Ancient Populations (Extended)

The following are categories of Paleolithic populations, their descriptions, and citations:

Ancient North Eurasians (ANE)

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Ancient North Eurasians (ANE) were a distinct population that lived in Upper Paleolithic Siberia, with their ancestry primarily associated with the Mal’ta-Buret culture . Ancient North Eurasians (ANE) were a group of mixed West and East Eurasian ancestry represented by the lineage of the Mal'ta-Buret' people (~24,000 years ago) and Upper Paleolithic groups from Afontova Gora. Their ancestry was composed of around 71% Ancient West Eurasian and 29% Ancient East Eurasian. The ANE were partially ancestral to the Ancient Beringians, Ancient Paleo-Siberians, Eastern Hunter Gatherers, and Ancestral Native Americans. Their genetic legacy is evident in later populations, including Indo-European steppe pastoralists (e.g., the Yamnaya culture) and Indigenous groups in the Americas. ANE ancestry remains prevalent in modern Central Asian, South Asian, and some Eastern European populations. 

 

1.Raghavan et al. (2014): "Upper Paleolithic Siberian genome reveals dual ancestry of Native Americans"

2.Lazaridis et al. (2016): "Genomic insights into the origin of farming in the ancient Near East"

Ancient Northern East Asians (ANEA)

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The Ancient Northern East Asians (ANEA) are a category consisting of multiple Northeast Asian ethnic groups which diverged from the lineage of the Ancient Southern East Asians (ASEA) between 22,000 - 28,000 BP. The first ANEA began appearing in the Amur region towards the end of the Last Glacial Maximum between 26,000 and 20,000 years ago. Prior to that, Tianyuan related ancestry was prevalent in the region. ANEA related ancestry is prevalent in Northern and Eastern Asian ethnic groups, in different proportions in modern times, and is partly found in the Han Chinese, Mongols, Koreans, and Siberian ethnic groups such as the Evenks and Nivkh [1][2][3].

1.Fu et al. (2016): "The genetic history of Ice Age Europe."

2.Gakuhari et al. (2020): "Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations."
3.Mao et al. (2021): "The deep population history of northern East Asia from the Late Pleistocene to the Holocene."

Ancient Southern East Asians (ASEA)

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The ANEA and ASEA groups were distinct from other ancient East Eurasian lineages and diverged from each other at least 19,000 years ago. In modern times, ASEA ancestry is most prominent today in populations in Southern China and Southeast Asia. Austronesian migrations brought ASEA ancestry to Island Southeast Asia and parts of Oceania. ASEA ancestry is best represented by samples from Liang Island (between China and Taiwan) and Qihe Cave in the Fujian province of China. 

1.McColl et al. (2018): "Ancient Genomics reveals four prehistoric migration waves into Southeast Asia" – One of the most comprehensive studies on ASEA and their contributions to modern Southeast Asian populations.

2.Lipson et al. (2018): "Ancient genomes document multiple waves of migration in Southeast Asian prehistory" – Highlights the genetic structure and migrations of ASEA populations.

Ancient San (South African Hunter-Gatherers)

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Modern South African hunter gatherer groups consist mostly of several tribes under the designation “Khoisan”. Along with the Rainforest Hunter Gatherers, they represent another major ancient divergence on the human family tree, and diverged from other lineages around 200,000 years ago. They have received genetic input over the millennia from East Africans, so many Khoisan groups now have varying degrees of East African ancestry. In a recent find of samples from Oakhurst rockshelter in South Africa, these 9,000 BP genomes were demonstrated to have genetic continuity with modern Khoisan groups. It’s also important to note that the Khoisan themselves have a major divergence within their group, dated to around 30,000 years ago [5]. Groups related to South African hunter gatherers were present in East Africa before being displaced by Pastoralists (practiced herding and farming), Southern Cushitic groups and then later Bantus during the timeframe of the Bantu expansion [4][7][8]. For the East African region, Bantu groups began entering the area around 2,000 years ago [6]. 

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1.Schlebusch et al. (2017): "Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago"
2.Pickrell et al. (2012): "The genetic prehistory of southern Africa"
3.Gretzinger et al. (2024): "9,000 years of genetic continuity in southernmost Africa demonstrated at Oakhurst rockshelter"
4.Skoglund et al. (2017): "Reconstructing prehistoric African population structure."
5.Prendergast et al. (2019): "Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa."
6.Serra-Vidal (2018): "Insights into the Human Demographic History of Africa Through Whole-Genome Sequence Analysis."
7.Mitchell (2014): "Sub-Saharan Africa archaeology."
8.Pfennig et al. (2023): "Evolutionary Genetics and Admixture in African Populations."
 

Basal East Eurasians (Onge)

The Onge people of the Andaman Islands are considered one of the closest modern representatives of an early-diverging branch of Basal East Eurasian ancestry. Genetic studies indicate that the Onge split from other East Asian-related populations before the differentiation of northern and southern East Asian lineages, possibly over 40,000 years ago. Their genetic distinctiveness is marked by low Neanderthal introgression and high genetic drift, likely due to long-term island isolation[1]. The Onge people and related Andaman Islands are considered one of the closest modern representatives of an early-diverging branch of Basal East Eurasian ancestry, and share a high genetic affinity to samples from the Tianyuan Man, a Basal East Asian that lived ~40,000 years ago in what is now Eastern China. A population genetically close to Tianyuan contributed between 32% and 50% to the Ancient North Eurasians (ANE). 

