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By c. 40kya, Northeast Siberia was occupied by a genetically distinctive population known as Ancient North Siberians (ANS). Ancient North Siberians diverged from a West Eurasian source that was itself the result of an earlier split into Western and Eastern Eurasian lineages following a migration out of Africa or West Asia. Ancient North Siberian ancestry is represented by genomes sequenced from human remains recovered from the Yana Rhinoceros Horn archaeological site, and from later genetically similar Ancient North Eurasians (ANE) from the Mal'ta and Afontova Gora sites.

Ancient North Siberians were once widely distributed across Northeast Eurasia, but this population had diminished in size and extent by the onset of the Late Glacial Maximum, and later Siberian populations were descendants of an East Asian group who migrated north and admixed with ANS-related populations to form Ancient Paleo-Siberians (APS), the ancestors of Ancestral Native Americans and modern Siberians.

Background
In 2009, geneticist David Reich and his team submitted a paper which tested the popular belief that Native Americans and East Asians are related groups that descend from a common ancestral population. Surprisingly, they found that Europeans were more closely related to Native Americans than to East Asians, and were able to show that this was not as a result of recent admixture between Europeans and Native Americans within the past 500 years. Subsequently, a study by Patterson et al. (2012) found evidence that North Europeans are descended from a mixture of populations, one of which shared more ancestry with contemporary native Americans than with any other modern population. According to Patterson, "an ancient northern Eurasian population contributed genetic material to both the ancestral population of the Americas and the ancestral population of northern Europe." This 'ghost' population of 'Ancient (or Ancestral) North Eurasians' (ANE) were hypothesized to have lived in Northern Eurasia more than 15,000 years ago, some of whom migrated to America via the Bering land bridge, while others migrated west and contributed ancestry to Europeans.

In 2013, the whole-genome data for the first representative of this ancestral population, a boy who lived at the Mal'ta archaeological site in south-central Siberia, c. 24,000 years ago ('MA-1'), was published. This child was found to be most closely related to modern Native Americans and Europeans, and much less closely related to modern Siberians, as predicted. This individual has been described as the 'prototype sample' for the Ancient North Eurasian lineage.

Origins
Anatomically modern humans probably expanded from Africa into Eurasia c. 70-60kya. The earliest sampled Eurasian individuals display a deep split between East Asian and European populations, which probably diversified no earlier than c. 45-40kya. Modern humans are documented in East Eurasia from c. 45kya. By the Upper Palaeolithic, human populations here had diversified into at least three distinct lineages; the first, represented by Ust' Ishim, a c. 45 kya individual from Western Siberia, was equally related to ancient West Eurasians and modern East Asians, and diverged before or at same time as the East/West Eurasian split, and did not contribute significantly to modern populations; a second group is represented by the c. 40 kya individual from Tianyuan Cave, China, who was genetically closer to modern East Asian and Native American populations than Europeans; and thirdly, Ancient North Siberians (ANS), represented by the earliest known inhabitants of northern Siberia, two unrelated 10 to 12 year-old males dated c. 31,630ybp from the Yana Rhinoceros Horn Site. ANS ancestry originates from a Western Eurasian source that diverged around 40kya from other Western Eurasian lineages and received significant gene flow (c. 22% to c. 50%) from an East Eurasian source population related to modern East and Southeast Asians. The two individuals from the Yana site were both mitochondrial haplogroup U, prevalent among West Eurasian hunter-gatherers, and Y chromosome haplogroup P1, which is upstream of haplogroups Q and R, commonly found among modern Native American and European populations respectively. By c. 32kya, populations carrying ANS-related ancestry were probably widely distributed across northeast Eurasia. As well as settling Siberia, Ancient North Siberians may have expanded as far as Alaska and the Yukon, but were forced to abandon high latitude regions following the onset of harsher climatic conditions that came with the Last Glacial Maximum.

Upper Paleolithic
Gene flow between early East Asian and Siberian populations is evidenced in a c. 34kya female from Salkhit Valley, northeast Mongolia, as this individual shares as many alleles with Tianyuan as it does with the Yana individuals, while Tianyuan and Yana share fewer alleles with each other than they do with Salkhit. The Salkhit genome is estimated to carry 75% East Eurasian (Tianyuan-related) ancestry and 25% ancestry related to the later Yana individuals.

