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.
Map
Archaic humans LGM and Post-LGM Europeans Ancient Middle East and North Africa Caucasus Upper Paleolithic Ancient Native Americans Initial Upper Paleolithic Ancient Eurasians (Zlatý Kůň / Ranis) Ancient East Asians Ancient Paleo-Siberians Ancient Northern Eurasians Ancient Africans Upper Paleolithic Europeans
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.
A 2024 study suggests this might not have happened
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 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)