Data from: Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in gray wolves
In an era of ever-increasing amounts of whole genome sequence data for individuals and populations, the utility of traditional single nucleotide polymorphisms (SNPs) array-based genome scans is uncertain. We previously performed a SNP array-based genome scan to identify candidate genes under selecti...
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ftdryad:oai:v1.datadryad.org:10255/dryad.96072 2023-05-15T15:00:01+02:00 Data from: Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in gray wolves Schweizer, Rena M. Robinson, Jacqueline Harrigan, Ryan Silva, Pedro Galaverni, Marco Musiani, Marco Green, Richard E. Novembre, John Wayne, Robert K. Canada United States Holocene 2015-11-16T15:29:05Z http://hdl.handle.net/10255/dryad.96072 https://doi.org/10.5061/dryad.8g0s3 unknown doi:10.5061/dryad.8g0s3/1 doi:10.5061/dryad.8g0s3/2 doi:10.5061/dryad.8g0s3/3 doi:10.5061/dryad.8g0s3/4 doi:10.5061/dryad.8g0s3/5 doi:10.5061/dryad.8g0s3/6 doi:10.5061/dryad.8g0s3/7 doi:10.5061/dryad.8g0s3/8 doi:10.5061/dryad.8g0s3/9 doi:10.5061/dryad.8g0s3/10 doi:10.5061/dryad.8g0s3/11 doi:10.5061/dryad.8g0s3/12 doi:10.5061/dryad.8g0s3/13 doi:10.5061/dryad.8g0s3/14 doi:10.5061/dryad.8g0s3/15 doi:10.5061/dryad.8g0s3/16 doi:10.5061/dryad.8g0s3/17 doi:10.5061/dryad.8g0s3/18 doi:10.5061/dryad.8g0s3/19 doi:10.5061/dryad.8g0s3/20 doi:10.5061/dryad.8g0s3/21 doi:10.5061/dryad.8g0s3/22 doi:10.5061/dryad.8g0s3/23 doi:10.5061/dryad.8g0s3/24 doi:10.5061/dryad.8g0s3/25 doi:10.5061/dryad.8g0s3/26 doi:10.5061/dryad.8g0s3/27 doi:10.5061/dryad.8g0s3/28 doi:10.1111/mec.13467 PMID:26562361 doi:10.5061/dryad.8g0s3 Schweizer RM, Robinson J, Harrigan R, Silva P, Galaverni M, Musiani M, Green RE, Novembre J, Wayne RK (2016) Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in gray wolves. Molecular Ecology 25(1): 357–379. http://hdl.handle.net/10255/dryad.96072 Genomics/Proteomics Adaptation Natural Selection and Contemporary Evolution Mammals Capture Array Climate Article 2015 ftdryad https://doi.org/10.5061/dryad.8g0s3 https://doi.org/10.5061/dryad.8g0s3/1 https://doi.org/10.5061/dryad.8g0s3/2 https://doi.org/10.5061/dryad.8g0s3/3 https://doi.org/10.5061/dryad.8g0s3/4 https://doi.org/10.5061/dryad.8g0s3/5 https://doi.org/1 2020-01-01T15:24:07Z In an era of ever-increasing amounts of whole genome sequence data for individuals and populations, the utility of traditional single nucleotide polymorphisms (SNPs) array-based genome scans is uncertain. We previously performed a SNP array-based genome scan to identify candidate genes under selection in six distinct gray wolf (Canis lupus) ecotypes. Using this information, we designed a targeted capture array for 1040 genes, including all exons and flanking regions, as well as 5000 1 kb non-genic neutral regions and resequenced these regions in 107 wolves. Selection tests revealed striking patterns of variation within candidate genes relative to non-candidate regions and identified potentially functional variants related to local adaptation. We found 27% and 47% of candidate genes from the previous SNP array study had functional changes that were outliers in SweeD and Bayenv analyses, respectively. This result verifies the use of genome wide SNP surveys to tag genes that contain functional variants between populations. We highlight non-synonymous variants in APOB, LIPG, and USH2A that occur in functional domains of these proteins, and that demonstrate high correlation with precipitation seasonality and vegetation. We find Arctic and High Arctic wolf ecotypes have higher numbers of genes under selection, which highlight their conservation value and heightened threat due to climate change. This study demonstrates that combining genome wide genotyping arrays with large scale resequencing and environmental data provides a powerful approach to discern candidate functional variants in natural populations. Article in Journal/Newspaper Arctic Canis lupus Climate change gray wolf Dryad Digital Repository (Duke University) Arctic Canada |
institution |
Open Polar |
collection |
Dryad Digital Repository (Duke University) |
op_collection_id |
ftdryad |
language |
unknown |
topic |
Genomics/Proteomics Adaptation Natural Selection and Contemporary Evolution Mammals Capture Array Climate |
spellingShingle |
Genomics/Proteomics Adaptation Natural Selection and Contemporary Evolution Mammals Capture Array Climate Schweizer, Rena M. Robinson, Jacqueline Harrigan, Ryan Silva, Pedro Galaverni, Marco Musiani, Marco Green, Richard E. Novembre, John Wayne, Robert K. Data from: Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in gray wolves |
