Genomic basis of deep‐water adaptation in Arctic Charr (Salvelinus alpinus) morphs
Colonization of extreme habitats requires extensive adaptation to novel environmental challenges. Deep-water environments (>50 m) have high hydrostatic pressure, low temperature, and low light, requiring physiological and visual system adaptation, but genomic mechanisms underlying evolution in th...
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ftzenodo:oai:zenodo.org:6029382 2024-09-15T17:52:24+00:00 Genomic basis of deep‐water adaptation in Arctic Charr (Salvelinus alpinus) morphs Kess, Tony Dempson, J. Brian Lehnert, Sarah J. Layton, Kara Einfeldt, Anthony Bentzen, Paul Salisbury, Sarah Messmer, Amber Duffy, Steven Ruzzante, Daniel Nugent, Cameron Ferguson, Moira Leong, Jong Koop, Ben O'Connell, Michael Bradbury, Ian Layton, Kara K. S. Salisbury, Sarah J. Messmer, Amber M. Ruzzante, Daniel E. Nugent, Cameron M. Ferguson, Moira M. Leong, Jong S. Koop, Ben F. O'Connell, Michael F. Bradbury, Ian R. 2022-02-09 https://doi.org/10.5061/dryad.gf1vhhmkh unknown Zenodo https://doi.org/10.1111/mec.16033 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.gf1vhhmkh oai:zenodo.org:6029382 info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode Axiom array SNP data Mitochondrial whole genome data info:eu-repo/semantics/other 2022 ftzenodo https://doi.org/10.5061/dryad.gf1vhhmkh10.1111/mec.16033 2024-07-26T14:32:01Z Colonization of extreme habitats requires extensive adaptation to novel environmental challenges. Deep-water environments (>50 m) have high hydrostatic pressure, low temperature, and low light, requiring physiological and visual system adaptation, but genomic mechanisms underlying evolution in these environments are rarely known. Post-glacial colonization of Gander Lake in Newfoundland, Canada, by Arctic Charr (Salvelinus alpinus) provides the opportunity to study the genomic basis of adaptation to extreme deep-water environments. Here, we compare genomic and morphometric divergence between a phenotypically divergent deep-water, demersal morph adapted to depths of up to 288m and a larger, piscivorous morph occupying shallower depths. Using a SNP array and resequencing of nuclear and mitochondrial genomes, we find moderate genetic divergence (FST = 0.15 - 0.11) between morphs, consistent with divergence in body shape and size, despite absence of mitochondrial genome divergence. Outlier analyses identified three key genes with very high divergence against a genome-wide distribution of diverged genomic islands containing genes with functions related to deep-water adaptation such as sensory processes, ligand binding and regulation of transcription. Quantification of SNP array signal intensity variation associated with complex polymorphisms (e.g. copy number variants), similarly uncovered genetic separation of morphs and coincided with several islands of genomic divergence, but also revealed additional genomic regions and molecular mechanisms associated with depth adaptation. Together, these results show that adaptation to an extreme deep-water environment has been facilitated by multiple polymorphism types with roles in cellular and physiological processes, providing insight into the genomic basis of adaptation in extreme environments. Funding provided by: Natural Sciences and Engineering Research Council of Canada Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100000038 Award Number: Funding ... Other/Unknown Material Arctic charr Newfoundland Salvelinus alpinus Zenodo |
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Axiom array SNP data Mitochondrial whole genome data |
spellingShingle |
Axiom array SNP data Mitochondrial whole genome data Kess, Tony Dempson, J. Brian Lehnert, Sarah J. Layton, Kara Einfeldt, Anthony Bentzen, Paul Salisbury, Sarah Messmer, Amber Duffy, Steven Ruzzante, Daniel Nugent, Cameron Ferguson, Moira Leong, Jong Koop, Ben O'Connell, Michael Bradbury, Ian Layton, Kara K. S. Salisbury, Sarah J. Messmer, Amber M. Ruzzante, Daniel E. Nugent, Cameron M. Ferguson, Moira M. Leong, Jong S. Koop, Ben F. O'Connell, Michael F. Bradbury, Ian R. Genomic basis of deep‐water adaptation in Arctic Charr (Salvelinus alpinus) morphs |
