Ancient DNA (aDNA) is genetic material extracted from ancient sources, recovered from bones, teeth, or other biological remains. Unlike DNA recovered from living organisms, aDNA is often highly degraded and present only in small quantities. Researchers extract it inside specialized clean rooms to avoid contamination and then sequence it to determine the order of nucleotides. Earlier studies focused on uniparental markers: mitochondrial DNA (mtDNA), inherited maternally, and Y chromosome DNA, inherited paternally, to trace single lines of ancestry. Advances in whole genome sequencing now allow researchers to reconstruct more detailed population histories and genetic relationships. Modern humans (Homo sapiens) and the ancestors of Neanderthals (Homo neanderthalensis) and Denisovans (Homo denisova) diverged from a common ancestral population between c. 500-700 thousand years ago (kya). Neanderthals and Denisovans subsequently split c. 350-450 kya, with Neanderthals occupying Europe and western Asia until their extinction c. 40 kya, and Denisovans inhabiting regions of central and eastern Asia. By the late Middle Pleistocene, Neanderthals had differentiated into eastern and western populations, undergoing repeated population expansions and replacements that reduced their genetic diversity, whereas Denisovans appear to have been genetically more diverse, forming at least a northern branch and an unsampled southern lineage. Modern humans evolved in Africa by 200 kya at the latest, by which time human populations had already differentiated into several distinct lineages. Early modern human dispersals Out-of-Africa between 130-90 kya reached Southeast Asia and Australia but left no genetic trace in most present-day populations. The major migration Out-of-Africa c. 70-60 kya is the primary source of ancestry in present-day non-African populations. During their expansion, the Main Eurasian lineage of modern humans admixed with Neanderthals in or near southwest Asia c. 60-50 kya, resulting in c. 2% Neanderthal ancestry in all present-day non-Africans. Some modern human groups subsequently admixed with Denisovans, likely in East Asia, contributing c. 2-3.5% of the ancestry of present day Oceanians, and small amounts to South Asians, East Asians, and Native Americans. Neanderthals and Denisovans also interbred with each other, as shown by a first generation c. 50 kya hybrid individual from Denisova cave. Basal Eurasians, a lineage that diverged from other non-Africans before c. 60 kya, carried little or no Neanderthal ancestry and later contributed to Upper Paleolithic and early Holocene populations in West Eurasia and South Asia, reducing the Neanderthal DNA of these groups and their descendants. After the initial Out-of-Africa dispersal, the Main Eurasian population likely remained in a single hub for several millennia, possibly in the Middle East or North Africa, before expanding across Eurasia in multiple waves: an early wave that contributed minimally to later populations; an Initial Upper Paleolithic wave (c. 45 kya) which expanded widely across most of Eurasia; and the Early Upper Paleolithic expansion (c. 40 kya) which largely replaced earlier lineages in Europe and admixed with descendants of Initial Upper Paleolithic populations in Siberia, producing lineages ancestral to present-day Europeans, Siberians, and Native Americans. Following the Campanian Ignimbrite eruption (c. 40 kya), Initial Upper Paleolithic lineages in West Eurasia were replaced by populations exhibiting the first significant genetic continuity with modern Europeans. Around the time of the Last Glacial Maximum (c. 25-19 kya), both western and eastern Eurasia underwent major population turnovers. In Europe, post-LGM groups largely replaced previous European populations, while in northern East Asia, late Pleistocene groups were replaced by groups closer to Holocene East Asian populations. By c. 12.5 kya, individuals such as Anzick 1 in Montana were present in the Americas, representing a population that had already diversified into multiple Native American lineages.
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Genomes and populations
Archaic humans Calabrian bottleneck (c. 930 Kya to 813 Kya) A genetic study from 2023 of 3154 individuals showed that human ancestors went through a severe population bottleneck with about 1280 breeding individuals between around 930,000 and 813,000 years ago. The bottleneck lasted for about 117,000 years and brought human ancestors close to extinction. This population crash would likely have had an impact on human genetic diversity, and may have driven the evolution of important features of modern humans, such as brain size. The geneticists suggest that the bottleneck may have led to increased inbreeding and a subsequent loss in human genetic diversity that has persisted to this day. The causes of the bottleneck are unknown.
Sima de los Huesos hominins (c. 430 kya)
Meyer et al. (2016) extracted nuclear DNA from two individuals recovered at the Sima de los Huesos site, Atapuerca, northern Spain, dated to around 430 kya. Analysis of their genomes indicates that these individuals were either Early Neanderthals or members of a population ancestral to Neanderthals on a lineage that had already diverged from Denisovans. Although their nuclear DNA is more closely related to Neanderthals than Denisovans, they carry a divergent mitochondrial DNA lineage that is more closely related to that of Denisovans. This suggests that the original mtDNA lineage of early Neanderthals, such as those from Sima de los Huesos, was later replaced as a result of gene flow from early modern humans from Africa.
