Data from: Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs
Population bottlenecks, inbreeding, and artificial selection can all, in principle, influence levels of deleterious genetic variation. However, the relative importance of each of these effects on genome-wide patterns of deleterious variation remains controversial. Domestic and wild canids offer a po...
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ftzenodo:oai:zenodo.org:4967926 2024-09-09T19:35:49+00:00 Data from: Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs Marsden, Clare D. Ortega-Del Vecchyo, Diego O'Brien, Dennis P. Taylor, Jeremy F. Ramirez, Oscar Vila, Carles Marques-Bonet, Tomas Schnabel, Robert D. Wayne, Robert K. Lohmueller, Kirk E. 2016-12-04 https://doi.org/10.5061/dryad.012s5 unknown Zenodo https://doi.org/10.1073/pnas.1512501113 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.012s5 oai:zenodo.org:4967926 info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode selective sweep deleterious mutations Canis familiaris Canis lupus info:eu-repo/semantics/other 2016 ftzenodo https://doi.org/10.5061/dryad.012s510.1073/pnas.1512501113 2024-07-26T14:27:06Z Population bottlenecks, inbreeding, and artificial selection can all, in principle, influence levels of deleterious genetic variation. However, the relative importance of each of these effects on genome-wide patterns of deleterious variation remains controversial. Domestic and wild canids offer a powerful system to address the role of these factors in influencing deleterious variation because their history is dominated by known bottlenecks and intense artificial selection. Here, we assess genome-wide patterns of deleterious variation in 90 whole-genome sequences from breed dogs, village dogs, and gray wolves. We find that the ratio of amino acid changing heterozygosity to silent heterozygosity is higher in dogs than in wolves and, on average, dogs have 2–3% higher genetic load than gray wolves. Multiple lines of evidence indicate this pattern is driven by less efficient natural selection due to bottlenecks associated with domestication and breed formation, rather than recent inbreeding. Further, we find regions of the genome implicated in selective sweeps are enriched for amino acid changing variants and Mendelian disease genes. To our knowledge, these results provide the first quantitative estimates of the increased burden of deleterious variants directly associated with domestication and have important implications for selective breeding programs and the conservation of rare and endangered species. Specifically, they highlight the costs associated with selective breeding and question the practice favoring the breeding of individuals that best fit breed standards. Our results also suggest that maintaining a large population size, rather than just avoiding inbreeding, is a critical factor for preventing the accumulation of deleterious variants. DOG_jackknife_on_sweep_nonsweep_data WOLF_jackknife_on_sweep_nonsweep_data Dogwolf_vcf_Filtered_coding_region_with_Miyata_and_GerpScore_annotated.vcf Gene_IDs_overlapping_sweep_regions.final Other/Unknown Material Canis lupus Zenodo |
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selective sweep deleterious mutations Canis familiaris Canis lupus |
spellingShingle |
selective sweep deleterious mutations Canis familiaris Canis lupus Marsden, Clare D. Ortega-Del Vecchyo, Diego O'Brien, Dennis P. Taylor, Jeremy F. Ramirez, Oscar Vila, Carles Marques-Bonet, Tomas Schnabel, Robert D. Wayne, Robert K. Lohmueller, Kirk E. Data from: Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs |
topic_facet |
selective sweep deleterious mutations Canis familiaris Canis lupus |
description |
Population bottlenecks, inbreeding, and artificial selection can all, in principle, influence levels of deleterious genetic variation. However, the relative importance of each of these effects on genome-wide patterns of deleterious variation remains controversial. Domestic and wild canids offer a powerful system to address the role of these factors in influencing deleterious variation because their history is dominated by known bottlenecks and intense artificial selection. Here, we assess genome-wide patterns of deleterious variation in 90 whole-genome sequences from breed dogs, village dogs, and gray wolves. We find that the ratio of amino acid changing heterozygosity to silent heterozygosity is higher in dogs than in wolves and, on average, dogs have 2–3% higher genetic load than gray wolves. Multiple lines of evidence indicate this pattern is driven by less efficient natural selection due to bottlenecks associated with domestication and breed formation, rather than recent inbreeding. Further, we find regions of the genome implicated in selective sweeps are enriched for amino acid changing variants and Mendelian disease genes. To our knowledge, these results provide the first quantitative estimates of the increased burden of deleterious variants directly associated with domestication and have important implications for selective breeding programs and the conservation of rare and endangered species. Specifically, they highlight the costs associated with selective breeding and question the practice favoring the breeding of individuals that best fit breed standards. Our results also suggest that maintaining a large population size, rather than just avoiding inbreeding, is a critical factor for preventing the accumulation of deleterious variants. DOG_jackknife_on_sweep_nonsweep_data WOLF_jackknife_on_sweep_nonsweep_data Dogwolf_vcf_Filtered_coding_region_with_Miyata_and_GerpScore_annotated.vcf Gene_IDs_overlapping_sweep_regions.final |
format |
Other/Unknown Material |
author |
Marsden, Clare D. Ortega-Del Vecchyo, Diego O'Brien, Dennis P. Taylor, Jeremy F. Ramirez, Oscar Vila, Carles Marques-Bonet, Tomas Schnabel, Robert D. Wayne, Robert K. Lohmueller, Kirk E. |
author_facet |
Marsden, Clare D. Ortega-Del Vecchyo, Diego O'Brien, Dennis P. Taylor, Jeremy F. Ramirez, Oscar Vila, Carles Marques-Bonet, Tomas Schnabel, Robert D. Wayne, Robert K. Lohmueller, Kirk E. |
author_sort |
Marsden, Clare D. |
title |
Data from: Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs |
title_short |
Data from: Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs |
title_full |
Data from: Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs |
title_fullStr |
Data from: Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs |
title_full_unstemmed |
Data from: Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs |
title_sort |
data from: bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs |
publisher |
Zenodo |
publishDate |
2016 |
url |
https://doi.org/10.5061/dryad.012s5 |
genre |
Canis lupus |
genre_facet |
Canis lupus |
op_relation |
https://doi.org/10.1073/pnas.1512501113 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.012s5 oai:zenodo.org:4967926 |
op_rights |
info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.012s510.1073/pnas.1512501113 |
_version_ |
1809905143666180096 |