Ancient genomes give insight into 160,000 years of East Asian population dynamics and biological adaptation

Guanglin He, Yuntao Sun, Shuhan Duan, Lintao Luo, Qiuxia Sun, Bowen Li, Libing Yun, Chao Liu & Mengge Wang

Abstract

Advances in ancient DNA research have transformed our understanding of human evolution, admixture-driven adaptation, and genetic underpinnings of traits. However, the evolutionary dynamics of Paleolithic and Neolithic East Asian remain fragmented. This review synthesizes 160,000 years of population interactions, highlighting three waves of archaic introgression and extensive population admixtures. We examine how ancestral lineages and agricultural innovations shaped East Asian populations, while migrations and admixture events linked to shifting subsistence strategies contributed to genomic and phenotypic diversity. Adaptive signatures from ancient genomes further elucidate the underpinnings of high-altitude adaptation, pigmentation, and morphological traits, offering new insights into human evolutionary biology.

Introduction

Ancient DNA (aDNA) research has advanced substantially over the past two decades, driven by innovations in DNA capture techniques, sequencing technologies, standardized laboratory preparation protocols, and computational methodologies [1, 2]. Insights derived from ancient genomes and large-scale genomic data from ethnolinguistically diverse modern populations have significantly enhanced our understanding of the evolutionary trajectory of anatomically modern humans (AMHs) and their relatives, including Neanderthals and Denisovans [3]. These advancements have provided invaluable perspectives on diverse aspects of human history, including genetic origins and evolutionary processes, complex admixture and genetic interactions, biological adaptations across spatiotemporally distinct ancient populations, and the genetic underpinnings of health and disease traits in geographically diverse modern groups [4]. Despite these achievements, existing studies have emphasized key milestones in human evolution, such as migration out of Africa, early settlement patterns, and subsequent migrations and admixture events in western Eurasia, Siberia, Oceania, and the Americas [1]. However, this focus has been characterized by persistent overrepresentation of European populations, resulting in significant biases in the broader understanding of human evolution [5].

Genomic investigations of Upper Paleolithic humans from East Asia and North Asia (Siberia and their neighbors) have significantly advanced the understanding of the early diversification of AMH lineages and their contributions to the genetic diversity and archaic introgression observed in contemporary populations following their migration out of Africa [1]. The successful sequencing of the Neanderthal and Denisovan genomes in 2010 provided critical insights into the genetic relationships between these archaic hominins and modern non-Africans [6,7,8]. Unlike uniparentally inherited genetic materials, autosomal data provide evidence of genetic connections, underscoring their shared ancestry with AMHs [9, 10]. Genealogical reconstructions based on shared genetic variants suggest that archaic hominins diverged from modern humans approximately 550 thousand years ago (kya), with Neanderthals and Denisovans diverging from each other by approximately 400 kya [11,12,13]. Patterns of haplotype diversity further elucidate the complexity of archaic introgression. The low diversity and consistent amounts and lengths of Neanderthal-related introgressed fragments across geographically diverse populations indicate a single major introgression episode. In contrast, Denisovan-related haplotypes exhibit substantial diversity, with differentiated match rates, quantities, and fragment lengths observed among Indigenous Australians, Melanesians, Philippine Negritos, and other Asian and American populations [6,7,8]. These patterns suggest a more intricate history of Denisovan genetic introgression [3]. Statistical reconstructions estimate approximately 2.5 ± 0.6% Neanderthal ancestry in non-Africans and approximately 5% Denisovan ancestry in Melanesians and Philippine Negritos [14]. Findings from aDNA further demonstrate that adaptive introgression has played a critical role in human evolution, introducing genetic variants that facilitate rapid adaptation to novel environmental conditions [15]. These genomic insights continue to deepen the understanding of human evolutionary history and the genetic interplay between modern and archaic populations.

During the Holocene, most aDNA studies shifted focus toward continental-scale migrations across Eurasia, Oceania, and the Americas, closely linked to the expansions of agriculture and language [16]. The aDNA data have transformed our understanding of European genetic diversity, revealing that the gene pool of modern Europeans was shaped primarily by three ancestral sources: Near Eastern farmers, Yamnaya-related pastoralists, and local hunter-gatherers [17]. Additionally, aDNA from Siberia has provided evidence of complex population interactions and the replacement of genetically distinct ancestry components associated with Ancient Northern Eurasians (ANE), Ancient Northeast Asians (ANA), Ancient Paleo-Siberians, Neo-Siberians, and Ancient Northern Siberians (ANS) [18]. The recovery and sequencing of DNA from human remains have also advanced the study of the initial peopling of the Americas, the divergence between northern and southern Native American groups, the separation of northern North American Amerindians from southern North Americans, the migration of Paleolithic populations to Oceania, and the Neolithic Austronesian expansion to Vanuatu [4, 19].

East Asia, including China, Mongolia, Japan, and neighboring regions, harbors numerous historical relics and archaeological human remains, making human genetic data an essential resource for uncovering key aspects of human origins and addressing health-related enigmas [20,21,22,23,24]. As such, genetic data from biobank-based cohorts have become a critical national strategic resource and key tool to illuminate the genetic history and genetic evolutionary determinants of human disease and health [25]. However, relatively few studies have been conducted to trace the evolutionary trajectory of human origins and the genetic variations associated with adaptation using genomic data from both ancient and contemporary individuals in East Asia. Statistical analysis revealed that large-scale aDNA from East Asia is limited, with fewer than 1,000 spatiotemporally distinct aDNA samples available in the Allen Ancient DNA Resource (AADR) database (Fig. 1A-C) [26]. Consequently, it is crucial to systematically summarize the complete evolutionary history and adaptive processes of ancient Chinese populations.

This review systematically summarizes recent advances in diverse ecosystems, encompassing aDNA studies from key agricultural origin centers in low-altitude regions, including the Yellow River Basin (YRB), Yangtze River Basin (YZRB), and West Liao River Basin (WLRB), as well as high-altitude regions such as the Tibetan Plateau (TP) and the surrounding Tibetan-Yi Corridor (TYC), which are characterized by extreme environments. Additional insights are drawn from trans-Eurasian regions, including the Tianshan Mountain (TSM), Mongolian Plateau (MP), and Amur River Basin (ARB), which are situated at the crossroads of Siberia, western Eurasia, and northern China (Fig. 1D). This review offers new perspectives on the historical evolution and ancient evolutionary adaptations of individuals from ancient East Asia, spanning the Pleistocene to Holocene periods, structured around seven key themes: (Ⅰ) Archaic introgression from the Neanderthal and Denisovan populations: We explored the contributions of archaic lineages to the gene pool of East Asians with an emphasis on introgression events from Neanderthals and Denisovans. (Ⅱ) Initial peopling of East Asia and basal Asian ancestry: This review highlights basic East Asian-related ancient individuals during the Pleistocene, shedding light on the early peopling of East Asia. (III) North-to-south differentiation of millet and rice farmers and their population dynamics: The genetic differentiation between ancient northern East Asian (ANEA) and ancient southern East Asian (ASEA) populations during the Paleolithic period is examined, alongside an admixture event resulting from the Neolithic expansion of millet-farming populations in the YRB and rice-farming populations in the YZRB. (Ⅳ) Genetic profile of ancient highlanders: The genetic makeup of ancient TP populations is analyzed, as are the genetic relationships of ancient southwestern Chinese groups involved in mixed farming. (Ⅴ) Genetic interaction between ancient farmer-related and herder-related populations in trans-Eurasian regions: This section discusses the genetic continuity of ancient northwestern Chinese populations and shifts in human populations associated with subsistence changes in northeastern China. (VI) Biological adaptation inferred from aDNA and its influence on human health and disease: Evolutionary and genetic determinants of human health and disease are summarized, with a focus on allele trajectory changes across different periods and spatial regions in ancient hominins. (Ⅶ) aDNA-related technological innovations and the reconstruction of complex social organizations: We finally discussed prospects for future aDNA-related technological advancements and their applications in reconstructing ancient human social organizations.