Denisova 2 Denisovan (c. 250-200 kya)
Denisova 2 is a female Denisovan sequenced from a molar recovered in the Main Chamber of Denisova Cave, layer 22.1, dated to between 250-200 kya. Her mitochondrial DNA is most closely related to that of Denisova 8. Denisova 2 carried recent Neanderthal ancestry from introgression c. 1,500 years before her lifetime.
Denisova Cave Denisovans (c. 200 kya) Denisovan DNA dating to c. 217-187 kya has been extracted from three bone fragments (Denisova 19, Denisova 20, and Denisova 21) recovered from Layer 15 of the East Chamber of Denisova Cave, Siberia. Denisova 19 and 21 have identical mitochondrial DNA sequences, indicating they may represent the same individual or close maternal relatives. Their mtDNA differs from that of Denisova 20 by only four substitutions. All three mtDNA sequences form a clade with Denisova 2 and Denisova 8.
Scladina Neanderthal (c. 127 kya) Scladina I-4A is an approximately eight-year-old Neanderthal child sequenced from a maxillary bone recovered from Scladina Cave, Sclayn, Belgium. The nuclear DNA of Scladina is more closely related to Vindija than to the Altai Neanderthal. Scladina is thought to have diverged from the common ancestor of Vindija around 100 kya, close to the estimated divergence time of the Hohlenstein-Stadel (HST) individual. Like HST, Scladina may represent a population that was ancestral to later Neanderthals outside the Altai lineage. The mitochondrial DNA of Scladina is most similar to that of the Altai Neanderthal and, like HST, belongs to a lineage that is not found among later European Neanderthals.
Hohlenstein–Stadel Neanderthal (c. 124 kya) The Hohlenstein–Stadel Neanderthal ('HST') is represented by a femur recovered from Hohlenstein–Stadel cave in southwestern Germany within a Mousterian context. The nuclear DNA of HST is more closely related to the Western Neanderthal lineage (e.g. Vindija) than to the eastern Altai Neanderthal lineage. HST is estimated to have diverged from its common ancestor with Vindija around 100 kya and may represent a population ancestral to all currently sequenced Neanderthals outside the Altai lineage. HST carries the most deeply divergent Neanderthal mtDNA lineage sequenced to date, estimated to have diverged from other Neanderthal mtDNA lineages around 270 kya. A closely related mitochondrial DNA lineage has been identified at a c. 112 kya layer of the Galería de las Estatuas site, Spain, but this lineage is not found in the site's upper layers, suggesting it was later replaced by lineages related to Mezmaiskaya I, Vindija, and Chagyrskaya.
Stajnia S5000 Neanderthal (c. 116 kya) Stajnia S5000 is a Neanderthal sequenced from a molar recovered from Stajnia Cave in Poland, associated with Micoquien artefacts. The archaeological layer is at least 49 thousand years old, and the individual has been genetically dated to c. 116 kya. The mitochondrial DNA of Stajnia S5000 belongs to a clade that diverged from Denisova 5, Denisova 15, and Scladina around 170 kya, and is most closely related to the Mezmaiskaya 1 Neanderthal from the North Caucasus. It falls outside the range of variation observed in other European Neanderthal mtDNA lineages, including Scladina and Hohlenstein-Stadel.
Denisova 5 Neanderthal (c. 110.5 kya) Denisova 5, also known as the 'Altai Neanderthal', is an adult female sequenced from a toe phalanx recovered from Denisova Cave, Siberia. Her nuclear DNA represents the most deeply divergent Neanderthal lineage sequenced to date, other than the Sima de los Huesos hominins. Genetic studies indicate that late Neanderthals split into eastern and western populations, with Denisova 5 representing the eastern branch and Vindija 33.19, a c. 44 kya individual from Croatia, representing the western branch. The Denisova 5 lineage is estimated to have diverged from other Neanderthal populations around 150 kya. Denisova 5 descended from a population with a small effective population size. Long runs of homozygosity indicate that inbreeding was common among her recent ancestors, including her parents, who were second-degree relatives, such as half-siblings or double first cousins. Polygenic predictions suggest that Denisova 5 was at elevated genetic risk for a range of conditions including cancer, gastrointestinal and liver diseases, immune system and neurological disorders, metabolic conditions, and muscular abnormalities. Her mitochondrial DNA belongs to the more typical, non-HST Neanderthal lineage. Andreeva et al. (2022) assign Denisova 5 to the NE clade, along with Denisova 15 and Scladina I-4A. This haplogroup was likely widespread among Middle Paleolithic Neanderthals in Europe and Central Asia. Approximately 3.7% of the Denisova 5 genome derived from early modern humans, although she was not closely related to the Neanderthal population that contributed DNA to the ancestors of present-day humans.