 

Recent research has revealed that the Zagros Neolithic Farmers (~10,000 BP, Iran) carried approximately 10% Basal East Eurasian ancestry, best represented by Onge-related genetic components. Similarly, the Caucasus Hunter Gatherers were found in the same study to have around 8% Basal East Eurasian ancestry as represented by Tianyuan. This suggests that early interactions between populations from South Asia and the Near East may have played a more significant role in shaping early Eurasian genetic diversity than previously assumed[2].

The Onge, along with other Andamanese populations, exhibit a degree of genetic linkage with early Hoabinhian hunter-gatherers of Southeast Asia, and are associated with waves of migrations that eventually led to humans settling what would become Papua New Guinea and Australia.

1.Reich et al. (2009): “Reconstructing Indian Population History”

2.Lazaridis et al. (2018): “Paleolithic DNA from the Zagros reveals the genetic history of early farmers”
3.Sitalaximi et al. (2023): "Genetic differentiation of Andaman Islanders and their relatedness to Nicobar Islanders." 

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Basal Eurasian (Excess)

The term Basal Eurasian refers to a group that diverged from other Eurasians just after the Out of Africa migration. With the assumption that the Out Of Africa migration happened around 60,000 years ago, it's theorized that the Basal Eurasians split from the lineage of other Eurasians shortly afterwards at around 57,500 years ago, with some estimates ranging up to 79,800 years ago [1][2]. That preceded the split between the West Eurasian Core (WEC) and East Eurasian Core (EEC) around 46,000 years ago.The homeland of the Basal Eurasians was either in Northern Africa, the Levant, or the Arabian Peninsula [1]. It has been inferred that there was around 9% Basal Eurasian in Early European Farmers, with this admixture occurring around 33,000 years ago [2]. The Basal Eurasian lineage contributed around 28% to Dzudzuana, with the remaining 72% from a lineage associated with Villabruna [3].

Basal Eurasian is measured in this test in terms of the excess Basal Eurasian per group (the amount which isn't already included in any of the samples per reference category). In the study [3], Table 1 gives an idea as to the amount of Basal Eurasian (represented by Mbuti) in each of the main populations (CHG, Dzudzuana, Iran_N, Natufian, PPNB, Taforalt). 

1.Vallini et al. (2024): “The Persian plateau served as hub for Homo sapiens after the main out of Africa dispersal”
2.Kamm et al. (2020): “Efficiently inferring the demographic history of many populations with allele count data”
3.Lazaridis et al. (2018): “Paleolithic DNA from Caucasus reveals core of West Eurasian ancestry”

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Dzudzuana

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The Dzudzuana population represents a lineage of Upper Paleolithic foragers in West Eurasia, identified through ancient DNA analysis from Dzudzuana Cave in Georgia (~26,000 years ago). The Dzudzuana population has ancestry related to both the Villabruna (WHG) cluster and Basal Eurasians, with contributions from the Basal Eurasian lineage being around 28%, with the remaining 72% being from a Common West Eurasian lineage that contributed to the Villabruna cluster [1]. Dzudzuana were the largest contributor to the ancestry of all modern West Eurasian groups, and a major contributor to Neolithic populations in the Near East, parts of Europe, and North Africa. For example it has been estimated that ancestry similar to the Dzudzuana contributed around 64% to Caucasus Hunter Gatherers and 58% to Zagros Neolithic Farmers represented by Iran_N [1]. Note that these estimates are not conclusive.

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1.Lazaridis et al. (2018): "Paleolithic DNA from Caucasus reveals core of West Eurasian ancestry" – 
2.Feldman et al. (2019): "Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia"
 

 

Jomon
 

The Jomon people were a pre-agricultural population that inhabited prehistoric Japan, becoming isolated as sea levels rose, and diverged from other ancient East Asian populations over ~20,000 years ago. Because of this, they are included in both the Neolithic and Paleolithic breakdowns. A recent study found that the Jomon maintained an extremely low population size of ~1,000 over several millennia [3]. The Jomon practiced a hunter gatherer lifestyle, along with fishing, and were known for their usage of pottery and consistent usage of ceramics. Modern Japanese are a mixture of East Asian (arrived during the Kofun Period), Northeast Asian, and Jomon ancestry, with the Jomon ancestry being around 11% to 19%, and the East Asian related ancestry being the most major component in modern Japanese. The Ainu, a small ethnic group concentrated in Hokkaido, Japan, still have a majority of their genome (around 50% to 70%) descended from the Jomon people.

1.Gakuhari et al. (2019): "Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations"

2.Jinam et al. (2021): "Discerning the origins of the Japanese people from genome-wide data"

3.Cooke et al. (2021): "Ancient genomics reveals tripartite origins of Japanese populations"

 

Villabruna (WHG)

The Villabruna cluster is an early representation of the WHG (Western Hunter Gatherer)
lineage. It is likely this ancestry first started in the Balkans around 17,000 years ago and was associated with the Epigravettian culture. As the Villabruna cluster spread across Europe, it replaced Magdalenian peoples, whose main ancestral components are associated with Goyet Q116-1 and the earlier Aurignacian culture [1]. The Villabruna cluster is thought to have diverged from West Eurasians around the onset of the Last Glacial Maximum (LGM) 26,000 years ago [2]. Western Hunter Gatherers eventually spread out over a wide range from Southeastern Europe across Western Europe and Southern Italy [3].