160,000-year-old archaic lineages and their genetic influence on ancient and modern anatomically modern humans

Neanderthals and Denisovans have garnered significant attention because of their close evolutionary relationships with AMHs and the potential interactions between them and our ancestors [13]. However, the lack of morphological and genetic data has hindered the direct understanding of their genetic legacy through archaic introgression in East Asian populations. Chen et al. identified Denisovan mandibles from Baishiya Karst Cave (BKC) in Gansu Province, China, via ancient protein analysis. These findings indicate that archaic hominins inhabited the northeastern regions of the TP (NETP) during the middle Pleistocene, effectively adapting to the high-altitude hypoxic environment long before the arrival of modern populations [27]. Mitochondrial DNA extracted from BKC sediments confirmed the presence of Denisovans approximately 100,000 to 60,000 years ago [28]. Mitochondrial genomes and the ancient proteome from a 146,000-year-old Harbin cranium suggest that a Denisovan individual existed in the ARB during the late Middle Pleistocene [29, 30]. Further investigations into archaic introgression have substantiated genetic interactions between archaic and modern humans, highlighting the acquisition of beneficial variants that increase survival in new environments [31]. In detail, genetic studies have successfully reconstructed three waves of archaic introgression into present-day Chinese populations, particularly Tibetans [32]. One wave of Neanderthal gene flow occurred before the separation of non-African individuals [13]. At the same time, two distinct Denisovan admixture pulses were identified, one shared with Oceanians and the other specific to East Asians [15, 32]. Notably, East Asian-specific encounters with archaic hominins facilitated the introgression of adaptive genetic fragments into AMH, including EPAS1 variants in Tibetan people derived from Denisovans [33]. The five SNP-based core Denisovan haplotypes identified through haplotype sharing analysis are widely present in contemporary Tibetans, contributing to their rapid adaptation to extremely highland environments [33]. Paleogenomic studies have also demonstrated that archaic introgression affects the metabolism of drugs and endogenous compounds in the human body, paving the way for the development of targeted therapeutics based on susceptibility genes [25].

Currently, significant efforts focusing on archaic hominins have demonstrated their genetic legacy of adaptive introgression in both ancient and modern Chinese populations. However, these studies offer only a preliminary understanding of early human genetic history, leaving several gaps that require further investigation. With advances in DNA extraction and sequencing technologies, it is now crucial to obtain high-quality DNA data from other morphologically Denisovan-like Paleolithic archaic humans, including individuals from the Jinniushan, Xujiayao, Xuchang, Penghu, and Yunxian crania [34]. These data could provide a more complete genetic profile and enhance our understanding of the human evolutionary landscape in East Asia during the Pleistocene. This study also sheds light on the genetic relationships and admixture processes between these potentially distinct or genetically linked archaic populations and modern East Asians. To fully assess the extent of admixture with Denisovan, Neanderthal, and other super-archaic ancestries, high-depth genomes from additional archaic individuals are essential, as they would allow a more detailed exploration of the influence of archaic ancestry on modern humans.

Deep Pleistocene lineages in northeastern and southern China

A limited understanding of the genetic structure and population differentiation characterized human history during the Pleistocene epoch. Population turnover and migration were central themes of European Paleolithic history [35]. However, the demographic history of East Asia during this period, particularly before and after the Last Glacial Maximum (LGM), remains fragmented and poorly understood due to the scarcity of genetic material from human fossils [1, 36]. High-quality ancient genomic data from pre-LGM human lineages were utilized to investigate the genetic profiles of a 40-kya-old Tianyuan individual (Zhoukoudian, Beijing) and a 33.6-kya-old AR33K female sample (Fig. 2). Admixture and graph-based evolutionary models, which are based on allele sharing, provide a foundational framework for understanding the prehistorical settlement of anatomically and behaviorally modern humans in northern China. These genetic models suggest that these individuals represent basal ancestry for northern East Asians and highlight a significant excess of Denisovan introgression in their genomes compared with both modern and other ancient populations [37]. Although significant genetic similarity was observed between the Paleolithic AR33K and Tianyuan individuals, the AR33K sample did not share the same genetic affinity with ancient western Eurasians (e.g., GoyrtQ116-1 from Belgium) or present-day Native Americans (e.g., Surui from the Amazon) as Tianyuan did [38, 39]. Tianyuan/AR33K-related ancestry, genetically close to the 24,000-year-old MA-1 individuals from the Belaya River near Lake Baikal [40], was widespread across northern East Asia and Siberia, exhibiting a complex population structure before the LGM [41].

Substantial genetic turnover has occurred between pre-LGM and post-LGM populations at the crossroads of Siberia and East Asia. Mao et al. identified the AR19K individuals who inhabited the ARB at the end of the LGM as the earliest known northern East Asians. These individuals possessed a distinct genetic makeup, separate from Tianyuan/AR33K-related ancestry [41]. Genetic data from pre-LGM populations in other East Asian regions, particularly in the core areas of farming origins, remain limited. Recently, three late Paleolithic genomes from southern East Asia were reported: the 14,000-year-old Mengzi Ren (Red Deer Cave, Malu Dong, MZR), the 11,747–11,356-year-old Qihe3, and the 10,686–10,439-year-old Longlin (Laomaocao Cave) [42, 43]. The two-layer hypothesis posits that ancient hunter-gatherers in southern China and Southeast Asia were shaped by both deep Asian ancestors related to Hòabìnhian groups and southern Chinese Neolithic farmers [44]. Genomic analyses indicate that MZR represents an early, diversified southern East Asian lineage distinct from Hòabìnhian ancestry, with contributions to the genetic pool of the first Americans during the late Pleistocene [43]. The cranial morphology of Guangxi Longlin displayed a combination of archaic and early modern human features. aDNA analysis revealed that Longlin fell within the genetic diversity of modern East Asians, with distant relationships with divergent Asian ancestries [42]. Qihe3 exhibited a close genetic affinity to Neolithic populations from Fujian (Qihe2, Liangdao1, and Liangdao2), showing a different demographic pattern than other Paleolithic populations with southern Chinese Guangxi Longlin, Yunnan MZR, and Vietnam Hòabìnhian ancestries [42]. The scarcity of genetic and archaeological evidence presents a significant challenge in obtaining direct data on Paleolithic human genomes with both spatial and temporal resolution. Thus, comprehensive and systematic research is essential for characterizing the population history of the pre-LGM or early Upper Paleolithic periods to better understand their expansion and transition.

North–south genetic divergence and population dynamics inferred from farmer-related ancient genomes

The Neolithic transition, marked by a shift from hunting-gathering, nomadic, and fishing subsistence strategies to farming, was accompanied by complex population migrations, admixture events, language divergence, and the development of sophisticated social structures. China, one of the earliest centers of agricultural domestication, witnessed the rise of millet farming in the YRB, which included the cultivation of foxtail millet (Setaria italica) and broomcorn millet (Panicum miliaceum) [45], as well as rice farming in the YZRB with domesticated rice (Oryza sativa ssp. japonica) [46]. The expansion of these agricultural practices was closely associated with the proto-Sino-Tibetan expansion and divergence in northern China, as well as the diffusion of super-language families in southern China [47, 48]. Linguistic, archaeological, and genetic evidence have provided insights into the genetic origins and ancestry of Sino-Tibetan-speaking populations and their predecessors [49, 50]. Zhang et al. characterized the phylogenetic relationships among language groups, linking Sinitic- and Tibeto-Burman-speaking populations to the expansion of the Neolithic Yangshao and Longshan cultures, as well as the westward spread of the Majiayao/Qijia cultures [49]. Similarly, Sagart et al. reconstructed the phylogenetic topology of Sino-Tibetan languages and estimated that divergence times confirmed a direct connection between Sino-Tibetan languages and late Cishan and early Yangshao millet farmers in northern China, dating back approximately 7,200 years before present (BP) [51].

