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. 

Ethnic Segregation In 8th Century Austria

The Avars from Asia Steppes and European farmers co-existed in segregated communities in the early Middle Ages in Austria for at least six generations.

Researchers carried out an archeogenetic study of human remains from more than 700 individuals from the Early Middle Ages. Two large burial sites, Modling and Leobersdorf, have been genetically analyzed in their entirety. The surprising result was that the individuals from Leobersdorf were mostly of East Asian origin, while those buried in Modling mostly had European ancestry. Both communities lived next to each other for at least six generations. . . . 

[The result] emerged from a genetic study of burial grounds from the Avar period in the 8th century CE. The Avars had arrived in the 6th century from the East Asian Steppes and settled in East Central Europe among a mixed population.

From Science Direct. The article quoted above is based upon the academic paper whose abstract and citation are provided below:

After a long-distance migration, Avars with Eastern Asian ancestry arrived in Eastern Central Europe in 567 to 568 CE and encountered groups with very different European ancestry. 

We used ancient genome-wide data of 722 individuals and fine-grained interdisciplinary analysis of large seventh- to eighth-century ce neighbouring cemeteries south of Vienna (Austria) to address the centuries-long impact of this encounter. We found that even 200 years after immigration, the ancestry at one site (Leobersdorf) remained dominantly East Asian-like, whereas the other site (Mödling) shows local, European-like ancestry. These two nearby sites show little biological relatedness, despite sharing a distinctive late-Avar culture. 

We reconstructed six-generation pedigrees at both sites including up to 450 closely related individuals, allowing per-generation demographic profiling of the communities. Despite different ancestry, these pedigrees together with large networks of distant relatedness show absence of consanguinity, patrilineal pattern with female exogamy, multiple reproductive partnerships (for example, levirate) and direct correlation of biological connectivity with archaeological markers of social status. The generation-long genetic barrier was maintained by systematically choosing partners with similar ancestry from other sites in the Avar realm. Leobersdorf had more biological connections with the Avar heartlands than with Mödling, which is instead linked to another site from the Vienna Basin with European-like ancestry. Mobility between sites was mostly due to female exogamy pointing to different marriage networks as the main driver of the maintenance of the genetic barrier.

Ke Wang, et al., "Ancient DNA reveals reproductive barrier despite shared Avar-period culture." Nature (January 15, 2025) DOI: 10.1038/s41586-024-08418-5 (open access).

Ancient DNA From Siberia As A Source For Modern Populations

Different strains of Siberian ancestry spread east to the New World and west to Scandinavia.

Human populations across a vast area in northern Eurasia, from Fennoscandia to Chukotka, share a distinct genetic component often referred to as the Siberian ancestry. Most enriched in present-day Samoyedic-speaking populations such as Nganasans, its origins and history still remain elusive despite the growing list of ancient and present-day genomes from Siberia. 

Here, we reanalyze published ancient and present-day Siberian genomes focusing on the Baikal and Yakutia, resolving key questions regarding their genetic history. First, we show a long-term presence of a unique genetic profile in southern Siberia, up to 6,000 yr ago, which distinctly shares a deep ancestral connection with Native Americans. Second, we provide plausible historical models tracing genetic changes in West Baikal and Yakutia in fine resolution. Third, the Middle Neolithic individual from Yakutia, belonging to the Belkachi culture, serves as the best source so far available for the spread of the Siberian ancestry into Fennoscandia and Greenland. These findings shed light on the genetic legacy of the Siberian ancestry and provide insights into the complex interplay between different populations in northern Eurasia throughout history.

Haechan Gill, Juhyeon Lee, Choongwon Jeon, "Reconstructing the Genetic Relationship between Ancient and Present-Day Siberian Populations" 16(4) Genome Biology and Evolution evae063 (March 25, 2024) https://doi.org/10.1093/gbe/evae063

East Asian Historical Population Genetics Reviewed

A December 3, 2024 (open access) monograph published by the Cambridge University Press comprehensively reviews the historical population genetics of East Asia and its vicinity, with associated linguistic and cultural implications. It is one volume in a larger series about Ancient East Asia.

I'll discuss and analyze this wide ranging 90 page review article as time allows in the future. 

