Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems
Abstract Using massively parallel sequencing data from two species with different life history traits, American lobster ( Homarus americanus ) and Arctic Char ( Salvelinus alpinus ), we highlight how an unbalanced sex ratio in the samples and a few sex‐linked markers may lead to false interpretation...
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Online Access: | http://dx.doi.org/10.1111/mec.14217 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fmec.14217 https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.14217 |
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crwiley:10.1111/mec.14217 2024-09-09T19:20:29+00:00 Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems Benestan, Laura Moore, Jean‐Sébastien Sutherland, Ben J. G. Le Luyer, Jérémy Maaroufi, Halim Rougeux, Clément Normandeau, Eric Rycroft, Nathan Atema, Jelle Harris, Les N. Tallman, Ross F. Greenwood, Spencer J. Clark, Fraser K. Bernatchez, Louis Natural Sciences and Engineering Research Council of Canada Fisheries and Oceans Canada Natural Sciences and Engineering Research Council of Canada Fisheries and Oceans Canada Nunavut Wildlife Management Board P.E.I. Atlantic Shrimp Corporation Inc. Atlantic Lobster Sustainability Measures Program 2017 http://dx.doi.org/10.1111/mec.14217 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fmec.14217 https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.14217 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor http://doi.wiley.com/10.1002/tdm_license_1.1 http://onlinelibrary.wiley.com/termsAndConditions#vor Molecular Ecology volume 26, issue 24, page 6767-6783 ISSN 0962-1083 1365-294X journal-article 2017 crwiley https://doi.org/10.1111/mec.14217 2024-08-22T04:17:39Z Abstract Using massively parallel sequencing data from two species with different life history traits, American lobster ( Homarus americanus ) and Arctic Char ( Salvelinus alpinus ), we highlight how an unbalanced sex ratio in the samples and a few sex‐linked markers may lead to false interpretations of population structure and thus to potentially erroneous management recommendations. Here, multivariate analyses revealed two genetic clusters separating samples by sex instead of by expected spatial variation: inshore and offshore locations in lobster, or east and west locations in Arctic Char. To further investigate this, we created several subsamples artificially varying the sex ratio in the inshore/offshore and east/west groups and then demonstrated that significant genetic differentiation could be observed despite panmixia in lobster, and that F ST values were overestimated in Arctic Char. This pattern was due to 12 and 94 sex‐linked markers driving differentiation for lobster and Arctic Char, respectively. Removing sex‐linked markers led to nonsignificant genetic structure in lobster and a more accurate estimation of F ST in Arctic Char. The locations of these markers and putative identities of genes containing or nearby the markers were determined using available transcriptomic and genomic data, and this provided new information related to sex determination in both species. Given that only 9.6% of all marine/diadromous population genomic studies to date have reported sex information, we urge researchers to collect and consider individual sex information. Sex information is therefore relevant for avoiding unexpected biases due to sex‐linked markers as well as for improving our knowledge of sex determination systems in nonmodel species. Article in Journal/Newspaper Arctic Salvelinus alpinus Wiley Online Library Arctic Molecular Ecology 26 24 6767 6783 |
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Wiley Online Library |
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crwiley |
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English |
description |
Abstract Using massively parallel sequencing data from two species with different life history traits, American lobster ( Homarus americanus ) and Arctic Char ( Salvelinus alpinus ), we highlight how an unbalanced sex ratio in the samples and a few sex‐linked markers may lead to false interpretations of population structure and thus to potentially erroneous management recommendations. Here, multivariate analyses revealed two genetic clusters separating samples by sex instead of by expected spatial variation: inshore and offshore locations in lobster, or east and west locations in Arctic Char. To further investigate this, we created several subsamples artificially varying the sex ratio in the inshore/offshore and east/west groups and then demonstrated that significant genetic differentiation could be observed despite panmixia in lobster, and that F ST values were overestimated in Arctic Char. This pattern was due to 12 and 94 sex‐linked markers driving differentiation for lobster and Arctic Char, respectively. Removing sex‐linked markers led to nonsignificant genetic structure in lobster and a more accurate estimation of F ST in Arctic Char. The locations of these markers and putative identities of genes containing or nearby the markers were determined using available transcriptomic and genomic data, and this provided new information related to sex determination in both species. Given that only 9.6% of all marine/diadromous population genomic studies to date have reported sex information, we urge researchers to collect and consider individual sex information. Sex information is therefore relevant for avoiding unexpected biases due to sex‐linked markers as well as for improving our knowledge of sex determination systems in nonmodel species. |
author2 |
Natural Sciences and Engineering Research Council of Canada Fisheries and Oceans Canada Natural Sciences and Engineering Research Council of Canada Fisheries and Oceans Canada Nunavut Wildlife Management Board P.E.I. Atlantic Shrimp Corporation Inc. Atlantic Lobster Sustainability Measures Program |
format |
Article in Journal/Newspaper |
author |
Benestan, Laura Moore, Jean‐Sébastien Sutherland, Ben J. G. Le Luyer, Jérémy Maaroufi, Halim Rougeux, Clément Normandeau, Eric Rycroft, Nathan Atema, Jelle Harris, Les N. Tallman, Ross F. Greenwood, Spencer J. Clark, Fraser K. Bernatchez, Louis |
spellingShingle |
Benestan, Laura Moore, Jean‐Sébastien Sutherland, Ben J. G. Le Luyer, Jérémy Maaroufi, Halim Rougeux, Clément Normandeau, Eric Rycroft, Nathan Atema, Jelle Harris, Les N. Tallman, Ross F. Greenwood, Spencer J. Clark, Fraser K. Bernatchez, Louis Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems |
author_facet |
Benestan, Laura Moore, Jean‐Sébastien Sutherland, Ben J. G. Le Luyer, Jérémy Maaroufi, Halim Rougeux, Clément Normandeau, Eric Rycroft, Nathan Atema, Jelle Harris, Les N. Tallman, Ross F. Greenwood, Spencer J. Clark, Fraser K. Bernatchez, Louis |
author_sort |
Benestan, Laura |
title |
Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems |
title_short |
Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems |
title_full |
Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems |
title_fullStr |
Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems |
title_full_unstemmed |
Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems |
title_sort |
sex matters in massive parallel sequencing: evidence for biases in genetic parameter estimation and investigation of sex determination systems |
publisher |
Wiley |
publishDate |
2017 |
url |
http://dx.doi.org/10.1111/mec.14217 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fmec.14217 https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.14217 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Salvelinus alpinus |
genre_facet |
Arctic Salvelinus alpinus |
op_source |
Molecular Ecology volume 26, issue 24, page 6767-6783 ISSN 0962-1083 1365-294X |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor http://doi.wiley.com/10.1002/tdm_license_1.1 http://onlinelibrary.wiley.com/termsAndConditions#vor |
op_doi |
https://doi.org/10.1111/mec.14217 |
container_title |
Molecular Ecology |
container_volume |
26 |
container_issue |
24 |
container_start_page |
6767 |
op_container_end_page |
6783 |
_version_ |
1809760640419495936 |