PopGen 101 — Illustrative DNA

Out of Africa (OoA) and the East–West Eurasian Split

Upper Paleolithic · ~70,000–38,000 BP

It is widely acknowledged that the ancestors of all non-African (Eurasian) populations migrated out of the African continent approximately 70–60 kya (Vallini et al. 2022). During their initial expansion into Eurasia, possibly somewhere in the Near East, they interbred with Neanderthals, resulting in an estimated 2–3% Neanderthal admixture in the majority of later populations (Posth et al. 2023). This initial Eurasian population further split into West and East Eurasian groups, believed to have occurred between 45 and 38 thousand years ago.

The oldest Homo sapiens specimen sequenced to date is a female individual from Zlatý kůň (Czech Republic), radiocarbon dated to over 45 ka. The Zlatý kůň individual represents an ancestral lineage that is basal to both West and East Eurasians (Vallini et al. 2022). In contrast, the second-oldest human samples from the Bacho Kiro cave in Bulgaria, dated around 45 thousand years ago, exhibit a closer genetic affinity with ancient and contemporary East Asians than with Europeans. Moreover, individuals from Bacho Kiro display a notably higher proportion of Neanderthal admixture, suggesting recent interbreeding with Neanderthals within the last few generations (Vallini et al. 2022). On the other hand, the genetic positioning of the Ust'-Ishim individual (45 ka) from Omsk Oblast, Russia — contemporaneous with Bacho Kiro — remains ambiguous; statistical support nevertheless leans towards the East Eurasian lineage for Ust'-Ishim (Vallini et al. 2022, supplementary information).

To summarise, the latest findings on the oldest human samples indicate that the initial migration wave out of Africa, as represented by Zlatý kůň, had already populated Europe prior to 45 ka. Around 45 ka, individuals with a genetic affinity to East Eurasians emerged in locations such as Bacho Kiro cave in Bulgaria and Ust'-Ishim in Russia. Subsequently, Oase1 in Romania (40 ka, likely descended from Bacho Kiro) and the Tianyuan individual in China (40 ka) also displayed similar genetic profiles.

It is also noteworthy that the ancestral lineage represented by individuals predating 40 ka — with the exception of Tianyuan — appears to have either become extinct or assimilated into later migrating populations (Posth et al. 2023).

Some time after the appearance of the East-Eurasian-related samples, we see the occurrence of samples carrying ancestries that derive primarily from the lineage leading to present-day Europeans (West Eurasian). The oldest human genomes reflecting this lineage include Kostenki 14 (38 ka) from western Russia and Goyet Q116-1 (35 ka) from Goyet cave in Belgium. The ancestral signature found in Kostenki 14 later contributed to the Věstonice cluster (named after the Dolní Věstonice site in Czechia), associated with the archaeologically defined Gravettian Culture (33–26 ka). This ancestral lineage was shared among individuals from the Gravettian Culture in Central and Southern Europe but disappeared after the Last Glacial Maximum (LGM).

Conversely, the ancestry related to Goyet Q116-1 reappeared after the LGM in individuals associated with the archaeological Magdalenian Culture (19–14 ka) from Iberia across Central Europe to Eastern Europe. This lineage was later largely replaced by the Epigravettian-associated (24–12 ka) Villabruna (WHG) cluster (Posth et al. 2023).

Sources

Vallini, L., et al. (2022). Genetics and Material Culture Support Repeated Expansions into Paleolithic Eurasia from a Population Hub Out of Africa. Genome Biology and Evolution, 14(4), evac045. https://doi.org/10.1093/gbe/evac045
Posth, C., et al. (2023). Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers. Nature, 615(7950), 117–126. https://doi.org/10.1038/s41586-023-05726-0

Basal Eurasians

Upper Paleolithic – Mesolithic · "ghost" population

Basal Eurasians are considered a "ghost" population believed to have significantly influenced ancient populations in the Middle East and North Africa during the Upper Paleolithic to Mesolithic periods. The earliest sequenced sample with Basal Eurasian ancestry (~24%), known as NEO283, dates back to the Upper Paleolithic era (26,000 BP) from Kotias Cave in Georgia, with the remaining ancestry attributed to West Eurasian Upper-Paleolithic hunter-gatherers (Allentoft et al. 2024).

