Data from: 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 multi-faceted 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. 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 develop the pipeline JeDi (https://github.com/drobledoruiz/JeDi) for
estimating unbiased individual heterozygosity, population nucleotide
diversity,y 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 doubling of nucleotide
diversity compared to either source. Genetic diversity estimates using our
pipeline are comparable across studies, datasets and species, and suitable
for evaluating the rate of global biodiversity change.