Temporal variation in introgressed segments’ length statistics computed from a limited number of ancient genomes sheds light on past admixture pulses

Article Article scientifique Article Temporal variation in introgressed segments’ length statistics computed from a limited number of ancient genomes sheds light on past admixture pulses eng 2023-11-22 2023-11-22 author Di Santo Lionel Nicolas 0000-0002-8288-4860 981683 Département de génétique et évolution (Genev) (BIANI) author Quilodran Claudio 0000-0001-7197-9154 753257 Département de génétique et évolution (Genev) (BIANI) author Currat Mathias 0000-0001-5211-8922 89701 Département de génétique et évolution (Genev) (BIANI) msad252 10.1093/molbev/msad252 37992125 0737-4038 https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msad252/7441957 <p>Hybridization 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 genomic data for a two-population system and described temporal neutral introgression patterns under a single- and two-pulse admixture model. We computed six 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 and related measures. The first two statistics could confidently be used to infer inter-lineage hybridization history, peaking at the beginning and shortly after an admixture pulse. Temporal variation in introgression proportions and related statistics provided more limited insights, particularly when considering their application to ancient genomes still scant in number. Lastly, we computed these statistics on Homo sapiens paleogenomes and successfully inferred the hybridization pulse from 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 ancient genomes.</p> Homo neanderthalensis Homo sapiens Ancient DNA Forward-in-time simulations Genomic mixing Single genome Dewey 590 44 Département de génétique et évolution 162 23 Institut de génétique et de génomique 0DH false 828 Groupe Currat 682 Laboratory of Anthropology, Genetics and Peopling history (AGP) Molecular biology and evolution cbf8bf97-2c51-4719-99a8-1089136765bb Article (Published version) Public Article-scientifique-from-unpaywall.pdf 1042601 application/pdf CC BY-NC ed3147f64c102eaa9b5c3397733f88afe0f7361bcef987d12b3717912fc00d40 openAccess Faculté des sciences / Section de biologie / Département de génétique et évolution Centres et instituts / Institut de génétique et de génomique

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Temporal variation in introgressed segments’ length statistics computed from a limited number of ancient genomes sheds light on past admixture pulses	Molecular biology and evolution			2023	143	749

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Di Santo, Lionel Nicolas