Between the Upper Paleolithic and Mesolithic periods, there is an observed increase in Basal Eurasian ancestry in the Caucasus and Iran, coupled with an Ancient North Eurasian (ANE)-related admixture. This results in approximately 35% Basal Eurasian + ANE in Mesolithic Caucasus Hunter-Gatherers (CHG) and 65% Basal Eurasian + ANE in Mesolithic Iran (HotuIIIb) samples, respectively. However, the Basal Eurasian admixture decreases to less than 50% in Neolithic Iran (Lazaridis et al. 2016).

In contrast to the Caucasus and Iran, Basal Eurasian ancestry in Anatolian and Natufian Hunter-Gatherers in the Levant is accompanied by Western Hunter-Gatherer (WHG)-like admixture. Anatolian Hunter-Gatherers and their direct descendants, Anatolian Neolithic Farmers, are estimated to have approximately 25% Basal Eurasian + WHG ancestry (Feldman et al. 2019), while Natufian Hunter-Gatherers exhibit around 45% Basal Eurasian + WHG-like ancestry. It remains unclear whether this WHG-like ancestry later migrated from South Europe to the Middle East or was already present in the region (Lazaridis et al. 2016, supplementary information).

Ferreira et al. (2021) proposed that Basal Eurasians and the ancestors of East and West Eurasians were genetically close, with Basal Eurasians likely descending from the same group that left Africa but splitting earlier — either in southwest Asia or in Africa before the Out-of-Africa (OoA) event. In the latter scenario, they followed the "southern route" in the Arabian Peninsula and took refuge somewhere in the Persian Gulf while the sister group followed the "northern route", mixed with Neanderthals in the northern Arabian Peninsula, and moved further into Europe and Asia. Ferreira's estimations also suggest that Iberomaurusians from the Taforalt Culture (15,000–13,000 BP) in Morocco carry approximately 60% Basal Eurasian ancestry. Additionally, in contrast to Lazaridis et al. (2016), Natufians are estimated to have above 20% Basal Eurasian ancestry, while CHGs have approximately 40%.

Sources

Allentoft, M. E., et al. (2024). Population genomics of post-glacial western Eurasia. Nature, 625, 301–311. https://doi.org/10.1038/s41586-023-06865-0
Ferreira, J. C., et al. (2021). Projecting Ancient Ancestry in Modern-Day Arabians and Iranians: A Key Role of the Past Exposed Arabo-Persian Gulf on Human Migrations. Genome Biology and Evolution, 13(9), evab194. https://doi.org/10.1093/gbe/evab194
Feldman, M., et al. (2019). Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia. Nature Communications, 10, 1218. https://doi.org/10.1038/s41467-019-09209-7
Lazaridis, I., et al. (2016). Genomic insights into the origin of farming in the ancient Near East. Nature, 536, 419–424. https://doi.org/10.1038/nature19310

Ancient North Eurasians (ANE)

Upper Paleolithic · ~24,000–18,000 BP

The Ancient North Eurasian (ANE) is a distinctive ancestral component that emerged during the Upper Paleolithic Age. It is represented by a boy known as MA-1, associated with the Mal'ta–Buret' Culture (24,000 BP) in Irkutsk Oblast, Russia, and individuals from Afontova Gora (18,000 BP), situated on the left bank of the Yenisei River in Krasnoyarsk, Russia. The ANE population is considered intermediate between West and East Eurasians and can be modelled as a combination of 50% Sunghir/Kostenki 14 and 50% Tianyuan-like ancestry (Posth et al. 2023). This population played a pivotal role in shaping later ancient populations in Europe, the Middle East, and Siberia.

The ANE is believed to have descended either from Ancient North Siberians (ANS), represented by individuals associated with the preceding Yana Culture (32,000 BP) in Sakha, Russia, or from a common older population that is ancestral to both ANE and ANS. Yana individuals, much like those of the ANE, can be modelled as either 78% Sunghir and 22% Tianyuan or as a 50% Sunghir/Kostenki 14 and 50% Tianyuan-like combination.