Genomic history of millet farmers

Long-range spatiotemporal migrations of ancient Near Easterners from Anatolia, the Levant, and the Iranian Zagros Mountains have been shown to involve genetically differentiated early farmers who first intermixed and later spread beyond the Near East, significantly influencing the genetic makeup of East Africa, the Eurasian Steppe, Europe, and South Asia [52]. Ancient genomes from the upper (Gansu, Qinghai, and Shaanxi), middle (Henan), and lower (Shandong) regions of the YRB reflect similar population transitions, with genetic influences from surrounding populations [50, 53,54,55,56,57,58]. Yang et al. reported aDNA from Shandong, including early Neolithic ANEA individuals from Bianbian, Xiaogao, Boshan, and Xiaojinshan, which revealed coastal ANEA lineages closely related to Siberian hunter-gatherer populations [54]. Du and collaborators analyzed ancient genomes in Shandong from the middle Neolithic to historical periods, revealing complex regional population dynamics [55, 58]. These findings highlight the genetic contributions of Neolithic millet farmers to the Dawenkou people, the demic diffusion between the Dawenkou and Longshan populations, and intricate admixture scenarios among historical groups [55, 58]. Similarly, Li et al. investigated ancient genomic data from the Yangshaocun site, integrating it with spatiotemporally diverse genomes from the Central Plain [56, 57]. The population admixture modeling demonstrated long-term genetic stability between Yangshao populations and their descendants from the Central Plain despite complex regional cultural and demographic interactions [56, 57]. Neolithic Wuzhuangguoliang-related ancestry (approximately 3,000 BP) in the upper YRB contributed approximately 84% of the gene pool of Tibetans, and 59–84% contributed to modern Han populations, which also share close genetic ties with the geographically neighboring Yumin people (Fig. 2) [50]. Ning et al. analyzed one of the earliest ancient millet farmer-related genomic datasets from the YRB and WLRB (Fig. 3) and reported that genetic stratification in these populations was correlated with subsistence shifts [53]. This study highlighted a parallel increased genetic legacy of millet-related ancestry between middle Neolithic Yangshao, Wanggou and Xiaowu people and late Neolithic Longshan populations, alongside the late Neolithic Qijia-related ancestry (Jinchankou and Lajia) in present-day Tibeto-Burman groups, illustrating the shared genetic origin of Sino-Tibetan people in the YRB [53]. Wang et al. further confirmed the common genetic origin of Sino-Tibetan-speaking populations in northern China [50]. Subsequently, combined analyses of ancient YRB-related and modern genomes revealed genetic stability and continuity among spatially distinct YRB populations [59, 60]. The population history inferred from aDNA further clarified the associations between genetic turnover and shifts in subsistence strategies within China. Ning et al. demonstrated that the demic diffusion of northern YRB millet farmers significantly contributed to the genetic makeup of early Xiajiadian people in the WLRB, whereas later herder ancestry contributed to subsequent generations [53]. The expansion of millet farmers is thought to have spread westward into the TP and Hexi Corridor (HXC), northward into the Eurasian Steppe and WLRB, eastward into Japan and Korea, and southward to the YZRB and TYC [47, 50, 54, 61]. Future local Paleolithic hunter-gatherer populations in the YRB will provide valuable insights into the origins of farming and the transformation of hunter-gatherer societies into millet-farming communities (Fig. 4).

The genetic legacy of rice farmers and their influence on Southeast Asians

Archaeological studies from the Xianrendong and Kuahuqiao sites have provided insights into the existence of two distinct YZRB rice-related traditions in southern China, one primarily in coastal areas and the other predominantly in inland regions. Genetic evidence from aDNA recovered from individuals in Fujian and Guangxi has corroborated this distinction [42, 54]. The genetic profile of East Asian ancestry in southeastern China has also been characterized. Yang et al. recently sequenced the genomes of 58 individuals from the middle Neolithic to the late Bronze Age at Baligang, which is situated on the northern rim of the middle YZRB. These findings indicate that the Baligang population underwent multiple waves of admixture, alternating between southward and northward directions, across different periods [62]. Xiong et al. identified key ancient genomes from the Fuquanshan, Maqiao, and Daxi peoples in the key regions of the middle and lower YZRB, suggesting direct genetic connections between the YZRB Neolithic populations and proto-Austronesian populations [47]. Yang et al. analyzed 19 ancient coastal genomes from southern regions of the YZRB and reported that these individuals primarily shared East Asian-related ancestry [54]. Notably, the cranial morphology of early Neolithic populations from Qihe and Liangdao (8,400–7,500 BP) was initially thought to be closely related to that of hunter-gatherer populations [63], but aDNA evidence has since contradicted this hypothesis [54]. Wang et al. sequenced 31 ancient genomes from southern China (Guangxi and Fujian), revealing significant genetic differences between the Neolithic populations of Guangxi and those from early Neolithic sites in Fujian, Yunnan, and Vietnam [42]. The middle Neolithic hunter-gatherers (9–6 kya) presented three distinct ancestral sources, with contributions from populations in Guangxi (Dushan and Baojianshan) and neighboring regions in Fujian and Vietnam [42]. Strong genetic affinity was confirmed between the historical Guangxi populations of GaoHuaHua and BaBanQinCen (1,500–500 BP) and modern Tai-Kadai and Hmong-Mien speakers through genomic analysis [42]. Additionally, Wang et al. reported that ancient populations from Taiwan (Hanben and Gongguan, 3,300–1,200 BP) derived approximately 75% of their ancestry from YZRB rice-related farmers. These proto-Austronesian-related ancient populations, such as the Iron Age Hanben people, share significant genetic alleles with present-day Tai-Kadai speakers in southern China (Fig. 2B and 2) [50].

Bidirectional gene flow between the YRB and YZRB facilitated the spread of mixed rice- and millet-based farming systems along coastal, middle, and inland corridors [47, 62]. Ning et al. suggested that the Longshan and later Luoheguxiang populations in Henan presented more alleles associated with southern East Asians than did the geographically proximal Yangshao populations [53] (Fig. 3). Subsequent aDNA data from coastal southern China, reported by Wang et al. [42], revealed northern ancestry-related migration between 6,400 and 1,500 BP, a pattern also identified in the Neolithic Tanshishan and Xitoucun populations of Fujian [54]. Recent large-scale analyses of ancient genomes from the Dasongshan site, spanning the period from 990 to 1,649 AD on the Yunnan-Guizhou Plateau, revealed a substantial presence of YRB-related ancestry [64, 65]. Clearly, similar bidirectional genetic admixture patterns were present in the Baligang population and other ancient groups from the middle and lower YZRB [47, 62]. These findings suggest that the demic diffusion of Han Chinese ancestors from the Central Plain had a significant impact on the gene pool of South China [65]. Furthermore, triangulation evidence has supported a link between subsistence strategies and human migration, demonstrating that agriculture and language spread from proto-Sino-Tibetan-speaking populations in the YRB to WLRB millet-based agricultural centers [53, 66], as well as the Central Plains and Steppe groups [67]. Comprehensive genetic analysis through genome-wide aDNA data can provide insights into past population dynamics, particularly concerning the co-diffusion of language and agriculture associated with farmer expansion in and out of China [4, 50]. Additionally, Wang et al. proposed a notable admixture scenario involving ancient individuals with YZRB-related ancestry, dating from approximately 9,000 to 6,000 BP, prior to the advent of agriculture [42]. This admixture was linked to local southern Chinese ancestry and deep Asian ancestry from Southeast Asian Hòabìnhian hunter-gatherers (Fig. 4).

