Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years.

Autor: Bougiouri K; Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark., Aninta SG; School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.; Department of Biology, University of Copenhagen, Copenhagen, Denmark., Charlton S; BioArCh, Department of Archaeology, University of York, York, UK., Harris A; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Carmagnini A; School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.; Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany., Piličiauskienė G; Department of Archeology, Faculty of History, Vilnius University, Vilnius, Lithuania., Feuerborn TR; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Scarsbrook L; The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK., Tabadda K; The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK., Blaževičius P; Department of Archeology, Faculty of History, Vilnius University, Vilnius, Lithuania.; National Museum of Lithuania, Vilnius, Lithuania., Parker HG; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Gopalakrishnan S; Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark., Larson G; The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK., Ostrander EA; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA., Irving-Pease EK; Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark., Frantz LAF; School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.; Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany., Racimo F; Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
Jazyk: angličtina
Zdroj: BioRxiv : the preprint server for biology [bioRxiv] 2024 Jul 03. Date of Electronic Publication: 2024 Jul 03.
DOI: 10.1101/2024.03.15.585179
Abstrakt: 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 2 >0.9) imputation accuracy for dogs with coverage as low as 0.5x and for wolves as low as 1.0x. We then imputed a dataset of 90 ancient dog and wolf genomes, to assess changes in inbreeding during the last 10,000 years of dog evolution. Ancient dog and wolf populations generally exhibited lower inbreeding levels than present-day individuals. Interestingly, regions with low ROH density maintained across ancient and present-day samples were significantly associated with genes related to olfaction and immune response. Our study indicates that imputing ancient canine genomes is a viable strategy that allows for the use of analytical methods previously limited to high-quality genetic data.
Databáze: MEDLINE