hundred years before the Columbian exchange and the Renaissance, and that small pre-agricultural populations placed an effective limit on the number of languages spoken in the pre-Holocene era. The peak number of languages was on the order of 10,000 to 35,000 according to the study under various model assumptions.

A linguistic “golden age” flourished between 1,000 to 3,000 years ago when tens of thousands of languages were spoken throughout the world, according to a new study coauthored by Yale linguist Claire Bowern that traces trajectories in global language diversity over the past 12,000 years.

The golden age was followed by a period of rapid decline in linguistic diversity that coincided with the rise of large states and multinational empires, such as the Roman Empire, the researchers found. The finding challenges a commonly held view that widespread language extinction began later, about 500 years ago, with the onset of European colonial expansion.

The languages of expanding states and empires were disproportionately likely to survive while those of absorbed, displaced, or declining populations disappeared, the researchers concluded. This means that the roughly 7,600 languages spoken or signed today represent a small and historically biased sample of the languages that once existed, which has important implications for the study of global patterns in language and culture, they said. . . .

The study, which was published July 23 in the journal Science, is the result of a long international collaboration between experts in language, demography, and evolutionary biology. . . .

Direct evidence of languages doesn’t exist before the appearance of writing about 6,000 years ago. So for the study, the researchers combined ethnographic information, estimates of prehistoric population size, and statistical and social-computational modelling to estimate linguistic diversity over the course of the Holocene — the current geological epoch that began about 12,000 years ago.

To gauge the likely distribution and sizes of populations before the advent of agriculture, the researchers used ethnographic data from 171 hunter-gatherer and fisher societies whose traditional subsistence and mobility had not been profoundly transformed by contact with food-producing populations. They combined these estimates with independent analyses suggesting that the global human population 12,000 years ago was between approximately 4.4 and 7 million. Assuming that the number of languages in the early Holocene corresponded with the number of distinct groups that the total human population could accommodate at the time, between 4,500 and 6,200 languages were spoken 12,000 years ago, the study’s models estimated.

The world immediately before agriculture was probably not exceptionally rich in languages,” said lead author Damián Blasi, an ICREA (Catalan Institution for Research and Advanced Studies) research professor based at the Center for Brain & Cognition at the Pompeu Fabra University in Barcelona, Spain. “There were most likely fewer languages than there are today. Linguistic diversity then grew alongside the human population for thousands of years.”

To capture fluctuations in linguistic diversity as populations expanded dramatically following the onset of agriculture and technological innovation and then contracted through wars, plagues, and other ecological factors, the researchers modelled thousands of possible trajectories connecting language estimates at the beginning of the Holocene with the present.

The models consistently produced patterns indicating that language diversity peaked between 1,000 and 3,000 years ago when upwards of tens of thousands of languages were being spoken worldwide, this period that the researchers call the world’s linguistic “golden age.”

That golden age ended with the rise of states and multinational empires as the dominant groups spread their languages, cultures, and pathogens to previously independent populations, the study shows. European colonialism intensified the steep decline in linguistic diversity, but did not cause it, according to the study.

The loss of so much linguistic diversity over the course of two millennia affected the development of today’s languages, the researchers said.

“The languages we see today are the survivors of a massive and highly selective historical bottleneck,” said study coauthor Russell Gray, director of the Department of Linguistic and Cultural Evolution at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. “A linguistic feature may be common not because it is inherently efficient or better for communication, but because it happened to be carried by populations that expanded. Extinction may have shaped linguistic diversity much more profoundly than we previously appreciated.”

"Study uncovers lost ‘golden age’ of languages: A new study coauthored by Yale linguist Claire Bowern suggests that tens of thousands of languages were spoken between 1,000 and 3,000 years ago." via a Yale University press release.

Conventional linguistic reconstruction methods struggle to reconstruction linguistic pre-history much before 4,000 to 8,000 years ago.