Hat tip to Language Log.

Uralic And Yeniseian Origins

New ancient DNA data informs both that origins of the Siberian Yeniseian peoples, the Native American populations of North America, and the Uralic people. 

In Siberia, two genetically distinct populations emerged from admixture between the early Northeastern Siberian population that was a major source of Native American ancestry, and "groups from Inland East Asia and the Amur River Basin."

One of these populations, the Cis-Baikal Late Neolithic–Bronze Age, was ancestral to the Yeniseian peoples of Siberia, who in turn admixed with some other Northeast Asian and North Central Asia populations.

The other of these populations, the Yakutian Late Neolithic–Bronze Age, was the proto-Uralic population. They spread from an east Siberian origin ca. 2500 BCE, along with subclades of Y-chromosome haplogroup N occurring at high frequencies among present-day Uralic speakers, into Western and Central Siberia in communities associated with Seima-Turbino metallurgy, a suite of advanced bronze casting techniques that starteds to expand rapidly ca. 2000 BCE. As they expanded they admixed with many other people in the region, including Indo-Iranians and various hunter-gather peoples.

The North Eurasian forest and forest-steppe zones have sustained millennia of sociocultural connections among northern peoples. We present genome-wide ancient DNA data for 181 individuals from this region spanning the Mesolithic, Neolithic and Bronze Age. 

We find that Early to Mid-Holocene hunter-gatherer populations from across the southern forest and forest-steppes of Northern Eurasia can be characterized by a continuous gradient of ancestry that remained stable for millennia, ranging from fully West Eurasian in the Baltic region to fully East Asian in the Transbaikal region. 

In contrast, cotemporaneous groups in far Northeast Siberia were genetically distinct, retaining high levels of continuity from a population that was the primary source of ancestry for Native Americans. By the mid-Holocene, admixture between this early Northeastern Siberian population and groups from Inland East Asia and the Amur River Basin produced two distinctive populations in eastern Siberia that played an important role in the genetic formation of later people. 

Ancestry from the first population, Cis-Baikal Late Neolithic–Bronze Age (Cisbaikal_LNBA), is found substantially only among Yeniseian-speaking groups and those known to have admixed with them.

Ancestry from the second, Yakutian Late Neolithic–Bronze Age (Yakutia_LNBA), is strongly associated with present-day Uralic speakers. We show how Yakutia_LNBA ancestry spread from an east Siberian origin ∼4.5kya, along with subclades of Y-chromosome haplogroup N occurring at high frequencies among present-day Uralic speakers, into Western and Central Siberia in communities associated with Seima-Turbino metallurgy: a suite of advanced bronze casting techniques that spread explosively across an enormous region of Northern Eurasia ∼4.0kya. However, the ancestry of the 16 Seima-Turbino-period individuals—the first reported from sites with this metallurgy—was otherwise extraordinarily diverse, with partial descent from Indo-Iranian-speaking pastoralists and multiple hunter-gatherer populations from widely separated regions of Eurasia. 

Our results provide support for theories suggesting that early Uralic speakers at the beginning of their westward dispersal where involved in the expansion of Seima-Turbino metallurgical traditions, and suggests that both cultural transmission and migration were important in the spread of Seima-Turbino material culture.

Tian Chen Zeng, et al., "Postglacial genomes from foragers across Northern Eurasia reveal prehistoric mobility associated with the spread of the Uralic and Yeniseian languages" bioRxiv (October 2, 2023).

Yakut Epigenetics

Life in Siberia ages you faster than life in more mild places. Your body also adapts to these conditions at an epigenetic level in these places.

Yakuts are one of the indigenous populations of the subarctic and arctic territories of Siberia characterized by a continental subarctic climate with severe winters, with the regular January average temperature in the regional capital city of Yakutsk dipping below −40°C. 

The epigenetic mechanisms of adaptation to such ecologies and environments and, in particular, epigenetic age acceleration in the local population have not been studied before. This work reports the first epigenetic study of the Yakutian population using whole blood DNA methylation data, supplemented with the comparison to the residents of Central Russia. 

