Biology subjects

Quilodran, C. S.

Publications and source records attributed to Quilodran, C. S..

6 recordsLinked to original sources

bioRxiv2026

Tracing Neanderthal ancestry patterns through successive population expansions in Europe

During their expansion out of Africa, modern humans interbred with Neanderthals, leading to the introgression of Neanderthal DNA into their genomes. This initial dispersal created, in Europe, a Southeast-to-Northwest gradient of Neanderthal ancestry in European populations, which was preserved through later Neolithic migration. Here, we investigate the population dynamics that created and maintained this gradient across two successive expansions. We developed a three-population layered simulation framework to track the spatiotemporal evolution of Neanderthal ancestry under a model of interactions between Neanderthals, Palaeolithic hunter-gatherers, and Neolithic farmers. Our results indicate that the Neanderthal ancestry cline was shaped by the direction of the early hunter-gatherer expansion, the northern limit of the Neanderthal range, and strong reproductive isolation between lineages. We estimated that admixture between hunter-gatherers and Neolithic populations was an order of magnitude higher than that between Neanderthals and modern humans. These findings demonstrate how spatiotemporal analyses of ancient DNA provide insights into the dynamics and interactions of ancestral populations.

genomics↗

bioRxiv2026

Tracing the Neanderthal-Modern Human hybrid zone using paleogenomic data

Interbreeding between closely related lineages is a pervasive evolutionary feature across taxa1, including modern humans, who admixed with Neanderthals and other archaic hominins2,3. Identifying where gene flow between these lineages happened can shed light on ecological and adaptive contexts in which introgressed genes were acquired. However, mapping ancient hybrid zones is challenging because post-admixture population dynamics obscure their genetic signatures. Here, we determine the conditions under which spatial patterns of introgressed DNA in ancient genomes allow the inference of the geographic location of past hybridization events during population expansions. Using computational simulations, we identify the conditions under which introgression-based statistics provide informative signals about past hybridization events. We show that the mean genomic proportion of introgressed DNA, which can be readily calculated from low-coverage ancient genomes, reveals a cline that increases with distance from the population expansion source until reaching the hybrid zone boundary and persists over time. Comparison with empirical Neanderthal introgression distribution from an extended Eurasian paleogenomic dataset supports a prolonged admixture pulse extending far beyond the Levant in western Eurasia. Our findings highlight the power of paleogenomics to reconstruct the spatiotemporal dynamics of species interactions.

evolutionary biology↗

bioRxiv2024

Local increases in admixture with hunter-gatherers followed the initial expansion of Neolithic farmers across continental Europe

The replacement of hunter-gatherer lifestyles by agriculture represents a pivotal change in human history. The initial stage of this Neolithic transition in Europe was instigated by the migration of farmers from Anatolia and the Aegean basin. In this study, we modeled the expansion of Neolithic farmers into Central Europe from Anatolia, along the Continental route of dispersal. We employed spatially explicit simulations of palaeogenomic diversity and high-quality palaeogenomic data from 67 prehistoric individuals to assess how population dynamics between indigenous European hunter-gatherers and incoming farmers varied across space and time. Our results demonstrate that admixture between the two groups increased locally over time at each stage of the Neolithic expansion along the Continental route. We estimate that the effective population size of farmers was about five times that of the hunter-gatherers. Additionally, we infer that sporadic long distance migrations of early farmers contributed to their rapid dispersal, while competitive interactions with hunter-gatherers were limited. TeaserThe first farmers of continental Europe increasingly admixed over time with indigenous hunter-gatherers.

genomics↗

bioRxiv2023

Temporal variation in introgressed segments' length statistics sheds light on past admixture pulses

