Genomic vulnerability to climate change of a poorly dispersing and threatened fish, the southern pygmy perch ( Nannoperca australis )

Abstract

Small and isolated populations often have low levels of standing genetic variation, which limits their capacity to evolutionarily adapt to climate change. In freshwater ecosystems, habitat fragmentation caused by instream barriers and water regulation is a prominent global issue impacting on connectivity among populations. We investigated genomic vulnerability to climate change in a small-bodied and poorly dispersing species, the southern pygmy perch, in Australia’s Murray–Darling Basin (MDB). We used a genome-wide dataset for 467 individuals from 30 sites covering the range of the species in the MDB. This included temporal sampling of a population in the Lower Lakes region, prior to its extirpation during the Millennium Drought and after its re-establishment through a captive breeding and reintroduction program. Southern pygmy perch exhibited high levels of population structure, with 11 distinct genetic clusters mainly delineated by river catchments. Genetic diversity was low, especially in small and isolated headwater populations. Genomic vulnerability, assessed via a genomic offset approach, correlated positively with elevation, being generally higher in upland and lower in lowland populations. We suggest that elevation could potentially serve as a proxy for climate change vulnerability in dendritic freshwater systems, particularly for species with limited dispersal capacity. The signal of low genomic vulnerability for the Lower Lakes population was consistent both before and after ex situ captive breeding and reintroduction. This highlights the importance of downstream populations as sinks of diversity. It also shows that integrating genetic management into captive breeding programs can help maintain climatic adaptive potential in threatened populations.