Gene set enrichment analysis revealed, among others, geographic region-specific differentially methylated regions associated with adaptation to climatic conditions (water consumption, digestive system regulation), aging processes (actin filament activity, cell fate), and both of them (channel activity, regulation of steroid and corticosteroid hormone secretion). Further, it is demonstrated that the epigenetic age acceleration of the Yakutian representatives is significantly higher than that of Central Russia counterparts. For both geographic regions, we showed that epigenetically males age faster than females, whereas no significant sex differences were found between the regions.

Alena Kalyakulina, et al., "Epigenetic features of far northern Yakutian population" bioRxiv (July 21, 2023).

https://doi.org/10.1101/2023.07.19.549706

Ethnic Turkish Expansion

Razib Khan has been publishing a three part series on the genetics and human population history of Anatolia on his Unsupervised Learning platform. His latest, on how Anatolia became Turkish is here and opens with the useful summary map below. 

The site is worth subscribing to, if you have the time for it, and the quality is, as usual, first rate: artfully written and informed by Razib's wide historical, linguistic and genetic knowledge. I agree pretty much 100% with the narrative told by the map below.

Turkish invaders ca. 1100 CE (a quite accurate estimate, more specifically, it is historically attested to have happened in 1071 CE) led to language shift in Anatolia, even though genetic estimates are that these invaders account for only perhaps 8%-20% of modern Turkish genetic ancestry (probably closer to the low end of that range). Their expansion was a classic case of expanding herder tribes confronting sedentary farmers.

Turkish expansion predates the Mongolian Empire and postdates by centuries, the Bronze Age. Their expansion was arguably the last of a series of sweeps east to west and west to east across the general region of roughly comprised of the Pontic Caspian steppe, Central Asia and Siberia that persisted. The Mongolian Empire left only a weak trace after it collapsed, but one could arguably call Russian expansion to the east the last sweep.

The Testimony Of 14,000 Year Old Ancient DNA From SW China

In Xiaoming Zhang et al., "A Late Pleistocene human genome from Southwest China" (2022), the authors discuss their analysis of 14,000 year old ancient DNA from a woman at the Red Deer Cave named Mengzi Ren (MZR). (I tip my hat to Bernard's blog and to Razib who together alerted me to this paper.) I previously blogged this find, before ancient DNA analysis was available, on December 18, 2015.

Her "mosaic" of seemingly partially archaic bone features suggested that she might be an archaic hominin-modern human hybrid in Southwest China. 

As was the case with seemingly archaic featured remains in South America that were later genotyped to be ordinary indigenous Americans genetically, the reality was less flashy and was largely paradigm affirming. 

The results disfavor the late persistence of archaic hominins in mainland Asia, and demand a non-genetic explanation for her seemingly archaic features, as she is genetically a typical Southeast and southern East Asian anatomically modern human.

Perhaps the most novel conclusion of the paper is that it substantiates a strong genetic affinity between the Red Deer Cave people of Southwest China ca. 14,000 years ago, and the main founding population of the Americas which broke away from Asia at roughly the same time or a few thousand years earlier.

mtDNA

Her mtDNA was a now extinct basal branch of mtDNA M9, a non-African modern human mtDNA clade, that is fairly closely related to the mtDNA M9 clades that are common in China's interior and central Asia (and to a lesser extent in the rest of China). Her mtDNA deviates by just one mutation from the mtDNA M9 root.

In island Southeast Asia and Vietnam, in contrast, mtDNA E which is also a basal branch of mtDNA M is more common.

Autosomal DNA

She is definitively an anatomically modern human based upon her autosomal DNA, which is close on a PCA chart of overall genetic similarity to Hoabinhian hunter-gatherers who occupied Southeast Asia and adjacent regions in China from sometime in the Upper Paleolithic, a.k.a. Late Pleistocene, era until about 2000 BCE.  

There has been considerable genetic continuity from her to modern populations that were until recently hunter-gathers in the region over the last 14,000 years.

She shows an even greater autosomal genetic affinity to contemporaneous Northeast Asians on the brink of the Bering land bridge and to the oldest Native American ancient genomes, than she does with mainland Southeast Asian Hoabinhians.

Her autosomal DNA reflected most strongly an ancestral DNA component now associated with Southeast Asia with a significant minority of ancestry that was distinctively Northeast Asian, in addition to trace ancestry components that were distinctive African, specifically Native American, European or Papuan (and she has no distinctive South Asian ancestry component).

