The importance of replicating genomic analyses to verify phylogenetic signal for recently evolved lineages
Abstract Genomewide SNP data generated by nontargeted methods such as RAD and GBS are increasingly being used in phylogenetic and phylogeographic analyses. When these methods are used in the absence of a reference genome, however, little is known about the locations and evolution of the SNP s. In us...
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Online Access: | http://dx.doi.org/10.1111/mec.13708 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fmec.13708 https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.13708 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/mec.13708 https://onlinelibrary.wiley.com/doi/am-pdf/10.1111/mec.13708 |
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crwiley:10.1111/mec.13708 2023-12-03T10:13:53+01:00 The importance of replicating genomic analyses to verify phylogenetic signal for recently evolved lineages Fraser, Ceridwen I. McGaughran, Angela Chuah, Aaron Waters, Jonathan M. Australian Research Council University of Otago Australian Research Council University of Otago 2016 http://dx.doi.org/10.1111/mec.13708 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fmec.13708 https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.13708 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/mec.13708 https://onlinelibrary.wiley.com/doi/am-pdf/10.1111/mec.13708 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#am http://onlinelibrary.wiley.com/termsAndConditions#vor http://doi.wiley.com/10.1002/tdm_license_1 http://onlinelibrary.wiley.com/termsAndConditions http://onlinelibrary.wiley.com/termsAndConditions Molecular Ecology volume 25, issue 15, page 3683-3695 ISSN 0962-1083 1365-294X Genetics Ecology, Evolution, Behavior and Systematics journal-article 2016 crwiley https://doi.org/10.1111/mec.13708 2023-11-09T14:01:41Z Abstract Genomewide SNP data generated by nontargeted methods such as RAD and GBS are increasingly being used in phylogenetic and phylogeographic analyses. When these methods are used in the absence of a reference genome, however, little is known about the locations and evolution of the SNP s. In using such data to address phylogenetic questions, researchers risk drawing false conclusions, particularly if a representative number of SNP s is not obtained. Here, we empirically test the robustness of phylogenetic inference based on SNP data for closely related lineages. We conducted a genomewide analysis of 75 712 SNP s, generated via GBS , of southern bull‐kelp ( Durvillaea ). Durvillaea chathamensis co‐occurs with D. antarctica on Chatham Island, but the two species have previously been found to be so genetically similar that the status of the former has been questioned. Our results show that D. chathamensis , which differs from D. antarctica ecologically as well as morphologically, is indeed a reproductively isolated species. Furthermore, our replicated analyses show that D. chathamensis cannot be reliably distinguished phylogenetically from closely related D. antarctica using subsets (ranging in size from 400 to 10 000 sites) of the 40 912 parsimony‐informative SNP s in our data set and that bootstrap values alone can give misleading impressions of the strength of phylogenetic inferences. These results highlight the importance of independently replicating SNP analyses to verify that phylogenetic inferences based on nontargeted SNP data are robust. Our study also demonstrates that modern genomic approaches can be used to identify cases of recent or incipient speciation that traditional approaches (e.g. Sanger sequencing of a few loci) may be unable to detect or resolve. Article in Journal/Newspaper Antarc* Antarctica Wiley Online Library (via Crossref) Molecular Ecology 25 15 3683 3695 |
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Open Polar |
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Wiley Online Library (via Crossref) |
op_collection_id |
crwiley |
language |
English |
topic |
Genetics Ecology, Evolution, Behavior and Systematics |
spellingShingle |
Genetics Ecology, Evolution, Behavior and Systematics Fraser, Ceridwen I. McGaughran, Angela Chuah, Aaron Waters, Jonathan M. The importance of replicating genomic analyses to verify phylogenetic signal for recently evolved lineages |
topic_facet |
Genetics Ecology, Evolution, Behavior and Systematics |
description |
Abstract Genomewide SNP data generated by nontargeted methods such as RAD and GBS are increasingly being used in phylogenetic and phylogeographic analyses. When these methods are used in the absence of a reference genome, however, little is known about the locations and evolution of the SNP s. In using such data to address phylogenetic questions, researchers risk drawing false conclusions, particularly if a representative number of SNP s is not obtained. Here, we empirically test the robustness of phylogenetic inference based on SNP data for closely related lineages. We conducted a genomewide analysis of 75 712 SNP s, generated via GBS , of southern bull‐kelp ( Durvillaea ). Durvillaea chathamensis co‐occurs with D. antarctica on Chatham Island, but the two species have previously been found to be so genetically similar that the status of the former has been questioned. Our results show that D. chathamensis , which differs from D. antarctica ecologically as well as morphologically, is indeed a reproductively isolated species. Furthermore, our replicated analyses show that D. chathamensis cannot be reliably distinguished phylogenetically from closely related D. antarctica using subsets (ranging in size from 400 to 10 000 sites) of the 40 912 parsimony‐informative SNP s in our data set and that bootstrap values alone can give misleading impressions of the strength of phylogenetic inferences. These results highlight the importance of independently replicating SNP analyses to verify that phylogenetic inferences based on nontargeted SNP data are robust. Our study also demonstrates that modern genomic approaches can be used to identify cases of recent or incipient speciation that traditional approaches (e.g. Sanger sequencing of a few loci) may be unable to detect or resolve. |
author2 |
Australian Research Council University of Otago Australian Research Council University of Otago |
format |
Article in Journal/Newspaper |
author |
Fraser, Ceridwen I. McGaughran, Angela Chuah, Aaron Waters, Jonathan M. |
author_facet |
Fraser, Ceridwen I. McGaughran, Angela Chuah, Aaron Waters, Jonathan M. |
author_sort |
Fraser, Ceridwen I. |
title |
The importance of replicating genomic analyses to verify phylogenetic signal for recently evolved lineages |
title_short |
The importance of replicating genomic analyses to verify phylogenetic signal for recently evolved lineages |
title_full |
The importance of replicating genomic analyses to verify phylogenetic signal for recently evolved lineages |
title_fullStr |
The importance of replicating genomic analyses to verify phylogenetic signal for recently evolved lineages |
title_full_unstemmed |
The importance of replicating genomic analyses to verify phylogenetic signal for recently evolved lineages |
title_sort |
importance of replicating genomic analyses to verify phylogenetic signal for recently evolved lineages |
publisher |
Wiley |
publishDate |
2016 |
url |
http://dx.doi.org/10.1111/mec.13708 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fmec.13708 https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.13708 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/mec.13708 https://onlinelibrary.wiley.com/doi/am-pdf/10.1111/mec.13708 |
genre |
Antarc* Antarctica |
genre_facet |
Antarc* Antarctica |
op_source |
Molecular Ecology volume 25, issue 15, page 3683-3695 ISSN 0962-1083 1365-294X |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#am http://onlinelibrary.wiley.com/termsAndConditions#vor http://doi.wiley.com/10.1002/tdm_license_1 http://onlinelibrary.wiley.com/termsAndConditions http://onlinelibrary.wiley.com/termsAndConditions |
op_doi |
https://doi.org/10.1111/mec.13708 |
container_title |
Molecular Ecology |
container_volume |
25 |
container_issue |
15 |
container_start_page |
3683 |
op_container_end_page |
3695 |
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1784260844516802560 |