The 7,600 languages spoken today is rapidly falling (according to Ethnologue, there are approximately 7,159 known languages spoken around the world today). A very large share of all languages spoken today have a small number of speakers or are moribund and on the brink of extinction in the next couple of generations or sooner. 

The general consensus is that between 6,000 and 7,000 languages are currently spoken. Some linguists estimate that between 50% and 90% of them will be severely endangered or dead by the year 2100. The 20 most common languages, each with more than 50 million speakers, are spoken by 50% of the world's population, but most languages are spoken by fewer than 10,000 people. . . . More than 50% of the world's endangered languages are located in just eight countries: India, Brazil, Mexico, Australia, Indonesia, Nigeria, Papua New Guinea and Cameroon.

From Wikipedia. About 107 languages are spoken by 7 million people or more and about 200 languages are spoken by a million people or more. A list of the number of languages per country can be found here. 

Roughly 40% of languages have less than 1,000 speakers (that's a total of 3,193 endangered languages) spoken collectively by much less than 3 million people out of 8.3 billion people in the world. About 10 million people speak a language that is spoken by 10,000 or fewer people. About 46 languages have only a single speaker. The Ainu language of Japan has 10 speaker. The median Australian Aboriginal language has 10 speakers. The median Native American language in the U.S. has 12 speakers. The median Brazilian indigenous language has 210 speakers. The median Papuan language has 1,315 speakers. The median Indonesian language has 3,500 speakers. The median Mexican indigenous language has 4,730 speakers. The median languages spoken in Cameroon has 10,000 speakers. The median language in Nigeria has 14,000 speakers. The median language in India has 35,000 speakers. 

Reviving an extinct or endangered or purely liturgical language is not impossible but is very difficult and there have been only about twenty moderately successful attempts to do so. The most successful effort has been the Hebrew language.

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).

Red River

Red River (Japanese: 天は赤い河のほとり, Hepburn: Sora wa Akai Kawa no Hotori; lit. 'The Sky Is on the Banks of the Red River'), also known as Anatolia Story, is a Japanese manga series written and illustrated by Chie Shinohara. The series was published by Shōgakukan in their Sho-Comi magazine from January 1995 to June 2002 and was collected in 28 tankōbon volumes. It is published in English in North America by Viz Media. An anime television series adaptation produced by Tatsunoko Production is set to premiere in July 2026. 

As of March 2019, the manga had over 20 million copies in circulation, making it one of the best-selling manga series. In 2001, Red River won the Shogakukan Manga Award for the shōjo category.

From Wikipedia.

The river after which the series was named, the "Kızılırmak (Turkish pronunciation: [kɯˈzɯɫɯɾmak], Turkish for "Red River"), historically known as the Halys River (Ancient Greek: Ἅλυς), is the longest river flowing entirely within Turkey.

I read this manga series when my children were in middle school, basically in the early twenty-tens, not long after I began this blog, as one of the first really epic manga series that I'd read. American comics and graphic novels have almost no sub-genre that approximates this series. 

It is back on my radar screen because the first episode of an anime based upon this manga series was released today, and so far, so good. It is a pretty faithful and successful adaptation so far.

Why am I writing about it here?

Because this manga series was instrumental in spurring my interest in prehistory, anthropology, and historical linguistics, in a story that brought the late Bronze Age Hittite Empire to life and contributed a lot to me caring about all of these fields. Some of my own writing on the Hittites can be found here.

And honestly, while it has fictional and magical elements, much like Bronze Age legendary history works actually written at or within a few centuries of that time period, by and large, this series has stood the test of time and is broadly consistent with what archaeologists, anthropologists, ancient historians, and historical linguistics scholars still believe now.

What all of those disciplines lack, however, that historical fiction like this can provide, is synthesis, relatability, and meaning. Academic scholars tend to focus in on tiny details and cower from providing a larger narrative or connecting the dots for fear of being wrong. But doing so takes away the joy and allure of that once captivated the people who are doing the work and keeps them motivated enough to continue to do so. Historical fiction can give the dry piecemeal reconstructions life and a "vibe" allowing you to feel some sense of what life was like back then.