This indicates that 14,000 years ago, there was already differentiation and population structure between Northeast Asia and mainland Southeast Asia that had formed, and then produced admixed populations again, of which she was a member.

Archaic Hominin Ancestry

Her percentages of Neanderthal (1.27%) and Denisovan (1.29%) autosomal DNA admixture is similar to that other modern humans of that era and does not show enhanced or recent archaic admixture. Her Neanderthal and Denisovan ancestry percentages are broadly similar to modern Asian people from this region today.

This is what the paradigm would expect since there are no really definitive examples of archaic hominins in mainland Southeast Asia or China more recent than about 100,000 years ago. 

Evidence of a Neanderthal presence has never been found east of South Asia in places south of the Altai. 

The History Of Two Asian Genetic Variants

She lacks a derived genetic variant associated with light skin in modern East Asians that an analysis of many ancient and modern DNA samples in the papers concludes arose only in the early Holocene era (i.e. in the last 10,000 years) with the oldest isolated example from 7,500 years ago and some examples in the las 5,000 years and predominance in the last hundred years.

The paper also analyzes the emergence of the derived EDAR variant which is the source of some of the distinctively "Asian" phenotype. This arises many thousands of years earlier than the light skin genetic variant, but apparently the ancient DNA sample from this woman was missing the part of her genome that would have contains the EDAR variant, so we don't know if she had it or not. The oldest example of the derived EDAR variant is from the Amur region in Northeast Asia from about 19,000 years ago (although mutation rate estimates suggest it originated 30,000 years ago), and it is fairly widespread in East Asia, Northeast Asia, and the Americas from 11,600 years ago onward, becoming predominant in Southeast Asia, East Asia, Northeast Asia and the Americas by 4,900 years ago.

Both of these derived genetic variants that are distinguishing features of modern Southeast and East Asians post-dated the Last Glacial Maximum which led to essentially total population replacement in Northern Asia (and preceded any significant modern human population that left lasting traces in the Americas).

The Paper's Analysis

The discussion section of the paper generally sums up these themes and adds some additional cross-disciplinary speculation, most of which is plausible, although the bold underlined conjecture really has no solid support.

Southern East Asia harbors rich archaeo-anthropological sites with rich morphological diversities, including the ∼100 kya Zhiren Cave and ∼120–80 kya Fuyan Cave in southern China (although a recent study suggested much younger dates for these two sites), the ∼190–50 kya H. floresiensis, and the 67 kya H. luzonensis in Southeast Asia.  

Indeed, based on the published mitochondrial genome data, the matrilineal lineage diversity of the Late Pleistocene hominins in eastern Eurasia is quite high, including the reported Ust’-Ishim (45.0 kya, novel N∗), Salkhit (34.0 kya, independent novel N∗), Tianyuan (40.0 kya, basal B∗), Yana-old (32.0 kya, U), MA-1 (24.3 kya, novel U∗), LLR (11.0 kya, M27d), and MZR (14.0 kya, basal M9∗) in this study, many of which were lost during the post Pleistocene (<11.7 kya) human evolutionary histories. 

In addition, the hominin fossils from these archaeological sites, such as MZR and LLR, all exhibit rich physical anthropological diversities, some of which were thought to overlap with the morphological characteristics of archaic hominins and triggered proposals of different scenarios of human evolution in this area.

In this study, we provide compelling evidence that the Late Pleistocene MZR from Malu Dong in Southwest China is an AMH. The nuclear genome data indicate that MZR represents an early diversified AMH lineage in East Asia. The mtDNA of MZR belongs to one of the root matrilineal lineages of AMHs in southern East Asia. Identified as a novel basal M9 lineage, MZR may represent one of the extinct pioneer hunter-gatherers ancestral to millet and rice farmers in China who emerged in the Yellow River and Yangtze River valley during the Early Neolithic period. Additionally, we observe obvious stratification and substructure of ancient human populations between southern China and mainland Southeast Asia, an indication of already diversified genetic backgrounds of the Late Pleistocene populations in southern East Asia. . . .

