Designing meta-population genetic management for a small, endangered passerine with fragmented range

Context Genetic diversity is essential for the persistence and future adaptation of species. However, human-driven habitat fragmentation results in population isolation, often leading to rapid loss of genetic diversity and adaptive capacity. Genetic management of focal taxa may be overlooked in many threatened species conservation programs. The Endangered southeastern Australian mallee emu-wren Stipiturus mallee is a species that may benefit from genetic management. Its current range encompasses patchily distributed sub-populations, prone to bottlenecks and genetic drift. Thus, the reintroduction to areas from which the species has been locally extirpated requires careful selection of founders to maximise genetic diversity. Aims We analyse reduced-representation genomic data from seven sampling areas across the global meta-population to design a translocation strategy that maximises heterozygosity and retention of mallee emu-wren allelic diversity. Methods We estimated genetic structure, genetic diversity within, and differentiation between subpopulations, thus testing previous inference based on 12 length-variable loci of low population differentiation with 10,840 genome-wide SNP loci. We also estimated effective population sizes to identify populations in need of genetic augmentation, Finally, we used metapop2 simulations to estimate the relative contributions of each population to global genetic diversity of the species and to estimate the source and number of founders that would maximise heterozygosity and allelic richness in a hypothetical newly established population. Key results We found weak genetic structure across all sampling areas, supporting previous conclusions that the global mallee emu-wren population should be considered a single genetic unit for management purposes. Low but significant Weir and Cockerham pairwise F ST among locations indicated differentiation between sampling areas, suggesting that contemporary gene flow is restricted. Effective population sizes for the two regions supporting the largest numbers of mallee emu-wrens were below the threshold associated with reduced adaptive potential. Conclusions The genetic health and adaptive potential of sampled mallee emu-wren sub-populations are at risk. Implications The global mallee emu-wren meta-population would likely benefit from genetic augmentation, including reciprocal gene flow between extant sub-populations. To maximise genetic diversity in newly established populations, managers should prioritise gene-pool mixing with founders sourced from all sampled areas.