Applicability of RAD-tag genotyping for interfamilial comparisons: empirical data from two cetaceans
International audience; Restriction site-Associated DNA tag (RAD-tag) sequencing has become a popular approach to generate thousands of SNPs used to address diverse questions in population genomics. Comparatively, the suitability of RAD-tag genotyping to address evolutionary questions across diverge...
Published in: | Molecular Ecology Resources |
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Main Authors: | , , , |
Other Authors: | , , , , |
Format: | Article in Journal/Newspaper |
Language: | unknown |
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Wiley
2014
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Online Access: | https://hal.archives-ouvertes.fr/hal-00908459/file/mer_viricel_rad_phocoena_25Oct13.pdf https://doi.org/10.1111/1755-0998.12206 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1755-0998.12206 https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.12206 https://hal.archives-ouvertes.fr/hal-00908459 https://www.ncbi.nlm.nih.gov/pubmed/24267050 https://hal.archives-ouvertes.fr/hal-00908459/document https://academic.microsoft.com/#/detail/2123205615 |
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RAD sequencing inter-familial divergence Delphinidae Phocoenidae envir scipo |
spellingShingle |
RAD sequencing inter-familial divergence Delphinidae Phocoenidae envir scipo Amélia Viricel Willy Dabin Benoit Simon-Bouhet Eric Pante Applicability of RAD-tag genotyping for interfamilial comparisons: empirical data from two cetaceans |
topic_facet |
RAD sequencing inter-familial divergence Delphinidae Phocoenidae envir scipo |
description |
International audience; Restriction site-Associated DNA tag (RAD-tag) sequencing has become a popular approach to generate thousands of SNPs used to address diverse questions in population genomics. Comparatively, the suitability of RAD-tag genotyping to address evolutionary questions across divergent species has been the subject of only a few recent studies. Here, we evaluate the applicability of this approach to conduct genome-wide scans for polymorphisms across two cetacean species belonging to distinct families: the short-beaked common dolphin (Delphinus delphis; n = 5 individuals) and the harbor porpoise (Phocoena phocoena; n = 1 individual). Additionally, we explore the effects of varying two parameters in the Stacks analysis pipeline on the number of loci and level of divergence obtained. We observed a 34% drop in the total number of loci that were present in all individuals when analyzing individuals from the distinct families compared to analyses restricted to intra-specific comparisons (i.e., within D. delphis). Despite relatively stringent quality filters, 3,595 polymorphic loci were retrieved from our inter-familial comparison. Cetaceans have undergone rapid diversification and the estimated divergence time between the two families is relatively recent (14 to 19 My). Thus, our results showed that, for this level of divergence, a large number of orthologous loci can still be genotyped using this approach, which is on par with two recent in silico studies. Our findings constitute one of the first empirical investigations using RAD-tag sequencing at this level of divergence and highlights the great potential of this approach in comparative studies and to address evolutionary questions. |
author2 |
LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs) Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS) Observatoire PELAGIS UMS 3462 (PELAGIS) Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS) CPER Poitou-Charente 2007-2013, Action Internationales et Rayonnement de l'Université de La Rochelle, UMR 7266 LIENSs CNRS-Université de La Rochelle |
format |
Article in Journal/Newspaper |
author |
Amélia Viricel Willy Dabin Benoit Simon-Bouhet Eric Pante |
author_facet |
Amélia Viricel Willy Dabin Benoit Simon-Bouhet Eric Pante |
author_sort |
Amélia Viricel |
title |
Applicability of RAD-tag genotyping for interfamilial comparisons: empirical data from two cetaceans |
title_short |
Applicability of RAD-tag genotyping for interfamilial comparisons: empirical data from two cetaceans |
title_full |
Applicability of RAD-tag genotyping for interfamilial comparisons: empirical data from two cetaceans |
title_fullStr |
Applicability of RAD-tag genotyping for interfamilial comparisons: empirical data from two cetaceans |
title_full_unstemmed |
Applicability of RAD-tag genotyping for interfamilial comparisons: empirical data from two cetaceans |
title_sort |
applicability of rad-tag genotyping for interfamilial comparisons: empirical data from two cetaceans |
publisher |
Wiley |
publishDate |
2014 |
url |