It should be noted that the MZR morphological data are indeed informative in reconstructing human morphological diversity during the Late Pleistocene in southern East Asia. However, due to the limited human remains as well as the limited number of morphological traits, it would be hard to confidently reveal the identity of the studied subject. To this end, genome sequence data are critical for unequivocal species identification, quantification of genetic introgression, and reconstruction of population history.

Spatiotemporal tracing of mutations related to phenotypic changes in human populations can help reconstruct the prehistoric patterns of how natural selection has shaped these adaptive events. We observed that the OCA2-HiS615Arg (rs1800414) variant, a key adaptive mutation causing skin lightening in East Asians, initially emerged in the southern coastal region of China during the early Neolithic (Liangdao2-7.5kya). The rapid dispersal of this variant during the past 4,000 years in East Asia is consistent with the proposed Darwinian positive selection on the adaptive allele (OCA2-615Arg), leading to skin lightening in East Asians to cope with the relatively low UV radiation in high-latitude areas. Interestingly, the rapid explosion of OCA2-615Arg coincides with the known major population expansion in China during the Late Holocene epoch. It should be noted that due to the limited aDNA data in East Asia, the inferred time of selection onset for OCA2-HiS615Arg is a rough estimation. With more aDNA data available in the future, we expect more accurate time estimation and high-resolution spatial-temporal tracking of adaptive genetic variants in East Asia.

Consistent with the dating of MZR (14.0 kya), following the end of the LGM (26.5–19.0 kya) and the earliest securely dated sites in Beringia (15–14 kya), we demonstrate that MZR has a higher affinity to First Americans than to Tianyuan (40 kya) and all the pre-LGM Late Pleistocene Siberians. MZR, Amur-19K, and UKY are cladal with respect to First Americans, while Amur-14kya and UKY exhibit a higher affinity to the Americans compared to MZR. Thus, MZR is linked deeply and indirectly to the ancestry that contributed to First Americans. We speculate that during the Late Pleistocene, there was an express northward expansion of AMHs starting in southern East Asia through the coastal line of China, possibly by way of the Japanese Islands, and eventually crossing the Bering Strait and reaching the Americas. However, the scenario that MZR shows a higher affinity to Americans compared to Jomon likely reflects that the 2.6 kya Jomon population does not represent the early post-LGM humans who settled in the Japanese archipelago. 

The proposed migratory route along the east coast of East Asia by way of the Japanese Islands is supported by a recent finding of a Paleolithic site (∼16 kya) at Cooper’s Ferry of western Idaho, USA, where they found the use of unfluted stemmed projectile point technologies before the appearance of the Clovis Paleoindian tradition. Notably, it exhibits early cultural connections with Paleolithic nonfluted projectile point traditions in Japan. The bifacial point and backed blade technologies (∼22–16 kya) in Honshu, Japan, lend technological correlates to the shared ecological and geographical factors with the Americas.

This scenario is also supported by the current distribution pattern of the ancient Y-chromosome lineage Hg C in coastal East Asia, Siberia, and North America. Approximately 40 kya, stemming from southern East Asia, the Hg C carriers started a northward expansion along the coastal regions of mainland China, the Korean Peninsula, and the Japanese archipelago, reaching Siberia ∼15 kya, and finally made their way to the Americas.  

In addition, unlike all other East Asian populations, the indigenous Ainu people in northern Japan and Sakhalin Island, Russia, show a closer genetic affinity with northeastern Siberians than with central Siberians. Hence, the Japanese Islands may serve as the midway station along the proposed migratory route, and aDNA data of Late Pleistocene human remains from Japan will be highly informative in testing the proposed coastal route. 

Finally, the spatial-temporal distribution of the East Asian-specific EDAR-V370A variant, as well as its early presence in the LosRieles-12.0kya sample from coastal Chile of South America, supported a clear contribution of the Late Pleistocene East Asians to the first Americans.

In summary, we generated ancient genome sequences of MZR, a Late Pleistocene female who lived in Southwest China, one of the global biodiversity hotspots and the ice age refuge region. The aDNA data confirm that she possesses diverse genetic components and represents an early diversified population, suggesting the scenario of more diverse AMH lineages than previously thought during the Late Pleistocene in southern East Asia. Our study paves the way to explore genetic explanations of morphological complexities of early hominins. MZR also shows a deep and indirect link to the ancestry that contributed to First Americans, which may help reconstruct the earliest migratory route from East Asia to the Americas.

