Data from: Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans
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...
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ftdryad:oai:v1.datadryad.org:10255/dryad.56790 2023-05-15T17:41:39+02:00 Data from: Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans Viricel, Amélia Pante, Eric Dabin, Willy Simon-Bouhet, Benoît Northeast Atlantic 2013-11-21T14:28:54Z http://hdl.handle.net/10255/dryad.56790 https://doi.org/10.5061/dryad.mk364 unknown doi:10.5061/dryad.mk364/1 doi:10.5061/dryad.mk364/2 doi:10.5061/dryad.mk364/3 doi:10.5061/dryad.mk364/4 doi:10.5061/dryad.mk364/5 doi:10.5061/dryad.mk364/6 doi:10.5061/dryad.mk364/7 doi:10.5061/dryad.mk364/8 doi:10.5061/dryad.mk364/9 doi:10.5061/dryad.mk364/10 doi:10.5061/dryad.mk364/11 doi:10.5061/dryad.mk364/12 doi:10.5061/dryad.mk364/13 doi:10.5061/dryad.mk364/14 doi:10.5061/dryad.mk364/15 doi:10.5061/dryad.mk364/16 doi:10.5061/dryad.mk364/17 doi:10.5061/dryad.mk364/18 doi:10.5061/dryad.mk364/19 doi:10.5061/dryad.mk364/20 doi:10.5061/dryad.mk364/21 doi:10.5061/dryad.mk364/22 doi:10.5061/dryad.mk364/23 doi:10.1111/1755-0998.12206 PMID:24267050 doi:10.5061/dryad.mk364 Viricel A, Pante E, Dabin W, Simon-Bouhet B (2013) Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans. Molecular Ecology Resources 14(3): 597–605. http://hdl.handle.net/10255/dryad.56790 Phylogenetic Theory and Methods Genomics/Proteomics Mammals Article 2013 ftdryad https://doi.org/10.5061/dryad.mk364 https://doi.org/10.5061/dryad.mk364/1 https://doi.org/10.5061/dryad.mk364/2 https://doi.org/10.5061/dryad.mk364/3 https://doi.org/10.5061/dryad.mk364/4 https://doi.org/10.5061/dryad.mk364/5 https://doi.org/1 2020-01-01T15:05:04Z 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 Northeast Atlantic Phocoena phocoena Dryad Digital Repository (Duke University) |
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Open Polar |
collection |
Dryad Digital Repository (Duke University) |
op_collection_id |
ftdryad |
language |
unknown |
topic |
Phylogenetic Theory and Methods Genomics/Proteomics Mammals |
spellingShingle |
Phylogenetic Theory and Methods Genomics/Proteomics Mammals Viricel, Amélia Pante, Eric Dabin, Willy Simon-Bouhet, Benoît Data from: Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans |
topic_facet |
Phylogenetic Theory and Methods Genomics/Proteomics Mammals |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Viricel, Amélia Pante, Eric Dabin, Willy Simon-Bouhet, Benoît |
author_facet |
Viricel, Amélia Pante, Eric Dabin, Willy Simon-Bouhet, Benoît |
author_sort |
Viricel, Amélia |
title |
Data from: Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans |
title_short |
Data from: Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans |
title_full |
Data from: Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans |
title_fullStr |
Data from: Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans |
title_full_unstemmed |
Data from: Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans |
title_sort |
data from: applicability of rad-tag genotyping for inter-familial comparisons: empirical data from two cetaceans |
publishDate |
2013 |
url |
http://hdl.handle.net/10255/dryad.56790 https://doi.org/10.5061/dryad.mk364 |
op_coverage |
Northeast Atlantic |
genre |
Northeast Atlantic Phocoena phocoena |
genre_facet |
Northeast Atlantic Phocoena phocoena |
op_relation |
doi:10.5061/dryad.mk364/1 doi:10.5061/dryad.mk364/2 doi:10.5061/dryad.mk364/3 doi:10.5061/dryad.mk364/4 doi:10.5061/dryad.mk364/5 doi:10.5061/dryad.mk364/6 doi:10.5061/dryad.mk364/7 doi:10.5061/dryad.mk364/8 doi:10.5061/dryad.mk364/9 doi:10.5061/dryad.mk364/10 doi:10.5061/dryad.mk364/11 doi:10.5061/dryad.mk364/12 doi:10.5061/dryad.mk364/13 doi:10.5061/dryad.mk364/14 doi:10.5061/dryad.mk364/15 doi:10.5061/dryad.mk364/16 doi:10.5061/dryad.mk364/17 doi:10.5061/dryad.mk364/18 doi:10.5061/dryad.mk364/19 doi:10.5061/dryad.mk364/20 doi:10.5061/dryad.mk364/21 doi:10.5061/dryad.mk364/22 doi:10.5061/dryad.mk364/23 doi:10.1111/1755-0998.12206 PMID:24267050 doi:10.5061/dryad.mk364 Viricel A, Pante E, Dabin W, Simon-Bouhet B (2013) Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans. Molecular Ecology Resources 14(3): 597–605. http://hdl.handle.net/10255/dryad.56790 |
op_doi |
https://doi.org/10.5061/dryad.mk364 https://doi.org/10.5061/dryad.mk364/1 https://doi.org/10.5061/dryad.mk364/2 https://doi.org/10.5061/dryad.mk364/3 https://doi.org/10.5061/dryad.mk364/4 https://doi.org/10.5061/dryad.mk364/5 https://doi.org/1 |
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