Influence of drainage divides versus arid corridors on genetic structure and demography of a widespread freshwater turtle, Emydura macquarii krefftii, from Australia

Abstract

The influence of Pleistocene climatic cycles on Southern Hemisphere biotas is not yet well understood. Australia's eastern coastal margin provides an ideal setting for examining the relative influence of landscape development, sea level fluctuation, and cyclic climatic aridity on the evolution of freshwater biodiversity. We examined the impact of climatic oscillations and physical biogeographic barriers on the evolutionary history of the wide-ranging Krefft's river turtle (Emydura macquarii krefftii), using range-wide sampling (649 individuals representing 18 locations across 11 drainages) and analysis of mitochondrial sequences (∼1.3-kb control region and ND4) and nuclear microsatellites (12 polymorphic loci). A range of phylogeographic (haplotype networks, molecular dating), demographic (neutrality tests, mismatch distributions), and population genetic analyses (pairwise FST, analysis of molecular variance, Bayesian clustering analysis) were implemented to differentiate between competing demographic (local persistence vs. range expansion) and biogeographic (arid corridor vs. drainage divide) scenarios. Genetic data reveal population genetic structure in Krefft's river turtles primarily reflects isolation across drainage divides. Striking north-south regional divergence (2.2% ND4 p-distance; c. 4.73 Ma, 95% higher posterior density (HPD) 2.08–8.16 Ma) was consistent with long-term isolation across a major drainage divide, not an adjacent arid corridor. Ancient divergence among regional lineages implies persistence of northern Krefft's populations despite the recurrent phases of severe local aridity, but with very low contemporary genetic diversity. Stable demography and high levels of genetic diversity are inferred for southern populations, where aridity was less extreme. Range-wide genetic structure in Krefft's river turtles reflects contemporary and historical drainage architecture, although regional differences in the extent of Plio–Pleistocene climatic aridity may be reflected in current levels of genetic diversity.

<strong>A revision of African helmeted terrapins (Testudines: Pelomedusidae: <em>Pelomedusa</em>), with descriptions of six new species</strong>

“…Vargas-Ramírez et al 2010Praschag et al 2011;Fritz et al 2012a, b;Kindler et al 2012;Iverson et al 2013;Todd et al 2014). Important insights of these studies were that there is a wide range of divergence values among congeneric species, and that there is no general threshold of sequence divergence that 'axiomatically' indicates distinct species (see also Shen et al 2013).…”

Genomewide SNP markers breathe new life into phylogeography and species delimitation for the problematic short‐necked turtles (Chelidae: Emydura) of eastern Australia

“…Many of the above‐mentioned species shared alleles at all loci, even rare alleles (Georges & Adams, ). The allozyme data provided evidence that the southern Emydura is a single polytypic species comprising a series of reasonably well‐defined but closely related ESUs (Cogger, ; Georges & Thomson, ; Todd, Blair, & Jerry, ). We anticipated that the large numbers of nuclear SNP markers and comprehensive spatial sampling of sequenced individuals would resolve species boundaries in the southern Emydura , and so resolve the disparity arising from the morphological and allozyme studies.…”

Significant genetic structure despite high vagility revealed through mitochondrial phylogeography of an Australian freshwater turtle (Chelodina longicollis)

“…We applied a mitochondrial divergence rate of 0.895% per million years (Zamudio and Greene 1997;Rabosky et al 2007) scaled per lineage per million years and modelled under a normal distribution. This divergence rate is consistent with a rate estimated from fossil chelid turtles by Georges et al (2014) (0.86% per million years) and has been applied successfully elsewhere Todd et al 2014). MCMC chains were run for 40 million generations with sampling every 1000 steps yielding a total of 40 000 trees.…”

“…A similar pattern characterises the Burdekin Gap in the Eastern Province. There, an arid corridor contributes to vicariance in terrestrial faunal lineages yet freshwater turtle species are relatively insensitive to the north-south 'gap' (Todd et al 2014).…”

“…Mitochondrial nucleotide divergence between the MDB and Eastern Province bioregions in this species is 2.41%, and deeper divergence of 4.61% is found between the Mary and Brisbane drainages in the Eastern Province itself . Eastern Province drainage divides similarly dictate deep phylogeographic structure in the Australian snapping turtle (Elseya albagula) and Krefft's river turtle (Emydura macquarii krefftii) (Todd et al 2013(Todd et al , 2014. Compared with C. longicollis, C. expansa and Em.…”