topic_facet |
Genomics/Proteomics Adaptation Natural Selection and Contemporary Evolution Mammals Capture Array Climate |
description |
In an era of ever-increasing amounts of whole genome sequence data for individuals and populations, the utility of traditional single nucleotide polymorphisms (SNPs) array-based genome scans is uncertain. We previously performed a SNP array-based genome scan to identify candidate genes under selection in six distinct gray wolf (Canis lupus) ecotypes. Using this information, we designed a targeted capture array for 1040 genes, including all exons and flanking regions, as well as 5000 1 kb non-genic neutral regions and resequenced these regions in 107 wolves. Selection tests revealed striking patterns of variation within candidate genes relative to non-candidate regions and identified potentially functional variants related to local adaptation. We found 27% and 47% of candidate genes from the previous SNP array study had functional changes that were outliers in SweeD and Bayenv analyses, respectively. This result verifies the use of genome wide SNP surveys to tag genes that contain functional variants between populations. We highlight non-synonymous variants in APOB, LIPG, and USH2A that occur in functional domains of these proteins, and that demonstrate high correlation with precipitation seasonality and vegetation. We find Arctic and High Arctic wolf ecotypes have higher numbers of genes under selection, which highlight their conservation value and heightened threat due to climate change. This study demonstrates that combining genome wide genotyping arrays with large scale resequencing and environmental data provides a powerful approach to discern candidate functional variants in natural populations. |
format |
Article in Journal/Newspaper |
author |
Schweizer, Rena M. Robinson, Jacqueline Harrigan, Ryan Silva, Pedro Galaverni, Marco Musiani, Marco Green, Richard E. Novembre, John Wayne, Robert K. |
author_facet |
Schweizer, Rena M. Robinson, Jacqueline Harrigan, Ryan Silva, Pedro Galaverni, Marco Musiani, Marco Green, Richard E. Novembre, John Wayne, Robert K. |
author_sort |
Schweizer, Rena M. |
title |
Data from: Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in gray wolves |
title_short |
Data from: Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in gray wolves |
title_full |
Data from: Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in gray wolves |
title_fullStr |
Data from: Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in gray wolves |
title_full_unstemmed |
Data from: Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in gray wolves |
title_sort |
data from: targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in gray wolves |
publishDate |
2015 |
url |
http://hdl.handle.net/10255/dryad.96072 https://doi.org/10.5061/dryad.8g0s3 |
op_coverage |
Canada United States Holocene |
geographic |
Arctic Canada |
geographic_facet |
Arctic Canada |
genre |
Arctic Canis lupus Climate change gray wolf |
genre_facet |
Arctic Canis lupus Climate change gray wolf |
op_relation |
doi:10.5061/dryad.8g0s3/1 doi:10.5061/dryad.8g0s3/2 doi:10.5061/dryad.8g0s3/3 doi:10.5061/dryad.8g0s3/4 doi:10.5061/dryad.8g0s3/5 doi:10.5061/dryad.8g0s3/6 doi:10.5061/dryad.8g0s3/7 doi:10.5061/dryad.8g0s3/8 doi:10.5061/dryad.8g0s3/9 doi:10.5061/dryad.8g0s3/10 doi:10.5061/dryad.8g0s3/11 doi:10.5061/dryad.8g0s3/12 doi:10.5061/dryad.8g0s3/13 doi:10.5061/dryad.8g0s3/14 doi:10.5061/dryad.8g0s3/15 doi:10.5061/dryad.8g0s3/16 doi:10.5061/dryad.8g0s3/17 doi:10.5061/dryad.8g0s3/18 doi:10.5061/dryad.8g0s3/19 doi:10.5061/dryad.8g0s3/20 doi:10.5061/dryad.8g0s3/21 doi:10.5061/dryad.8g0s3/22 doi:10.5061/dryad.8g0s3/23 doi:10.5061/dryad.8g0s3/24 doi:10.5061/dryad.8g0s3/25 doi:10.5061/dryad.8g0s3/26 doi:10.5061/dryad.8g0s3/27 doi:10.5061/dryad.8g0s3/28 doi:10.1111/mec.13467 PMID:26562361 doi:10.5061/dryad.8g0s3 Schweizer RM, Robinson J, Harrigan R, Silva P, Galaverni M, Musiani M, Green RE, Novembre J, Wayne RK (2016) Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in gray wolves. Molecular Ecology 25(1): 357–379. http://hdl.handle.net/10255/dryad.96072 |
op_doi |
https://doi.org/10.5061/dryad.8g0s3 https://doi.org/10.5061/dryad.8g0s3/1 https://doi.org/10.5061/dryad.8g0s3/2 https://doi.org/10.5061/dryad.8g0s3/3 https://doi.org/10.5061/dryad.8g0s3/4 https://doi.org/10.5061/dryad.8g0s3/5 https://doi.org/1 |
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