A Eurasian Stone Age Ancient DNA Megapaper

A new preprint analyzes a huge number of new ancient DNA samples from stone age Eurasia (Hat tip to Razib Khan). Despite its claim "Eurasian" scope, it covers pretty much only Europe and part of Siberia. The paper largely confirms and refines existing paradigms and expectations.

LVN = ancestry maximized in Anatolian farmer populations. WHG = ancestry maximized in western European hunter gatherers. EHG = ancestry maximized in eastern European hunter-gatherers. IRN = ancestry maximized in Iranian Neolithic individuals and Caucasus hunter-gatherers.   

 

Razib clarifies beyond the abstract that:

New hunter-gatherer cluster with a focus in the eastern Ukraine/Russian border region. Between the Dnieper and Don. . . .

Scandinavia seems to have had several replacements even after the arrival of the early Battle Axe people. This is clear in Y chromosome turnover, from R1a to R1b and finally to mostly I1, the dominant lineage now. They claim that later Viking and Norse ancestry is mostly from the last pulse during the Nordic Bronze Age. . . .

it’s clear that Neolithic ancestry in North/Central/Eastern Europe was from Southeast Europe, while that in Western Europe was from Southwest Europe. . . .

They find the African R1b around Lake Chad in some Ukrainian samples.

The last point confirms my previous analysis of the origins of African Y-DNA R1b, in which I argue that Y-DNA R1b-V88 bearing Chadic people are derived from migrants who originated in the Bug-Dneister culture of Ukraine departing between 5400 BCE and 5200 BCE (this culture is also discussed in the body text of the main paper). 

The pertinent part of the first pdf of Supplemental Materials (at pdf page 42, lines 911-928) states:

Newly reported samples belonging to haplogroup R1b were distributed between two distinct groups depending on whether they formed part of the major European subclade R1b1a1b (R1b-M269). 

Individuals placed outside this subclade were predominantly from Eastern European Mesolithic and Neolithic contexts, and formed part of rare early diverging R1b lineages (Fig. S3b.6). Two Ukrainian individuals belonged to a subclade of R1b1b (R1b-V88) found among present-day Central and North Africans, lending further support5,10 to an ancient Eastern European origin for this clade. 

Haplogroup R1b1a1a (R1b-M73) was frequent among Russian Neolithic individuals. 

Individuals placed within the R1b-M269 clade on the other hand were from Scandinavian Late Neolithic and early Bronze Age contexts (Fig. S3b.6). Interestingly, more fine-scale sub-haplogroup placements of those individuals revealed that Y chromosome lineages distinguished samples from distinct genetic clusters inferred from autosomal IBD sharing (Fig. S3b.6, S3b.7). In particular, individuals associated with the Scandinavian cluster Scandinavia_4200BP_3200BP were all placed within the sub-haplogroup R1b1a1b1a1a1 (R1b-U106), whereas the two Scandinavian males associated with the Western European cluster Europe_4500BP_2000BP were placed within R1b1a1b1a1a2 (R1b-P312) (Fig. S3b.7). 

Figure S3b.6 is as follows and is basically unreadable since even when magnified 500% the resolution isn't fine enough to make it readable, but is presumably referencing the two most basal portions of the circular chart which start in approximately the three o'clock position and evolve counterclockwise. Presumably R1b-V88 is the tree closest to the three o'clock position because it has two samples from the current study in purple/pinkish, while the next tree counterclockwise from it is probably R1b-M73 which has many samples from the study, consistent with the text quoted above.

The footnoted references 5 and 10 to this part of the Supplemental Materials were:

5. Haber, M. et al. "Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations". Am. J. Hum. Genet. 0, (2016). The abstract of this paper states:

Understanding human genetic diversity in Africa is important for interpreting the evolution of all humans, yet vast regions in Africa, such as Chad, remain genetically poorly investigated. Here, we use genotype data from 480 samples from Chad, the Near East, and southern Europe, as well as whole-genome sequencing from 19 of them, to show that many populations today derive their genomes from ancient African-Eurasian admixtures. 

