DOI: 10.5061/dryad.t2c668d
title: Data from: Genome-wide SNP markers breathe new life into phylogeography and species delimitation for the problematic short-necked turtles (Chelidae: Emydura) of eastern Australia

description: Understanding the evolutionary history of diversifying lineages and the
 delineation of evolutionarily significant units and species remain major
 challenges for evolutionary biology. Low cost representational sampling of
 the genome for single nucleotide polymorphisms (SNPs) shows great
 potential at the temporal scales that are typically the focus of species
 delimitation and phylogeography. We apply these markers to a case study of
 a freshwater turtle, Emydura macquarii, whose systematics has so far
 defied resolution, to bring to light a dynamic system of incipient species
 held back by low level and episodic exchange of alleles across drainage
 divides on various timescales. Emydura macquarii is a polytypic species
 complex comprising a set of allopatric lineages and incipient species at
 various shallow levels of molecular (and morphological) divergence that
 can interbreed to exchange alleles and do so where their ranges come into
 contact. In the context of low-level episodic gene flow, speciation is
 often reticulate, not a bifurcating process. Species delimitation needs to
 take into account the pattern of ancestry and descent of diverging
 lineages in allopatry (phylogenetics) together with the recent and
 contemporary processes of dispersal and gene flow (population genetics)
 that retard and obscure that divergence. This combined approach provides a
 means for addressing the challenges of incompletely isolated populations
 with uncommon, but recurrent gene flow in studies of species delimitation,
 a combination likely to be frequently encountered. The accompanying
 taxonomic judgements can avoid the risk of the taxonomic inflation that
 can accompany phylogenetic or lineage approaches to species delimitation.
description: Emydura_sth_glEmydura_metadataSpecimen metadata to accompany the raw data file when read into a genlight object using gl.read.dart.2row.r in R package dartR.svdMBD_LEBAn input file for New Hybrids to examine admixture between the Murray Darling Basin and the Lake Eyre Basin, via the Paroo and Bulloo rivers. Generated using gl.nhybrids.r in the dartR package.Fitzroy_BurdekinAn input file for New Hybrids to examine admixture between the Fitzroy River basin and the Burdekin River basin. Generated using gl.nhybrids.r in dartR package.fitch_infileAn input file for Phylip to construct the distance phylogeny. Generated using gl2phylip.r in the dartR package.emsth_treemixA gzip file provided as input to treemix, generated by gl2treemix.r, for use with the unix commands treemix -i emsth_treemix.gz -o emsth_treemix9 -root EmvicVict -m 9 plot_tree("emsth_treemix9", cex=0.05) plot_resid("emsth_treemix9","poporder",cex=0.5)Emydura_SNPs_2RowCombined R scripts used to generate the results. Draws heavily on R package dartR (Gruber et al., 2018)full_analysis.rEmSth_mtDNAA PAUP* nexus file for conducting the RAXML analysis of mtDNA sequence data.READMEDescription of files and their relationship to the analysis.