One of the ANE population's most significant roles was forming the Eastern European Hunter-Gatherers (EHG) by mixing partially with the WHG and Upper Paleolithic Caucasus Hunter-Gatherer-related source in Eastern Europe sometime around the Mesolithic Age. The ANE ancestry was later exclusively carried by Western Siberian Hunter-Gatherers (WSHG) — primarily represented by an individual called Tyumen_HG — the Botai Culture, and Bronze Age Tarim populations (Tarim_EMBA) from the Tarim Basin, China.

Sources

Posth, C., et al. (2023). Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers. Nature, 615(7950), 117–126. https://doi.org/10.1038/s41586-023-05726-0
Vallini, L., et al. (2022). Genetics and Material Culture Support Repeated Expansions into Paleolithic Eurasia from a Population Hub Out of Africa. Genome Biology and Evolution, 14(4), evac045. https://doi.org/10.1093/gbe/evac045

Europe: From Paleolithic to Neolithic

~45,000 – 5,000 BP

In this section we briefly go through the genetic breakpoints of Europe, beginning from the Initial Paleolithic Age to the Neolithic farmer migrations. The information below relies on two extensive recent studies: Posth et al. 2023 and Allentoft et al. 2024.

Overview

The genetic history of Paleolithic Europe can be roughly categorised into two periods: pre- and post-Last Glacial Maximum (25,000–19,000 BP). In the pre-LGM era, Europe had two distinct ancestral groups. The first is represented by the individual Goyet Q116-1 (35,000 BP) in Belgium, and the second by individuals from Kostenki 14 (32,000 BP) and Sunghir (34,000 BP) in western Russia.

The ancestry associated with Goyet Q116-1 corresponds to the Aurignacian Period, a period that later transitioned into the Gravettian Culture (33–26,000 BP), giving rise to two ancestral clusters in Europe. Central, east, and southern Europe received a mixture related to Sunghir, resulting in an estimated 64% Sunghir and 36% Goyet Q116-1-like admixture, known as the Věstonice Cluster. In contrast, the genetic cluster in west and southwest Europe — known as the Fournol Cluster — was closely linked to the ancestry represented by Goyet Q116-1. This ancestry persisted during and after the LGM in west and southwest Europe.

The LGM period in southwest Europe is archaeologically associated with the Solutrean Culture. Samples from this period exhibit an intermediate genetic profile between the preceding Fournol ancestry (associated with the Gravettian Culture) and the succeeding Magdalenian Culture, represented by the oldest Magdalenian-associated sample, El Mirón.

The Magdalenian Culture had two genetic clusters of its own. The first is the Goyet Q2 cluster, with samples 15,000 years old (from France, Belgium, Germany); the second is the 19,000-year-old El Mirón cluster from Spain. Both clusters are distantly related to Goyet Q116-1 — although they also carry significant contribution from the Epi-Gravettian-associated Villabruna Cluster.

After the LGM, the Epi-Gravettian culture spread widely in south and southeast Europe. The ancestry related to this culture is called the Villabruna Cluster, which also became known as the Western European Hunter-Gatherer (WHG) ancestry. This ancestry was not related to the preceding Gravettian-associated Věstonice Cluster, which seemingly disappeared after the LGM. The Villabruna Cluster later largely replaced the Magdalenian culture which had spread in southwest, west, and central Europe. Villabruna / Oberkassel / WHG ancestry dominated most parts of Europe until the Neolithic Age, when it was largely replaced by the Anatolian Neolithic Farmer migrations.

Timeline

Pre-LGM

The oldest genomes carrying ancestries that derive primarily from the lineage leading to present-day Europeans are Kostenki 14 (37 ka, uncertain archaeological association, western Russia), Goyet Q116-1 (35 ka, Aurignacian-associated, Belgium) and Bacho Kiro 1653 (35 ka, probably Aurignacian-associated, Bulgaria).