We found evidence of early Eurasian backflow to Africa in people speaking the unclassified isolate Laal language in southern Chad and estimate from linkage-disequilibrium decay that this occurred 4,750–7,200 years ago. It brought to Africa a Y chromosome lineage (R1b-V88) whose closest relatives are widespread in present-day Eurasia; we estimate from sequence data that the Chad R1b-V88 Y chromosomes coalesced 5,700–7,300 years ago. 

This migration could thus have originated among Near Eastern farmers during the African Humid Period. We also found that the previously documented Eurasian backflow into Africa, which occurred ~3,000 years ago and was thought to be mostly limited to East Africa, had a more westward impact affecting populations in northern Chad, such as the Toubou, who have 20%–30% Eurasian ancestry today. 

We observed a decline in heterozygosity in admixed Africans and found that the Eurasian admixture can bias inferences on their coalescent history and confound genetic signals from adaptation and archaic introgression. 

and

10. Marcus, J. H. et al. "Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia." Nat. Commun. 11, 1–14 (2020) (pertinent Supplemental Information here). The abstract of this paper states:

The island of Sardinia has been of particular interest to geneticists for decades. The current model for Sardinia’s genetic history describes the island as harboring a founder population that was established largely from the Neolithic peoples of southern Europe and remained isolated from later Bronze Age expansions on the mainland. 

To evaluate this model, we generate genome-wide ancient DNA data for 70 individuals from 21 Sardinian archaeological sites spanning the Middle Neolithic through the Medieval period. The earliest individuals show a strong affinity to western Mediterranean Neolithic populations, followed by an extended period of genetic continuity on the island through the Nuragic period (second millennium BCE). Beginning with individuals from Phoenician/Punic sites (first millennium BCE), we observe spatially-varying signals of admixture with sources principally from the eastern and northern Mediterranean. Overall, our analysis sheds light on the genetic history of Sardinia, revealing how relationships to mainland populations shifted over time.

The relevant language in the Supplemental Information states:

The 1240k read capture data allowed us to call several R1b subclades in ancient individuals (see Supp. Fig. 7 for overview of available markers). While R1b-M269 was absent from our sample of ancient Sardinians until the Nuragic period, we detected R1b-V88 equivalent markers in 11 out of 30 ancient Sardinian males from the Middle Neolithic to the Nuragic with Y haplogroup calls. Two ancient individuals carried derived markers of the clade R, but we could not identify more refined subclades due to their very low coverage (Supp. Data 1B). The ancient geographic distribution of R1b-V88 haplogroups is particularly concentrated in the Seulo caves sites and the South of the island (Supp. Data 1B). 

At present, R1b-V88 is prevalent in central Africans, at low frequency in present-day Sardinians, and extremely rare in the rest of Europe58. By inspecting our reference panel of western Eurasian ancient individuals, we identified R1b-V88 markers in 10 mainland European ancient samples (Fig. 8), all dating to before the Steppe expansion (ą 3k years BCE). Two very basal R1b-V88 (with several markers still in the ancestral state) appear in Serbian HGs as old as 9,000 BCE (Fig. 9), which supports a Mesolithic origin of the R1bV88 clade in or near this broad region. The haplotype appears to have become associated with the Mediterranean Neolithic expansion - as it is absent in early and middle Neolithic central Europe, but found in an individual buried at the Els Trocs site in the Pyrenees (modern Aragon, Spain), dated 5,178-5,066 BCE59 and in eleven ancient Sardinians of our sample. Interestingly, markers of the R1b-V88 subclade R1b-V2197, which is at present day found in Sardinians and most African R1b-V88 carriers, are derived only in the Els Trocs individual and two ancient Sardinian individuals (MA89, 3,370-3,110 BCE, MA110 1,220-1,050 BCE) (Fig. 9). MA110 additionally carries derived markers of the R1b-V2197 subclade R1b-V35, which is at present-day almost exclusively found in Sardinians58. 

