The Hanging Coffin represents a distinctive mortuary tradition practiced across southern China, Southeast Asia (e.g., the Log Coffin), and the Pacific approximately 3,000 years. Historical records attribute this funerary practice to the Bo people, a group that largely disappeared from documented history by the end of the Ming Dynasty (1,368–1,644 AD). Here we report eleven ancient genomes from four Hanging Coffin sites in China, alongside thirty whole genomes from the extant Bo people in Southwest China. We also sequence four ancient genomes from Log Coffin sites in northwestern Thailand. Our findings indicate that present-day Bo people derive a substantial proportion of their ancestry from practitioners of the Hanging Coffin mortuary tradition. Both ancient and modern groups exhibit elevated genetic affinity with coastal Neolithic populations from southern East Asia, who are ancestral to Tai-Kadai and Austronesian speakers. Unexpectedly, we also find evidence of long-range interactions and cultural inclusivity between Northeast Asian and Yellow River farmers and Hanging Coffin communities over 1,200 years ago. Finally, shared genetic components between Hanging (Log) Coffin populations in China and Thailand point to a common origin and a broader genetic and cultural network underlying this distinctive mortuary tradition across southern China and Southeast Asia.

The advent of the First Agricultural Revolution, also referred to as the Neolithic Revolution, marked by the domestication of plants and animals, established a foundation for the development of complex societies. In East Asia, the Yellow River and Yangtze River basins served as primary centers for the domestication of millet (Panicum miliaceum and Setaria italica) and rice (Oryza sativa), respectively. In addition, the domestication of pigs (Sus scrofa domesticus) occurred independently from that in West Asia. The widespread in-tensive millet and rice cultivation during the Middle Neolithic period (~7000–5000 years ago) led to the proliferation of diverse archeological cultures across and beyond the Yellow River and Yangtze River basins. The demic and/or cultural diffusion during thisperiodhaspromptedre-evaluationofthefarming/languagedispersalhypothesisinEastAsia.

The Yuanmou Basin in Yunnan Province, southwestern China, preserves one of the latest surviving records of Eurasian hominoids, yet the chronological and paleoenvironmental framework for this region remains poorly constrained. Here we analyze hyena coprolites from hominoid-bearing strata to establish a robust chronology and reconstruct the paleoecology of the Late Miocene. In-situ LA-MC-ICP-MS U–Pb dating of carbonate crystals within coprolites yielded a geologically reliable age of 7.7 ± 1.4 Ma, providing the first direct radiometric constraint on hominoid survival in Yuanmou. Palynological analyses reveal a highly diverse vegetation assemblage encompassing coniferous, evergreen broadleaf, and deciduous taxa, with evidence of distinct vertical zonation. Bioclimatic Analysis (BA) indicates a subtropical humid climate, with mean annual temperature of 12.8–13.3 ◦C and mean annual precipitation of 1320–1409 mm, markedly cooler and wetter than today. These favorable climatic conditions, coupled with extensive dense forests, supplied abundant food resources for arboreal hominoids, as supported by dental adaptations for consuming hard fruits and nuts. Regional comparisons demonstrate that, unlike much of Eurasia where hominoids declined during the Late Miocene, Yunnan retained stable warm–humid environments buffered by the complex topography associated with Tibetan Plateau uplift and the evolving South Asian Monsoon. This long-term ecological stability made Yunnan a critical refuge for Late Miocene hominoids and underscores the importance of tectonic–climatic coupling in shaping primate evolutionary trajectories in East Asia.

Wild plants have been an important part of the diet of ancient people, and their remains at archaeological sites are therefore a good proxy for disentangling human exploitation of plant foods in the history. Yunnan in southwest China has been poorly explored in archaeobotany, especially for periods before the Neolithic when gathering was still dominant in plant utilization. Here, we present an archaeobotanical assemblage consisting of fruit and seed remains from the regionally terminal Paleolithic (8740 ± 30 BP) Tangzigou site in western Yunnan. Our taxonomic identification shows that the archaeobotanical assemblage is poor in diversity with only four taxa, i.e., Celtis sp. (hackberry), Prunus persica (wild peach), Vitis sp. (wild grape) and Choerospondias axillaris (Nepal hog plum), which have served as potential food resources to ancient people of the site. However, the full picture of plant exploitation by the Tangzigou people cannot be gained only from the low abundance and diversity of plant remains at the site itself. Based on what is known of the practices of hunter-gatherers today, most fruits and seeds were probably eaten by Tangzigou people during the course of foraging trips, with only a small fraction being carried back to the site for processing and consumption. The fruit stone remains of C. axillaris have been processed with fire accidently or intentionally; the intentional fire-processing was probably for consumption of the seeds inside, which is compatible with the processing of animal foods with fire by the Tangzigou people. Our study brings to light the possible incorporation of plant food resources into the diet of the latest Paleolithic Tangzigou people who are suggested to have lived under a warm subtropical climate. It also enriches our knowledge of the historical use of wild plants by early Holocene humans in southwest China.

