Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole‐genome sequencing
Abstract Selection can create complex patterns of adaptive differentiation among populations in the wild that may be relevant to management. Atlantic cod in the Northwest Atlantic are at a fraction of their historical abundance and a lack of recovery within the Gulf of Maine has created concern rega...
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ftdoajarticles:oai:doaj.org/article:7d581b178dac45d2994c0f35ed270701 2023-05-15T15:27:00+02:00 Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole‐genome sequencing Gemma V. Clucas R. Nicolas Lou Nina O. Therkildsen Adrienne I. Kovach 2019-12-01T00:00:00Z https://doi.org/10.1111/eva.12861 https://doaj.org/article/7d581b178dac45d2994c0f35ed270701 EN eng Wiley https://doi.org/10.1111/eva.12861 https://doaj.org/toc/1752-4571 1752-4571 doi:10.1111/eva.12861 https://doaj.org/article/7d581b178dac45d2994c0f35ed270701 Evolutionary Applications, Vol 12, Iss 10, Pp 1971-1987 (2019) adaptive differentiation allochronic reproduction Atlantic cod chromosomal inversions fisheries management heat shock proteins Evolution QH359-425 article 2019 ftdoajarticles https://doi.org/10.1111/eva.12861 2022-12-31T14:55:34Z Abstract Selection can create complex patterns of adaptive differentiation among populations in the wild that may be relevant to management. Atlantic cod in the Northwest Atlantic are at a fraction of their historical abundance and a lack of recovery within the Gulf of Maine has created concern regarding the misalignment of fisheries management structures with biological population structure. To address this and investigate genome‐wide patterns of variation, we used low‐coverage sequencing to perform a region‐wide, whole‐genome analysis of fine‐scale population structure. We sequenced 306 individuals from 20 sampling locations in U.S. and Canadian waters, including the major spawning aggregations in the Gulf of Maine in addition to spawning aggregations from Georges Bank, southern New England, the eastern Scotian Shelf, and St. Pierre Bank. With genotype likelihoods estimated at almost 11 million loci, we found large differences in haplotype frequencies of previously described chromosomal inversions between Canadian and U.S. sampling locations and also among U.S. sampling locations. Our whole‐genome resolution also revealed novel outlier peaks, some of which showed significant genetic differentiation among sampling locations. Comparisons between allochronic winter‐ and spring‐spawning populations revealed highly elevated relative (FST) and absolute (dxy) genetic differentiation near genes involved in reproduction, particularly genes associated with the brain‐pituitary‐gonadal axis, which likely control timing of spawning, contributing to prezygotic isolation. We also found genetic differentiation associated with heat shock proteins and other genes of functional relevance, with complex patterns that may point to multifaceted selection pressures and local adaptation among spawning populations. We provide a high‐resolution picture of U.S. Atlantic cod population structure, revealing greater complexity than is currently recognized in management. Our genome‐scan approach likely underestimates the full suite of ... Article in Journal/Newspaper atlantic cod Northwest Atlantic Directory of Open Access Journals: DOAJ Articles Evolutionary Applications 12 10 1971 1987 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
adaptive differentiation allochronic reproduction Atlantic cod chromosomal inversions fisheries management heat shock proteins Evolution QH359-425 |
spellingShingle |
adaptive differentiation allochronic reproduction Atlantic cod chromosomal inversions fisheries management heat shock proteins Evolution QH359-425 Gemma V. Clucas R. Nicolas Lou Nina O. Therkildsen Adrienne I. Kovach Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole‐genome sequencing |
topic_facet |
adaptive differentiation allochronic reproduction Atlantic cod chromosomal inversions fisheries management heat shock proteins Evolution QH359-425 |
description |
Abstract Selection can create complex patterns of adaptive differentiation among populations in the wild that may be relevant to management. Atlantic cod in the Northwest Atlantic are at a fraction of their historical abundance and a lack of recovery within the Gulf of Maine has created concern regarding the misalignment of fisheries management structures with biological population structure. To address this and investigate genome‐wide patterns of variation, we used low‐coverage sequencing to perform a region‐wide, whole‐genome analysis of fine‐scale population structure. We sequenced 306 individuals from 20 sampling locations in U.S. and Canadian waters, including the major spawning aggregations in the Gulf of Maine in addition to spawning aggregations from Georges Bank, southern New England, the eastern Scotian Shelf, and St. Pierre Bank. With genotype likelihoods estimated at almost 11 million loci, we found large differences in haplotype frequencies of previously described chromosomal inversions between Canadian and U.S. sampling locations and also among U.S. sampling locations. Our whole‐genome resolution also revealed novel outlier peaks, some of which showed significant genetic differentiation among sampling locations. Comparisons between allochronic winter‐ and spring‐spawning populations revealed highly elevated relative (FST) and absolute (dxy) genetic differentiation near genes involved in reproduction, particularly genes associated with the brain‐pituitary‐gonadal axis, which likely control timing of spawning, contributing to prezygotic isolation. We also found genetic differentiation associated with heat shock proteins and other genes of functional relevance, with complex patterns that may point to multifaceted selection pressures and local adaptation among spawning populations. We provide a high‐resolution picture of U.S. Atlantic cod population structure, revealing greater complexity than is currently recognized in management. Our genome‐scan approach likely underestimates the full suite of ... |
format |
Article in Journal/Newspaper |
author |
Gemma V. Clucas R. Nicolas Lou Nina O. Therkildsen Adrienne I. Kovach |
author_facet |
Gemma V. Clucas R. Nicolas Lou Nina O. Therkildsen Adrienne I. Kovach |
author_sort |
Gemma V. Clucas |
title |
Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole‐genome sequencing |
title_short |
Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole‐genome sequencing |
title_full |
Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole‐genome sequencing |
title_fullStr |
Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole‐genome sequencing |
title_full_unstemmed |
Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole‐genome sequencing |
title_sort |
novel signals of adaptive genetic variation in northwestern atlantic cod revealed by whole‐genome sequencing |
publisher |
Wiley |
publishDate |
2019 |
url |
https://doi.org/10.1111/eva.12861 https://doaj.org/article/7d581b178dac45d2994c0f35ed270701 |
genre |
atlantic cod Northwest Atlantic |
genre_facet |
atlantic cod Northwest Atlantic |
op_source |
Evolutionary Applications, Vol 12, Iss 10, Pp 1971-1987 (2019) |
op_relation |
https://doi.org/10.1111/eva.12861 https://doaj.org/toc/1752-4571 1752-4571 doi:10.1111/eva.12861 https://doaj.org/article/7d581b178dac45d2994c0f35ed270701 |
op_doi |
https://doi.org/10.1111/eva.12861 |
container_title |
Evolutionary Applications |
container_volume |
12 |
container_issue |
10 |
container_start_page |
1971 |
op_container_end_page |
1987 |
_version_ |
1766357467469447168 |