This configuration suggests that the V88 branch first appeared in eastern Europe, mixed into Early European farmer individuals (after putatively sex-biased admixture60), and then spread with EEF to the western Mediterranean. Individuals carrying an apparently basal V88 haplotype in Mesolithic Balkans and across Neolithic Europe provide evidence against a previously suggested central-west African origin of V88 61. A west Eurasian R1b-V88 origin is further supported by a recent phylogenetic analysis that puts modern Sardinian carrier haplotypes basal to the African R1b-V88 haplotypes 58. The putative coalescence times between the Sardinian and African branches inferred there fall into the Neolithic Subpluvial (“green Sahara”, about 7,000 to 3,000 years BCE). Previous observations of autosomal traces of Holocene admixture with Eurasians for several Chadic populations 62 provide further support for a speculative hypothesis that at least some amounts of EEF ancestry crossed the Sahara southwards. Genetic analysis of Neolithic human remains in the Sahara from the Neolithic Subpluvial would provide key insights into the timing and specific route of R1b-V88 into Africa - and whether this haplogroup was associated with a maritime wave of Cardial Neolithic along Western Mediterranean coasts 63 and subsequent movement across the Sahara 58,64. 

Overall, our analysis provides evidence that R1b-V88 traces back to eastern European Mesolithic hunter gatherers and later spread with the Neolithic expansion into Iberia and Sardinia. These results emphasize that the geographic history of a Y-chromosome haplotype can be complex, and modern day spatial distributions need not reflect the initial spread.

The abstract and paper are as follows:

The transitions from foraging to farming and later to pastoralism in Stone Age Eurasia (c. 11-3 thousand years before present, BP) represent some of the most dramatic lifestyle changes in human evolution. We sequenced 317 genomes of primarily Mesolithic and Neolithic individuals from across Eurasia combined with radiocarbon dates, stable isotope data, and pollen records. 

Genome imputation and co-analysis with previously published shotgun sequencing data resulted in >1600 complete ancient genome sequences offering fine-grained resolution into the Stone Age populations. 

We observe that: 

1) Hunter-gatherer groups were more genetically diverse than previously known, and deeply divergent between western and eastern Eurasia. 

2) We identify hitherto genetically undescribed hunter-gatherers from the Middle Don region that contributed ancestry to the later Yamnaya steppe pastoralists; 

3) The genetic impact of the Neolithic transition was highly distinct, east and west of a boundary zone extending from the Black Sea to the Baltic. Large-scale shifts in genetic ancestry occurred to the west of this "Great Divide", including an almost complete replacement of hunter-gatherers in Denmark, while no substantial ancestry shifts took place during the same period to the east. This difference is also reflected in genetic relatedness within the populations, decreasing substantially in the west but not in the east where it remained high until c. 4,000 BP; 

4) The second major genetic transformation around 5,000 BP happened at a much faster pace with Steppe-related ancestry reaching most parts of Europe within 1,000-years. Local Neolithic farmers admixed with incoming pastoralists in eastern, western, and southern Europe whereas Scandinavia experienced another near-complete population replacement. Similar dramatic turnover-patterns are evident in western Siberia; 

5) Extensive regional differences in the ancestry components involved in these early events remain visible to this day, even within countries. Neolithic farmer ancestry is highest in southern and eastern England while Steppe-related ancestry is highest in the Celtic populations of Scotland, Wales, and Cornwall (this research has been conducted using the UK Biobank resource); 

6) Shifts in diet, lifestyle and environment introduced new selection pressures involving at least 21 genomic regions. Most such variants were not universally selected across populations but were only advantageous in particular ancestral backgrounds. Contrary to previous claims, we find that selection on the FADS regions, associated with fatty acid metabolism, began before the Neolithisation of Europe. Similarly, the lactase persistence allele started increasing in frequency before the expansion of Steppe-related groups into Europe and has continued to increase up to the present. Along the genetic cline separating Mesolithic hunter-gatherers from Neolithic farmers, we find significant correlations with trait associations related to skin disorders, diet and lifestyle and mental health status, suggesting marked phenotypic differences between these groups with very different lifestyles. 

This work provides new insights into major transformations in recent human evolution, elucidating the complex interplay between selection and admixture that shaped patterns of genetic variation in modern populations.

Morten E. Allentoft, et al., "Population Genomics of Stone Age Eurasia" bioRxiv (May 5, 2022).

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