Denisova 11 Denisovan-Neanderthal hybrid (c. 98.7 kya) Denisova 11 ("Denny") is a female individual sequenced from a small bone fragment recovered from the East Chamber of Denisova Cave, Siberia, dated to around 118-79 kya. Denisova 11 was the first-generation offspring of a Denisovan father and a Neanderthal mother. Her father was a Denisovan but also carried traces of Neanderthal ancestry from one or more Neanderthal ancestors who lived approximately 300 to 600 generations before his lifetime. Her father's Neanderthal ancestry was genetically more similar to Denisova 5 than that of her mother, who was more closely related to Chagyrskaya 8 and Vindija 33.19. This difference in parental ancestry suggests that a population turnover occurred among Neanderthal populations in the Altai mountains prior to Denisova 11's lifetime.
Mezmaiskaya Neanderthals (c. 97-50 kya) Genetic data from three Neanderthal individuals has been recovered from Mezmaiskaya cave, North Caucasus, Russia. Mezmaiskaya 1, a near-complete skeleton of a two-week old child (c. 70-60 kya), and Mezmaiskaya 3, a 5-6 year old female (c. 90-100 kya), are both from layer 3 and associated with the early Eastern Micoquien industry, and represent an earlier lineage. The third individual, Mezmaiskaya 2, is more closely related to other late Western European Neanderthals. Mezmaiskaya 1 and Mezmaiskaya 3 are most closely related to Stajnia S5000. Mezmaiskaya 3 shows greater affinity to Chagyrskaya 8 and Vindija 33.19 than to the Altai Neanderthal, sharing c. 17% of derived alleles with Chagyrskaya 8 and c. 13% with Vindija 33.19. Both individuals are assigned to the NM2 mitochondrial haplogroup by Andreeva et al. (2022), which falls outside the variation of later European Neanderthals. Mezmaiskaya3, Mezmaiskaya1, and Stajnia S5000 belong to a mtDNA clade that is separate from that of Altai, Denisova 15, and Scladina I-4A.
Chagyrskaya 8 Neanderthal (c. 80 kya) Chagyrskaya 8 is a female Neanderthal from Chagyrskaya Cave in the Altai Mountains, genetically dated to c. 80 kya, though the Micoquien archaeological layer she is associated with dates to around 60 kya. She is more closely related to Neanderthals from western Eurasia such as Vindija than to the earlier Altai Neanderthal from the nearby Denisova Cave, which is located about 100 km away, suggesting that her population was part of an eastward Neanderthal expansion that occurred around 120-80 thousand years ago. Chagyrskaya 8 is the closest known relative to the mother of Denisova 11, the Denisovan-Neanderthal hybrid. Her genome contains approximately 12.9% of regions homozygous by descent, consistent with descent from a small, isolated population of fewer than 60 individuals.
Denisova 3 Denisovan (c. 64 kya) Denisova 3, a female estimated to have been around 13 years old at the time of her death, was recovered from the East Chamber of Denisova Cave, Siberia in 2008. Molecular dating places her between around 76-52 kya. Analysis of her nuclear and mitochondrial DNA provided the first genetic evidence of an archaic human group, subsequently named Denisovans. Denisova 3 carried lower levels of Neanderthal ancestry than Denisova 2 and Denisova 8, with at least 0.5% of her genome deriving from a lineage similar to that of Denisova 5 (the 'Altai Neanderthal'). Her genome exhibits low heterozygosity, suggesting that she belonged to a population with small effective size, but she carried few long runs of homozygosity, indicating that less inbreeding occurred in her ancestral population compared with Neanderthals. Denisova 3 carried genetic variants that in modern humans are associated with dark skin, brown hair, and brown eyes, along with other derived pigmentation alleles with unknown effects. She also carried genetic variants linked to dental morphology, impulsivity, cerebral cortex development, hand structure, and nasal speech, as well as a nonfunctional FUT2 gene, which may have provided protection against intestinal viral infections. Present-day East Asians, Siberians, and Native Americans carry ancestry closely related to Denisova 3, resulting from admixture between Denisovans and the ancestors of these groups. The limited geographical distribution of Denisova 3-related ancestry in present-day human populations suggests that this admixture occurred in mainland Asia, possibly in East Asia.
Vindija 33.19 Neanderthal (c. 52 kya) Vindija 33.19 is a female Neanderthal from Vindija Cave, Croatia, dated to c. 52 kya. Her genome represents the 'Western' Eurasian Neanderthal population, which diverged from the 'Eastern' Altai lineage c. 130-145 kya, and subsequently from the Mezmaiskaya (Caucasus) lineage between c. 80-100 kya. Vindija 33.19 is genetically more similar to the Neanderthals who interbred with the ancestors of non sub-Saharan African present-day humans than the Altai Neanderthal. Her genome carried c. 2.5% modern human ancestry, similar to that of the Altai Neanderthal, suggesting that gene flow from early modern humans into Neanderthal populations occurred prior to the separation of eastern and western Neanderthal lineages. Low heterozygosity in the Vindija 33.19 genome indicates that she belonged to a relatively small and isolated population, though it was likely larger than those of the Chagyrskaya and Altai Neanderthals.