Gravettian Period (33–26 ka):

Věstonice genetic cluster — Named after the Dolní Věstonice site in Czechia. Comprises Gravettian-associated individuals from central-east and southern Europe (Dolní Věstonice, Pavlov, Krems-Wachtberg, Paglicci, Ostuni). Emerged by the genetic contribution from a Sunghir / Kostenki 14-related source. This genetic signature is shared among individuals associated with the archaeologically defined Gravettian culture in central and southern Europe and seemingly disappeared after the Last Glacial Maximum.
Fournol genetic cluster — Comprises Gravettian-associated individuals from western and southwestern European sites (Ormesson, La Rochette, Fournol, and two Serinyà cave sites — Mollet III and Reclau Viver). The Fournol cluster is closely related to Aurignacian-associated individuals from Belgium dated to 35 ka (Goyet Q116-1 and Goyet Q376-3).

During this period, genetically intermediate samples between Věstonice and Fournol are also observed.

During the LGM

Solutrean culture (24–19 ka): Emerged during the LGM in southwest Europe. The LGM is considered to have caused a demographic decline in large parts of Europe, with populations retracting to southern latitudes, to the Iberian peninsula and southern France.

Epi-Gravettian culture (24–12 ka): During the LGM the Epi-Gravettian culture seems to have gradually spread from the Balkans to Italy. The distinct ancestry represented by Epi-Gravettian-associated individuals is called the Villabruna or Oberkassel cluster. This ancestry initially replaced the Věstonice Cluster in the region and later largely replaced Magdalenian-associated ancestry in much of Europe.

Post-LGM

Magdalenian Culture (19–14 ka): Succeeded the Solutrean Culture in Iberia and France and spread across eastern and central Europe. Ancestry represented by Magdalenian-associated individuals (Goyet Q2) is distantly linked to the Goyet Q116-1 individual from Belgium dated to 35 ka. Magdalenian Culture and the ancestry associated with it were largely replaced by the Epi-Gravettian Culture.

Epi-Gravettian culture (24–12 ka): Upon mostly replacing the Magdalenian Culture, the Epi-Gravettian-associated Villabruna / Oberkassel (WHG) ancestry became the dominant and most widespread ancestry in Europe until the Mesolithic era. Around the Mesolithic, an ANE-related population mixed with WHG appears in Eastern Europe, giving rise to Eastern European Hunter-Gatherers (EHG / Sidelkino Cluster).

Neolithic Transition

The arrival of Anatolian Farmer-related ancestry in different regions of Europe spans an extensive time period of over 3,000 years, from its earliest evidence in the Balkans (Lepenski Vir) at ~8,700 BP to c. 5,900 BP in Denmark. These Neolithic migrations caused an East–West distinction along a boundary zone running from the Black Sea to the Baltic, causing the "Great Divide" in Europe. To the west of this division, Anatolian Farmer-related ancestry largely replaced the local hunter-gatherers (WHG).

However, on the eastern side of the "Great Divide" no ancestry shifts can be observed during this period. In the East Baltic region, Ukraine, and Western Russia, local HG ancestry (represented by the EHG) prevailed until ~5,000 BP without noticeable input of Anatolian-related farmer ancestry.

Sources

Allentoft, M. E., et al. (2024). Population genomics of post-glacial western Eurasia. Nature, 625, 301–311. https://doi.org/10.1038/s41586-023-06865-0
Posth, C., et al. (2023). Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers. Nature, 615(7950), 117–126. https://doi.org/10.1038/s41586-023-05726-0

Asia: Primary Ancestral Groups

East Eurasia · primary clusters

The genetic history of East Eurasian populations is a complex topic and still under ongoing debate. Here we summarise the major ancestral clusters that played a significant role in shaping the later populations in the region, under the guidance of the latest studies.

Abbreviations

MMesolithic

NNeolithic

ENEarly Neolithic

EMNEarly–Middle Neolithic

MNMiddle Neolithic

LNLate Neolithic

LNBALate Neolithic – Bronze Age

Northeast Asia

Khairygas_16.7kya. One of the oldest samples recovered from Northeast Asia, this sample may be a near-unadmixed representative of Ancient Paleosiberian (APS) ancestry and is likely a near-unadmixed descendant of a population closely related to the founding population of the Americas. This sample can be modelled as ~97% Native-American-like (represented by Peru_Laramate_900B) and ~7% ANE-related (represented by AfontovaGora3). (Zeng et al. 2023, sup. mat. p. 172–173)