Genetic evidence suggests that the prehistoric peopling of Southeast Asia involved five distinct southward migrations from South China [44, 68]. These migrations facilitated the dispersal of Austronesian and Tai-Kadai languages across coastal regions, as well as Hmong-Mien, Austroasiatic, and Tibeto-Burman languages in inland areas. Furthermore, Yang et al. identified genetic connections between the YZRB rice-farming populations of southern China and the Lapita culture of Oceania, indicating that proto-Austronesian ancestors originated in South China and spread with the expansion of rice farming [54]. Wang et al. reported that the movement of individuals with YZRB rice farmer-related ancestry coincided with the dispersal of Austronesian, Hmong-Mien, and Tai-Kadai language groups [50]. Collectively, these findings highlight the prevalence of gene flow among ancient farmer populations, underscoring the genetic links between southwestern China, mainland Southeast Asia, the coastal regions of southern China, Siberia, Japan, Vietnam, and Oceania (Fig. 4) [42, 50, 54]. Following the LGM, the climate transitioned to a warmer environment, driving frequent population dynamics among ancient Chinese populations. This included a sequence of demic and cultural co-diffusions, as well as north‒south migrations and interactions beyond China. However, sampling has been limited to a small number of ancient Chinese individuals, particularly those from the upper and middle YZRB regions, which have warm and humid environments. This sampling bias may not have fully captured the genetic diversity and demographic history of these populations.

Dynamic population histories in the crossroad regions of northern China and the eastern Eurasian Steppe since the Neolithic

The Paleolithic separation between the western Eurasian Steppe and eastern MP hunter-gatherer populations, along with the large-scale westward migrations during the Bronze Age, are central themes in the history of the Eurasian Steppe [69]. These migrations included the movements of the Yamnaya, Afanasievo, Chemurchek, and Sintashta cultures and, to a lesser extent, Bactria-Margiana Archaeological Complex (BMAC)-related barley farmers. Post-Bronze Age migrations, such as those of the Xiongnu, Xianbei, Rouran, Türk, and Mongolian nomadic regimes, further shaped the demographic landscape of the Eurasian Steppe. In addition to these large-scale migrations, the long-term genetic stability observed in Neolithic populations from Devils Cave and Boisman in the Far East of Russia, the western region of the ARB, and modern Tungusic speakers is noteworthy. Extensive interactions between Siberian hunter-gatherers or herders and millet farmers in the YRB also significantly influenced the genetic diversity and population structure of both ancient and modern populations within these farming–pastoral transitional zones. This review summarizes the population history and demographic patterns at the crossroads between Siberia, Central Asia, and North China, where shared ancient genetic and cultural elements, including wheat, barley, millet, kefir cheese, bronze technology, cattle, and sheep/goats, reflect extensive trans-Eurasian cultural and population exchanges [2, 70]. These elements also suggest shared Altaic or trans-Eurasian language families, including the Turkic, Mongolic, and Tungusic languages. For this work, the crossroad regions are collectively referred to as the “trans-Eurasian region”, which encompasses the TSM, MP, ARB, and WLRB in North China and neighboring regions. These areas, situated at a critical ecotone, were where sedentary millet agriculturalists and nomadic pastoralists converged (Fig. 1D). These regions served as the cradle for multiple ancient civilizations, facilitating the exchange of material cultures, agricultural technologies, and subsistence strategies among diverse and complex societies [71].

Complex admixture of ancient Tianshan Mountain populations

The Altai Mountains served as a primary barrier to early trans-Eurasian population migration and cultural exchange. Similarly, the TSM, which is situated in the central and western regions of Chinese Xinjiang, divides the southern Altai Mountains into northern and southern Xinjiang, encompassing the Dzungarian and Tarim Basins, respectively. The ancient TSM regions harbored deep genetic lineages from proto-Indo-European people, particularly the Tocharian-speaking populations in the Tarim Basin, as well as complex western-eastern physical features observed in naturally mummified human remains [72]. The Xinjiang Autonomous Region, a historically crucial geographical corridor in northwestern China, has played a central role in facilitating migration and interactions between eastern and western Eurasian populations since the Han dynasty (approximately 2,200–1,800 BP) [2, 24, 73,74,75]. Three significant hypotheses, including the Inner Asian Mountain Corridor (IAMC) inland biogeography hypothesis, the Bactrian Oasis hypothesis, and the Yamnaya/Afanasievo steppe hypothesis, have been proposed to explain the formation of early TSM populations [73, 76]. However, craniometric analyses have failed to provide strong evidence to support any of these models [77]. High-quality genome-wide data from individuals in the Dzungarian (Ayituohan, Songshugou, and Nileke) and Tarim Basin (Gumugou, Baifang, and Xiaohe) regions, which represent the earliest human remains discovered from the TSM, have offered new insights into regional population dynamics. The early-middle Bronze Age Tarim group in southern Xinjiang, which comprises a genetically isolated population, exhibited a high degree of genetic affinity, although there was no evidence of close kinship [76]. Genetic analyses of the Tarim individuals revealed their connections to two ancient East Asian groups: one related to ANA-associated Baikal_EB and another represented by the Upper Paleolithic Afontova Gora site (AG3) individuals from the upper Yenisei River region (Fig. 3) [76]. Additionally, both genetic and dental calculus proteomic analyses suggest that the earliest Tarim Basin cultures were derived from a locally isolated group. This earliest Tarim Basin group likely adopted pastoralist and farming practices from neighboring TSM populations, which sharply contrasts with earlier theories that suggested that the Tarim mummies (proto-Tocharian-speaking pastoralists) were migrants from Afanasievo, BMAC, or IAMC cultures [73, 77].

The Dzungaria group presented a genetic legacy related to Afanasievo culture, with substantial Afanasievo contributions and minor local influence observed in early Bronze Age Dzungarian individuals [76]. A large-scale aDNA study, including 201 ancient genomes from 39 archaeological sites, focused on TSM-related populations spanning from the Bronze Age to the historical period. This study highlighted the complex and persistent admixture events that have shaped the demographic history of the TSM region [78]. Kumar et al. reported that Bronze Age populations in the TSM region presented high genetic diversity and regional genetic affinities with steppe and northeastern Asian populations. The Iron Age intensified admixture between TSM-related groups and populations associated with the steppe and Northeast Asia. Historical evidence suggests that there has been continued genetic admixture with surrounding populations and genetic continuity since the Iron Age [72]. Recent analysis of 24 Bronze to Iron Age genomes from western Tarim revealed early Tarim populations and rapidly expanding westward steppe migrants, with these groups initially interacting with BMAC people, followed by interactions with Tarim populations [79]. Local ancestry remained dominant across the Tarim Basin even during the Iron Age, highlighting the region’s complex and fascinating history. Mitogenomic data further corroborated significant admixture with both agriculturalist and pastoralist populations [78]. Fine-scale demographic reconstructions of genetically diverse individuals from the Shirenzigou site, dated to approximately 2,200 years ago, revealed that genetic exchanges between eastern and western Eurasians influenced culturally homogeneous populations (Fig. 4) [80]. Additionally, aDNA findings were primarily concentrated in the western regions of the Altai and TSM areas, with limited data available from the eastern sides of these mountain ranges. This disparity is crucial for understanding the boundaries of the influence of Western Eurasian Steppe pastoralists on East Asian populations. While the Yamnaya culture disrupted the Bronze Age genetic structure of eastern MP populations, the extent of western Eurasian genetic contributions to spatiotemporally distinct HXC populations remains a pivotal issue in aDNA research.