1. Posth et al. (2023): "Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers"

2. Marsh & Bello (2023): "Cannibalism and burial in the late Upper Palaeolithic: Combining archaeological and genetic evidence"

3. Mathieson et al. (2018): "The genomic history of Southeastern Europe"

The following are reconstructed Paleolithic populations:

Ancient East African

 

The Ancient East African category is a genetic approximation of an East African population ancestral to genetically distinct modern day populations of Nilotes (Dinka, Nuer), South Omotics (Aari), and Cushitics (Somalis, Ethiopians). A representative approximation ancestral to all three was constructed using DNA from modern Dinka samples, Mota (4,500 BP) and Pastoral Neolithic (~3,000 BP) samples.

The oldest fossils of anatomically modern humans in East Africa (Ethiopia) have been dated to around 200,000 years ago [5]. The split between West Africans (Niger-Congo) and East Africans (Nilo-Saharan, Afroasiastic) occurred around 28,000-34,000 years ago. The split between Nilo-Saharans (Dinka) and Afroasiastics (Cushitics) happened around 16,000 years ago [4]. Because of these deep divergence times, this Ancient East African population category is an attempt to model the ancestors of these particular East African groups prior to 30,000 years ago, since there are no genetic samples to work with from this time frame.


 

1.Lucas-Sánchez et al. (2021): "Population history of North Africa based on modern and ancient genomes"

2.Shriner et al. (2018): "Genetic ancestry of Hadza and Sandawe peoples reveals ancient population structure in Africa"

3.Skoglund et al. (2017): "Reconstructing prehistoric African population structure."

4.Prendergast et al. (2019): "Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa."
5.Vidal et al. (2022): "Age of the oldest known Homo sapiens from eastern Africa."

Ancestral North African

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The Ancestral North African population is inferred by analyzing the genetic structure of early North African groups before significant Eurasian admixture. This reconstruction is approximated from the non-Eurasian portion of the Taforalt samples. The Iberomaurusian culture (~15,000 BP, Morocco, Algeria, and Tunisia) provides the earliest ancient DNA evidence from the region, particularly the Taforalt individuals (~15,000 BP, Morocco). 
This lineage is genetically distinct from both sub-Saharan African and West Eurasian populations, positioning it as an intermediate population between early Africans and Eurasians.

The Epipaleolithic Taforalt Iberomaurusian samples from ~15,000 years ago share genetic continuity with the Early Neolithic samples from ~7,000 years ago at Ifri n'Amr Ou Moussa in Morocco. Late Neolithic samples from Kelif el Boroud in Morocco have around half of their ancestry from this lineage with the rest from a Neolithic lineage from southern Iberia [3]. Following the introduction of Neolithic European ancestry into the region, around 1,400 years ago Middle Eastern ancestry was introduced into the region, followed by Sub-Saharan African ancestry [4]. Berbers have the highest amounts of ancestry correlating to the Iberomaurusian lineage but it should be noted that Berbers are not genetically homogenous [3]. The Taforalt samples were found to have a component corresponding to around 45% Ancient North African and 55% Dzudzuana
[5]. The reconstructed approximation of Ancient North African genetic data was based on the non-Dzudzuana portions of the Taforalt lineage. The Natufian lineage was also found to have 27% Taforalt related and 73% Dzudzuana related ancestry [5]. Taforalt related ancestry may have also contributed to West Africans such as the Yoruba which have been found to have ~13% Taforalt related ancestry [5]. 

1.Lucas-Sánchez et al. (2021): "Population history of North Africa based on modern and ancient genomes"
2.Henn et al. (2012): "Genomic ancestry of North Africans supports back-to-Africa migrations"
3.Serra-Vidal (2018): "Insights into the Human Demographic History of Africa Through Whole-Genome Sequence Analysis."
4.Pfennig et al. (2023): "Evolutionary Genetics and Admixture in African Populations."
5.Lazaridis et al. (2018): "Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry"
 

 

Ancient Rainforest Hunter-Gatherers (Ancient RHG)

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The category Ancient Rainforest Hunter-Gatherers (RHG) represents a derived population meant to genetically approximate the ancient population ancestral to Central Africa’s modern Rainforest Hunter Gatherer tribes, also known as Central African Foragers or by their tribal names (Mbuti, Biaka, etc). These modern populations are mixed to varying degrees with adjacent Bantu groups, but retain a high degree of ancestry stemming from earlier groups in the region. It’s generally accepted their lineage began diverging from other African groups around 200,000 years ago around the same time the Khoisan began diverging. However, researchers have also noted that there is a lineage of mtDNA shared between RHG and Bantus, indicating their common ancestors diverged around 70,000 years ago. Modern RHG groups also had their own divergence between Eastern and Western groups around 20,000 years ago. The only ancient samples partially representing ancient RHG are the Shum Laka samples from 8,000 BP and 3,000 BP, which are around 65% West African (Basal) and 35% RHG. Modern day RHG are admixed, with the Biaka being around 59% Bantu, while the Mbuti are around 17% East African agro-pastoralist and 26% Bantu [3].