The c. 24ky old child from Mal'ta (MA-1) originates from the same West Eurasian source that is ancestral to the Yana individuals, who are in fact more closely related to MA-1 than to any other ancient Eurasian. MA-1, the typical representative of the Ancient North Eurasians (ANE), can be either modelled as a direct descendent of the ANS lineage, with minor gene flow from a Eurasian lineage ancestrally related to the Caucasus Hunter Gatherers (CHG), an Upper Paleolithic population from the Caucasus region, or as stemming from a separate admixture event of the same West Eurasian and East Asian ancestral sources that contributed to Yana, but with a slightly higher proportion of the West Eurasian source than in Yana. The 17ky old male found at the Afontova Gora II archaeological site in south-central Siberia in the 1920s, ('AG-2') and another c. 18kya female (AG-3) discovered at the same site in 2014 descend from the same ancestral population as MA-1. These three individuals have together been described as forming a genetically-related 'Mal'ta cluster', who lived in Siberia c. 24-17kya.. These individuals show some significant differences in their genetic substructure. MA-1 shares more genetic drift with AG-3 than it does with European hunter gatherers, and AG-3 seems to descend from a lineage that contributed more ancestry to later populations than MA-1. Sikhora et al. concluded that, although the Yana and ANE populations can both be modeled as a mixture of East Asian and West Eurasian sources, ANE had a higher proportion of W Eurasian ancestry, and do not come from the same population as the Yana individuals.

The Yana, Mal'ta, and Afontova Gora individuals are sometimes collectively referred to as 'Ancient North Siberians'.

Native Americans, Ancient Beringians, and Ancient Paleo-Siberians are all descended from populations that formed as a result of gene flow between ANE-related and EA-related groups that occurred c. 23-20kya, perhaps near Lake Baikal or in Eastern Beringia. Several scenarios are possible; in the first, an ANE/ANS-related population diverges into basal American and Ancient Paleo-Siberian lineages, each of which then receives different proportions of admixture from an East Asian source.. In the second, an ANE/ANS related and an East Asian population admix (between 58% and 70% East Asian contribution), followed by divergence of basal Americans from the UKY and Kolyma lineages. UKY and Kolyma then each receive separate additional admixture from an East Asian related source.

Also Flegontov et al. (2019)?

In either case, this process resulted in the formation of at least two distinct populations with different admixture proportions; Ancient Paleo-Siberians, the ancestors of modern populations of northeast Siberia, a population with additional East Asian ancestry; and the basal American lineage, ancestral to Native Americans and Ancient Beringians. Estimated divergence of Ancient Paleo-Siberians (UKY, Kolyma-1) and a population ancestral to Ancient Beringians and Ancestral Native American lineages occurred c. 23kya, with Native Americans diverging from Ancient Beringians (USR, Trail Creek) c. 20kya.

At Khaiyrgas Cave, on the middle Lena, Sakha Republic, the genome of a c. 17kya juvenile female ('Khaiyrgas-1') demonstrates that a major genetic shift had occurred in the region by the end of the Last Glacial Maximum. Khaiyrgas-1 represents a new lineage in Northeast Asia distinct from the earlier individuals, sharing more genetic drift with the Ancient North Eurasian (Mal'ta) lineage than the Ancient North Siberians (Yana), suggesting gene flow from west Eurasia into Siberia during the LGM. The lineage represented by Khaiyrgas-1 directly contributed ancestry to later populations such as the Ancient Paleo-Siberians.

Ancient Paleo-Siberians, represented by a 14ky old Upper Paleolithic individual from near Lake Baikal, (Ust-Kyakhta-3, 'UKY') and a 10ky old Mesolithic individual from the Duvanny Yar site in North East Siberia (Kolyma-1), are a population who were probably once widely distributed across north Eurasia from northeastern Siberia to Lake Baikal, descended from an East Asian population with some admixture from Ancient North Eurasians. Yu et al. model UKY and Kolyma-1 as descendents of a population consisting of 30% ANE and 70% East Asian ancestry, with an additional East Asian contribution of 27% to the UKY genome and 21% to the Kolyma-1 genome. A study by Mao et al. (2021) concludes that AR14K is the closest source for the East Asian ancestry in Ancient Paleo-Siberians, and that a population related to AR14K from the Amur river basin region could have been the direct source population for this ancestry in the APS. The Ancient North Eurasian ancestry component in Ancient Paleo-Siberians is genetically closer to the Mal'ta sample than it is to the Yana individuals, and so the Yana lineage did not contribute ancestry directly to Ancient Paleo-Siberians. Shared identity-by-descent segments suggest that UKY and Kolyma-1 were genetically closely related, and long runs of homozygosity in the Kolyma-1 individual suggest that the population size of North East Siberia in the Mesolithic was comparatively small.