Population dynamics of ancient Mongolian Plateau people

The demographic history of ancient MP populations, particularly those in Inner Mongolia, remains poorly defined compared with that of the TSM, mainly due to the limited availability of large-scale aDNA data. This review provides fundamental insights into population history by analyzing reported genomes from sporadic regions and data from neighboring northern areas of the MP. Genetic features derived from hunter-gatherers in the eastern (SOU001, eastMongolia_preBA) and northern (Fofonovo_EN) regions of the MP suggest that the pre-Bronze Age population structure in the MP exhibited a genetic pattern closely associated with ANA ancestry. This pattern shares similarities with that of the 7,200–6,200-year-old Baikal_EN from the western Baikal region and the 7,700-year-old DevilsCave_N from the Russian Far East [81]. During the Bronze Age, the genetic structure of the MP was characterized by a tripartite division consisting of distinct dairy pastoralist groups linked to northern Khovsgol_LBA, western Altai_MLBA, and southeastern Ulaanzuukh_SlabGrave populations. This structure facilitated the emergence of mixed genetic and cultural patterns, driven by interactions between the Xiongnu and other historical pastoral groups [81, 82]. Only one 8,400-year-old Neolithic population, the Yumin people from Ulanqab, Inner Mongolia, has been identified. This population exhibits genetic ties to inland Neolithic ANEA and shares a close phylogenetic relationship with ANA-related Neolithic Siberians and modern Tibetans [54].

Recent paleogenomic studies have confirmed that the population history of the MP is characterized by repeated admixture between distinct eastern and western Eurasians [81]. Historical records document that Xianbei, a prominent pastoral nomadic group in the MP region, established political dynasties, such as the Northern Wei Dynasty. Cai et al. analyzed ancient genomes from nine Xianbei individuals dating back approximately 1,800 BP and revealed genetic changes linked to the southward migration of the Xianbei population [83]. This evidence supports the notion of genetic admixture with millet farmers or their descendants from the ARB. Furthermore, genetic data indicate that Xianbei underwent a substantial transformation from nomadic tribes to sedentary agriculturalists, with notable admixture upon their settlement in the Central Plains of China [83]. Additionally, Yang et al. traced the Northeast Asian origin of the Göktürk Khanate and reconstructed genetic connections between the Northern Zhou Dynasty and the Türks through political marriages, based on aDNA extracted from Empress Ashina dating to approximately 1,300 BP [84]. Ancient genomes from Emperor Wu of China indicate a genetic origin linked to ANA-related Xianbei populations, with additional admixture from Han Chinese individuals [85]. Recent admixture analysis using modern genomic data has also confirmed this interaction between Han Chinese and northern herders, as well as more ancient long-distance migrations [67, 86]. Y-chromosome evidence from time-calibrated phylogenies supports the hypothesis that the Emperor Wu-related lineage and subsistence-related migrations have introduced and promoted the dispersal of ANA ancestry [20, 87, 88]. Nevertheless, it reveals its limited direct paternal contributions to the modern Chinese paternal gene pool. Recent historical and contemporary genomes from the HXC and geographically different Hui people also suggest that western Eurasian influences permeated the eastern MP regions [24, 61, 89]. Therefore, elucidating the genetic interactions with Western Steppe herders, especially considering the unique geographical position of Inner Mongolia, is essential. A broader analysis of ancient genomes from both within and beyond the Great Wall is crucial for a more comprehensive understanding of population dynamics.

Long-term genetic stability of ancient Northeast Asians

The ARB and WLRB regions, located in northeastern China, encompass a vast expanse of mountains and plains that extend into part of the Eastern Steppe. The population dynamics of these areas are of particular interest because of their close genetic links with Native Americans and modern Tungusic speakers [19]. Mao et al. demonstrated that human populations in northern China have maintained genetic continuity since approximately 14,000 BP (Fig. 3) [41]. Demographic patterns inferred from qpWave-/qpGraph-based models indicated that early Neolithic individuals from DevilsGate and Boisman, along with modern Tungusic speakers from the ARB, exhibited substantial genomic homogeneity [50]. Ning et al. further confirmed the long-term genetic stability of early Neolithic hunter-gatherers and Iron Age populations in the upper ARB region [53]. Unpublished ancient genomes from the Houtaomuga site also support the genetic continuity and significant contribution of these initial populations to Native American ancestry [90]. Additional population genetic structure analyses revealed clear genetic stratification, with present-day Tungusic-related ancestry shared by AR_EN and AR_Xianbei_IA individuals. Moreover, probable Mongolic-related ancestry was identified in AR_IA individuals, which supports the hypothesis of gene flow between different ARB populations during the formation of present-day Altaic-speaking populations [53].

The WLRB, situated between the YRB and ARB regions, has undergone frequent genetic transformations throughout history, reflecting shifts in subsistence strategies. Unlike the stable genetic composition observed in ancient ARB populations, the genetic makeup of ancient WLRB populations has fluctuated significantly over the past 6,000 years, in parallel with changes in subsistence practices [53]. Ning et al. presented ancient Banlashan genomes from northern China associated with Hongshan-related cultures in the WLRB, revealing that an increased reliance on millet farming during the middle to late Neolithic was linked to a stronger genetic affinity with YRB millet farmers [53]. Wang et al. sequenced 19 Zhengjiagou genomes from Hongshan individuals, confirming that ANA and farmers linked to the middle Neolithic Dawenkou culture contributed to the development of the Neolithic Hongshan population [91]. Late Neolithic groups from the lower Xiajiadian culture (Erdaojingzi_LN) were also influenced by similar demic diffusion patterns. In contrast, populations linked to the Bronze Age Upper Xiajiadian culture (Longtoushan_BA) exhibited a closer genetic relationship to ARB populations, which probably signifies a move toward pastoralism as their primary subsistence strategy [53]. Zhu et al. identified a distinct genetic substructure within upper Xiajiadian culture populations, noting that individuals from the Majiazishan site in the late Bronze Age traced their ancestry entirely to YRB millet-related populations, which differed from the genetic profile of Longtoushan_BA [92]. Additionally, the late Bronze Age was characterized by extensive cultural exchange across the Eurasian Steppe, leading to the admixture of WLRB and Eastern Steppe populations with Western Eurasian genetic lineages [50, 66]. Prehistoric genetic changes were further aligned with the intensified practice of rice farming in the YZRB region, suggesting potential demic diffusion driven by shifts in subsistence strategies (Fig. 4) [53, 66]. Building on these associations, Robbeets et al. linked the origins of Neolithic and Bronze Age millet farming in northern China to the emergence of Sino-Tibetan and trans-Eurasian language families. These findings suggest that linguistic and demic diffusion occurred as early as the late Neolithic, driven primarily by the gradual admixture of millet farmers with substantial ANA, ANEA, and western Eurasian ancestries [66].

Genetic studies have underscored the significant contributions of ancient Chinese millet farmers to neighboring regions. For example, the modeling of ancient Koreans from the Three Kingdoms period suggests their ancestry as a mixture of Bronze Age northern Chinese populations and Jomon-related groups (Fig. 4) [93]. Robbeets et al. analyzed ancient genomes from Korea, the Ryukyu Islands, and early cereal-farming communities and demonstrated that the movement of the first farmers across Northeast Asia left a profound genetic legacy [66]. Similarly, Cooke et al. examined pre- and post-farming Japanese genomes, revealing deep divergence between Jomon populations and continental groups [94]. Liu et al. reconstructed population dynamics from the ShanDong region, dating to approximately demonstrate that Shandong’s ancient ancestry is the closest to the mainland East Asian ancestry of post-Yayoi populations from the Japanese archipelago [95]. These findings highlight the diffusion of ANA and millet farmer ancestry, which facilitated the introduction of rice and millet cultivation to Japan, as well as the role of continuous East Asian gene flow in reshaping the tripartite model of Japanese genomic origins and reshaping their adaptive biological landscape [94, 96]. These studies highlighted the profound historical connections among ancient Eurasian populations, providing insights into the population dynamics of trans-Eurasian regions in China and neighboring regions. Future investigations into the human history of these regions should prioritize the acquisition of representative genomic sequences, particularly aDNA from the eastern sides of the TSM, eastern MP, and HXC, with a focus on early agricultural populations. Such efforts will facilitate a more nuanced understanding of the relationship between agricultural diffusion and its impact on language, culture, and the adaptive genetic foundations of this vast geographical territory.

