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Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout

Aquatic ectotherms are predicted to harbour genomic signals of local adaptation resulting from selective pressures driven by the strong influence of climate conditions on body temperature. We investigated local adaptation in redband trout (Oncorhynchus mykiss gairdneri) using genome scans for 547 sa...

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Autores principales: Andrews, Kimberly R., Seaborn, Travis, Egan, Joshua P., Fagnan, Matthew W., New, Daniel D., Chen, Zhongqi, Hohenlohe, Paul A., Waits, Lisette P., Caudill, Christopher C., Narum, Shawn R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9905331/
https://www.ncbi.nlm.nih.gov/pubmed/36478624
http://dx.doi.org/10.1111/mec.16810
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author Andrews, Kimberly R.
Seaborn, Travis
Egan, Joshua P.
Fagnan, Matthew W.
New, Daniel D.
Chen, Zhongqi
Hohenlohe, Paul A.
Waits, Lisette P.
Caudill, Christopher C.
Narum, Shawn R.
author_facet Andrews, Kimberly R.
Seaborn, Travis
Egan, Joshua P.
Fagnan, Matthew W.
New, Daniel D.
Chen, Zhongqi
Hohenlohe, Paul A.
Waits, Lisette P.
Caudill, Christopher C.
Narum, Shawn R.
author_sort Andrews, Kimberly R.
collection PubMed
description Aquatic ectotherms are predicted to harbour genomic signals of local adaptation resulting from selective pressures driven by the strong influence of climate conditions on body temperature. We investigated local adaptation in redband trout (Oncorhynchus mykiss gairdneri) using genome scans for 547 samples from 11 populations across a wide range of habitats and thermal gradients in the interior Columbia River. We estimated allele frequencies for millions of single nucleotide polymorphism loci (SNPs) across populations using low‐coverage whole genome resequencing, and used population structure outlier analyses to identify genomic regions under divergent selection between populations. Twelve genomic regions showed signatures of local adaptation, including two regions associated with genes known to influence migration and developmental timing in salmonids (GREB1L, ROCK1, SIX6). Genotype–environment association analyses indicated that diurnal temperature variation was a strong driver of local adaptation, with signatures of selection driven primarily by divergence of two populations in the northern extreme of the subspecies range. We also found evidence for adaptive differences between high‐elevation desert vs. montane habitats at a smaller geographical scale. Finally, we estimated vulnerability of redband trout to future climate change using ecological niche modelling and genetic offset analyses under two climate change scenarios. These analyses predicted substantial habitat loss and strong genetic shifts necessary for adaptation to future habitats, with the greatest vulnerability predicted for high‐elevation desert populations. Our results provide new insight into the complexity of local adaptation in salmonids, and important predictions regarding future responses of redband trout to climate change.
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spelling pubmed-99053312023-04-18 Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout Andrews, Kimberly R. Seaborn, Travis Egan, Joshua P. Fagnan, Matthew W. New, Daniel D. Chen, Zhongqi Hohenlohe, Paul A. Waits, Lisette P. Caudill, Christopher C. Narum, Shawn R. Mol Ecol ORIGINAL ARTICLES Aquatic ectotherms are predicted to harbour genomic signals of local adaptation resulting from selective pressures driven by the strong influence of climate conditions on body temperature. We investigated local adaptation in redband trout (Oncorhynchus mykiss gairdneri) using genome scans for 547 samples from 11 populations across a wide range of habitats and thermal gradients in the interior Columbia River. We estimated allele frequencies for millions of single nucleotide polymorphism loci (SNPs) across populations using low‐coverage whole genome resequencing, and used population structure outlier analyses to identify genomic regions under divergent selection between populations. Twelve genomic regions showed signatures of local adaptation, including two regions associated with genes known to influence migration and developmental timing in salmonids (GREB1L, ROCK1, SIX6). Genotype–environment association analyses indicated that diurnal temperature variation was a strong driver of local adaptation, with signatures of selection driven primarily by divergence of two populations in the northern extreme of the subspecies range. We also found evidence for adaptive differences between high‐elevation desert vs. montane habitats at a smaller geographical scale. Finally, we estimated vulnerability of redband trout to future climate change using ecological niche modelling and genetic offset analyses under two climate change scenarios. These analyses predicted substantial habitat loss and strong genetic shifts necessary for adaptation to future habitats, with the greatest vulnerability predicted for high‐elevation desert populations. Our results provide new insight into the complexity of local adaptation in salmonids, and important predictions regarding future responses of redband trout to climate change. John Wiley and Sons Inc. 2022-12-19 2023-02 /pmc/articles/PMC9905331/ /pubmed/36478624 http://dx.doi.org/10.1111/mec.16810 Text en © 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ (https://creativecommons.org/licenses/by-nc-nd/4.0/) License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.
spellingShingle ORIGINAL ARTICLES
Andrews, Kimberly R.
Seaborn, Travis
Egan, Joshua P.
Fagnan, Matthew W.
New, Daniel D.
Chen, Zhongqi
Hohenlohe, Paul A.
Waits, Lisette P.
Caudill, Christopher C.
Narum, Shawn R.
Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout
title Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout
title_full Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout
title_fullStr Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout
title_full_unstemmed Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout
title_short Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout
title_sort whole genome resequencing identifies local adaptation associated with environmental variation for redband trout
topic ORIGINAL ARTICLES
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9905331/
https://www.ncbi.nlm.nih.gov/pubmed/36478624
http://dx.doi.org/10.1111/mec.16810
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