The importance of replicating genomic analyses to verify phylogenetic signal for recently evolved lineages
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 SNPs. In using such d...
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ftanucanberra:oai:openresearch-repository.anu.edu.au:1885/144647 2024-01-14T10:02:21+01:00 The importance of replicating genomic analyses to verify phylogenetic signal for recently evolved lineages Fraser, Ceridwen McGaughran, Angela Chuah, Aaron Waters, Jonathan M application/pdf http://hdl.handle.net/1885/144647 https://doi.org/10.1111/mec.13708 https://openresearch-repository.anu.edu.au/bitstream/1885/144647/5/Fraser%20et%20al.%202016_The%20Importance.pdf.jpg unknown Wiley http://purl.org/au-research/grants/arc/DE140101715 0962-1083 http://hdl.handle.net/1885/144647 doi:10.1111/mec.13708 https://openresearch-repository.anu.edu.au/bitstream/1885/144647/5/Fraser%20et%20al.%202016_The%20Importance.pdf.jpg © 2016 John Wiley & Sons Ltd http://www.sherpa.ac.uk/romeo/issn/0962-1083/."author can archive post-print (ie final draft post-refereeing). 12 months embargo" from SHERPA/RoMEO site (as at 29/06/18). This is the peer reviewed version of the following article: Fraser, C. I., McGaughran, A. , Chuah, A. and Waters, J. M. (2016), The importance of replicating genomic analyses to verify phylogenetic signal for recently evolved lineages. Mol Ecol, 25: 3683-3695. doi:10.1111/mec.13708, which has been published in final form at https://dx.doi.org/10.1111/mec.13708. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. Molecular ecology genotyping by sequencing single nucleotide polymorphism kelp macroalgae marine speciation genetic speciation genomics sequence analysis dna phylogeny polymorphism single nucleotide Journal article ftanucanberra https://doi.org/10.1111/mec.13708 2023-12-15T09:38:22Z 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 SNPs. In using such data to address phylogenetic questions, researchers risk drawing false conclusions, particularly if a representative number of SNPs 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 SNPs, 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 SNPs 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. This research was supported by an Australian Research Council Discovery Early Career Research Award (DE140101715 to CIF) and University of Otago Performance Based Research Funding (to JMW). Article in Journal/Newspaper Antarc* Antarctica Australian National University: ANU Digital Collections Molecular Ecology 25 15 3683 3695 |
institution |
Open Polar |
collection |
Australian National University: ANU Digital Collections |
op_collection_id |
ftanucanberra |
language |
unknown |
topic |
genotyping by sequencing single nucleotide polymorphism kelp macroalgae marine speciation genetic speciation genomics sequence analysis dna phylogeny polymorphism single nucleotide |
spellingShingle |
genotyping by sequencing single nucleotide polymorphism kelp macroalgae marine speciation genetic speciation genomics sequence analysis dna phylogeny polymorphism single nucleotide Fraser, Ceridwen McGaughran, Angela Chuah, Aaron Waters, Jonathan M The importance of replicating genomic analyses to verify phylogenetic signal for recently evolved lineages |
topic_facet |
genotyping by sequencing single nucleotide polymorphism kelp macroalgae marine speciation genetic speciation genomics sequence analysis dna phylogeny polymorphism single nucleotide |
description |
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 SNPs. In using such data to address phylogenetic questions, researchers risk drawing false conclusions, particularly if a representative number of SNPs 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 SNPs, 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 SNPs 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. This research was supported by an Australian Research Council Discovery Early Career Research Award (DE140101715 to CIF) and University of Otago Performance Based Research Funding (to JMW). |
format |
Article in Journal/Newspaper |
author |
Fraser, Ceridwen McGaughran, Angela Chuah, Aaron Waters, Jonathan M |
author_facet |
Fraser, Ceridwen McGaughran, Angela Chuah, Aaron Waters, Jonathan M |
author_sort |
Fraser, Ceridwen |
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 |
url |
http://hdl.handle.net/1885/144647 https://doi.org/10.1111/mec.13708 https://openresearch-repository.anu.edu.au/bitstream/1885/144647/5/Fraser%20et%20al.%202016_The%20Importance.pdf.jpg |
genre |
Antarc* Antarctica |
genre_facet |
Antarc* Antarctica |
op_source |
Molecular ecology |
op_relation |
http://purl.org/au-research/grants/arc/DE140101715 0962-1083 http://hdl.handle.net/1885/144647 doi:10.1111/mec.13708 https://openresearch-repository.anu.edu.au/bitstream/1885/144647/5/Fraser%20et%20al.%202016_The%20Importance.pdf.jpg |
op_rights |
© 2016 John Wiley & Sons Ltd http://www.sherpa.ac.uk/romeo/issn/0962-1083/."author can archive post-print (ie final draft post-refereeing). 12 months embargo" from SHERPA/RoMEO site (as at 29/06/18). This is the peer reviewed version of the following article: Fraser, C. I., McGaughran, A. , Chuah, A. and Waters, J. M. (2016), The importance of replicating genomic analyses to verify phylogenetic signal for recently evolved lineages. Mol Ecol, 25: 3683-3695. doi:10.1111/mec.13708, which has been published in final form at https://dx.doi.org/10.1111/mec.13708. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. |
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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1788057339911208960 |