Highland Tibetan Plateau peopling processes and genetic connections to Neolithic millet farmers and Tibetan-Yi Corridor populations

The TP is characterized by extreme environmental conditions, including low atmospheric pressure, hypoxia, cold temperatures, and intense ultraviolet radiation [97]. Despite these formidable challenges, Tibetans and other ethnic groups, as well as their ancestors, have demonstrated remarkable adaptability to these harsh conditions for millennia [98]. However, several key questions remain unclear about who the early ancestors of highland people were and how they adapted to highland environments, including their genetic origins, highlander-specific ancestry, early migrations onto the plateau, the timing of permanent settlement, and the development of gene pools that led to the modern Tibetans. Archaeological evidence from the BKC site indicates that Denisovan-related populations inhabited the NETP at elevations of 3,280 m above sea level (masl), approximately 160 to 60 kya [27]. Nwya Devu hunter-gatherers are believed to have reached the central core regions of the TP (4,600 masl) between 30–40 kya [99]. Permanent settlement of the TP may have occurred through the Chusang hunter-gatherers, who lived between 7.4 kya and 12.7 kya, or via later barley-based agricultural populations from the lowlands [100, 101]. Complex demographic models, which are based on high-coverage whole-genome sequencing and uniparental Y-chromosome and mitochondrial DNA data, suggest that both Paleolithic occupation and Holocene expansion contributed to the formation of the gene pool of contemporary highland TP populations [102, 103].

Paleolithic occupation and Neolithic expansion of ancient Tibetan Plateau groups

A decade ago, archaic Denisovan-like genetic material was identified in modern Tibetans, providing early insights into the peopling history of the TP [33]. Recent genomic data from large-scale population studies of highland populations have further enhanced our understanding of these populations [104,105,106,107,108]. Ancient genomes from the Annapurna Conservation Area, including samples from Chokhopani (3,150–2,400 years ago), Mebrak (2,400–1,850 years ago), and Samdzong (1,750–1,250 years ago), supported the hypothesis of a high-altitude East Asian origin for ancient Himalayan populations and indicated long-term genetic stability [108]. Zongri genomes, dating to approximately 5,100 BP, revealed plateau-specific genetic structures that were closely linked to ANEA millet farmers [106]. A graph-based model fitted to 38 genomes from seven sites across the Mustang and Manang districts, including new sites such as Suila, Lubrak, Rhirhi, and Kyang, suggested that ancient TP populations primarily derived their ancestry from late Neolithic populations in the NETP, with minor contributions from deep Paleolithic Eurasian ancestry [107]. This model aligns with previously proposed hypotheses that multiple waves of migration shape the peopling history of the TP [60]. Recent work on the Neolithic Xingyi people in Yunnan Province has provided the closest link to Basal Asian ancestry, which was previously considered a vital ghost ancestral source in the formation of highlanders [48]. Wang et al. conducted a large-scale, spatiotemporally diverse genomic study, revealing significant genetic differences among TP populations from the western, southern, central, and northern regions, which date back more than 2,500 years. Yang et al. analyzed ancient genomes from the Mabu Co site, one of the highest-elevation sedentary settlements globally [105]. Genomic modeling of the indigenous lake-centered sedentary population from Mabu Co indicated that they possessed predominantly southern plateau ancestry [105]. These studies also highlighted substantial gene flow between the TP and regions of East Asia and Southeast Asia, further shaping the genetic composition of present-day Tibetans (Fig. 3) [105, 106]. Bai et al. performed in-depth genetic modeling to investigate the population dynamics of ancient western Tibetans from Ngari Prefecture [104]. These findings revealed 3,500 years of regional genetic continuity, multiple westward expansions from the southern Plateau, and gene flow between the Guge kingdom and populations in Central and South Asia [104]. Additionally, historical populations have undergone extensive genetic exchange with other Eurasian populations. Zhu et al. reported 10 Tubo-related samples from the Dulan site dating to 1,308–1,130 BP, which indicated that the Tubo Empire influenced the NETP through both demic and cultural diffusion. This influence affected core Tibetan populations and Eurasian Steppe-related ancestry groups during the historical period [109].

Northern China origin of the ancient Tibetan-Yi Corridor people

The NETP has long served as a crucial corridor for the peopling of the TP, with ancient genomes from Zongri, Lajia, and Jinchankou revealing a close genetic connection between millet farmers and highland populations. Liu et al. identified a distinct genetic history for Tibeto-Burman people residing at mid-elevations, marking one of the geographic passages of the TYC along the southern and eastern margins of the TP [107]. TYC, as one of the parallel routes for north‒south migration, functions as a corridor for the dispersal of Tibeto-Burman-speaking populations from southwestern China to lowland Southeast Asia [107]. Located on the eastern periphery of TP, the region is characterized by complex geographical conditions. While millet-related ancestry from northern China is prevalent in the YRB, present-day Tibeto-Burman-speaking populations residing in the TYC exhibit significant genetic differentiation, likely due to variations in selective pressures and adaptive genetic traits [22]. Recent advances in aDNA have provided greater insight into the processes of agricultural dispersal, cultural diffusion, and the evolutionary trajectories of demic movements since prehistoric times [110, 111]. Tao et al. reported genome-wide data from Neolithic Gaoshan and Bronze Age Haimenkou sites in southwestern China, where a combination of millet-based and rice-based agriculture was practiced from 4,500 to 3,000 BP [111]. The populations from Gaoshan and Haimenkou displayed approximately 90% YRB millet-related ancestry during the Neolithic period, maintaining hunter-gatherer-related lineages with no detectable genetic traces of rice farmers. These findings suggest that millet farmers in the TYC adopted rice-related agriculture without significant genetic assimilation, supporting the notion of distinct agricultural traditions [111]. Moreover, ancient populations discovered along the northeastern slopes and Yarlung Tsangpo River of the TP show notable genetic affinities with ancient TYC groups, indicating that these two routes likely contributed to their shared genetic makeup (Fig. 2). Genomic data from four historic cliff tombs in Meishan, Sichuan, also revealed a close genetic relationship with ANEA farmers [112]. Collectively, these ancient genetic data reinforce the view that both modern and ancient TYC populations, as well as Tibeto-Burman speakers, originated from millet farming populations in northern China.

The history of human occupation on the TP has been elucidated through multidisciplinary evidence, particularly from recent advancements in archaeological and aDNA research. Archaeological records document a long history of human presence on the TP, with notable sites, including the BKC site [28], the Nwya Devu site [85], and the Chusang site [100, 101]. The earliest aDNA data from northwestern China were derived from hunter-gatherers at the Zongri site, dating to approximately 5,100 BP [106]. However, this temporal range is insufficient to establish the precise timing of the initial colonization of the TP based solely of genetic evidence. Moreover, further aDNA sampling across both temporal and spatial ranges from adjacent TYC populations is necessary to clarify the genetic relationships and divergence times between ancient TP populations and the early inhabitants of the TYC.

Ancient biological adaptation among East Asian populations

Influence of aDNA on tracing the genetic origin of human disease

The evolutionary determinants of human diseases and complex traits have been shaped by diverse forces, including extreme environments on the TP, pathogen exposure (e.g., malaria in South China), and shifts in prehistoric subsistence strategies. These determinants have traditionally been inferred through advanced statistical and computational techniques based on patterns of genomic variation [113]. Ancient genetic analysis with comprehensive spatiotemporal coverage has provided direct insight into previously undisclosed population dynamics underlying human disease susceptibility, elucidating the evolutionary foundations of adaptive signatures and suggesting why diseases emerge in modern environments [114,115,116,117]. aDNA has yielded valuable insights into evolutionary medicine by revealing how beneficial variants in past environments have influenced modern human health and disease susceptibility, as well as by applying evolutionary principles to disease risk prediction and treatment.