Gibraltar Neanderthals (c. 50 kya) The Gibraltar Neanderthals are represented by two partial crania: Gibraltar 1, an adult female from Forbes' Quarry; and Gibraltar 2, a 3-to-5 year-old male child, from Devil's Tower. Gibraltar 1 is equally closely related to Vindija 33.19 and Chagyrskaya 8, but less closely related to the Altai Neanderthal. She is genetically more similar to older Neanderthals such as Scladina, HST, and Mezmaiskaya 1, than to roughly contemporaneous individuals such as the c. 49 thousand year-old El Sidrón 1253. Her divergence from Vindija 33.19 is estimated at around 94 kya, and from Chagyrskaya 8 at around 101.6 kya. The mitochondrial DNA of Gibraltar 1 clusters with Thorin, Stajnia S5000, and Mezmaiskaya 1. Andreeva et al. (2022) place her within the NM1 haplogroup, together with Stajnia S5000. Gibraltar 1 and Thorin form a distinct mtDNA clade, and the close genetic relationship these individuals suggests that Gibraltar Neanderthals may have been a part of a larger interconnected Neanderthal population in southwest Europe.
El Sidrón Neanderthals (c. 49 kya) The El Sidrón site in northern Spain, dated to c. 49 kya, has yielded the remains of at least 13 Neanderthal individuals, who form a closely related group. The Y chromosome of El Sidrón 1253 is most closely related to that of Thorin, while his mitochondrial DNA clusters with other late European Neanderthals. The mtDNA haplotypes of the El Sidrón Neanderthals suggests male philopatry: all males share a closely related mtDNA lineage, whereas three out of four females carried mtDNA lineages originating from outside the group. One female had the same mtDNA haplotype as two juveniles, suggesting they may have been her children. The El Sidrón Neanderthals exhibit a higher proportion of runs of homozygousity than the Vindija, Altai, and Denisova Neanderthals, indicating a long history of inbreeding. Two individuals carried a version of the FOX2P gene associated with language ability, identical to the version found in modern humans. One individual carried a variant of the MC1R gene, suggesting that some Neanderthals had pale skin and red hair, and El Sidrón 1253 also carried a variant of the TAS2R38 gene, making them sensitive to bitter tasting compounds.
Goyet Neanderthals (c. 45.5-40.5 kya) The Goyet Caves in Belgium were excavated in the late 19th and 20th centuries, revealing evidence of Middle and Upper Paleolithic human occupation associated with the Mousterian, Lincombian-Ranisian-Jerzmanowician, Aurignacian, Gravettian, and Magdalenian industries. The Goyet Neanderthals are dated to c. 40.5-45.5 kya, though the remains may represent a single occupation of c. 44-45.5 kya Their mitochondrial DNA is most closely related to central and western European late Neanderthal mtDNA lineages such as that carried by Feldhofer 1, El Sidron, and Vindija. All these sequences exhibit only minor genetic variation, consistent with a low effective population size among late Neanderthals. Three distinct mtDNA lineages have been identified among the Goyet neanderthals: Goyet Q305-4, who forms a clade with Feldhofer 2; Goyet Q56-1, Q374a-1, and Q305-7, who form a clade with Vindija; and Goyet Q57-3, Q57-1, and Q57-2, who form a clade with Feldhofer 1.
Okladnikov Cave Neanderthals (c. 44 kya) Three Neanderthal individuals associated with a Mousterian context have been recovered from Layer 3 of Okladnikov Cave, in the Altai Mountains of southern Siberia. These are Okladnikov 2 (also known as Okladnikov 14), Okladnikov A (or Okladnikov 11), a 7–11 year old male represented by a partial femur, and Okladnikov B (or Okladnikov 15), an adult female represented by a humerus fragment. The Okladnikov individuals were genetically distinct from the Neanderthals at nearby Chagyrskaya Cave, although both groups were equally closely related to European Neanderthals. Late European, Chagyrskaya and Okladnikov Neanderthals are thought to be descendants of a common Neanderthal population that expanded rapidly across Eurasia between c. 100-115 kya. Okladnikov 2 carries a mitochondrial DNA lineage basal to that of Mezmaiskaya 1, while Okladnikov B carried an identical mtDNA haplotype to that of Chagyrskaya G, suggesting that these individuals lived within a few thousand years of each other.
