In the course of the peopling of the World by Homo sapiens, East Asia was reached about 50,000 years ago (50 kya). The "recent African origin" lineage from 70 kya diverged into identifiable East Eurasian and West Eurasian lineages by about 50 kya. The East Eurasian ancestors of East Asians used a southern route to reach South and Southeast Asia, along which they rapidly diverged into the ancestors of Ancient Ancestral South Indians (AASI), Papuans, East Asians and Andamanese peoples (such as the Onge). This early East Asian lineage diverged further during the Last Glacial Maximum, spreading northwards from Mainland Southeast Asia where it significantly contributed to the peopling of the Americas via Beringia about 25 kya. After the last ice age, China was cut off from neighboring island groups. The phenotypes of early East Asians were either replaced or prevailed among more geographically distant groups.
Genetic history
Overview A "Basal-East Asian population", referred to as the East and Southeast Asian lineage (ESEA), is ancestral to the Hoabinhian hunter-gatherers of Southeast Asia and the Tianyuan lineage found in Northern China and also, modern East Asians, Southeast Asians, Polynesians, and Siberians. The ESEA lineage descend from an earlier "eastern non-African" (ENA) or "Ancient East Eurasian" meta-population, which used a single southern route to reach South, Southeast Asia, and Oceania, and along which they rapidly diverged into the ancestors of Ancient South Asians (AASI), East/Southeast Asians (ESEA), as well as Australasians. This ESEA lineage later diverged into the Hoabinhian, the Tianyuan, and Ancient East Asian lineages, and expanded northward. The Ancient East Asian lineage later split into Ancient Southern East Asians and Ancient Northern East Asians. There is "a strong correlation with latitude, with diversity decreasing from south to north".
Basal Asian-related populations related to the Tianyuan man were widespread in across northern East Asia at least 40,000 years ago. However, they were replaced by an AR19K-related population near the end of the Last Glacial Maximum. This AR19K-related population carried EDAR_V370A variants, which was previously absent in East Asia. The AR19K-related population was basal to younger samples of Ancient Northern East Asians, who form a sister lineage to Ancient Southern East Asians, with both lineages diverging at least 19,000 years ago. There's also evidence of a distinct Ancient Northern East Asian lineage that diverged around the same time as the AR19K-related lineage and is represented by the ~11,000-year-old Donghulin individual from Beijing, China. Other studies suggest that the ancestors of ancient East Asians were a mixture of Tianyuan-related and Early Neolithic Xingyi-related lineages. Several ancient Northeast Asian individuals from inland East Asia (Yumin) and the Devil's Gate Cave (NEO240) can also be modeled as mixtures of deep lineages that are ancestral to the Jōmon and Tianyuan respectively, despite the latter being more related to the Jōmon.
Archaeogenetic studies in the Central Plains Neolithic Northern China can be divided into 4 periods: the Pre-Peiligang period (before 7000 BC), the Peiligang period (7000–5000 BC), the Yangshao period (5000–3000 BC), and the Longshan period (3000–2000 BC). The first two correlate with the initial development of Neolithic Chinese culture whilst the latter two correlate with the accelerated development of the Chinese civilization. Modern-day Shandong province in Northern China is home to a series of Neolithic archaeological cultures: Houli culture (6300–5400 BC), Beixin culture (5400–4200 BC), Dawenkou culture (4200–2600 BC), Shandong Longshan culture (2600–2000 BC) and Yueshi culture (1900–1500 BC).
The progenitors of the Han Chinese were Neolithic Yellow River farmers from the Central Plains, who constitute a distinct sublineage within Ancient Northern East Asians. They descend from Proto-Sino-Tibetan-speaking groups in the Yellow River regions, who diverged into Sinitic and Tibeto-Burman groups about 4–8 kya, and show high genetic affinities to Yumin hunter-gatherers. Yellow River groups were also genetically distinguishable from Early Neolithic Shandong hunter-gatherers, who have affinities with Ancient Northeast Asians (ANA) from the Amur River Basin and Mongolian Plateau, as well as Tibetan populations. Other studies suggest that Early Neolithic Shandong hunter-gatherers were distinct from ANA and might even precede ANA groups from coastal Northern China. Populations from coastal Northern China also contributed to the East Asian ancestries of East Asians, Jōmon peoples, East Siberians and Native Americans since the Last Glacial Maximum. According to a 2024 study, Early Neolithic Shandong hunter-gatherers were closely related to Yellow River populations but were slightly shifted towards ANA populations. Other studies likewise show notable genetic input from AR14K-related or Donghulin-related sources in Early Neolithic Shandong hunter-gatherers.
Yangshao-related Yellow River populations show high genetic similarities with the Dahecun and Wenshaobei populations from Henan and Shandong respectively. They are estimated to receive 43.5 ± 5.3% input from groups who show affinities to Yumin. Longshan-related populations show genetic differentiation, with those from Shandong receiving more input from local Shandong hunter-gatherers and Southern East Asians than those from the Central Plains. Successors of Longshan-related Yellow River population show continuity and they've impacted several East Asian groups such as West Liao River populations, Songshan populations and modern Han Chinese.