Ancestral gene flows have been examined to determine how trait evolution relevant to health was shaped, as noted in recent genetic research focused on the possible genetic origin of multiple sclerosis (MS) in modern and ancient Europeans [114]. Another promising aspect of aDNA research for human disease involves spatiotemporal windows to test evolutionary hypotheses, including the thrifty gene hypothesis, hygiene hypothesis, antagonistic pleiotropy hypothesis, and others [115, 118]. By capitalizing on the time-series nature of aDNA, the genetic trajectories of past adaptations can be traced to identify changes critical for survival under distinct environmental pressures, such as disease resistance, dietary tolerance, or adaptation to climate stressors. Akbari et al. reported numerous genome-wide significant signals and strong directional selection signatures related to celiac disease, blood type B disease, tuberculosis risk, rheumatoid arthritis, and 31 other aDNA-attested disease traits associated with selection [115]. This large-scale aDNA research has also illuminated complex directional selection that reshaped dozens of complex human traits and diseases. Such investigations are beneficial for understanding complex conditions (e.g., diabetes, cardiovascular disease, and cancer), which may carry an evolutionary component driven by ancestral gene flows.

The genetic legacy of ancient populations has also been characterized more accurately through aDNA, indicating how ancestral gene flows have shaped the genetic architectures of the complex disease traits of the contemporary human gene pool [119]. Marnetto et al. used combined genomic admixture modeling of ancient and modern Europeans to elucidate differentiated ancient European ancestral sources that contributed to varying effective sizes of anthropometric, pigmentation, and metabolic traits, such as the distinct influences of local hunter-gatherer and Yamnaya steppe ancestry on cholesterol levels [119]. In addition, genes transmitted during archaic human migrations, including those involving early Homo sapiens or Neanderthals, have clarified the genetic underpinnings of disease susceptibility and resistance [6,7,8]. The introgression of Neanderthal DNA, for example, has been associated with immune system responses necessary for coping with infections.

Genetic changes associated with the agricultural revolution, spanning thousands of years during the Holocene, have been documented through aDNA, particularly those linked to immune-related host–pathogen co-evolution, chronic diseases, aging, or metabolic disorders [114, 116, 118]. These findings suggest that genetic variants associated with disease risk have evolved, as variants that protect against ancient pathogens continue to influence modern disease susceptibility. By examining these variants, evolutionary medicine can identify pathways that influence present-day health and disease. Kerner et al. recently reported that the Holocene host‒pathogen interaction landscape illuminated genetic adaptation to increased infectious disease, which also affected susceptibility to inflammatory disorders [116].

A more comprehensive picture of human evolution and its bearing on health was also promoted via the integration of aDNA with modern genomic data. If ancient populations are found to carry immune-related genetic variants that confer resistance to human diseases, comparisons with modern groups possessing similar variants can clarify how these traits affect current disease outcomes [116]. This approach can inform precision medicine and genetic counseling. Barrie et al. combined the risk of MS among modern northern and southern Europeans with ancient human migration and admixture dates [114]. A strong association was observed between the elevated genetic risk of MS and the ancestry of steppe pastoralist populations [114]. However, recent large-scale analyses of modern and ancient European genomes suggest that the elevated MS risk in northern Europe was not attributable to selection by steppe pastoralists, despite the positive selection of HLA-DRB1*15:01 increasing to 18% between ~ 6,000 and 2,000 years ago [115].

Evolutionary trajectory reconstruction among East Asians through the lens of aDNA

aDNA resources from East Asia also provide a unique opportunity to unravel the evolutionary history of traits that affect health today, offering potential advancements in preventive strategies, personalized medicine, and the understanding of genetic predispositions [114,115,116,117,118,119]. The rich narrative offered by ancestral gene flows, coupled with insights derived from aDNA, deepens our knowledge of the genetic foundations of health and disease. The limited availability of aDNA from China impedes the systematic exploration of the evolutionary determinants of East Asian-related traits (Figs. 5–6). Kumar et al. explored the phenotypic effects resulting from changes in ancestry in TSM populations, confirming the emergence of lighter hair pigmentation and skin tone in individuals from western and northern TSM regions, particularly from the late Bronze Age to the Iron Age. Additionally, blue-eyed alleles were present in these regions during the Iron Age. Notably, all five historical samples presented darker eye and hair pigmentation, reflecting a period of increased ancestry from East, South, and Central Asia [72].

To better understand the East Asian-specific evolutionary trajectory of the EDAR V370A genetic variant, which regulates traits related to thicker hair shafts, Mao et al. analyzed genome-wide data from 25 ARB individuals, supplemented with data from a previously published Tianyuan individual. This dataset spans the pre- and post-LGM periods (40–6 kya) and provides valuable insights (Fig. 5). The study revealed that the V370A mutation was present in all post-LGM ancient East Asians, suggesting that its prevalence emerged during or shortly after the LGM (Fig. 5) [41]. In a separate study, Zhang et al. traced the emergence of the OCA2-HiS615Arg (rs1800414) variant to the early Neolithic in the coastal region of southern China (Liangdao). Over the past 4,000 years, this variant has experienced a significant increase in frequency, likely due to Darwinian positive selection. This selection mechanism may have contributed to the lightening of skin tone in Chinese populations as an adaptation to relatively lower UV radiation levels at higher latitudes (Fig. 5) [43].

Introgression can introduce genetic variations from archaic hominins into modern populations, potentially subjecting these variations to natural selection. This process offers valuable insights into the genetic mechanisms underlying phenotypic variation and adaptive traits [120]. The EPAS1 gene, associated with high-altitude adaptation, was identified in a 5,100-year-old plateau individual and recently published Dadiwan people [47, 106], with its frequency increasing over the past 2,800 years (Fig. 6). Additionally, Gao et al. reported that Chinese-specific introgression of archaic-derived alleles was linked to various functional traits, including keratinization, ultraviolet radiation response, DNA repair, immune system functions, and lifespan, based on pangenomic data from 36 Chinese populations [121]. Large-scale genomic datasets from contemporary populations also suggest that the evolutionary trajectory of East Asian-specific adaptive traits, such as alcohol metabolism-related ADH/ALDH and agricultural diet-related MTHFR, warrants further exploration through aDNA evidence. Spatiotemporal tracing of genetic variants associated with phenotypic alterations in human populations provides valuable insights into prehistoric patterns of genetic diversity, highlighting how natural selection influences the timing of biological adaptations. However, owing to the limited availability of Chinese aDNA data, the precise timing of the emergence and selection of adaptive variants, as well as the detailed evolutionary trajectories of complex traits, remains imprecise. As the availability of aDNA data increases, more accurate temporal estimations and higher-resolution spatiotemporal tracing are anticipated [43].

Challenges and future directions

Evolutionary basis of the genetic architecture of complex human traits

Ancient genomic data offer critical insights into local adaptation and the genetic underpinnings of human health and disease [122]. A prominent example of this progress is the identification of a genetic risk factor from Neanderthals associated with increased susceptibility to severe COVID-19 [123]. The signatures of natural selection in post-Neolithic Europe suggest that genetic adaptation to disease pathogens reshaped immunity-related genes, increasing the risk of inflammatory disorders [116]. Marnetto et al. reported that ancestral components from barley farmers, Steppe herders, and local European hunter-gatherers contributed to the complex trait variability observed in modern Europeans [119]. Recent aDNA studies in China have enhanced our understanding of the evolutionary trajectory of local adaptation, highlighting genetic markers such as EPAS1, which is linked to extreme environmental adaptation on the TP [106], and the well-documented EDAR V370A variant, which influences morphological traits in the Central China Plain region [41]. Additionally, genetic evidence indicates the influence of eastward-moving western Eurasians on pigmentation traits in ancient populations in the TSM region [72]. However, the available aDNA data from China remain limited in both spatial and temporal scopes, hindering a complete exploration of the genetic basis for human health and disease across evolutionary time. The advent of new methodologies, including sediment DNA analysis, paleoproteomics, isotopic studies, microbiome research, and epigenetic profiling, combined with advanced bioinformatics tools tailored for aDNA analysis, promises to deepen our understanding of ancestral health and genetic influences on human evolution [1, 124,125,126]. Omics-based research on ancient human remains or sediment samples could yield novel insights into the evolution of both ancient and modern humans, as well as their coevolution with bacteria.