Settlement of the Americas


The basal American lineage must have emerged by c. 21kya to 20kya at the latest, as it had started to diversify into distinct lineages by this time. Absence of subsequent Ancient Paleo-Siberian or East Asian gene flow or additional ancestral components in Native Americans suggests that the basal American lineage was geographically isolated at an early date, perhaps in Western Beringia as a consequence of the LGM separating population groups and resulting in the separation and diversification of the basal American group. This suggested period of isolation aligns with the Standstill Hypothesis, which proposes a period of settlement in the Beringian land bridge area prior to the settlement of the Americas. This isolated population then split into at least three distinct lineages, all of which eventually entered North America, probably at separate times: a currently unsampled 'ghost' population; Ancient Beringians, represented by the USR-1 individual and a c. 9kya young child from Trail Creek Cave 2; and Ancestral Native Americans, which then split somewhere south of Eastern Beringia c. 17.5-14.5kya into North Native Americans (NNA, restricted to northern North America) and South Native Americans (SNA, widely distributed across the rest of North and South America) and rapidly diversified into distinct groups.

Holocene
In the early Holocene, northern Eurasian populations formed a west-to-east cline with four major source populations: While in the easternmost part of Eurasia, Paleolithic Siberian (specifically, ANE-related) ancestry was largely replaced by continuous geneflow from East Asian ancestry sources (related to the Upper Pleistocene Tianyuan individual and ultimately to most modern East and Southeast Asians), high levels of Paleolithic Siberian ancestry persisted in the EHG- and WSHG-related populations until the Bronze Age.
 * Western Hunter-Gatherers (WHG), distributed over much of western and central Europe
 * Eastern Hunter-Gatherers (EHG), covering northeastern Europe down to the western Steppe
 * West Siberian hunter-gatherers (WSHG), represented by individuals from Tyumen (c. 5000 BCE) in Western Siberia close to the Ural Mountains
 * East Siberian hunter-gatherers, represented by individuals from Lake Baikal.

Along the eastern cline that connects WSHG to East Siberian hunter-gatherers were e.g. the early horse herders of the Botai culture (c. 3500–3000 BCE) or the Bronze Age mummies from the Tarim Basin (c. 2000 BCE). Many Early and Middle Bronze Age samples in Central Asia and southern Siberia (e.g. from the central Steppe and the Okunevo culture in the Altai mountains) carry lower levels of ANE-related ancestry as a result of further admixture with populations originating from the western Steppe and the Bactria–Margiana Archaeological Complex (or other groups with a high proportion of ancestry from Neolithic Iranian farmers), but still provide evidence that ANE-related ancestry must have been widespread in this area before the introduction of pastoralism.

Further west outside of Siberia, Mesolithic hunter-gatherers formed a cline of ANE-related ancestry across Western Eurasia. These can be grouped into distinct clusters, with differing proportions of ANE ancestry. At one end of the cline, Eastern Hunter Gatherers (EHGs) who are found in Northwest Russia from c. 10000 BCE, are represented by individuals from Karelia, in Northwest Russia, and Samara, near the Ural Mountains on the Pontic-Caspian steppe. Although their exact Upper Paleolithic origins are still poorly understood, EHGs carried significant levels of ANE ancestry. According to one model, Eastern Hunter Gatherers (EHG) derived around 75% of their ancestry from Ancient North Eurasians. To the west and south, Western Hunter Gatherers (WHGs), including individuals from Luxembourg and Spain, who had already occupied Europe for thousands of years before the Mesolithic, form the other end of this cline, with the lowest levels of ANE ancestry. The Scandinavian Hunter-Gatherers (SHG) are intermediate between EHG and WHG, while Mesolithic Ukrainian individuals are intermediate between EHG and SHGs.

From the mid-fifth millennium BCE, admixture between populations related to EHGs and Caucasus Hunter-Gatherers (CHG) occurred, resulting in the formation of so-called Steppe ancestry that was first documented in the Eneolithic Khvalynsk culture. This ancestral component, commonly associated with the spread of Indo-European languages, became widespread by the third millennium BCE, throughout the Western Eurasian steppe in individuals in the Yamnaya culture, in the Altai mountains in the Afanasievo culture, and in Europe via the Corded Ware culture. A back migration from Europe to the Pontic-Caspian steppe resulted in the formation of Steppe MLBA ancestry, which later spread to the Sintashta culture south of the Ural mountains and then to the Andronovo culture further east in the 2nd millennium BCE.

Modern populations
The Ancient North Eurasian ancestral lineage contributed substantially to modern West Eurasian, South Asian, Siberian, and Native American populations.

Siberia
Successful three-way admixture modelling of modern Siberian populations in Jeong et al. (2019) required an ANE-related (Afontova Gora 3) contribution for Mansi (~8.4%), Selkup (~16%), Enets (~3.9%), and Ket (~12.6%) populations.