Biology subjects

Heyer, E.

Publications and source records attributed to Heyer, E..

6 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↗

bioRxiv2024

Ancient tree-topologies and gene-flow processes among human lineages in Africa

The deep history of human evolution in Africa remains intensely debated, with increasingly complex models being proposed. To investigate this, we sequenced and analysed 73 novel high-quality whole genomes from 14 Central and Southern African populations with diverse cultural practices. Using extensive simulations and machine-learning Approximate Bayesian Computation (ABC), we jointly reconstructed their demographic history of divergences and migrations. We find extensive genome-wide diversity within and among populations, including substantial local genetic differentiation not fully explained by geography or cultural practices. These patterns highlight the importance of explicitly considering local genomic diversity when reconstructing human evolutionary history. We find that tree-like population histories with long periods of drift separated by short pulses of unidirectional gene-flow better explain the data than continuous gene-flow. Without invoking archaic admixture, our models accurately fit observed genomic variation and identify multiple episodes of gene-flow coinciding with major ecological and cultural changes in Sub-Saharan Africa.

genetics↗

bioRxiv2022

Cultural transmission of reproductive success impacts genomic diversity, coalescent tree topologies and demographic inferences

Cultural Transmission of Reproductive Success (CTRS) has been observed in many human populations as well as other animals. It consists in a positive correlation of non-genetic origin between the progeny size of parents and children. This correlation can result from various factors, such as the social influence of parents on their children, the increase of childrens survival through allocare from uncle and aunts, or the transmission of resources. Here, we study the evolution of genomic diversity through time under CTRS. We show that CTRS has a double impact on population genetics: (1) effective population size decreases when CTRS starts, mimicking a population contraction, and increases back to its original value when CTRS stops; (2) coalescent trees topologies are distorted under CTRS, with higher imbalance and higher number of polytomies. Under long-lasting CTRS, effective population size stabilises but the distortion of tree topology remains, which yields U-shaped Site Frequency Spectra (SFS) under constant population size. We show that this CTRS impact yields a bias in SFS-based demographic inference. Considering that CTRS was detected in numerous human and animal populations worldwide, one should be cautious that inferring population past histories from genomic data can be biased by this cultural process.

genetics↗

bioRxiv2021

Genetic continuity of Indo-Iranian speakers since the Iron Age in southern Central Asia.

Since prehistoric times, South Central Asia has been at the crossroads of the movement of people, culture, and goods. Today, the Central Asias populations are divided into two cultural and linguistic groups: the Indo-Iranian and the Turko-Mongolian groups. Previous genetic studies unveiled that migrations from East Asia contributed to the spread of Turko-Mongolian populations in Central Asia and the partial replacement of the Indo-Iranian population. However, little is known about the origin of the latter. To shed light on this, we compare the genetic data on two current-day populations- Yaghnobis and Tajiks - with genome-wide data from published ancient individuals. The present Indo-Iranian populations from Central Asia display a strong genetic continuity with Iron Age samples from Turkmenistan and Tajikistan. We model Yaghnobis as a mixture of 93% Iron Age individual from Turkmenistan and 7% from Baikal. For the Tajiks, we observe a higher Baikal ancestry and an additional admixture event with a South Asian population. Our results, therefore, suggest that in addition to a complex history, Central Asia shows a remarkable genetic continuity since the Iron Age, with only limited gene flow.

genomics↗

bioRxiv2017

A Genome Scan for Genes Underlying Adult Body Size Differences between Central African Pygmies and their Non-Pygmy Neighbors

BackgroundCentral African hunter-gatherer Pygmy populations have reduced body size compared with their often much larger agricultural non-Pygmy neighbors, potentially reflecting adaptation to the anatomical and physiological constraints of their lifestyle in tropical rainforests. Earlier studies investigating the genetics of the pygmy phenotype have focused on standing height, one aspect of this complex phenotype that is itself a composite of skeletal components with different growth patterns. Here, we extend the investigations of standing height to the variability and genetic architecture of sitting height and subischial leg length as well as body mass index (BMI) in a sample of 406 unrelated West Central African Pygmies and non-Pygmies.\n\nResultsIn addition to their significantly reduced standing height compared with non-Pygmies, we find Pygmies to have significantly shorter sitting heights and subischial leg lengths as well as higher sitting/standing height ratios than non-Pygmies. However, while male Pygmies had significantly lower BMI compared with male non-Pygmies, the BMI of females were instead similar. Consistent with prior observations with standing height, sitting height and subischial leg length were strongly correlated with inferred levels of non-Pygmy genetic admixture while BMI was instead weakly correlated, likely reflecting the greater contribution of non-genetic factors to the determination of body weight compared with height. Using 196,725 SNPs on the Illumina Cardio-MetaboChip with genotypes on 358 Pygmy and 169 non-Pygmy individuals together with single-and multi-marker association approaches, we identified a single genomic region and seven genes associated with Pygmy/non-Pygmy categorization as well as 9, 10, 9, and 10 genes associated with standing and sitting height, sitting/standing height ratio, and subischial leg length, respectively. Many of the genes identified have putative functions consistent with a role in determining their associated trait as well as the complex Central African pygmy phenotype.\n\nConclusionsThese findings highlight the potential of modestly sized datasets of Pygmies and non-Pygmies to detect biologically meaningful associations with traits contributing to the Central African pygmy phenotype. Moreover, they provide new insights into the phenotypic and genetic bases of the complex pygmy phenotype and offer new opportunities to facilitate our understanding of its complex evolutionary origins.

genetics↗