Evidence of subdivisions on evolutionary timescales in a large, declining marsupial distributed across a phylogeographic barrier

Major prehistoric forces, such as the climatic shifts of the Pleistocene, can remain visible in a species' population genetics. Inference of refuges via genetic tools is useful for conservation management as it can identify populations whose preservation may help retain a species' adaptive potential. Such investigation is needed for Australia's southern hairy-nosed wombat (Lasiorhinus latifrons), whose conservation status has recently deteriorated, and whose phylogeographic history during the Pleistocene may be atypical compared to other species. Its contemporary range spans approximately 2000 km of diverse habitat on either side of the Spencer Gulf, which was a land bridge during periods of Pleistocene aridity that may have allowed for migration circumventing the arid Eyrean barrier. We sampled from animals in nearly all known sites within the species' current distribution, mainly using non-invasive methods, and employed nuclear and mitochondrial DNA analyses to assess alternative scenarios for Pleistocene impacts on population structure. We found evidence for mildly differentiated populations at the range extremes on either side of Spencer Gulf, with secondary contact between locations neighbouring each side of the barrier. These extreme western and eastern regions, and four other regions in between, were genetically distinct in genotypic clustering analyses. Estimates indicate modest, but complex gene flow patterns among some of these regions, in some cases possibly restricted for several thousand years. Prior to this study there was little information to aid risk assessment and prioritization of conservation interventions facilitating gene flow among populations of this species. The contributions of this study to that issue are outlined

Southern blot RFLP compound haplotypes and frequencies, and nucleotide diversity (as percentages) in seven sites of SHN wombats.

<p>Southern blot RFLP compound haplotypes and frequencies, and nucleotide diversity (as percentages) in seven sites of SHN wombats.</p

Network Analysis.

<p>Minimum-spanning tree based on pairwise genetic distances [(δμ)²] arranged approximately by geographic layout of sampling locations. Size of nodes and edges are scaled to the degree of ‘connectedness’ to other populations, lighter colours of edges indicate decreasing connectedness. Dashed lines enclose structure microsatellite clusters.</p

Microsatellite Clusters.

<p>Proportion of each of six microsatellite structure clusters represented in individuals from each sampling site, using the four loci in the combined dataset (sets A and B). Columns represent data from individual SHN wombats, divided into sampling sites by vertical narrow dark lines, and organized into geographic regions.</p

Fu’s <i>F</i>_<i>S</i> and Tajima’s <i>D</i> values, based on RFLP haplotypes, for seven sites of SHN wombats.

<p>Fu’s <i>F</i>_<i>S</i> and Tajima’s <i>D</i> values, based on RFLP haplotypes, for seven sites of SHN wombats.</p

Table of (δμ)² distances between 24 collection sites, calculated by Arlequin from microsatellite data (lower diagonal) and divergence times in years, calculated from these distances (upper diagonal).

<p><b>Bold</b> indicates sites within the same cluster identified by STRUCTURE.</p

RFLP Haplotypes.

<p>Unrooted neighbour-joining tree of six whole mtDNA RFLP haplotypes in <i>L</i>. <i>latifrons</i> populations. E = east of the Eyrean barrier, W = west of it.</p

Hierarchical analysis of molecular variance (amova) based on microsatellite data for 24 SHN wombat sample sites, (a) among the six geographic groups identified by structure, and (b) among two groups (East v. West) identified by forcing <i>K</i> = 2.

<p>Hierarchical analysis of molecular variance (amova) based on microsatellite data for 24 SHN wombat sample sites, (a) among the six geographic groups identified by structure, and (b) among two groups (East v. West) identified by forcing <i>K</i> = 2.</p