Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves
Abstract In an era of ever‐increasing amounts of whole‐genome sequence data for individuals and populations, the utility of traditional single nucleotide polymorphisms ( SNP s) array‐based genome scans is uncertain. We previously performed a SNP array‐based genome scan to identify candidate genes un...
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crwiley:10.1111/mec.13467 2024-03-31T07:50:54+00:00 Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves Schweizer, Rena M. Robinson, Jacqueline Harrigan, Ryan Silva, Pedro Galverni, Marco Musiani, Marco Green, Richard E. Novembre, John Wayne, Robert K. National Science Foundation University of California, Los Angeles Natural Sciences and Engineering Research Council of Canada National Institutes of Health National Science Foundation NSF Graduate Research Fellowship University of California, Los Angeles Portuguese Science Foundation Natural Sciences and Engineering Research Council of Canada National Institutes of Health 2015 http://dx.doi.org/10.1111/mec.13467 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fmec.13467 https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.13467 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/mec.13467 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor http://doi.wiley.com/10.1002/tdm_license_1.1 Molecular Ecology volume 25, issue 1, page 357-379 ISSN 0962-1083 1365-294X Genetics Ecology, Evolution, Behavior and Systematics journal-article 2015 crwiley https://doi.org/10.1111/mec.13467 2024-03-05T05:41:34Z Abstract In an era of ever‐increasing amounts of whole‐genome sequence data for individuals and populations, the utility of traditional single nucleotide polymorphisms ( SNP s) array‐based genome scans is uncertain. We previously performed a SNP array‐based genome scan to identify candidate genes under selection in six distinct grey 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 nongenic neutral regions, and resequenced these regions in 107 wolves. Selection tests revealed striking patterns of variation within candidate genes relative to noncandidate 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 genomewide SNP surveys to tag genes that contain functional variants between populations. We highlight nonsynonymous variants in APOB , LIPG and USH 2A 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 genomewide 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 Wiley Online Library Arctic Molecular Ecology 25 1 357 379 |
institution |
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Wiley Online Library |
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crwiley |
language |
English |
topic |
Genetics Ecology, Evolution, Behavior and Systematics |
spellingShingle |
Genetics Ecology, Evolution, Behavior and Systematics Schweizer, Rena M. Robinson, Jacqueline Harrigan, Ryan Silva, Pedro Galverni, Marco Musiani, Marco Green, Richard E. Novembre, John Wayne, Robert K. Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves |
topic_facet |
Genetics Ecology, Evolution, Behavior and Systematics |
description |
Abstract In an era of ever‐increasing amounts of whole‐genome sequence data for individuals and populations, the utility of traditional single nucleotide polymorphisms ( SNP s) array‐based genome scans is uncertain. We previously performed a SNP array‐based genome scan to identify candidate genes under selection in six distinct grey 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 nongenic neutral regions, and resequenced these regions in 107 wolves. Selection tests revealed striking patterns of variation within candidate genes relative to noncandidate 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 genomewide SNP surveys to tag genes that contain functional variants between populations. We highlight nonsynonymous variants in APOB , LIPG and USH 2A 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 genomewide genotyping arrays with large‐scale resequencing and environmental data provides a powerful approach to discern candidate functional variants in natural populations. |
author2 |
National Science Foundation University of California, Los Angeles Natural Sciences and Engineering Research Council of Canada National Institutes of Health National Science Foundation NSF Graduate Research Fellowship University of California, Los Angeles Portuguese Science Foundation Natural Sciences and Engineering Research Council of Canada National Institutes of Health |
format |
Article in Journal/Newspaper |
author |
Schweizer, Rena M. Robinson, Jacqueline Harrigan, Ryan Silva, Pedro Galverni, Marco Musiani, Marco Green, Richard E. Novembre, John Wayne, Robert K. |
author_facet |
Schweizer, Rena M. Robinson, Jacqueline Harrigan, Ryan Silva, Pedro Galverni, Marco Musiani, Marco Green, Richard E. Novembre, John Wayne, Robert K. |
author_sort |
Schweizer, Rena M. |
title |
Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves |
title_short |
Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves |
title_full |
Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves |
title_fullStr |
Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves |
title_full_unstemmed |
Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves |
title_sort |
targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves |
publisher |
Wiley |
publishDate |
2015 |
url |
http://dx.doi.org/10.1111/mec.13467 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fmec.13467 https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.13467 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/mec.13467 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Canis lupus Climate change |
genre_facet |
Arctic Canis lupus Climate change |
op_source |
Molecular Ecology volume 25, issue 1, page 357-379 ISSN 0962-1083 1365-294X |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor http://doi.wiley.com/10.1002/tdm_license_1.1 |
op_doi |
https://doi.org/10.1111/mec.13467 |
container_title |
Molecular Ecology |
container_volume |
25 |
container_issue |
1 |
container_start_page |
357 |
op_container_end_page |
379 |
_version_ |
1795029378788229120 |