Toddalia Juss. is a genus in Rutaceae, with a modern geographical range that extends from West and East Africa to South, East and Southeast Asia. The genus has a good fossil record in Europe, where it has become extinct, but is poorly represented in the geological record of Asia, where it flourishes today. This study reports the second fossil record of Toddalia in Asia, based on three-dimensional seed remains recovered from the latest Miocene Baoshan Basin in western Yunnan, southwestern China. The fossil seeds are characterized by their reniform shape, smooth surface, large hilar scar, unique raphe excrescence and layered seed coat. Following morphological and anatomical comparisons with both extant and other fossil species, the fossil seeds were assigned to T. nanlinensis, a species first reported from the Early-Middle Miocene Longchuan Basin in southwestern Yunnan. This new fossil finding suggests that the Baoshan Basin probably had forest vegetation in a warm, humid climate at some time during the latest Miocene. This is in line with previous suggestions based on other fossils, such as hominoids (Lufengpithecus sp.) and other mammals, found from the same sedimentary layer of the basin. Together with the previous record, our fossil discovery mirrors continuous presence of Toddalia in southwestern China since at least the Early-Middle Miocene. This provides insight into how the modern distribution range of the genus formed in this region and even in Asia.

Over 80 million people worldwide live at high altitudes (> 2500 m), where numerous studies have documented the remarkable biological adaptations of highland populations to these extreme environments. However, current resources for accessing and analyzing highlander-specific data remain limited. To address this gap, we present the HiLand Resource (HLR), a comprehensive database that integrates phenomic, genomic, and genetic association data from 29,977 highlanders across three major high-altitude regions: the Qinghai–Xizang Plateau, the Andean Plateau, and the Ethiopian Plateau. HLR offers six key functions: (1) visualization of phenotypic pattern among Qinghai– Xizang highlanders across different altitudes, as well as comparison between highlanders and lowlanders, and between sexes; (2) an interactive interface to explore genomic diversity, population structure, ancestral composition, and signatures of natural selection of high-altitude populations; (3) access to a comprehensive catalog of genome-wide variants and genes identified in highlanders; (4) a genome browser built on a high-quality Tibetan genome assembly; (5) a curated collection of genotype phenotype associations derived from genome-wide association studies (GWAS) in highland populations; and (6) an online, user-friendly tool for genotype imputation using a highland-specific reference panel. Collectively, HLR provides a novel and in54
depth resource for understanding the biological features of high-altitude human populations. It holds significant potential for advancing research on human adaptation to hypoxic environments and improving medical studies focused on highland communities. The HLR database is freely available at: https://ngdc.cncb.ac.cn/hiland/.

Mainland Southeast Asia (MSEA) has rich ethnic and cultural diversity with a population of nearly 300 million1,2. However, people from MSEA are underrepresented in the current human genomic databases. Here we present the SEA3K genome dataset (phase I), generated by deep short-read whole-genome sequencing of 3,023 individuals from 30 MSEA populations, and long-read whole-genome sequencing of 37 representative individuals. We identified 79.59 million small variants and 96,384 structural variants, among which 22.83 million small variants and 24,622 structural variants are unique to this dataset. We observed a high genetic heterogeneity across MSEA populations, reflected by the varied combinations of genetic components. We identified 44 genomic regions with strong signatures of Darwinian positive selection, covering 89 genes involved in varied physiological systems such as physical traits and immune response. Furthermore, we observed varied patterns of archaic Denisovan introgression in MSEA populations, supporting the proposal of at least two distinct instances of Denisovan admixture into modern humans in Asia3. We also detected genomic regions that suggest adaptive archaic introgressions in MSEA populations. The large number of novel genomic variants in MSEA populations highlight the necessity of studying regional populations that can help answer key questions related to prehistory, genetic adaptation and complex diseases.