Mezmaiskaya 2 Neanderthal (c. 43 kya) Mezmaiskaya 2, a 1-2 year old male child from layer 2 of Mezmaiskaya cave, Russia, is associated with the later Eastern Micoquien, and has been directly dated to c. 44.4-42.6 kya. Mezmaiskaya 2 is more closely related to other late Western Neanderthals than with the earlier population represented by Mezmaiskaya 1 and Mezmaiskaya 3 from the same site. He is assigned to the NL1 mtDNA haplogroup, shared with other late Neanderthals in Western and Central Europe, by Andreeva et al.
Les Cottés Neanderthal (c. 43 kya) The Les Cottés Neanderthal ('Les Cottés Z4-1514'), is a female individual from Les Cottés cave, France, dated to c. 43.7-42.7 kya. She is genetically closer to Vindija 33.19 than to the Altai Neanderthal, and shows highest affinity to the nearby Goyet Q56-1 and Spy 94a Neanderthals. She is less closely related to the Mezmaiskaya Neanderthals: among the late Neanderthals, Les Cottés Z4-1514 is the most genetically distant individual from Mezmaiskaya 2. Her genome shows evidence of gene flow from an unsampled lineage that diverged from the most recent common ancestor of the European Neanderthals over 80 kya. According to Andreeva et al. (2022), Les Cottés Z4-1514 carries the NL2 mitochondrial haplogroup, a sister clade to other late Neanderthals.
Grotte Mandrin Neanderthal (c. 42 kya) A male Neanderthal from Mandrin Cave, France ('Thorin'), dated to c. 42 kya and associated with the Post-Neronian II tradition, belonged to a distinct Neanderthal lineage that diverged from the main ancestral European Neanderthal population c. 100 kya. D-statistics indicate that his lineage diverged before other late Neanderthals of the Vindija lineage, with the possible exception of the Forbes' Quarry Neanderthal, who shares some excess alleles with Thorin. Thorin's genome did not show evidence of recent gene flow from modern humans. Thorin exhibits elevated homozygosity compared to other late European Neanderthals, consistent with recent inbreeding and descent from a small population that was genetically isolated for up to 50,000 years. His mitochondrial DNA was most closely related to the Stajnia S5000, Mezmaiskaya 1, and Forbes' Quarry individuals, and distinct from other late European Neanderthals. His Y-chromosome diverged from a lineage ancestral to Spy94a and Mezmaiskaya 2, forming a clade with the earlier Chagyrskaya Neanderthals. Thorin's Y-chromosome is closest to El Sidrón 1253.
Feldhofer Neanderthals (c. 40 kya) The Feldhofer Neanderthals, Feldhofer 1 and Feldhofer 2, were discovered in Feldhofer Cave in the Neander Valley, Germany, dated to c. 40 kya. Feldhofer 1 provided the first published Neanderthal (mitochondrial) DNA sequence. Both Feldhofer individuals are associated with the Micoquien industry. They are assigned to the NL1 mtDNA haplogroup by Andreeva et al. (2022), along with other Late European Neanderthals.
Spy I Neanderthal (c. 39 kya) Spy 94a, an upper right molar from Spy I, is one of 2 incomplete adult Neanderthal skeletons discovered in Spy Cave, Belgium. The tooth, directly associated with Mousterian tools, is dated to c. 39.2-37.9 kya. The nuclear DNA of Spy 94a is most closely related to Vindija 33.19. His Y-chromosome haplogroup forms a clade with Mezmaiskaya 2, while his mtDNA is closely related to Goyet Q56-1, Goyet Q305-7, and Goyet Q374a-1. Like other late Neanderthals, Spy 94a shows low levels of heterozygosity, consistent with small effective Neanderthal population sizes near the end of their history.
Modern humans
Ancient southern African Hunter-Gatherers (c. 200-160 kya) Ancient southern African Hunter-Gatherers (AncSA) represent one of the earliest branches of modern humans, estimated to have diverged from all other lineages around the same time as central African rainforest Hunter-Gatherers, c. 200-160 kya, and possibly even earlier, c. 270 kya. The AncSA lineage subsequently split into northern and southern lineages sometime between 170-30 kya. This lineage is not directly represented by any ancient or present day individuals. The closest available proxies are c. 2 kya hunter-gatherers from Ballito Bay, Faraoskop rock shelter, and St. Helena. The AncSA lineage was likely widespread in southern Africa, and may have been the only human population in southern Africa for most of the prehistoric period. Their present-day descendants in southern Africa, the Khoisan, carry some of the most deeply divergent human lineages and the highest number of unique genetic variants of any human populations, reflecting this early separation. The Khoisan carry ancestry primarily derived from a population that separated from ancient southern African foragers c. 20-30 kya, with an additional c. 9-22% mixed Eurasian-East African ancestry introduced during the spread of farming into southern Africa.