Citations:

 

1.Patin et al. (2014): "The impact of agricultural emergence on the genetic history of African rainforest hunter-gatherers and agriculturalists"

2.Hsieh et al. (2016): "Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in African hunter-gatherers"

3.Lipson et al. (2020): "Ancient West African foragers in the context of African population history."

Ancient West African

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The Ancient West African category here is meant to represent the lineage of West Africans just after their separation from the Nilo-Saharans (~28,000 years ago) and upon their entry into the West African region [16]. The West African region remains mostly unsampled in terms of ancient DNA relative to other regions, aside from the Shum Laka samples from Cameroon which date to ~ 8,000 BP and ~ 3,000 BP. These samples are a genetic combination of around 65% Basal West African and 35% of a lineage related to Rainforest Hunter Gatherers. The group represented at Shum Laka is not closely related to modern West Africans, but a study did note elevated allele sharing between this group and modern populations in the Grassfields region of Cameroon [1]. 
Our reconstructed statistical approximation of an Ancient West African genome is partially based on the West African portion of these samples.To create simulated samples of Ancient West Africans, a combination of the Basal West African portion of the Shum Laka genomes was combined with the non-Iberomaurusian portions of modern West African genomes mostly sourced from Yoruba, Lemande, Mende, and Gambian genetic files.

Ancient artifacts from West Africa are fairly numerous in contrast to the lack of ancient DNA from the region. Human settlements in the area are associated with artifacts found at several sites, including Korounkorokale rockshelter (~10,000 BP) in Mali [9], Faleme Valley in Senegal (13,000 BP - 17,000 BP) [14], along with Iho Eluru (Nigeria) and Bingerville (Ivory Coast) which both range from 13,000 BP to 15,000 BP  [15].

Ceramics were produced throughout the region around the same time, as found on the Bandiagara Plateau in Mali dated to ~12,450 BP [12][13] and Bosumpra Cave, Ghana within a similar timeframe [11].

It has been found that West African groups like the Yoruba have ~13% ancestry corresponding to the North African Taforalt samples, so the non-Taforalt associated portions of the Yoruba genome were used as well during the creation of the Ancient West African approximation [7]. The split between West Africans (Niger-Congo) and East Africans (Nilo-Saharan, Afroasiastic) occurred around 28,000-34,000 years ago [3].  West African genes are widespread throughout the African continent, and this process was perpetuated throughout the timeframe of the Bantu expansion, which began around 4,000 to 6,000 years ago in the region between Nigeria and Cameroon and spread throughout Central, Eastern, and Southern Africa [4][5][6].

 

1.Lipson et al. (2020): "Ancient West African foragers in the context of African population history"
2.Schlebusch & Jakobsson (2018): "African genomic diversity and its implications for human evolution"
3.Prendergast et al. (2019): "Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa."
4.Mitchell (2014): "Sub-Saharan Africa archaeology."
5.Fortes-Lima et al. (2023): "The genetic legacy of the expansion of Bantu-speaking peoples in Africa."
6.Pfennig et al. (2023): "Evolutionary Genetics and Admixture in African Populations."
7.Lazaridis et al. (2018): "Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry"
8.Skoglund et al. (2017): "Reconstructing prehistoric African population structure."
9.MacDonald, K. C. (1997): "Korounkorokalé revisited: The Pays Mande and the West African microlithic technocomplex"
10.Cerasoni et al. (2023): "Human interactions with tropical environments over the last 14,000 years at Iho Eleru, Nigeria"
11.Watson et al. (2017): "Bosumpra revisited: 12,500 years on the Kwahu Plateau, Ghana, as viewed from ‘On top of the hill’."
12.Huysecom (2020): "The first emergence of ceramic production in Africa."
13.Huysecom et al. (2009): "The emergence of pottery in Africa during the tenth millennium cal BC: new evidence from Ounjougou (Mali)."
14.Ndiaye et al. (2024): "Two new Later Stone Age sites from the Final Pleistocene in the Falémé Valley, eastern Senegal."
15.Lebrun et al. (2024): "Establishing a West African chrono-cultural framework: First luminescence dating of sedimentary formations from the Falémé Valley, Eastern Senegal."
16.Fan et al. (2019): “African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations”
 

The following are Neolithic populations:

Amur River Hunter-Gatherers

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The Amur River Hunter-Gatherers were a foraging population that occupied the Russian Far East and northeastern China during the Late Pleistocene and early Holocene. Genomic analysis suggests that they were closely related to Ancient Northern East Asians (ANEA) [1]. 

The Boisman samples (~7,000 BP) were used to represent Amur River Basin hunter gatherer ancestry since they are around 87% of this lineage with the remaining 13% being related to the Jomon. [4]. Genetic samples of hunter gatherers from the Amur River Basin, Japan, Neolithic Taiwan, and the Tibetan region are part of a deep lineage likely linked to a coastal migration during the Late Pleistocene era. The modern day populations closest to the Amur River ancestry are typically Tungusic language speakers along with the Nivkh ethnic group in Siberia [4].

