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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ftzenodo:oai:zenodo.org:4940810 2024-09-09T19:24:34+00:00 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. 2015-11-16 https://doi.org/10.5061/dryad.8g0s3 unknown Zenodo https://doi.org/10.1111/mec.13467 https://www.ncbi.nlm.nih.gov/nuccore/.%2Fsra%2F%3Fterm%3DSRP065570 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.8g0s3 oai:zenodo.org:4940810 info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode Genomics/Proteomics Natural Selection and Contemporary Evolution Capture Array Holocene Canis lupus info:eu-repo/semantics/other 2015 ftzenodo https://doi.org/10.5061/dryad.8g0s310.1111/mec.13467 2024-07-25T23:19:05Z 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. AllSamples_n107_EnvData_wLatLong These data represent latitude and longitude coordinates for the 107 wolves used in this study for selection tests. The 12 environmental variables for each coordinate were downloaded within ArcGIS from various WORLDCLIM databases (http://www.worldclim.org/). Please see descriptions on website for information on what each variable measures. From the website: "Please note that the ... Other/Unknown Material Arctic Canis lupus Climate change gray wolf Zenodo Arctic |
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op_collection_id |
ftzenodo |
language |
unknown |
topic |
Genomics/Proteomics Natural Selection and Contemporary Evolution Capture Array Holocene Canis lupus |
spellingShingle |
Genomics/Proteomics Natural Selection and Contemporary Evolution Capture Array Holocene Canis lupus 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 Natural Selection and Contemporary Evolution Capture Array Holocene Canis lupus |
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. AllSamples_n107_EnvData_wLatLong These data represent latitude and longitude coordinates for the 107 wolves used in this study for selection tests. The 12 environmental variables for each coordinate were downloaded within ArcGIS from various WORLDCLIM databases (http://www.worldclim.org/). Please see descriptions on website for information on what each variable measures. From the website: "Please note that the ... |
format |
Other/Unknown Material |
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 |
publisher |
Zenodo |
publishDate |
2015 |
url |
https://doi.org/10.5061/dryad.8g0s3 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Canis lupus Climate change gray wolf |
genre_facet |
Arctic Canis lupus Climate change gray wolf |
op_relation |
https://doi.org/10.1111/mec.13467 https://www.ncbi.nlm.nih.gov/nuccore/.%2Fsra%2F%3Fterm%3DSRP065570 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.8g0s3 oai:zenodo.org:4940810 |
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.8g0s310.1111/mec.13467 |
_version_ |
1809894451898744832 |