title: 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 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.
authors.affiliation: Fenner School of Environment and Society, Australian National University, Canberra, Act, 2601, Australia.
authors.forename: Ceridwen I
authors.initials: CI
authors.lastname: Fraser
authors.affiliation: CSIRO Land and Water, Black Mountain Laboratories, Clunies Ross Street, Canberra, Act, 2601, Australia.|School of BioSciences, University of Melbourne, 30 Flemington Road, Melbourne, Vic, 3010, Australia.
authors.forename: Angela
authors.initials: A
authors.lastname: McGaughran
authors.affiliation: John Curtin School of Medical Research, Australian National University, Canberra, Act, 2601, Australia.
authors.forename: Aaron
authors.initials: A
authors.lastname: Chuah
authors.affiliation: Department of Zoology, University of Otago, Dunedin, 9016, New Zealand.
authors.forename: Jonathan M
authors.initials: JM
authors.lastname: Waters
mesh_terms: D049810:Genetic Speciation; D023281:Genomics; D044423:Kelp / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
keywords: Genotyping by Sequencing; Single Nucleotide Polymorphism; kelp; macroalgae; marine; speciation