Unfiltered VCF for pink salmon rapid adaptation
Introduced and invasive species make excellent natural experiments for investigating rapid evolution. Here, we describe the effects of genetic drift and rapid genetic adaptation in pink salmon (Oncorhynchus gorbuscha) that were accidentally introduced to the Great Lakes via a single introduction eve...
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ftzenodo:oai:zenodo.org:8256947 2023-09-26T15:21:44+02:00 Unfiltered VCF for pink salmon rapid adaptation Sparks, Morgan Schraidt, Claire Yin, Xiaoshen Seeb, Lisa Christie, Mark 2023-08-24 https://zenodo.org/record/8256947 https://doi.org/10.5281/zenodo.8256947 unknown https://www.authorea.com/users/594602/articles/628973-rapid-genetic-adaptation-to-a-novel-ecosystem-despite-a-massive-bottleneck doi:10.5061/dryad.0vt4b8h2w doi:10.5281/zenodo.8256946 https://zenodo.org/communities/dryad https://zenodo.org/record/8256947 https://doi.org/10.5281/zenodo.8256947 oai:zenodo.org:8256947 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode agent-based models genetic adaptation introduced species Genetic drift pink salmon Rapid evolution info:eu-repo/semantics/other other 2023 ftzenodo https://doi.org/10.5281/zenodo.825694710.5061/dryad.0vt4b8h2w10.5281/zenodo.8256946 2023-08-29T22:59:08Z Introduced and invasive species make excellent natural experiments for investigating rapid evolution. Here, we describe the effects of genetic drift and rapid genetic adaptation in pink salmon (Oncorhynchus gorbuscha) that were accidentally introduced to the Great Lakes via a single introduction event 31-generations ago. Using whole-genome resequencing for 134 fish spanning five sample groups across the native and introduced range, we estimate that the source population's effective population size was 146,886 at the time of introduction, whereas the founding population's effective population size was just 72—a 2040-fold decrease. As expected with a severe founder event, we show reductions in genome-wide measures of genetic diversity, specifically a 37.7% reduction in the number of SNPs and an 8.2% reduction in observed heterozygosity. Despite this decline in genetic diversity, we provide evidence for putative selection at 47 loci across multiple chromosomes in the introduced populations, including missense variants in genes associated with circadian rhythm, immunological response, and maturation, which match expected or known phenotypic changes in the Great Lakes. For one of these genes, we use a species-specific agent-based model to rule out genetic drift and conclude our results support a strong response to selection that occurred in a period gene (per2) that plays a predominant role in determining an organism's daily clock, matching large day-length differences experienced by introduced salmon during important phenological periods. Together, these results inform how populations might evolve rapidly to new environments, even with a small pool of standing genetic variation. Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: DEB-1856710 This VCF file contains whole-genome resequence data with SNPs called from GATK best practices. This file has been filtered for GATK flagged SNPs but otherwise is unfiltered (to allow users to filter ... Other/Unknown Material Oncorhynchus gorbuscha Pink salmon Zenodo |
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agent-based models genetic adaptation introduced species Genetic drift pink salmon Rapid evolution |
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agent-based models genetic adaptation introduced species Genetic drift pink salmon Rapid evolution Sparks, Morgan Schraidt, Claire Yin, Xiaoshen Seeb, Lisa Christie, Mark Unfiltered VCF for pink salmon rapid adaptation |
topic_facet |
agent-based models genetic adaptation introduced species Genetic drift pink salmon Rapid evolution |
description |
Introduced and invasive species make excellent natural experiments for investigating rapid evolution. Here, we describe the effects of genetic drift and rapid genetic adaptation in pink salmon (Oncorhynchus gorbuscha) that were accidentally introduced to the Great Lakes via a single introduction event 31-generations ago. Using whole-genome resequencing for 134 fish spanning five sample groups across the native and introduced range, we estimate that the source population's effective population size was 146,886 at the time of introduction, whereas the founding population's effective population size was just 72—a 2040-fold decrease. As expected with a severe founder event, we show reductions in genome-wide measures of genetic diversity, specifically a 37.7% reduction in the number of SNPs and an 8.2% reduction in observed heterozygosity. Despite this decline in genetic diversity, we provide evidence for putative selection at 47 loci across multiple chromosomes in the introduced populations, including missense variants in genes associated with circadian rhythm, immunological response, and maturation, which match expected or known phenotypic changes in the Great Lakes. For one of these genes, we use a species-specific agent-based model to rule out genetic drift and conclude our results support a strong response to selection that occurred in a period gene (per2) that plays a predominant role in determining an organism's daily clock, matching large day-length differences experienced by introduced salmon during important phenological periods. Together, these results inform how populations might evolve rapidly to new environments, even with a small pool of standing genetic variation. Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: DEB-1856710 This VCF file contains whole-genome resequence data with SNPs called from GATK best practices. This file has been filtered for GATK flagged SNPs but otherwise is unfiltered (to allow users to filter ... |
format |
Other/Unknown Material |
author |
Sparks, Morgan Schraidt, Claire Yin, Xiaoshen Seeb, Lisa Christie, Mark |
author_facet |
Sparks, Morgan Schraidt, Claire Yin, Xiaoshen Seeb, Lisa Christie, Mark |
author_sort |
Sparks, Morgan |
title |
Unfiltered VCF for pink salmon rapid adaptation |
title_short |
Unfiltered VCF for pink salmon rapid adaptation |
title_full |
Unfiltered VCF for pink salmon rapid adaptation |
title_fullStr |
Unfiltered VCF for pink salmon rapid adaptation |
title_full_unstemmed |
Unfiltered VCF for pink salmon rapid adaptation |
title_sort |
unfiltered vcf for pink salmon rapid adaptation |
publishDate |
2023 |
url |
https://zenodo.org/record/8256947 https://doi.org/10.5281/zenodo.8256947 |
genre |
Oncorhynchus gorbuscha Pink salmon |
genre_facet |
Oncorhynchus gorbuscha Pink salmon |
op_relation |
https://www.authorea.com/users/594602/articles/628973-rapid-genetic-adaptation-to-a-novel-ecosystem-despite-a-massive-bottleneck doi:10.5061/dryad.0vt4b8h2w doi:10.5281/zenodo.8256946 https://zenodo.org/communities/dryad https://zenodo.org/record/8256947 https://doi.org/10.5281/zenodo.8256947 oai:zenodo.org:8256947 |
op_rights |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/legalcode |
op_doi |
https://doi.org/10.5281/zenodo.825694710.5061/dryad.0vt4b8h2w10.5281/zenodo.8256946 |
_version_ |
1778147020799737856 |