AbstractHybridization is recognized as an important evolutionary force, but identifying and timing admixture events between divergent lineages remains a major aim of evolutionary biology. While this has traditionally been done using inferential tools on contemporary genomes, the latest advances in paleogenomics have provided a growing wealth of temporally distributed genomic data. Here, we used individual-based simulations to generate chromosome-level genomics data for a two-population system and described temporal neutral introgression patterns under a single- and two-pulse admixture model. We computed three summary statistics aiming to inform the timing and number of admixture pulses between interbreeding entities: lengths of introgressed sequences and their variance within-genomes, as well as genome-wide introgression proportions. The first two statistics can confidently be used to infer inter-lineage hybridization history, peaking at the beginning and shortly after an admixture pulse. Temporal variation in introgression proportions provided more limited insights. We then computed these statistics on Homo sapiens paleogenomes and successfully inferred the hybridization pulse with Neanderthal that occurred approximately 40 to 60 kya. The scarce number of genomes dating from this period prevented more precise inferences, but the accumulation of paleogenomic data opens promising perspectives as our approach only requires a limited number of genomes.

genomics↗

bioRxiv2022

Past human expansions shaped the spatial pattern of Neanderthal ancestry

The worldwide expansion of modern humans (Homo sapiens) from Africa started before the extinction of Neanderthals (Homo neanderthalensis). Both species coexisted and interbred, as revealed by the sequencing of Neanderthal genomes, leading to ~2% Neanderthal DNA in modern Eurasians1,2, with slightly higher introgression in East Asians than in Europeans3-6. These distinct levels of ancestry have been argued to result from selection processes7,8. However, recent theoretical simulations have shown that range expansions could be another explanation9,10. This hypothesis would lead to the generation of spatial gradients of introgression, increasing with the distance from the source of the expansion, i.e., Africa for modern humans. Here, we investigate the presence of Neanderthal introgression gradients after past human expansions by analysing an extended palaeogenomic dataset of Eurasian populations. Our results show that the Out-of-Africa expansion of modern humans into Eurasia resulted in spatial gradients of Neanderthal ancestry that persisted through time. Moreover, while keeping the same gradient orientation, the expansion of early Neolithic farmers into western Eurasia contributed decisively to reducing the average level of Neandertal genomic introgression in European compared to Asian populations. This is because Neolithic farmers carried less Neanderthal DNA than preceding Palaeolithic hunter-gatherers. This study shows that inferences about past population dynamics within our species can be made from the spatiotemporal variation in archaic introgression.

evolutionary biology↗

bioRxiv2019

The multiple population genetic and demographic routes to islands of genomic divergence

1. The way that organisms diverge into reproductively isolated species is a major question in biology. The recent accumulation of genomic data provides promising opportunities to understand the genomic landscape of divergence, which describes the distribution of differences across genomes. Genomic areas of unusually high differentiation have been called genomic islands of divergence. Their formation has been attributed to a variety of mechanisms, but a prominent hypothesis is that they result from divergent selection over a small portion of the genome, with surrounding areas homogenised by gene flow. Such islands have often been interpreted as being associated with divergence with gene flow. However other mechanisms related to genetic architecture and population history can also contribute to the formation of genomic islands of divergence.\n\n2. We currently lack a quantitative framework to examine the dynamics of genomic landscapes under the complex and nuanced conditions that are found in natural systems. Here, we develop an individual-based simulation to explore the dynamics of diverging genomes under various scenarios of gene flow, selection and genotype-phenotype maps.\n\n3. Our modelling results are consistent with empirical observations demonstrating the formation of genomic islands under genetic isolation. Importantly, we have quantified the range of conditions that produce genomic islands. We demonstrate that the initial level of genetic diversity, drift, time since divergence, linkage disequilibrium, strength of selection and gene flow are all important factors that can influence the formation of genomic islands. Because the accumulation of genomic differentiation over time tends to erode the signal of genomic islands, genomic islands are more likely to be observed in recently divergent taxa, although not all recently diverged taxa will necessarily exhibit islands of genomic divergence. Gene flow primarily slows the swamping of islands of divergence with time.\n\n4. By using this framework, further studies may explore the relative influence of particular suites of events that contribute to the emergence of genomic islands under sympatric, parapatric and allopatric conditions. This approach represents a novel tool to explore quantitative expectations of the speciation process, and should prove useful in elucidating past and projecting future genomic evolution of any taxa.

genomics↗