1.Sikora et al. (2019): "The population history of northeastern Siberia since the Pleistocene"
2.He et al. (2023): "Extensive ethnolinguistic diversity at the crossroads of North China and South Siberia reflects multiple sources of genetic diversity"
3.Bennett et al. (2024): "Reconstructing the Human Population History of East Asia through Ancient Genomics"
4.Wang et al. (2021): "Genomic insights into the formation of human populations in East Asia."
5.Ning et al. (2020): "Ancient genomes from northern China suggest links between subsistence changes and human migration."
 

Anatolia Neolithic Farmers

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Agriculture first became widely practiced in the Fertile Crescent region of Southwest Asia (~12,000 BP) and spread throughout Western Eurasia, replacing local foraging techniques, before finally reaching parts of Central Anatolia by around 10,000 BP.  By around 8,900 BP, farmers expanding from Anatolia began moving into Southeastern Europe, and became known as EEF (Early European Farmers) after migrating throughout parts of Europe and gaining small amounts of admixture from Western Hunter Gatherers. 

 

Genetic studies show that Anatolia Neolithic Farmers (ANF) descended ultimately from populations related to Dzudzuana, but had additional Levantine and West Asian admixture [2]. The population immediately preceding them, which they shared a majority of their genome with (~90%), were the Anatolian Hunter Gatherers (AHG), represented by the Pinarbasi sample (~15,000 BP) [5]. The farming practices of the ANF expanded via the Aegean route, replacing most hunter-gatherer populations in Europe while mixing with Western Hunter-Gatherers (WHG). They later contributed to Caucasus populations and Indo-European steppe pastoralists[3]. ANF ancestry peaks in modern populations in southern Europe, such as the Sardinians, and are generally concentrated around the Mediterranean basin, the Near East and North Africa, including the Horn of Africa [7][8].

 

As an example of the widespread nature of ANF genes in modern populations, Eurasian sources with ancestry corresponding to ANF can also be found in the Horn of Africa’s modern populations, with the Eurasian components of the Amhara, Oromo, and Wolayta being composed of ~85% Anatolia_N and ~15% CHG, and the Ethiopian Somali Eurasian component being estimated to be slightly different at ~92% Anatolia_N and 8% CHG [4]. Note that these breakdowns are just examples of percentage estimates for the Eurasian portion of these modern groups, and the Eurasian portion only makes up part of their genome. 

 

Citations:

1.Liu et al. (2021): "Insights into human history from the first decade of ancient human genomics"

2.Schurr & Pipes (2011): "The prehistory of Mongolian populations as revealed by studies of osteological, dental, and genetic variation"

3.Nägele et al. (2022): "Ancient genomic research-From broad strokes to nuanced reconstructions of the past"

4.Molinaro et al. (2019): "West Asian sources of the Eurasian component in Ethiopians: a reassessment"
5.Feldman et al. (2019). “Late Pleistocene Human Genome Suggests a Local Origin for the First Farmers of Central Anatolia”

6.Allentoft et al. (2024): "Population genomics of post-glacial western Eurasia."

7.Clemente et al. (2021): "The genomic history of the Aegean palatial civilizations."
8.Irving-Pease et al. (2024): "The selection landscape and genetic legacy of ancient Eurasians."

Ancient Australians

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Human habitation in Australia began 50,000 to 65,000 years ago, when sea levels were lower towards the late Pleistocene [6]. The ancestors of the Australians and Papuans migrated out of Southeast Asia, over (now sunken) landmasses and over islands before reaching Sahul (the combined landmass of Australia and Papua New Guinea at the time). The ancestors of the Australians and Papuans diverged ~25,000 years ago. Prior to that, the Negrito populations of the Philippines diverged from the same lineage 37,000-46,000 years ago. The Basal Australasian lineage diverged from the ancestors of East Asians around 50,000 years ago [3]. Within the Australian continent, the Aboriginal Australian communities exhibit deep structure, and began diverging 26,000-35,000 years ago, on the basis of geographical distance and language in some cases [4][5]. They reached the (now) Sydney area on the other end of the Australian continent around 36,000 years ago [7]. The modern descendents of the ancient Aboriginal Australians overwhelmingly (traditionally) speak native languages belonging to the Pama-Nyungan language family [8].

 

1.Bennett et al. (2024): "Reconstructing the Human Population History of East Asia through Ancient Genomics"

2.Rogers (2016): "Understanding ancient human population genetics of the eastern Eurasian steppe through mitochondrial DNA analysis"
3.Larena et al. (2021): "Multiple migrations to the Philippines during the last 50,000 years."

4.Silcocks et al. (2023): "Indigenous Australian genomes show deep structure and rich novel variation."
5.Wright et al. (2018):"Ancient nuclear genomes enable repatriation of Indigenous human remains."
6.Clarkson et al. (2017):"Human occupation of northern Australia by 65,000 years ago."
7.Williams et al. (2014): "A glacial cryptic refuge in south-east Australia: human occupation and mobility from 36,000 years ago in the Sydney Basin, New South Wales."

8.Zuckermann et al. (2021):"LARA in the Service of Revivalistics and Documentary Linguistics: Community Engagement and Endangered Languages."