Ust_Kyakhta_14kya. The second-oldest sample in the APS cluster, this individual can be modelled as ~53–69% preceding Khairygas plus an undefined East Asian source, possibly related to KhatystyrCave_M_10.2kya. (Zeng et al. 2023, sup. mat. p. 173)

KhatystyrCave_M_10.2kya. Appearing to be of mixed ancestry, in a 3-way model this individual primarily inherits the majority of its genetic heritage from China_AmurRiver_Mesolithic (~57–78% — alternatively as ~61% from China_AmurRiver_Mesolithic + ~24% from Cisbaikal_LNBA + ~15% from China_SEastAsia_Coastal_EN), with the remaining portion originating from Ust_Kyakhta and another East Asian source (either China_NEastAsia_Inland_EN or China_SEastAsia_Coastal_EN). (Zeng et al. 2023, sup. mat. p. 173–174)

Kolyma_M_10.1kya. While models for Kolyma_M_10.1kya are quite varied, they are highly consistent in suggesting that this population is mostly descended from Ancient Paleosiberians (~65–73% Khairygas_16.7kya-like) and is less admixed with East Asian ancestry compared to Ust_Kyakhta_14kya. The remaining East Asian ancestry of Kolyma_M_10.1kya seems to be derived from either Yumin- or Amur-related sources. (Zeng et al. 2023, sup. mat. p. 174 / 196)

Dzhilinda1_M_N_8.4kya. This individual can be modelled as having all its ancestry coming from Ust_Kyakhta_14kya, or alternatively as an admixture of Kolyma_M_10.1kya or Khairygas with an East-Asian-related source — with much ancestry from KhatystyrCave_M_10.2kya or Transbaikal_EMN_old. (Zeng et al. 2023, sup. mat. p. 176)

Transbaikal_EMN_old. Consists of two individuals within the Transbaikal_EMN cluster (irk007.SG and cta016.SG), both older than the others at approximately 8,300 and 8,800 BP respectively. This genetic make-up can be represented as a two-way admixture between the Yumin individual (China_NEastAsia_Inland_EN) and KhatystyrCave_M_10.2kya. (Zeng et al. 2023, sup. mat. p. 176)

Altai_N_old. The oldest individuals under the Altai_N group label — uniting Kemerovo_N, Firsovo_N, and West_Siberia_N (extremely similar populations found in the Altai region) — older than ~8,000 BP (including individuals I2137 and I13098) can be successfully modelled as a 2-way admixture between a minor fraction of ancestry from AG3 and a major fraction from the three APS populations Khairygas, Ust_Kyakhta_14kya, and Kolyma_M_10.1kya. The same models pass in set B; no simpler models pass. (Zeng et al. 2023, sup. mat. p. 177)

Altai_N. This group — comprising all individuals in the Altai_N group label younger than 8,000 BP — can be modelled as descending completely from the older individuals in this cluster (Altai_N_old). (Zeng et al. 2023, sup. mat. p. 178)

Transbaikal_EMN. Consisting of younger individuals in the Transbaikal_EMN cluster, can either be modelled as descending completely in a one-way model from Transbaikal_EMN_old or via a two-way model with a small additional contribution from China_NEastAsia_Inland_EN (represented by the Yumin individual). (Zeng et al. 2023, sup. mat. p. 178)

China_AmurRiver_N. Consisting of individuals from the Amur River Basin region younger than ~8,000 BP, can be modelled as descending almost entirely (~77–98%) from prior populations of the Amur River region (China_AmurRiver_EarlyN or China_AmurRiver_Mesolithic) in multiple 2-way models with the addition of a small contribution from one other, typically Northeast Asian or APS source. (Zeng et al. 2023, sup. mat. p. 178) The individuals labelled Russia_Boisman_MN and Devils_Gate_N from the Amur Basin region are also associated with this ancestral cluster. Present-day Tungusic populations from the region also show strong correlation with this ancestry.