https://hal.archives-ouvertes.fr/hal-00908459/file/mer_viricel_rad_phocoena_25Oct13.pdf https://doi.org/10.1111/1755-0998.12206 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1755-0998.12206 https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.12206 https://hal.archives-ouvertes.fr/hal-00908459 https://www.ncbi.nlm.nih.gov/pubmed/24267050 https://hal.archives-ouvertes.fr/hal-00908459/document https://academic.microsoft.com/#/detail/2123205615 |
genre |
Phocoena phocoena |
genre_facet |
Phocoena phocoena |
op_source |
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op_relation |
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Molecular Ecology Resources |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::5f25e4368c46ef848c7f77bd09202b5e 2023-05-15T17:59:14+02:00 Applicability of RAD-tag genotyping for interfamilial comparisons: empirical data from two cetaceans Amélia Viricel Willy Dabin Benoit Simon-Bouhet Eric Pante LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs) Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS) Observatoire PELAGIS UMS 3462 (PELAGIS) Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS) CPER Poitou-Charente 2007-2013, Action Internationales et Rayonnement de l'Université de La Rochelle, UMR 7266 LIENSs CNRS-Université de La Rochelle 2014-01-01 https://hal.archives-ouvertes.fr/hal-00908459/file/mer_viricel_rad_phocoena_25Oct13.pdf https://doi.org/10.1111/1755-0998.12206 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1755-0998.12206 https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.12206 https://hal.archives-ouvertes.fr/hal-00908459 https://www.ncbi.nlm.nih.gov/pubmed/24267050 https://hal.archives-ouvertes.fr/hal-00908459/document https://academic.microsoft.com/#/detail/2123205615 undefined unknown Wiley https://hal.archives-ouvertes.fr/hal-00908459/file/mer_viricel_rad_phocoena_25Oct13.pdf http://dx.doi.org/10.1111/1755-0998.12206 https://dx.doi.org/10.1111/1755-0998.12206 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1755-0998.12206 https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.12206 https://hal.archives-ouvertes.fr/hal-00908459 https://www.ncbi.nlm.nih.gov/pubmed/24267050 https://hal.archives-ouvertes.fr/hal-00908459/document https://academic.microsoft.com/#/detail/2123205615 undefined 10.1111/1755-0998.12206 2123205615 oai:HAL:hal-00908459v1 24267050 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|openaire____::55045bd2a65019fd8e6741a755395c8c 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|issn___print::b218938d02cd90e10a9c0a89780b4300 10|openaire____::8ac8380272269217cb09a928c8caa993 10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a 10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a openaire____::1256f046-bf1f-4afc-8b47-d0b147148b18 10|opendoar____::1534b76d325a8f591b52d302e7181331 10|opendoar____::18bb68e2b38e4a8ce7cf4f6b2625768c 10|openaire____::806360c771262b4d6770e7cdf04b5c5a 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c 10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357 RAD sequencing inter-familial divergence Delphinidae Phocoenidae envir scipo Journal Article https://vocabularies.coar-repositories.org/resource_types/c_6501/ 2014 fttriple https://doi.org/10.1111/1755-0998.12206 2023-01-22T17:08:33Z International audience; Restriction site-Associated DNA tag (RAD-tag) sequencing has become a popular approach to generate thousands of SNPs used to address diverse questions in population genomics. Comparatively, the suitability of RAD-tag genotyping to address evolutionary questions across divergent species has been the subject of only a few recent studies. Here, we evaluate the applicability of this approach to conduct genome-wide scans for polymorphisms across two cetacean species belonging to distinct families: the short-beaked common dolphin (Delphinus delphis; n = 5 individuals) and the harbor porpoise (Phocoena phocoena; n = 1 individual). Additionally, we explore the effects of varying two parameters in the Stacks analysis pipeline on the number of loci and level of divergence obtained. We observed a 34% drop in the total number of loci that were present in all individuals when analyzing individuals from the distinct families compared to analyses restricted to intra-specific comparisons (i.e., within D. delphis). Despite relatively stringent quality filters, 3,595 polymorphic loci were retrieved from our inter-familial comparison. Cetaceans have undergone rapid diversification and the estimated divergence time between the two families is relatively recent (14 to 19 My). Thus, our results showed that, for this level of divergence, a large number of orthologous loci can still be genotyped using this approach, which is on par with two recent in silico studies. Our findings constitute one of the first empirical investigations using RAD-tag sequencing at this level of divergence and highlights the great potential of this approach in comparative studies and to address evolutionary questions. Article in Journal/Newspaper Phocoena phocoena Unknown Molecular Ecology Resources 14 3 597 605 |