Baikal Hunter-Gatherers

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The Lake Baikal region has been important to anatomically modern human for millenia, and humans began entering this part of Siberia ~38,000 years ago [5]. The Baikal Hunter-Gatherers were a distinct foraging population in the Lake Baikal region of Siberia, and closely related to the lineage of Ancient Northern East Asians (ANEA). 

The Baikal Hunter Gatherers are represented by Neolithic Shamanka_EN samples (~7560–6690 cal. BP) and are associated with the Cis-Baikal Region of Eastern Siberia [4]. After the Early Neolithic, the area saw a genetic shift, with Late Neolithic/Bronze Age hunter gatherers displaying admixture from a source related to the Ancient North Eurasians, which may have been Ancient Paleo-Siberians [1][2].

 

There were numerous and recurrent genetic demographic shifts within the Cis-Baikal and Yakutia regions, which are contrasted with relative genetic continuity in other areas of Siberia like the Trans-Baikal [5].

 

1.de Barros Damgaard et al. (2018): "The first horse herders and the impact of early Bronze Age steppe expansions into Asia"

2.Sikora et al. (2019): "The population history of northeastern Siberia since the Pleistocene"
3.Wang et al. (2021): "Genomic insights into the formation of human populations in East Asia."
4.Moussa et al. (2024): "Insights into Lake Baikal's ancient populations based on genetic evidence from the Early Neolithic Shamanka II and Early Bronze Age Kurma XI cemeteries."
5.Kılınç et al. (2024): "Human population dynamics and Yersinia pestis in ancient northeast Asia."

Caucasus Hunter-Gatherers (CHG)

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The Caucasus Hunter-Gatherers (~13,000–10,000 BP) were an isolated Upper Paleolithic population inhabiting the Caucasus Mountains. Their genetic legacy contributed significantly to later Indo-European, Iranian, and South Asian gene pools[1].

 

CHG individuals were genetically distinct from Anatolia Neolithic Farmers and Eastern European Hunter-Gatherers (EHG) but later merged with them to form the Yamnaya steppe pastoralists (~5,000 BP), a key group in the spread of Indo-European languages[2]. Their DNA also contains a Basal Eurasian component, indicating early connections to Near Eastern populations[3].

 

CHG were closely related to Zagros Neolithic Farmers and at times these populations are grouped together when performing genetic analysis.The CHG clade diverged from the Western Hunter Gatherers around 45,000 years ago, and then further split from the ancestors of the Anatolian Neolithic Farmers around 25,000 years ago. The CHG (and Zagros Farmer ancestry) were a major ancestral contributor (around 40%) to the Western Steppe Herders who eventually migrated into Europe. [4]

Ancestry related to CHG and Zagros Farmers (when they are combined) is found most commonly in countries east of the Caucasus, along with Pakistan, India, Afghanistan and Iran [5].

1.Nägele et al. (2022): "Ancient genomic research-From broad strokes to nuanced reconstructions of the past"

2.Liu et al. (2021): "Insights into human history from the first decade of ancient human genomics"

3.He et al. (2021): "Genomic insights into the differentiated population admixture structure and demographic history of North East Asians"

4.Jones et al. (2015): "Upper Palaeolithic genomes reveal deep roots of modern Eurasians."
5.Irving-Pease et al. (2024): "The selection landscape and genetic legacy of ancient Eurasians."

East African Hunter-Gatherers (Mota/Bayira)

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The Mota individual (~4,500 BP, Ethiopia) represents one of the earliest sequenced genomes from an East African forager. His genetic profile confirms that West Eurasian admixture in East Africa occurred later (~3,000 BP), supporting the hypothesis that the Afroasiatic language family’s genetic input from the Near East postdates his existence[1]. 

Several modern tribes display elevated levels of Mota ancestry [3]. It is the highest in the Ari/ Aari, Bench, and Sheko tribes, but also present in lesser amounts in smaller tribes like the Chabu, Majang, and Hadza [4]. 

 

1.Gallego Llorente et al. (2015): "Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent"

2.Skoglund et al. (2017): "Reconstructing Prehistoric African Population Structure"

3.Gurdasani et al. (2021): "Insights into the genomic diversity of Africa."

4.Lipson et al. (2022): "Ancient DNA and deep population structure in sub-Saharan African foragers."

East African Pastoral Neolithic

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The East African Pastoral Neolithic period spanned from around 5,000 BP to 1,200 BP and coincided with the spread of nomadic pastoralism, small scale farming, pottery usage, and expansion of human populations in East Africa. It is theorized that East African Pastoralists were first found in the Nile Valley before their populations expanded and gradually moved southward. This is evidenced partly by genetic samples from East African Pastoralists who were found to be present in Upper Nubia (present day Northern Sudan) around 4,000 BP (Kerma culture) [4]. 

 

Pastoral Neolithic samples found in in the present day East African countries of Kenya and Tanzania, specifically in regions area around Lake Turkana, were used within the reference panel for this category. The two main groups in the area during this period are known as the Elmenteitan and the Savanna Pastoral Neolithic. The herding of domesticated cattle was prevalent, with cattle first being domesticated in the Near East, before spreading in North Africa at around 8,000 BP and then East Africa at around 5,000 BP [3].
It appears that migrations from pastoralist populations in the Sahara moving into Sudan and further south, starting around 4,500 years ago, introduced lactase persistence alleles into East African populations [5][6].
East African Pastoral Neolithic populations were approximately 40% of Eurasian ancestry, 40% Nilotic, and 20% Mota. They display the closest affinities to modern Cushitic speaking populations [1].