Ancient central African rainforest Hunter-Gatherers (c. 200 kya) Central African Rainforest Hunter-Gatherers (CRHGs) are one of the earliest diverging modern human lineages. They are inferred to have split from other human populations c. 200-160 kya, and perhaps as early as c. 220 kya. This lineage is not directly represented by any ancient or present day individuals. The Mbuti are their closest representatives among present-day populations. The CRHG lineage subsequently diverged into eastern (represented by the Mbuti) and western (represented by the Aka) branches between roughly 50-31 kya, with further differentiation within the western lineage occurring c. 18-12 kya. Ancient individuals from Malawi (I2967, c. 8.2 kya) and perhaps Kenya (I8930, c. 4.5 kya) carry mitochondrial DNA lineages typical of present-day central African foragers such as Mbuti and Aka.
Ancient eastern African Hunter-Gatherers (c. 140-70 kya) Ancient eastern African Hunter-Gatherers (closest to Hadza and Sandawe among present-day humans) split from all other African populations c. 140-70 kya. The c. 4.5 kya Mota individual from Ethiopia and the present day Hadza represent an ancient East African lineage that is more closely related to non-African populations than any other major African lineage.
Basal Eurasians (c. 80 kya) Basal Eurasians are a currently unsampled ('ghost') postulated lineage of modern humans that diverged from all other non-African populations before these groups differentiated from one another. This split likely occurred shortly after the main Out-of-Africa expansion and before the major Neanderthal admixture event into the Main Eurasian population, possibly as early as 80 kya. The geographical origin of the Basal Eurasian lineage is uncertain, with proposed homelands including the Arabian Peninsula, Southwest Asia, or North Africa. Basal Eurasians remained isolated from other Eurasian populations until c. 25 kya at the latest, when they are obeserved admixing with other groups in the Middle East. The earliest traces of Basal Eurasian ancestry are found in Upper Paleolithic individuals from Georgia (c. 26 kya), Morocco (c. 15 kya), and the Satsurblia cluster in the Caucasus (c. 13–9 kya). By the Holocene, this component was widespread the ancient Near East, contributing c. 44% of the ancestry in Natufians and c. 66% in Mesolithic Iranians. It later spread into Europe with the expansion of early Neolithic farmers. In present-day populations, Basal Eurasian ancestry is highest in the eastern Arabian Peninsula (c. 45%), followed by Iran (c. 38%), the Levant (c. 32%), the Caucasus (c. 20-25%), and Europe (under c. 20%). Because the Basal Eurasian lineage had little, if any, Neanderthal admixture, populations with higher proportions of Basal Eurasian ancestry, such as early Near Easterners and some modern Middle Eastern groups, tend to have reduced levels of Neanderthal DNA.
Main Eurasians (c. 80-54 kya) Genetic evidence suggests that the ancestral Out-of-Africa population remained largely isolated for a prolonged period, perhaps between c. 82-55 kya in refugia such as now-submerged areas such as the Arabian Gulf or the Red Sea, or in southern Iran. Around 80 kya, this population divided into two lineages: the Basal Eurasians, and the Main Eurasians who subsequently admixed with Neanderthals and expanded rapidly across Eurasia, reaching Europe by c. 54 kya and Australia by c. 50 kya. According to Vallini et al. (2024), the Persian Plateau functioned as a major population hub for the Main Eurasian population during the early stages of the Out-of-Africa dispersal. In their model, the Main Eurasian population occupied this region between the time of the initial migration Out-of-Africa and the colonization of Eurasia. From this hub, successive population waves are thought to have originated: an early wave before c. 45 kya, represented by Zlatý kůň; a later Initial Upper Paleolithic ('East Eurasian Core') expansion c. 45 kya (represented by Bacho Kiro, Tianyuan, and the ancestors of most present-day East Asians and Oceanians); and an Upper Paleolithic ('West Eurasian Core') expansion c. 40 kya (represented by Kostenki 14, Sunghir, and later West Eurasians). The relatively high proportion of Neanderthal ancestry in present-day populations indicates that the Main Eurasian group was small, consistent with having only two mitochondrial lineages (haplogroups M and N).