According to a 2025 study, Middle Neolithic Yellow River groups exhibit distinct substructure. For example, lower Yellow River groups are characterized by Middle Neolithic Yellow River ancestry (24%–73.1%), hunter-gatherer ancestry from Early Neolithic coastal Northern China (23.8%–46.8%), Southern East Asian-related ancestry (7.1%–57.3%; average 32.3%) and ANA-related ancestry (5.2%–16.5%). Meanwhile, upper Yellow River groups are characterized by Middle Neolithic Yellow River ancestry (21%–87.9%), Zongri5.1k-related ancestry (8.3%–55%) and ANA-related ancestry (6.5%–91.7%). Conversely, middle Yellow River groups do not exhibit significant admixture with non-Yellow River groups although admixture with ANA-related groups peak in higher-latitude regions. Zongri5.1k-related ancestry is also found in some local sites from Shaanxi and Shanxi. Some middle Yellow River groups have input from a Southern East Asian-related ancestry called "Yangtzean ancestry", which also constitutes the Southern East Asian ancestry found within lower Yellow River groups. Yangtzean ancestry derives 60% of its ancestry from Southeast China and the rest from Yellow River groups.
Among modern Han subgroups, Han Chinese from Henan, Shandong and Shanxi show the most continuity with post-Late Neolithic Yellow River groups and can even be modeled as their direct descendants. Other Han subgroups have more southern East Asian-related ancestry, especially in Southern China, although studies show that all Han subgroups have matrilineal admixture with minorities in their respective localities. Modern northern Han Chinese are also shown to be closely related to Late Neolithic Yellow River-related populations from Shimao or Neolithic Wuzhuangguoliang-related populations. Siberian and West Eurasian-related ancestry is also detected in some Northern and Central Han Chinese, along with highland Tibetan-related ancestry. Another study states that Central Plains populations show continuity from the Tang dynasty, with no signifcant admixture with northern Asian steppe ethnic groups, although Tang-era populations received some minimal Central Asian-related input. Post-Tang populations were also directly ancestral to modern Han Chinese from Henan and Shandong. Besides the Han Chinese, populations who are closely related to Neolithic Yellow River farmers include Naxi, Yi, Gelao, indigenous populations from the Himalayan region and western Japanese (i.e. Kansai) people.
Archaeogenetic studies in southern China According to Wang et al. (2021), these ancient individuals from Southern China play a key role in the ethnogenesis of present-day Southern Chinese populations and the Austroasiatic and Austronesian diaspora:
Archaic individuals from 12,000 to 10,000 BP: Qihe-3 () (11,747–11,356 cal BP; Qihe Cave , Zhangping, Fujian) is an Upper Paleolithic individual from the mountainous interior of Fujian, located about 100 km north of present-day Zhangzhou city. Like other late Homo sapiens, Qihe-3 exhibited a long head, large cranial capacity, high narrow face, broad and low/short nasal shape and exhibits features from northern and southern populations in Neolithic China. They also have large prominent cheekbones, flat upper faces, thin narrow cheeks, larger heads and facial hair. Their features are not necessarily representative of populations living during the Neolithic and Paleolithic transition but rather, reflect the great phenotypic variation that exists. Like the Qihe-2 individual, Qihe-3 clusters closely with Austronesians and are a mixture of Longlin-related and Tianyuan-related ancestries. Alternatively, Qihe individuals can also be described as mixtures of Dushan-related and either Longlin-related or Tianyuan-related ancestries. Qihe-2, a more recent specimen from a different layer of the same site dating to 8,428–8,359 cal BP, was sequenced and found to be closely related to Iron Age Taiwanese and Austronesians like Qihe-3. Longlin () (10,686–10,439 cal BP; Laomocao Cave , Longlin Autonomous County, Guangxi, China) is an Upper Paleolithic individual with deeply diverging East Asian ancestry. Longlin is closely related to the Maludong, or Red Deer Cave people, and Ikawazu (ca. 2,700 BP; Ikawazu Shell Midden site (伊川津貝塚), Atsumi Peninsula, southern Aichi Prefecture, central Honshu, Japan), a Jōmon individual. They are also closely related to Ancient East Asians from Shandong and Fujian than to basal lineages like Hoabinhian before the former split into present Northern East Asians and Southern East Asians. Longlin, Ikawazu and Ancient East Asians likely all diverged from each other at the same time, with Longlin being located at the basal position on the lineage leading to M71d, sharing a maternal genetic connection with present-day populations from mainland Southeast Asia. Although diverged from Ancient East Asians like Jōmon, they were not geographically isolated. Longlin can also be modeled as an admixture of Early Neolithic Xingyi (48.8–71.5%), which is closely related to deeply diverged ghost ancestry found in ancient Tibetans, and Qihe-3-related East Asian ancestry. Despite Longlin's uniquely archaic phenotypes, they carried similar levels of archaic human ancestry as Neolithic and present-day East Asians although it is likely that their phenotypes arose from hybridization with archaic hominins.