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

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.