A Shift to Metapopulation Genetic Management for Persistence of a Species Threatened by Fragmentation: The Case of an Endangered Australian Freshwater Fish

In a world where habitats are degrading and the climate is warming and becoming unpredictable, biodiversity conservation efforts and funding remain grossly inadequate. As part of a multifaceted approach to halting extinctions, shifting from preserving small, remnant populations to a practice of genetically connecting populations that recreate larger and more diverse populations is expected to be beneficial. This harnesses key evolutionary processes to promote species' abilities to adapt to changing environments and to increase the likelihood of population persistence. Here, we use the endangered Macquarie perch (Macquaria australasica) as a case study to develop a genetic strategy for metapopulation management aimed at promoting population growth and persistence. The Macquarie perch's range has been highly fragmented and its remaining habitat is at risk of catastrophic degradation due to climate change. We integrate results of new and existing genetic analyses to illustrate how genetically depauperate populations can benefit from admixture, and how the outcomes of management interventions can be quantified through genetic monitoring. We also develop the pipeline JeDi (https://github.com/drobledoruiz/JeDi) for estimating unbiased individual heterozygosity, population nucleotide diversity, and pairwise-population divergence, using reduced-representation genome sequencing data and an assembled reference genome. We use this pipeline to estimate baseline data for monitoring of Macquarie perch populations and show that combining two genetic sources of migrants during population restoration resulted in a doubling of nucleotide diversity compared to either source. Genetic diversity estimates using our pipeline are comparable across studies, data sets and species, and suitable for evaluating the rate of global biodiversity change.