Zlatý kůň and Ranis (c. 50-42 kya) The Zlatý kůň woman, a near-complete skull discovered in Koněprusy Caves, Czech Republic, along with six individuals from Ilsenhöhle in Ranis, Germany associated with the Lincombian-Ranisian-Jerzmanowician culture, are dated to c. 49.5–42 kya. These individuals represent a distinct population that separated from other non-African lineages prior to than any previously analysed individual, preceding the split between East and West Eurasians. Outgroup f₃-statistics indicate that Zlatý kůň, together with Bacho Kiro IUP, Ust'Ishim, and Oase 1, comprise a distinct, 'pre-40 kya' genetic group. Some of the Ranis individuals were close kin: Ranis 6 was the daughter of Ranis 4, while Ranis 12 was a second- or third-degree relative of Ranis 4. Zlatý kůň was a fifth or sixth degree relative of both Ranis 12 and Ranis 4, and more distantly related to the other Ranis individuals. Long runs of homozygosity in Ranis 13 and Zlatý kůň suggest that these individuals were part of a population with recent low effective population size, and indicate consanguinity in their recent ancestors. Ranis and Zlatý kůň lacked genetic variants for lactose tolerance, light skin, and light hair. Neanderthal ancestry was estimated at around 2.9% in the Ranis13 and ZKU individuals, with longer Neanderthal-derived segments than in other contemporaneous individuals. Bennett et al. (2023) found support for gene flow from Zlatý Kůň into Early to Middle Upper Paleolithic individuals, including Buran-kaya, and the Fournol and Věstonice clusters. Other studies have concluded that the population represented by Ranis and Zlatý kůň, like Ust'-Ishim and Oase1, did not contribute genetically to later Eurasians.
Bacho Kiro Initial Upper Paleolithic (c. 46-43 kya) Human remains from the Initial Upper Paleolithic layers (IUP) of Bacho Kiro cave, near Dryanovo, Bulgaria, are associated with the Bachokirian or Pre-Aurignacian industry, and are dated to c. 45.9-42.6 kya. The Bacho Kiro IUP individuals form a distinct genetic cluster, more closely related to ancient and present-day East Asians than to Europeans. Their presence in Europe from 45 kya has been interpreted as part of a broader Initial Upper Paleolithic population expansion, originating from the Persian Plateau and extending eastward as far as Tianyuan. Vallini et al. (2022) model the Bacho Kiro IUP lineage as a sister group to Tianyuan Man, and suggest that Bacho Kiro IUP, Tianyuan, and Ust'-Ishim may have shared a brief evolutionary history. Hajdinjak et al. (2021) found support for gene flow from the lineage represented by Bacho Kiro IUP to Ust'-Ishim, Tianyuan, and GoyetQ116-1. Alternatively, Meier et al. (2023) suggest that the apparent genetic connection between Bacho Kiro IUP and Tianyuan may not reflect a direct relationship, and that instead, the shared ancestry could be the result of sequential expansions of modern humans out of West Asia, first contributing to Bacho Kiro, then to early East Asians, followed by Ust'-Ishim, and lastly to later European hunter-gatherers. Vallini et al. (2022) also suggest that a Bacho Kiro IUP-like population contributed the majority of the ancestry of the Oase 1 individual, with Oase 1 receiving additional Neanderthal admixture. Trace Bacho Kiro IUP-related ancestry has been proposed to be present in a later Early Upper Paleolithic individual ('BK1653') from the same site, as well as in members of the Fournol cluster. The Bacho Kiro IUP individuals carried unusually high Neanderthal ancestry ranging from 3.0-3.8%. All three Bacho Kiro IUP individuals analysed by Hajdinjak et al. (2021) had Neanderthal ancestors within a few generations of their lifetimes.
Ust'-Ishim (c. 42 kya) Ust'-Ishim man is represented by a near-complete femur discovered along the Irtysh River, near Ust' Ishim, Siberia, dated to c. 42 kya. He belonged to a population that diverged from the ancestors of East and West Eurasians either before or around the time of their separation. This population can be described as forming a near-trifurcation with West Eurasian (Kostenki 14) and East Eurasian (Tianyuan) groups, possibly representing a basal split on the lineage leading to Bacho Kiro IUP and Tianyuan Man. Ust'-Ishim man carried Neanderthal admixture at levels similar to that of present day populations, but with significantly longer Neanderthal-derived segments, indicating recent admixture. His mtDNA lies at the root of haplogroup R, which is widespread across present-day Eurasia, while his Y-chromosome was ancestral to haplogroup K(xLT).
Basal East Asian (c. 40-33 kya) Basal East Asian ancestry, also called 'Tianyuan' or 'Tianyuan/AR33K' ancestry, is represented by two early modern humans from China: Tianyuan man (c. 40 kya) from Tianyuan Cave, Zhoukoudian; and AR33K, (c. 33 kya) from the Amur River region. These individuals form a distinct genetic cluster that is basal to later East Asian populations. This ancestry was likely widespread in northern East Asia before the Last Glacial Maximum, but was later replaced by other lineages such as that represented by the AR19K individual. Tianyuan Man is more closely related to present-day East Eurasians, Oceanians, and Native Americans than to modern Europeans, and shows greatest similarity to East and Southeast Asians. While not directly ancestral to present-day East or Southeast Asians, Tianyuan man represents a population that diverged early from the ancestors of these groups. He shares excess alleles with Native American groups, particularly Amazonians, and also shares excess alleles with Goyet Q116-1, which may be explained by their common shared ancestry with populations such as Bacho Kiro Initial Upper Paleolithic. His mitochondrial DNA belongs to a lineage ancestral to haplogroup B, widespread among present-day Asian and Native American populations. AR33K, who lived around 7,000 years later and over 1,000 km northeast of Tianyuan carried similar ancestry, but has less affinity to Goyet Q116-1 and no excess affinity to Amazonians than to other Native American groups. Both Tianyuan Man and AR33K had elevated Denisovan-related ancestry compared to later individuals from this region.
