Inferring Domestic Goat Demographic History Through Ancient Genome Imputation

Goats were among the earliest managed animals, making them a natural model to explore the genetic consequences of domestication. However, a challenge in ancient genomic analysis is the relatively low genome coverage for most samples, limiting analysis to pseudohaploid genotypes. Genotype imputation offers potential to alleviate this limitation by improving information content and accuracy in low coverage genomes. To test this, we used published high coverage (>8✕) goat palaeogenomes, imputing downsampled genomes using the VarGoats dataset (1,372 individuals) as a reference panel. Measuring concordance between imputed and high coverage genotypes, we find high concordance after filtering for common (>5%), high confidence variants, with 0.5✕ genomes reaching >0.97 concordance. There is a trade-off between coverage, genotype probability (GP) thresholds, and genotype recovery, where higher coverage and more lenient GP thresholds result in higher recovery, and a reduction in heterozygous false-positive rates with stricter thresholds. We then imputed 36 goat palaeogenomes with ≥0.5✕ coverage to examine runs-of-homozygosity (ROH) and identity-by-descent (IBD) patterns. Using a novel approach combining ROH profiles across tools, we find that among Neolithic goats, ROH increases with distance from the Zagros Mountains, suggesting a large effect of the initial dispersal of managed herds. Inbreeding levels decrease across Southwest Asia in more recent periods. IBD mirrored this pattern, with less relatedness in the early herding site of Ganj Dareh compared to higher relatedness in goats from later in the dispersal process. These findings provide insights into the genetic consequences of early goat management on demography, and confirm the utility of imputation in leveraging low coverage palaeogenomes.

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Journal
Genome Biology and Evolution
Published
2025-10-29
DOI
https://doi.org/10.1093/gbe/evaf181
Primary Topic
Genetic and phenotypic traits in livestock
Type
article
Field-Weighted Citation Impact
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article

Inferring Domestic Goat Demographic History Through Ancient Genome Imputation

Emily L. Clark, Curtis P. Van Tassell, Andrea Talenti, Philippe Bardou et al.
Genome Biology and Evolution
Genetic and phenotypic traits in livestock
article

Inferring Domestic Goat Demographic History Through Ancient Genome Imputation

Emily L. Clark, Curtis P. Van Tassell, Andrea Talenti, Philippe Bardou, Alessandra Stella, François Pompanon, Marjan Mashkour, Jolijn A. M. Erven, Marcel Amills, Gwenola Tosser‐Klopp, Bertrand Servin, Licia Colli, Paola Crepaldi, Marco Milanesi, Kevin G. Daly, Clet Wandui Masiga, Mahesh Neupane, Benjamin D. Rosen, Alice Etourneau
article en

Abstract

Goats were among the earliest managed animals, making them a natural model to explore the genetic consequences of domestication. However, a challenge in ancient genomic analysis is the relatively low genome coverage for most samples, limiting analysis to pseudohaploid genotypes. Genotype imputation offers potential to alleviate this limitation by improving information content and accuracy in low coverage genomes. To test this, we used published high coverage (>8✕) goat palaeogenomes, imputing downsampled genomes using the VarGoats dataset (1,372 individuals) as a reference panel. Measuring concordance between imputed and high coverage genotypes, we find high concordance after filtering for common (>5%), high confidence variants, with 0.5✕ genomes reaching >0.97 concordance. There is a trade-off between coverage, genotype probability (GP) thresholds, and genotype recovery, where higher coverage and more lenient GP thresholds result in higher recovery, and a reduction in heterozygous false-positive rates with stricter thresholds. We then imputed 36 goat palaeogenomes with ≥0.5✕ coverage to examine runs-of-homozygosity (ROH) and identity-by-descent (IBD) patterns. Using a novel approach combining ROH profiles across tools, we find that among Neolithic goats, ROH increases with distance from the Zagros Mountains, suggesting a large effect of the initial dispersal of managed herds. Inbreeding levels decrease across Southwest Asia in more recent periods. IBD mirrored this pattern, with less relatedness in the early herding site of Ganj Dareh compared to higher relatedness in goats from later in the dispersal process. These findings provide insights into the genetic consequences of early goat management on demography, and confirm the utility of imputation in leveraging low coverage palaeogenomes.

Genome Biology and EvolutionVol. 17(11)
University College Dublin (IE), Università Cattolica del Sacro Cuore (IT), Centre National de la Recherche Scientifique (FR), European Bioinformatics Institute (GB), Agricultural Research Service (US), United States Department of Agriculture (US), Roslin Institute (GB), Università degli Studi della Tuscia (IT), École Nationale Vétérinaire de Toulouse (FR), University of Milan (IT), Trinity College Dublin (IE), University of Tehran (IR), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR), International Institute of Tropical Agriculture (UG), Beltsville Agricultural Research Center (US), Archéozoologie et Archéobotanique (FR), Bioinformatics Institute (RU), Laboratoire d'Écologie Alpine (FR), Génétique Physiologie et Systèmes d'Elevage (FR), National Research Council (IT), Center for Research in Agricultural Genomics (ES), Université Savoie Mont Blanc (FR), Université Grenoble Alpes (FR), University of Edinburgh (GB)
Agence Nationale de la Recherche, University of Tsukuba, Directorate for Biological Sciences, Biotechnology and Biological Sciences Research Council
Openalex Percentile: Top 64%
Genetic and phenotypic traits in livestock
DOIOpen Access PDFOpenAlex
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