topic_facet |
Axiom array SNP data Mitochondrial whole genome data |
description |
Colonization of extreme habitats requires extensive adaptation to novel environmental challenges. Deep-water environments (>50 m) have high hydrostatic pressure, low temperature, and low light, requiring physiological and visual system adaptation, but genomic mechanisms underlying evolution in these environments are rarely known. Post-glacial colonization of Gander Lake in Newfoundland, Canada, by Arctic Charr (Salvelinus alpinus) provides the opportunity to study the genomic basis of adaptation to extreme deep-water environments. Here, we compare genomic and morphometric divergence between a phenotypically divergent deep-water, demersal morph adapted to depths of up to 288m and a larger, piscivorous morph occupying shallower depths. Using a SNP array and resequencing of nuclear and mitochondrial genomes, we find moderate genetic divergence (FST = 0.15 - 0.11) between morphs, consistent with divergence in body shape and size, despite absence of mitochondrial genome divergence. Outlier analyses identified three key genes with very high divergence against a genome-wide distribution of diverged genomic islands containing genes with functions related to deep-water adaptation such as sensory processes, ligand binding and regulation of transcription. Quantification of SNP array signal intensity variation associated with complex polymorphisms (e.g. copy number variants), similarly uncovered genetic separation of morphs and coincided with several islands of genomic divergence, but also revealed additional genomic regions and molecular mechanisms associated with depth adaptation. Together, these results show that adaptation to an extreme deep-water environment has been facilitated by multiple polymorphism types with roles in cellular and physiological processes, providing insight into the genomic basis of adaptation in extreme environments. Funding provided by: Natural Sciences and Engineering Research Council of Canada Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100000038 Award Number: Funding ... |
format |
Other/Unknown Material |
author |
Kess, Tony Dempson, J. Brian Lehnert, Sarah J. Layton, Kara Einfeldt, Anthony Bentzen, Paul Salisbury, Sarah Messmer, Amber Duffy, Steven Ruzzante, Daniel Nugent, Cameron Ferguson, Moira Leong, Jong Koop, Ben O'Connell, Michael Bradbury, Ian Layton, Kara K. S. Salisbury, Sarah J. Messmer, Amber M. Ruzzante, Daniel E. Nugent, Cameron M. Ferguson, Moira M. Leong, Jong S. Koop, Ben F. O'Connell, Michael F. Bradbury, Ian R. |
author_facet |
Kess, Tony Dempson, J. Brian Lehnert, Sarah J. Layton, Kara Einfeldt, Anthony Bentzen, Paul Salisbury, Sarah Messmer, Amber Duffy, Steven Ruzzante, Daniel Nugent, Cameron Ferguson, Moira Leong, Jong Koop, Ben O'Connell, Michael Bradbury, Ian Layton, Kara K. S. Salisbury, Sarah J. Messmer, Amber M. Ruzzante, Daniel E. Nugent, Cameron M. Ferguson, Moira M. Leong, Jong S. Koop, Ben F. O'Connell, Michael F. Bradbury, Ian R. |
author_sort |
Kess, Tony |
title |
Genomic basis of deep‐water adaptation in Arctic Charr (Salvelinus alpinus) morphs |
title_short |
Genomic basis of deep‐water adaptation in Arctic Charr (Salvelinus alpinus) morphs |
title_full |
Genomic basis of deep‐water adaptation in Arctic Charr (Salvelinus alpinus) morphs |
title_fullStr |
Genomic basis of deep‐water adaptation in Arctic Charr (Salvelinus alpinus) morphs |
title_full_unstemmed |
Genomic basis of deep‐water adaptation in Arctic Charr (Salvelinus alpinus) morphs |
title_sort |
genomic basis of deep‐water adaptation in arctic charr (salvelinus alpinus) morphs |
publisher |
Zenodo |
publishDate |
2022 |
url |
https://doi.org/10.5061/dryad.gf1vhhmkh |
genre |
Arctic charr Newfoundland Salvelinus alpinus |
genre_facet |
Arctic charr Newfoundland Salvelinus alpinus |
op_relation |
https://doi.org/10.1111/mec.16033 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.gf1vhhmkh oai:zenodo.org:6029382 |
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.gf1vhhmkh10.1111/mec.16033 |
_version_ |
1810294435944071168 |