ArticlebioRxiv : the preprint server for biology2024
Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years.
Katia Bougiouri, Sabhrina Gita Aninta, Sophy Charlton, Alex Harris, Alberto Carmagnini, Giedrė Piličiauskienė, Tatiana R Feuerborn, Lachie Scarsbrook, Kristina Tabadda, Povilas Blaževičius and 7 more
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In one paragraphArticle in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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17 authors.
Katia BougiouriSection for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark.ORCID 0000-0002-7890-2755 Sabhrina Gita AnintaSchool of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.ORCID 0000-0002-0736-4750 Alex HarrisNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.ORCID 0000-0002-6868-5363 Alberto CarmagniniSchool of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.ORCID 0000-0002-5215-4269 Giedrė PiličiauskienėDepartment of Archeology, Faculty of History, Vilnius University, Vilnius, Lithuania.ORCID 0000-0002-5168-8568 Tatiana R FeuerbornNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.ORCID 0000-0003-1610-3402 Lachie ScarsbrookThe Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.ORCID 0000-0003-2558-4455 Kristina TabaddaThe Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.
Povilas BlaževičiusDepartment of Archeology, Faculty of History, Vilnius University, Vilnius, Lithuania.ORCID 0000-0003-2869-4895 Heidi G ParkerNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.ORCID 0000-0002-9707-6380 Shyam GopalakrishnanCenter for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark.ORCID 0000-0002-2004-6810 Greger LarsonThe Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.ORCID 0000-0002-4092-0392 Elaine A OstranderNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.ORCID 0000-0001-6075-9738 Evan K Irving-PeaseSection for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark.ORCID 0000-0003-1940-2192 Laurent A F FrantzSchool of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.ORCID 0000-0001-8030-3885 Fernando RacimoSection for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark.ORCID 0000-0002-5025-2607 Funding
Comparative Mammalian GenomicsZIAHG200377 · NHGRI · NATIONAL HUMAN GENOME RESEARCH INSTITUTE · PI OSTRANDER, ELAINE · 2012 to 2025
$24.8MWellcome Trust
6 · The paper itselfAbstract
The multi-millenia long history between dogs and humans has placed them at the forefront of archeological and genomic research. Despite ongoing efforts including the analysis of ancient dog and wolf genomes, many questions remain regarding their geographic and temporal origins, and the microevolutionary processes that led to the diversity of breeds today. Although ancient genomes provide valuable information, their use is hindered by low depth of coverage and post-mortem damage, which inhibits confident genotype calling. In the present study, we assess how genotype imputation of ancient dog and wolf genomes, utilising a large reference panel, can improve the resolution provided by ancient datasets. Imputation accuracy was evaluated by down-sampling high coverage dog and wolf genomes to 0.05-2x coverage and comparing concordance between imputed and high coverage genotypes. We measured the impact of imputation on principal component analyses and runs of homozygosity. Our findings show high (R
Indexed as
ancient DNAdog evolutiongenotype imputationinbreedingruns of homozygosity
Identifiers
PMID38903121
PMCPMC11188068
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