The fictional account does so in ways big and small. For example, while the dialog is in Japanese (and translated into English in the versions I consume), this series retains enough of the historically accurate Hittite proper names to make those names relatable and not so intimidating, when you encounter them as you study the actual history of the Hittite people, a culture the remains the source of pivotal and important open questions in the broader picture of the Bronze Age and Indo-European linguistics.

Even the magical and supernatural and religious aspects of the story, while not actually things that happened in the past, are largely consistent with the religious and metaphysical worldviews of the people who lived in that era in Anatolia.

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.

Cracking Linear Elamite

Four years ago, French archaeologist François Desset reportedly cracked the 4,000 year old Linear Elamite script, "[m]ade up of 77 signs – diamonds, curves, and other geometric patterns – the writing system comes from the Bronze Age civilisation of Elam" in Southwest Iran that collapsed long ago. The script was rediscovered in 1903, but has eluded decipherment until now. 

Elam is shown in red.

The Elamite language has partially been known long before this breakthrough from inscriptions of the language made in an Elamite cuneiform script, which was adapted from Akkadian cuneiform. This language was still spoken in the first century CE, and probably went extinct around the eleventh century CE. Most linguists consider it to be a language isolate (and in my review of this literature, I have not found that Elamo-Dravidian hypothesis to be a credible one).

Elamite is regarded by the vast majority of linguists as a language isolate,[31][32] as it has no demonstrable relationship to the neighbouring Semitic languages, Indo-European languages, or to Sumerian, despite having adopted the Sumerian-Akkadian cuneiform script.

An Elamo-Dravidian family connecting Elamite with the Brahui language of Pakistan and Dravidian languages of India was suggested in 1967 by Igor M. Diakonoff[33] and later, in 1974, defended by David McAlpin and others.[34][35] In 2012, Southworth proposed that Elamite forms the "Zagrosian family" along with Brahui and, further down the cladogram, the remaining Dravidian languages; this family would have originated in Southwest Asia (southern Iran) and was widely distributed in South Asia and parts of eastern West Asia before the Indo-Aryan migration.[36] Recent discoveries regarding early population migration based on ancient DNA analysis have revived interest in the possible connection between proto-Elamite and proto-Dravidian.[37][38][39][40] A critical reassessment of the Elamo-Dravidian hypothesis has been published by Filippo Pedron in 2023.[41]

Václav Blažek proposed a relation with the Semitic languages.[42]

In 2002 George Starostin published a lexicostatistic analysis finding Elamite to be approximately equidistant from Nostratic and Semitic.[43]

None of these ideas have been accepted by mainstream historical linguists.[31]

Desset accomplished this primarily by using proper names to decode the meaning of those signs and applying that method to ten new Linear Elamite texts inscribed on vases, according an April 28, 2026 story from France 24. This story of breakthrough is also reported in National Geographic, January 2026, pp. 110-131, entitled, "Decoding the Lost Scripts of the Ancient World", by Joshua Hammer. Hat top to Language Log. The Smithsonian magazine also has a recent article on the topic. It isn't entirely clear to me why this development is making headlines now, four years after the leading article on the topic was published (which I blogged at the time, see also an earlier post on a related topic).