High-quality population-specific ancient genome database and haplotype reference panel

The integration of aDNA technologies, including DNA extraction and sequencing from fossilized or human remains, with aDNA phasing and imputation, remains an area in need of further innovations [114, 127]. However, accurate genotype calling from ancient genomes remains limited by low coverage, primarily due to post-mortem DNA degradation and contamination. As a result, genome imputation via population-specific, high-quality haplotype reference panels derived from ancestry-specific modern populations has emerged as a reliable method for enhancing genotyping accuracy, even for low-coverage aDNA [128]. The rapid expansion of aDNA data suggests that more ancestry-diverse and spatiotemporally varied ancient genomes will soon become available. This underscores the urgent need to develop population-specific haplotype reference panels for East Asian populations and to establish widely accepted standards for imputation protocols [128, 129]. Furthermore, most aDNA studies currently focus on SNP-based allele-sharing patterns rather than on fine-scale population structures derived from haplotype data. It is essential to define simulation-based benchmarks and accelerate the development of population-specific haplotype reference panels, haplotype-based phasing, and imputation software and databases for aDNA analysis to address this gap [130].

Necessity of multidisciplinary collaboration and indigenous engagement

Interdisciplinary collaboration and effective communication are crucial for developing balanced narratives in aDNA research [131]. Engaging archaeologists, geneticists, anthropologists, and specialists in animal and plant sciences has significantly advanced aDNA studies. By integrating recent insights into the origins and adaptations of ancient domesticated plants and animals within agricultural centers and their surrounding regions, along with their biological adaptations, we can gain a better understanding of the complex dynamics of human movements and biological evolution [46, 132, 133]. On the other hand, one significant challenge in both aDNA and forensic research is the extraction of DNA profiles from degraded samples. Childebayeva et al. highlighted the computational workflows involved in analyzing low-coverage NGS data, addressing the limitations and decision-making processes at each stage of analysis, which is crucial for the progress of both aDNA and forensic studies [134]. Forensic genetics focuses on linking DNA recovered from fragmented evidence to specific individuals, employing DNA profiling alongside phenotype, genetic ancestry, and familial connections to narrow the scope of investigations [134]. In contrast, aDNA research uses DNA from ancient remains, often obtained through capture sequencing, to explore prehistoric demographic interactions [53, 72, 111], test migration hypotheses [54, 66, 76], and examine genetic relationships between ancient and modern populations [1, 4, 41, 42, 50, 106]. Given these diverse applications, it is crucial to extensively validate studies on Chinese populations in both aDNA and forensic genetics to ensure their practical relevance. Moreover, integrating knowledge from genetics, genomics, archaeology, ethnology, and linguistics is necessary to enhance the depth and comprehensiveness of aDNA research.

Fine-scale reconstruction of ancient social development and family genealogy

Recent advances in aDNA have revolutionized our understanding of cultural transitions and complex social organizations [131]. The biological aspects of familial structures in prehistoric societies have gained more precise insights through aDNA studies [135]. Several key aDNA studies have examined genetic relatedness in co-burials, successfully reconstructing complex social structures and shedding light on various facets of past human societies. These studies have revealed important information on the social and reproductive behaviors of Paleolithic hunter-gatherers; the diverse kinship structures in Neolithic Anatolian populations; and the descent, marriage, and residence practices of Bronze Age nomads [135,136,137]. Recent findings from two aDNA works at the Fujia and Baligang archaeological sites have begun to explore how matrilineal and patrilineal communities contributed to social organization in the Neolithic YRB and YZRB populations [62, 138]. To construct a comprehensive profile of ancient East Asian social organizations, integrating insights from cultural traditions, marriage customs, and burial practices across different historical periods, which can help reconstruct the entire landscape of the demographic history of East Asia and possible influencing factors, is essential [112].

Conclusion

This work systematically summarizes the population history of deeply diverged East Asian hunter-gatherer ancestry, including AR19K, Longlin, Qihe, and MZR, which represent ANA, Guangxi, Fujian, and Yunnan ancestries, respectively. This study also provides a comprehensive overview of Holocene eastern Eurasian population dynamics, specifically among millet and rice farmers and herders, indicating that complex movements and admixture have shaped the genomic diversity of modern and ancient East Asians. The Central Plain, particularly the YRB, is regarded as the origin of the Sino-Tibetan language family and an early agricultural center, whose hunter-gatherers or cultivators, in concert with rice farmers from the YZRB, contributed the primary ancestries of populations across other East Asian regions. Challenges associated with preserving aDNA in hot, humid environments, especially among upper and middle YZRB rice farmers in South China, have hindered the recovery of critical spatiotemporal sequences. The relative scarcity of genomic resources from geographically distinct Holocene East Asian populations underscores the need for a high-quality, high-coverage, and spatiotemporally resolved ancient genomic database. Such a database would advance the understanding of the evolutionary origins of human disease and biological adaptations in Paleolithic hunter-gatherers, Neolithic farmers, Bronze Age pastoralists, and contemporary East Asian populations. Although recent advances in aDNA research in East Asia have refined our view of human evolutionary history on the eastern Eurasian continent, the spatiotemporal gap in aDNA data continues to impede a complete understanding of the genetic profiles of rice and millet farmers and their ancestors and descendants. Establishing a robust genomic record from spatiotemporally high-coverage remains vital for illuminating the origins and evolutionary trajectories of East Asian populations.

Materials and methods

We present detailed information on the methods in Additional file 1. Ancient genomic resources from the AADR were merged with recently reported modern and ancient DNA from diverse East Asian populations, resulting in a final dataset of 929 individuals [3, 26, 42, 43, 50, 53, 80, 106, 111, 139,140,141]. ADMIXTURE analysis was performed on linkage disequilibrium-pruned SNPs to infer ancestral components via ADMIXTURE v1.3.0 [142], identifying four primary sources and distinguishing geographically distinct groups at K = 6 [142, 143]. Principal component analysis via the smartpca algorithm implemented in EIGENSOFT [144] clustered ancient and modern populations, revealing genetic substructure across East Asia. BAM files from ancient individuals were processed to assess post-mortem DNA damage [41,42,43, 50, 53,54,55,56, 58, 61, 64, 72, 76, 80, 84, 85, 92, 104, 106, 109, 111, 145,146,147,148], with genotype imputation performed via GLIMPSE2 using the population-specific reference panel [127, 128]. Strict quality control ensured high-resolution genomic analysis, advancing insights into East Asian population history.

Data availability

All data and codes are available at Zenodo. The repository includes the imputed ancient genomic datasets generated in this study, detailed information and references for the ancient genomes analyzed, and scripts used for data processing and analysis. Imputed genomes can be found at Zenodo: [https://zenodo.org/records/17270846] [149]. Code and detailed information for analysis can be found at Zenodo: [https://zenodo.org/records/17270850] [150]. The code for visualization, including PCA and ADMIXTURE, is also available at Zenodo: [https://doi.org/10.5281/zenodo.17271668] [151]. All the other data generated in this study are included in the article and the Additional files.

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