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The importance of replicating genomic analyses to verify phylogenetic signal for recently evolved lineages

Fraser, Ceridwen; McGaughran, Angela; Chuah, Aaron; Waters, Jonathan M

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...[Show more]

dc.contributor.authorFraser, Ceridwen
dc.contributor.authorMcGaughran, Angela
dc.contributor.authorChuah, Aaron
dc.contributor.authorWaters, Jonathan M
dc.date.accessioned2018-06-29T03:57:21Z
dc.identifier.issn0962-1083
dc.identifier.urihttp://hdl.handle.net/1885/144647
dc.description.abstractGenomewide 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.
dc.description.sponsorshipThis 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).
dc.format.mimetypeapplication/pdf
dc.publisherWiley
dc.rights© 2016 John Wiley & Sons Ltd
dc.rightshttp://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.
dc.sourceMolecular ecology
dc.subjectgenotyping by sequencing
dc.subjectsingle nucleotide polymorphism
dc.subjectkelp
dc.subjectmacroalgae
dc.subjectmarine
dc.subjectspeciation
dc.subjectgenetic speciation
dc.subjectgenomics
dc.subjectkelp
dc.subjectsequence analysis, dna
dc.subjectphylogeny
dc.subjectpolymorphism, single nucleotide
dc.titleThe importance of replicating genomic analyses to verify phylogenetic signal for recently evolved lineages
dc.typeJournal article
local.identifier.citationvolume25
dc.date.issued2016
local.type.statusAccepted Version
local.contributor.affiliationFraser, C. I., Fenner School of Environment and Society, The Australian National University
dc.relationhttp://purl.org/au-research/grants/arc/DE140101715
local.identifier.essn1365-294X
local.bibliographicCitation.issue15
local.bibliographicCitation.startpage3683
local.bibliographicCitation.lastpage3695
local.identifier.doi10.1111/mec.13708
dcterms.accessRightsOpen Access
dcterms.accessRightsOpen Access
CollectionsANU Research Publications

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