 

1.Prendergast et al. (2019): "Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa"

2.Wang et al. (2022): "Genomic insights into the formation of human populations in East Africa"
3. McTavish et al. (2013): "New World cattle show ancestry from multiple independent domestication events."

4.Wang et al. (2022): "4000-year-old hair from the Middle Nile highlights unusual ancient DNA degradation pattern and a potential source of early eastern Africa pastoralists."

5.Lucas-Sánchez et al. (2021): "Population history of North Africa based on modern and ancient genomes."
6.Ranciaro et al. (2014): "Genetic Origins of Lactase Persistence and the Spread of Pastoralism in Africa."

Eastern European Hunter-Gatherers (EHG)

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The EHG, also called the Sidelkino cluster, emerged in Eastern Europe around 14,000 years ago and are a mix of WHG and ANE ancestries [3]. Both the WHG and EHG remained relatively isolated in Western and Eastern Europe until around 8,000 years ago. The EHG also ended up forming around 50% of the ancestry of Western Steppe Herders who contributed heavily to the genetics of several regions [1][2]. In terms of haplogroups, there was a marked contrast between the WHG and EHG, with the WHG (also called the Oberkassel cluster) being predominantly Y-chromosome haplogroup I and mtDNA haplogroup U5, while the EHG predominantly had Y-chromosome haplogroups J, Q, and R along with mtDNA haplogroups R1b, U2, and U4.
EHG related ancestry is highest in Finland and Estonia, and is also a significant component in the genomes of populations found in Central Asia and Mongolia [4].

 

1.Mathieson et al. (2018): "The Genomic History of Southeastern Europe"

2.Haak et al. (2015): "Massive migration from the steppe was a source for Indo-European languages in Europe"

3.Posth et al. (2023):"Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers."
4.Irving-Pease et al. (2024): "The selection landscape and genetic legacy of ancient Eurasians."

Hoabinhian Hunter-Gatherers

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The Hoabinhian hunter gatherers were a collection of foraging populations found in Southeast Asia and Southern China, and occupied the region around 13,000 years ago to 3,000 years ago [1][2]. Anatomically modern humans entered Southeast Asia somewhere between 50,000 to 70,000 years ago, and this was possibly done by taking a coastal route [2][5]. The Hoabinhian were displaced starting around 4,000 years ago as East Asian agricultural populations started to expand and move southward [1].The closest modern populations to the Hoabinhian are the Orang Asli tribes of hunter gatherers that live in Southeast Asia, which are a mix of ancestral components related to East Asians and Hoabinhian [2][3].


1.Wu et al. (2022): "Dedan Cave: Extending the evidence of the Hoabinhian technocomplex in southwest China."
2.Aghakhanian et al. (2022): "Sequence analyses of Malaysian Indigenous communities reveal historical admixture between Hoabinhian hunter-gatherers and Neolithic farmers."
3.Göllner et al. (2022): "Unveiling the Genetic History of the Maniq, a Primary Hunter-Gatherer Society."
4.McColl et al. (2018): "The prehistoric peopling of Southeast Asia."
5.McColl et al. (2018): "Ancient Genomics reveals four prehistoric migration waves into Southeast Asia"
 

Iberomaurusians
 

Humans have been present in North Africa for at least 300,000 years, as evidenced by fossilized remains from Jebel Irhoud, Morocco [6].
The Iberomaurusian culture (~15,000 BP, Morocco, Algeria, and Tunisia) provides the earliest ancient DNA evidence from the region, particularly the Taforalt individuals (~15,000 BP, Morocco).

Ancient DNA from Taforalt (~15,000 BP, Morocco) reveals that Iberomaurusians were a mix of West Eurasian and Ancestral North African, having roughly 55% Dzudzuana related ancestry and 45% Ancestral North African related ancestry[2]. The Epipaleolithic Taforalt Iberomaurusian samples from ~15,000 years ago share genetic continuity with the Early Neolithic samples from ~7,000 years ago at Ifri n'Amr Ou Moussa in Morocco. Late Neolithic samples from Kelif el Boroud in Morocco have around half of their ancestry from this lineage with the rest from a Neolithic lineage from southern Iberia [4].
Following the introduction of Neolithic European ancestry into the region, around 1,400 years ago Middle Eastern ancestry was introduced into the region, followed by Sub-Saharan African ancestry [5]. Berbers have the highest amounts of ancestry correlating to the Iberomaurusian lineage but it should be noted that Berbers are not genetically homogenous [4]. There were Iberomaurusian contributions to West African ancestry, with groups such as the Yoruba being modeled as ~13% Iberomaurusian [2]. The Natufian lineage was also found to have 27% Taforalt related and 73% Dzudzuana related ancestry [2]. Sahelian groups such as the Fulani received admixture from ancient North African sources ~7,000-8,000 years ago, with the source best being modeled as similar to Late Neolithic Moroccans (5,000 BCE) or Moroccan Early Neolithic (KTG, ~7000 years BP) which has Iberomaurusian as one of its components. The introgression of North African sources into the Fulani corresponds to the Green Sahara time period [3].