Cisbaikal_EN. Models of Cisbaikal_EN — which includes individuals from the Cisbaikal region from ~8,000 to ~6,800 BP — show major contributions from Transbaikal_EMN_old (~65–79%) and minor contributions from an APS population (Ust_Kyakhta_14kya ~35% or Khairygas_16.7kya ~31%). (Zeng et al. 2023, sup. mat. p. 178)

Mongolia_N_North. A two-way model for Mongolia_N_North — from the northern region of the Mongolian plateau just south of Lake Baikal at approximately 7,500 BP — as an admixture between Transbaikal_EMN_old (~65%) + China_NEastAsia_Inland_EN (~35%), alternatively with the addition of a small fraction (<7%) of ancestry from an ANE-rich source (either Altai_N_old or an APS-related population such as Khairygas_16.7kya, Ust_Kyakhta_14kya, Dzhilinda1_M_N_8.4kya, or Kolyma_M_10.1kya). (Zeng et al. 2023, sup. mat. p. 178)

Syalakh-Belkachi. The Syalakh-Belkachi population in the Middle Lena river valley in Central Yakutia from 6,800–6,300 BP can be modelled as descending entirely from the Mesolithic Northern Buryatian Dzhilinda1_M_N_8.4kya. In other passing 2-way models with higher p-values, Syalakh-Belkachi continues to demonstrate majority descent from Dzhilinda1_M_N_8.4kya with a minor contribution (~10–20%) from a broadly East-Asian-related population whose identity is poorly resolved. In other passing models, a major contribution from Dzhilinda1_M_N_8.4kya (~76%) and a minor contribution (~24%) from a population rich in Inland Northeast Asian ancestry (Yumin under the China_NEastAsia_Inland_EN label) — either Cisbaikal_EN, Transbaikal_EMN_old, or Mongolia_N_North — is observed. (Zeng et al. 2023, sup. mat. p. 178–179)

This population shows high affinity with the Paleo-Eskimo / Inuit cultures and may represent the major ancestral source contributed to them. A close genetic relationship was found between the Paleo-Inuit individual from the Saqqaq site in Greenland and the Syalakh-Belkachi population. 3-way models for the Saqqaq individual result in ~64–79% Syalakh-Belkachi-like admixture with the remainder from Kolyma_M_10.1kya and an East Asian source rich in Inland Northeast Asian ancestry. (Zeng et al. 2023, sup. mat. p. 204)

In turn, Saqqaq-related ancestry persisted on either side of the Bering Strait among ancient populations related to Eskimo-Aleut speakers. It is present at high levels in individuals from Old Bering Sea sites (up to ~43%) and in an individual from the classic Thule culture (up to ~59%), who is very similar to present-day Inuit. A Native-American-related source is also present in passing models for all of these groups — which in the case of the Old Bering Sea culture suggests back-migration from the New World to Chukotka. (Zeng et al. 2023, sup. mat. p. 212)

Saqqaq.SG ancestry persists along the northern shores of the Sea of Okhotsk in a population from the Tokarev culture from ~3,000 BP (Magadan_BA). This population is very similar to present-day Chukotko-Kamchatkans, and has very complex ancestry, with contributions from at least a Kolyma_M_10.1kya-related source and a Native-American-related source on top of Saqqaq.SG ancestry; the remainder is drawn from East Asian-related sources. (Zeng et al. 2023, sup. mat. p. 212) Ancestry related to that found in Syalakh-Belkachi also persists in an Iron Age Yakutian (~2,600 BP) from the Middle Lena River Valley, who can be modelled as cladal with Yakutia_LNBA. This individual is extremely similar to present-day Yukaghirs and Nganasans. (Zeng et al. 2023, sup. mat. p. 212)

While all ancient populations from Beringia and Arctic North America require a Saqqaq.SG-related source for passing models, ancient Athabaskans surprisingly do not share in this pattern. The models indicate that ancient Athabaskans can be modelled without any ancestry from Saqqaq.SG (i.e., with Saqqaq.SG retained in the reference populations); rather, in a 3-way model where most ancestry comes from a Native-American-related and a Kolyma_M_10.1kya-related source, model p-values are maximised by a minor (~9–13%) contribution from a third source that may be either Cisbaikal_LNBA or the closely-related Ust_Kyakhta_14kya. (Zeng et al. 2023, sup. mat. p. 213)