Nitric oxide (NO) is a key vasodilator that regulates vascular pressure and blood flow. Tibetans have developed a “blunted” mechanism for regulating NO levels at high altitude, with GTP cyclohydrolase 1 (GCH1) identified as a key candidate gene. Here, we present comprehensive genetic and functional analyses of GCH1, which exhibits strong Darwinian positive selection in Tibetans. We show that Tibetan-enriched GCH1 variants down-regulate its expression in the blood of Tibetans. Based on this observation, we generate the heterozygous Gch1 knockout (Gch1 þ/e) mouse model to simulate its downregulation in Tibetans. We find that under prolonged hypoxia, the Gch1 þ/e mice have relatively higher blood NO and blood oxygen saturation levels compared with the wild-type (WT) controls, providing better oxygen supplies to the cardiovascular and pulmonary systems. Markedly, hypoxia-induced cardiac hypertrophy and pulmonary remodeling are significantly attenuated in the Gch1 þ/e mice compared with the WT controls, likely due to the adaptive changes in molecular regulations related to metabolism, inflammation, circadian rhythm, extracellular matrix, and oxidative stress. This study sheds light on the role of GCH1 in regulating blood NO, contributing to the physiological adaptation of the cardiovascular and pulmonary systems in Tibetans at high altitude.

Understanding the cellular and genetic mechanisms driving human-specific features of cortical development remains a challenge. We generated a cell-type resolved atlas of transcriptome and chromatin accessibility in the developing macaque and mouse prefrontal cortex (PFC). Comparing with published human data, our findings demonstrate that although the cortex cellular composition is overall conserved across species, progenitor cells show significant evolutionary divergence in cellular properties. Specifically, human neural progenitors exhibit extensive transcriptional rewiring in growth factor and extracellular matrix (ECM) pathways. Expression of the human-specific progenitor marker ITGA2 in the fetal mouse cortex increases the progenitor proliferation and the proportion of upper-layer neurons. These transcriptional divergences are primarily driven by altered activity in the distal regulatory elements. The chromatin regions with human-gained accessibility are enriched with human-specific sequence changes and polymorphisms linked to intelligence and neuropsychiatric disorders. Our results identify evolutionary changes in neural progenitors and putative gene regulatory mechanisms shaping primate brain evolution.

Dichobunoids were the most basal artiodactyl group, widely distributed throughout the Eocene of Eurasia and North America, but were rarely reported from southern China. In this paper, we report the first dichobunoid artiodactyl, Shilinhyus chowi n. gen. n. sp., from the middle Eocene of Lunan Basin (Shilin County), China. Shilinhyus is characterized by its relatively large size, bunoselenodont tooth morphology with a highly developed p4 metaconid, and a mesially interrupted paracristid formed by a weak premetacristid and a strong preprotocristid. This morphology distinguishes Shilinhyus from all known dichobunoid artiodactyls. Within dichobunoids, Shilinhyus resembles Pakkokuhyus from the Eocene of Southeast Asia and ‘‘Gobiohyus” yuanchuensis from the Eocene of Shanxi, China, by the relatively large size, the absence of the paraconid, and the well-development of the hypolophid. However, Shilinhyus still differs from Pakkokuhyus and ‘‘Gobiohyus” yuanchuensis in the complete interruption of the paracristid and in the alignment of the entoconid and hypoconid as well as the protoconid and metaconiod. Shilinhyus, Pakkokuhyus, and ‘‘Gobiohyus” yuanchuensis might have derived from the Eocene Gobiohyus from northern China, constituting a distinct group. The discovery of Shilinhyus chowi enhances our understanding of the early evolution of dichobunoid artiodactyls, especially in southern China.

Aurochs (Bos primigenius), once widely distributed in Afro-Eurasia, became extinct in the early 1600s.
However, their phylogeography and relative contributions to domestic cattle remain unknown. In this
study, we analyzed 16 genomes of ancient aurochs and three mitogenomes of ancient bison (Bison priscus) excavated in East Asia, dating from 43,000 to 3,590 years ago. These newly generated data with previously published genomic information on aurochs as well as ancient/extant domestic cattle worldwide
through genome analysis. Our findings revealed significant genetic divergence between East Asian aurochs and their European, Near Eastern, and African counterparts on the basis of both mitochondrial
and nuclear genomic data. Furthermore, we identified evidence of gene flow from East Asian aurochs into
ancient and present-day taurine cattle, suggesting their potential role in facilitating the environmental
adaptation of domestic cattle.

The anterior cingulate cortex (ACC) of the human brain is involved in higher-level cognitive functions such as emotion and self-awareness. We generated profiles of human and macaque ACC gene expression and chromatin accessibility at single-nucleus resolution. We characterized the conserved patterns of gene expression, chromatin accessibility, and transcription factor binding in different cell types. Combining the published mouse data, we discovered the molecular identities and cell-lineage origin of the primate von Economo neurons (VENs). Our in vitro and in vivo experiments identified a group of primate-shared and human-specific VEN marker genes, such as PCSK6, ADAMTSL3, and CDHR3, potentially contributing to VEN morphogenesis. We demonstrated that the human-specific sequence changes account for the cellular and functional innovations in the ACC during primate evolution and human origin. These findings provide new insights into understanding the cellular composition and molecular regulation of ACC and its evolutionary role in shaping human-owned higher cognitive skills.