1.van de Loosdrecht et al. (2018): “Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations”

2.Lazaridis et al. (2018): “Paleolithic DNA from Caucasus reveals core of West Eurasian ancestry”
3.D’Atanasio et al. (2023): The genomic echoes of the last Green Sahara on the Fulani and Sahelian people

4.Serra-Vidal (2018): "Insights into the Human Demographic History of Africa Through Whole-Genome Sequence Analysis."

5.Pfennig et al. (2023): "Evolutionary Genetics and Admixture in African Populations."
6.Hublin et al. (2017): "New fossils from Jebel Irhoud, Morocco and the pan-African origin of Homo sapiens."

Jomon

The Jomon lineage is estimated to have diverged from other East Asian populations around 22,000–25,000 years ago. Genetic analyses of Jomon remains, such as the IK002 individual, confirm that the Jomon formed a distinct clade separate from later East Asians[1].

A 2021 study by Adachi et al. estimated that the Jomon genetic divergence occurred approximately 22,000 years ago, predating major migrations that shaped the genetic structure of mainland East Asians[2]. Other studies suggest that the Jomon carried a unique genetic signature, possibly influenced by Northern Eurasian and early East Asian populations, but remained highly isolated from continental populations for thousands of years[3].

The Jomon divergence is further supported by their high levels of genetic drift, which resulted from their long-term isolation on the Japanese archipelago. This distinct lineage remained largely intact until the arrival of Yayoi agriculturalists (~3,000 BP), which significantly altered the genetic landscape of Japan[4].

1.Gakuhari et al. (2020): “Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations”

2.Adachi et al. (2021): “Ancient genomes from the initial Jomon period: new insights into the genetic history of the Japanese archipelago”

3.Kanzawa-Kiriyama et al. (2019): “Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan”

4.Gakuhari et al. (2019): “Jomon genome sheds light on East Asian population history”

Ancient Melanesians
 

The “Ancient Melanesians” grouping is inclusive of both Ancient Papuans and Ancient Melanesian Islanders. Upon leaving Southeast Asia, lower sea levels allowed humans to move gradually into Sahul (New Guinea and Australia) around 55,000 years ago [7]. Using genetic evidence (mtDNA) it seems two groups of settlers moved separately into Northern and Southern Sahul, with Northern Sahul corresponding to Papua New Guinea and Near Oceania, and Southern Sahul corresponding to Australia. The crossing from Southeast Asia (Sunda) appears to have been planned, since there was around 56 miles of ocean between the two landmasses and large numbers of people were involved. The settlement of New Guinea was probably initiated from its southeast region, where the oldest archaeological sites have been found [6].  Eventually after Papua New Guinea, people reached the North Solomon Islands by ~ 33,000 years ago [7].

The Pacific Islands in modern times have a mixture of ancestries derived from two divergent ancestral populations, the Melanesians with origins in Papua, and the Austronesians with an ultimate origin in Taiwan and mainland East Asia. The sample used to represent these ancient Melanesians is from Vanuatu and dated to around 2,300 BP [5].

Islands proximal to Papua (Near Oceania) were settled by Melanesians 30,000-40,000 years ago, and other islands in remote Oceania (Fiji, Samoa, Tonga,...) were then settled by Neolithic Austronesians (also called First Remote Oceanians) belonging to the Lapita culture (~2,700 BP) during the Austronesian expansion period which began around 6,000 years ago. Different pulses of admixture and migrations occurred, leaving the modern populations of the region with varying proportions of these two ancestral sources [2][4][5].

 

The Basal Australasian lineage diverged from the ancestors of East Asians around 50,000 years ago. Then, the Negrito populations of the Philippines diverged from the same lineage 37,000-46,000 years ago.  Following that, the ancestors of the Australians and Papuans diverged ~25,000 years ago [3]. Papuans also have around 2% of their genome traced to an earlier out-of-Africa migration of anatomically modern humans (~120,000 years ago) [9]. Additionally, both Papuans and Aboriginal Australians have around 4% of their genomes traced to Denisovans [8] [9]. The Ayta Magbukon of the Philippines have the highest amount of Denisovan, and diverged from the ancestors of the Papuans around 53,000 years ago [10].
 

 

1.Reich et al. (2011): "Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania"

2.Skoglund et al. (2016):"Ancient Genomics and the Peopling of the Southwest Pacific."

3.Larena et al. (2021): "Multiple migrations to the Philippines during the last 50,000 years."
4. Pawley et al. (2007): "The origins of Early Lapita culture: the testimony of historical linguistics."

5.Lipson et al. (2018): "Population Turnover in Remote Oceania Shortly after Initial Settlement."
6.Brucato et al. (2021):"Papua New Guinean Genomes Reveal the Complex Settlement of North Sahul."
7.Pedro et al. (2020):"Papuan mitochondrial genomes and the settlement of Sahul."

8.Browning et al. (2019): "Multiple Deeply Divergent Denisovan Ancestries in Papuans."
9.Pagani et al. (2016):"Genomic analyses inform on migration events during the peopling of Eurasia."
10.Larena et al. (2021):"Philippine Ayta possess the highest level of Denisovan ancestry in the world."