10.5061/DRYAD.T2C668D
Georges, Arthur
University of Canberra
Gruber, Bernd
University of Canberra
Pauly, Greg B.
Natural History Museum of Los Angeles County
White, Duanne
University of Canberra
Adams, Mark
University of Adelaide
University of Canberra
Young, Matthew J.
University of Canberra
Kilian, Andzrej
University of Canberra
Zhang, Xiuwen
University of Canberra
Shaffer, H. Bradley
University of California Los Angeles
Unmack, Peter J.
University of Canberra
Kilian, Andrzej
University of Canberra
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
Dryad
dataset
2018
Emydura macquarii
tokogenesis
cladogeneisis
Pleistocene to present
2018-10-23T20:55:03Z
2018-10-23T20:55:03Z
en
https://doi.org/10.1111/mec.14925
42022170 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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.
Australia