Yakutia_LNBA. Comprising individuals dating to ~4,500–3,200 BP from a region stretching from the Kan river valley in southeastern Krasnoyarsk to the Middle-Lower Lena valley in Central Yakutia and the Kolyma River basin in far northeastern Yakutia close to Beringia, Yakutia_LNBA can be modelled as a three-way admixture between Syalakh-Belkachi (~50%), Transbaikal_EMN (~42%), and a source related to Amur-River-related populations (~8%). (Zeng et al. 2023, sup. mat. p. 182) The Yakutia_LNBA genetic cluster has strong correlation with Uralic-speaking populations. The recent comprehensive analysis shows that this ancestry distinguishes Uralic-speaking populations from their non-Uralic-speaking neighbours; Uralic peoples derive the majority — and in some cases all — of their East-Asian-related ancestry from this source. (Zeng et al. 2023, sup. mat. p. 214–215)

Cisbaikal_LNBA. A model of Cisbaikal_LNBA as deriving most of its ancestry (~86%) from Ust_Kyakhta_14kya, with some ancestry from Inland Northeast Asians (~14%), is the only model passing with a high p-value. The origin of Cisbaikal_LNBA is not clear and is thought to be descended from an unsampled population that is related to but younger than Ust_Kyakhta_14kya. (Zeng et al. 2023, sup. mat. p. 184) Cisbaikal_LNBA ancestry — represented mostly by individuals associated with the Glazkov Culture — shows strong correlation with Yeniseian speakers and is constantly required as a source when modelling populations in the Yenisei Basin such as Yeniseian-speaking Kets, Uralic-speaking Enets and Selkup, and Turkic-speaking populations (Tuvinian, Tofalar, Tubalar, Altaian, Altaian_Chelkan, Khakass, Khakass_Kachin, Shor, Shor_Mountain, and Todzin), which is not the case for other Turkic or Uralic peoples. (Zeng et al. 2023, sup. mat. p. 219–220)

China_NEastAsia_Inland_EN. Represented by the Yumin (~8,000 BP) individual. This ancestry seems to have significantly contributed to many later populations in Northeast Asia.

Jomon Ancestry. Represented by 8,000–3,000-year-old hunter-gatherer individuals in Japan. The oldest individual sampled to date is Higashimyo, from Kyushu, Japan. Populations associated with this ancestry contributed partially to present-day Japanese populations. (Yang et al. 2022)

Southeast Asia

China_YellowRiver_N. Represented by Neolithic individuals from the Yellow River region, China. This ancestry is associated with the Proto Tibeto-Sinitic languages and is the major ancestral source that contributed to present-day South and East Asian populations (Han Chinese, Tibetan, Korean, Japanese, etc.). The Neolithic individuals grouped under the China_NEastAsia_Coastal_EN label are also closely related to the Neolithic Yellow River ancestry. (Yang et al. 2022)

Fujian Ancestry. The ancestry described in Yang et al. 2020 and 2021, consisting of 4 groups based on the Neolithic-era samples obtained from Fujian, China:

China_SEastAsia_Coastal_EN
China_SEastAsia_Coastal_LN
China_SEastAsia_Island_EN
China_SEastAsia_Island_LN

This ancestry is found in high levels in Austronesian populations and is thought to be associated with Austronesian expansions. It is also one of the most significant ancestries shared in high levels among present-day East and Southeast Asians.

South Asia

Ancient Ancestral South Indian (AASI). AASI is another "ghost" population, detected by indirect methods. Ancestry associated with the AASI lineage was found at low levels in almost all present-day Indian populations, particularly southern Indians. This ancestry has deep relationships with the other ancient East Eurasian ancestries; Onge or Irula populations are frequently used as a proxy to represent this ancestry. (Yang et al. 2022)

Sources

Zeng, T. C., et al. (2023). Postglacial genomes from foragers across Northern Eurasia reveal prehistoric mobility associated with the spread of the Uralic and Yeniseian languages (pre-print). bioRxiv. https://doi.org/10.1101/2023.10.01.560332
Yang, M. (2022). A genetic history of migration, diversification, and admixture in Asia. Human Population Genetics and Genomics, 2(1), 0001. https://doi.org/10.47248/hpgg2202010001
Yang, M., et al. (2020). Ancient DNA indicates human population shifts and admixture in northern and southern China. Science, 369, 282–288. https://doi.org/10.1126/science.aba0909