Wikipedia (at the link above) explains that:

In 2022, Desset et al. (2022) argued that Linear Elamite is an alpha-syllabary, which would make it the oldest known purely phonographic writing system.[5] However, they admit that some logograms may have been used, although only rarely and not systematically, arguing that Elamite scribes rejected logographic writing in the 3rd millennium BCE.[30] Other researchers, such as the linguist Michael Mäder, dispute this, arguing that only around 70 percent of Linear Elamite characters are likely to be purely phonographic and that the remainder are logograms, as evidenced by mathematical analyses of Linear Elamite inscriptions.[3][31]

His 2022 article is the capstone of the project. Its abstract states:

Linear Elamite writing was used in southern Iran in the late 3rd/early 2nd millennium BCE (ca. 2300–1880 BCE). First discovered during the French excavations at Susa from 1903 onwards, it has so far resisted decipherment. The publication of eight inscribed silver beakers in 2018 provided the materials and the starting point for a new attempt; its results are presented in this paper. A full description and analysis of Linear Elamite of writing, employed for recording the Elamite language, is given here for the first time, together with a discussion of Elamite phonology and the biscriptualism that characterizes this language in its earliest documented phase.

Desset's main publications on the subject are as follows: 

Desset, François (2018a). "Linear Elamite Writing". In Álvarez-Mon, Javier; Basello, Gian Pietro; Wicks, Yasmina (eds.). The Elamite World. Abingdon, Oxon: Routledge. pp. 397–415. ISBN 978-1-315-65803-2.

Desset, François (2018b). "Nine Linear Elamite Texts Inscribed on Silver "Gunagi" Vessels (X, Y, Z, F', H', I', J', K' and L'): New Data on Linear Elamite Writing and the History of the Sukkalmaḫ Dynasty". Iran. 56 (2): 105–143. doi:10.1080/05786967.2018.1471861. S2CID 193057655.

Desset, François (2020a). "Breaking the Code: The Decipherment of Linear Elamite, a Forgotten Writing System of Ancient Iran (3rd Millenium BC)". Canal-U.

Desset, François (2020b). A New History of Writing on The Iranian Plateau – via YouTube.

Desset, François (1 September 2021). "On The Decipherment of Linear Elamite Writing". The Postil (Interview). Interviewed by Robert M. Kerr.

Desset, François; Tabibzadeh, Kambiz; Kervran, Matthieu; Basello, Gian Pietro; Marchesi, Gianni (2022). "The Decipherment of Linear Elamite Writing". Zeitschrift für Assyriologie und vorderasiatische Archäologie. 112 (1): 11–60. doi:10.1515/za-2022-0003. ISSN 0084-5299. S2CID 250118314.

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).

Astronomy Meets Climate

A 100,000 year climate cycle on Earth can be explained by Earth's orbit.

The 100,000-year problem concerns the dominant period of glacial-interglacial cycles over the past 800,000 years and their correlation with Earth's orbital eccentricity, despite eccentricity's weak influence on solar radiation. 

Two theories compete: the astronomical theory, in which orbital forcing drives the cycles with amplification from Earth system feedbacks, and the geochemical theory, in which internal dynamics dominate with orbital forcing synchronising oscillations. We investigate these theories using conceptual models. 

Augmentations to the Budyko energy balance model fail to reproduce the 100,000-year period, revealing formulation limitations. Linearised versions of existing non-linear ice volume models perform comparably to their full counterparts, indicating the data does not necessitate non-linear dynamics. We develop two simple linear models: a feedforward model aligned with the astronomical theory and a feedback model aligned with the geochemical theory. 

The feedforward model reproduces the ice volume record well and offers a novel explanation for the absence of eccentricity's 400,000-year period, arising from oceanic heat storage and tropospheric energy responding with differing phase lags. Conservative estimates show bulk ocean temperature variation can be explained by eccentricity alone, challenging the geochemical theory's core assumption. 

We also show that widespread use of Q65 may bias models towards geochemical explanations by underrepresenting eccentricity. The feedback model's improvement is concentrated around Marine Isotope Stage 11, suggesting this anomalous interglacial reflects Earth-based events rather than a general requirement for feedback mechanisms. We conclude that 800,000 years of glacial cycles can be largely reproduced by a linear astronomical model, emphasising the importance of parsimony when interpreting palaeoclimate data.

Liam Wheen, "A First Principles Approach to the 100,000-year Problem" arXiv:2604.12143 (April 14, 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.