Conservation genomics of an endangered subspecies of Southern Emu-Wren, <i>Stipiturus malachurus</i> (Passeriformes: Maluridae)

<p>The endangered subspecies of Southern Emu-Wren (<i>Stipiturus malachurus intermedius</i>) in the Mount Lofty Ranges (MLR), South Australia has a fragmented distribution and poor dispersal capability. These factors make it susceptible to local population extinction, as evidenced by declining distribution and abundance since 1993. We documented genetic diversity by genotyping thousands of nuclear markers from samples collected in the 1990s to inform genetic management. We found that Southern Emu-Wrens from south-eastern South Australia and the MLR, which are separate subspecies that share mitochondrial haplotypes, are genetically distinct based on nuclear DNA, albeit at a low level (<i>F_ST</i> = 0.21). Within the MLR, differentiation between southern and northern sites is consistent with the presence of two populations, with the boundary reflecting a disjunction in the distribution of historical records. Although Southern Emu-Wrens are now absent from our MLR sample sites, nearby occupied sites within each of the populations require continued management, and our results suggest these may warrant treatment as separate management units. At one site where birds had disappeared over an 8-year period, our retrospective genotyping found low levels of inbreeding, reinforcing the need to distinguish factors impacting on population viability to mitigate extinction likelihood.