Biology subjects

Chaix, R.

Publications and source records attributed to Chaix, R..

3 recordsLinked to original sources

bioRxiv2026

The genetic legacy of archaic hominins in Central and Southeast Asia uncovers three distinct Denisovan populations

The sequencing of Neanderthal and Denisovan genomes has provided new insights into human evolution. Today, interactions between Neanderthals, Denisovans, and populations of European, East Asian, and Oceanian descent are well documented. However, neighboring regions such as Central and Southeast Asia remain understudied for archaic admixture despite their key geographic location and complex migration histories. To fill this gap, we investigate archaic ancestry in 16 populations from Central Asia and 14 from mainland Southeast Asia. Our results show that Neanderthal and Denisovan ancestry in these populations is of the same order of magnitude as in other Eurasian populations. However, although Denisovan ancestry accounts for less than 1% in mainland Asian populations, it originates from several admixture events involving different Denisovan populations. In particular, we find in Southeast Asia that Denisovan ancestry results from three distinct admixture events with three different Denisovan populations, highlighting the complexity of Denisovan contact with the ancestors of present-day Southeast Asian populations and providing new insights into the extensive geographic distribution of Denisovan populations.

evolutionary biology↗

bioRxiv2026

Genomic insights into adaptation to eco-regional and cultural variables across human populations from North, Central and Southeast Asia

Natural selection has been extensively studied in humans, providing many examples of how climate, diet, and pathogens can translate into local selective pressures and thus phenotypic diversity across populations. However, most studies have focused either on a global scale, with a limited number of populations per geographic area, or on a very local scale. To complement these approaches, we collected and studied a large genomic dataset at a continental scale covering North, Central, and mainland Southeast Asia, and consisting of 863 individuals from 25 culturally diverse populations. We aimed to decipher the selective pressures across the Asian continent, comparing populations from different geographic areas and having contrasted subsistence strategies, using both intra-populations (iHS) and inter-populations (Fst) statistics. We detected both local and continental-wide signals, with some geographically and culturally complex patterns emerging when being compared to the literature. Interestingly, among the regions detected as significant only in mainland Southeast Asia, we found two of them clearly pointing to selective pressures associated with immunity. The first one, detected with iHS only, contains three peptidoglycan binding genes (REG1A, REG1B and REG3A) interacting with bacterial cell walls. The second region, the most significant one when intersecting iHS and Fst, contains PELI1, previously shown to modulate the immune and inflammatory response and to be under selection in Han Chinese and Oceanians. In addition, in North and Central Asia, we uncovered a region overlapping with PTPRC, a gene associated with viruses recognition, as well as another region including GPHB5, associated with lipid and carbohydrate metabolism. Interestingly, we further identified a signal on PTPRG, where variants have previously been associated with alcohol flushing in East Asia, not only in farmers but also in herders and hunter-gatherers, challenging the hypothesis that this phenotype was selected for in response to the transition to agriculture. In turn, when focusing on signals specific to given subsistence strategies, we found two genes related to immune functions (TUBA1B and HERC1 ) exclusively in herders. In conclusion, while many signals of selection likely remain to be uncovered in less studied human groups, deciphering whether they are linked to immune, dietary or climatic factors is challenging, as subsistence strategies often covary with climate, which further influence pathogenic loads.

genomics↗

bioRxiv2025

Historic Genomes Uncover Demographic Shifts and Kinship Structures in Post-Roman Central Europe

Many European towns and villages trace their origins to Early Medieval foundations. In former Roman territories, their emergence has traditionally been linked to mass migrations from outside the Roman Empire. However, recent studies have emphasised local continuity with some individual-level mobility. We generated and analysed 248 historic genomes from Late Roman (3rd and 4th century CE) and Early Medieval (5th-8th century CE) burial sites in southern Germany, comparing them to over 2,500 contemporary and Iron Age genomes in addition to 1,344 modern-day genomes from Germany, Italy and Great-Britain. Despite small inferred Early Medieval period community sizes, genetic diversity exceeded that of modern German cities. In the Altheim graveyard, established in the 5th century by a group of Northern European descent, we inferred a demographic shift in the 6th century with the integration of newcomers with ancestry typical of a nearby Roman military camp, likely as a result of the collapse of Roman state structures. We reconstructed multigenerational pedigrees and, using a novel approach to infer ancestry of unsampled relatives, inferred immediate intermarriage between incoming and local groups, with a distinct tendency for men from former Roman background marrying women of northern descent. Burial proximity correlates strongly with kinship, in some cases spanning six generations. These communities were organized around small family units, exhibited loosely patrilineal or bilateral descent patterns, practiced reproductive monogamy, and avoided close-kin marriages. Such practices reflect broader transformations in family structures that began during the Late Roman period, were transferred to small agrarian societies in the Early Medieval period, and continued to shape European societies. By the 7th century, ongoing admixture had shaped genetic diversity patterns into those resembling Central Europe today.

genetics↗