Archaic ancestry inference in imputed ancient human genomes
Abstract
When modern humans expanded from Africa into Eurasia, they interbred with archaic hominins such as Neanderthals and Denisovans. This introgression shaped human evolution, yet most insights have been gained from present-day genomes, leaving little known about how archaic variants evolved after interbreeding. Ancient genomes offer a direct view of this process, but low coverage and poor quality have limited their use. Recent advances in genotype imputation offer a way to overcome these challenges by reconstructing missing information from reference panels and recovering evolutionary signals from low-coverage data. Here, we show that imputation enables accurate detection and quantification of archaic introgression in ancient genomes, improves local archaic ancestry inference, and that regions of archaic ancestry are imputed with especially high accuracy. We further demonstrate that imputed genomes can reconstruct the trajectories of introgressed haplotypes, distinguish populations across time and geography, and identify both known and additional candidates for adaptive introgression.
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BibTeX
@article{capodiferro2026archaic,
title = {{Archaic ancestry inference in imputed ancient human genomes}},
author = {Marco Rosario Capodiferro and Léo Planche and Emily M Breslin and Linda Ongaro and María C Ávila-Arcos and Flora Jay and Lara M Cassidy and Emilia Huerta-Sanchez},
journal = {Nature Communications},
year = {2026},
month = sep,
doi = {10.1038/s41467-026-76204-0},
url = {https://hal.science/hal-05747161v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Archaic ancestry inference in imputed ancient human genomes
AU - Marco Rosario Capodiferro
AU - Léo Planche
AU - Emily M Breslin
AU - Linda Ongaro
AU - María C Ávila-Arcos
AU - Flora Jay
AU - Lara M Cassidy
AU - Emilia Huerta-Sanchez
PY - 2026
DA - 2026/09/11
JO - Nature Communications
DO - 10.1038/s41467-026-76204-0
UR - https://hal.science/hal-05747161v1
AB - When modern humans expanded from Africa into Eurasia, they interbred with archaic hominins such as Neanderthals and Denisovans. This introgression shaped human evolution, yet most insights have been gained from present-day genomes, leaving little known about how archaic variants evolved after interbreeding. Ancient genomes offer a direct view of this process, but low coverage and poor quality have limited their use. Recent advances in genotype imputation offer a way to overcome these challenges by reconstructing missing information from reference panels and recovering evolutionary signals from low-coverage data. Here, we show that imputation enables accurate detection and quantification of archaic introgression in ancient genomes, improves local archaic ancestry inference, and that regions of archaic ancestry are imputed with especially high accuracy. We further demonstrate that imputed genomes can reconstruct the trajectories of introgressed haplotypes, distinguish populations across time and geography, and identify both known and additional candidates for adaptive introgression.
SN - 2041-1723
SN - 2041-1723
ER -