Oase 1 (c. 40 kya) Oase 1 is a male sequenced from a mandible discovered at Peștera cu Oase, Romania, directly dated to c. 40 kya with no clear archaeological context. Oase 1 is not closely genetically related to ancient or present-day East Asians or Europeans, although he shows some affinity to present day East Asian and Native American populations. Prüfer et al. (2021) place Oase 1 basal to the divergence of East and West Eurasians. Alternatively Vallini et al. (2022) model Oase 1 as deriving the majority of his ancestry (97%) from Bacho Kiro IUP, with the remaining 3% from recent Neanderthal admixture. Oase 1 is closely related to Muierii2, a c. 33 kya individual from Romania. Oase 1 carries 6.0-9.4% Neanderthal ancestry, significantly higher than the levels found in present-day Eurasians, indicating a recent Neanderthal ancestor within the last 4 to 6 generations, or less than 200 years before he lived. His mitochondrial DNA belongs to a basal lineage of macrohaplogoup N, and his Y-DNA falls within haplogroup F.
Oase 2 (c. 38 kya) Oase 2 is represented by a near-complete cranium discovered at Peștera cu Oase, Romania. The remains are dated to c. 38 kya and not associated with any archaeological culture. Oase 2 was genetically related to, but distinct from, the population represented by Oase 1 and, like Oase 1, is not closely related to present-day populations. Siska concludes that Oase 2 belonged to a population that formed an outgroup to the ancestors of present-day non-African human populations, but was more closely related to the ancestors of Asians and Native Americans than to Europeans. Compared with Oase 1, Oase 2 shows slightly more affinity to Asian and Native American populations. Oase 2 carried a basal mitochondrial lineage of macrohaplogoup N and carried 6.06% Neanderthal-related ancestry, lower than Oase 1 but still high compared to contemporaneous individuals.
Kostenki 14 (c. 38 kya) Kostenki 14 ('Markina Gora') is the skeleton of a 20-25 year old male discovered along the Middle Don at the Kostyonki–Borshchyovo site in Russia, directly dated to c. 38.7-36.2 kya. He represents the earliest known example of the West Eurasian Core population (genetically closer to present-day European populations than to East Asians) which replaced earlier European lineages after the Heinrich Stadial 4 cold period that followed the Campanian Ignimbrite eruption. His lineage diverged from East Eurasians and Ust' Ishim by 45 kya, subsequently separating from the Sunghir lineage. Kostenki 14 ancestry later contributed to the Věstonice cluster in Europe, and to ancient populations in Siberia, represented by the Mal'ta and Yana individuals. At Kostyonki–Borshchyovo, groups closely related to Sunghir, represented by Kostenki 12, likely replaced populations represented by Kostenki 14 by c. 31 kya.
Buran-Kaya (c. 37-36 kya) The remains of two male individuals, BuKa3C (c. 37 kya) and BuKa3A (c. 36 kya) were recovered from the Early Upper Paleolithic layers of the Buran-Kaya III rock shelter, Crimea. These layers have been variously interpreted as 'proto-Gravettian', early Gravettian, or part of a non-Aurignacian Caucasus-related culture. BuKa3A and BuKa3C were closely genetically related but were not genetically uniform, reflecting complex population dynamics during the 1,000-year interval separating them. Both individuals are more similar to post-38 kya Europeans than to pre-40 kya individuals. Bennett et al. model both individuals as primarily descending from a population ancestral to Kostenki-14 and Sunghir-3 (83% for BuKa3A and 94% for BuKa3C), with the remainder from a population related to Zlatý kůň. However Sümer et al. (2024) did not find support for Zlatý kůň/Ranis-like ancestry contributing to these individuals. BuKa3C carried a mitochondrial DNA lineage that was basal to haplogroup U. His Y-chromosome DNA was a basal branch of F. BuKa3A carried an early branch of mtDNA haplogroup N1, and carried Y-chromosome haplogroup CT. Neanderthal ancestry was estimated at c. 3.8% in BuKa3A and 2.2% in BuKa3C, indicating no recent admixture. BuKa3A and BuKa3C share the most genetic drift with the later Gravettian-associated Fournol and, to a lesser extent, Věstonice clusters, with Fournol being more closely-relat