Author: Emily Booth
Booth, Emily, 2025 Genomic vulnerability of Murray–Darling Basin fishes to climate change, Flinders University, College of Science and Engineering
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Predicting how species may respond to climate change is a pressing topic in conservation and evolutionary biology. This requires developing an understanding of which intrinsic traits might benefit or disadvantage a species facing novel environments, as well as cataloguing variation in climate change vulnerability among intraspecific populations. Evolutionary adaptation is one of the main processes that allows populations to cope with climate change. The potential for a population to respond through evolutionary adaptation is determined largely by its standing genetic variation, but also by local adaptation, population size and connectivity to other populations. Genomic vulnerability is an increasingly popular metric that describes the amount of genomic change a population will require to maintain contemporary genotype-environment associations under projected climates. It can be used to determine which populations across a species’ range are more likely to be resilient under climate change, and conversely, where management interventions such as assisted gene flow might be necessary. The Murray–Darling Basin (MDB) is one of Australia’s most valuable, yet highly threatened ecosystems. In this region, habitat fragmentation and altered flow regimes are already interacting with climate change to produce negative impacts on its aquatic biodiversity. The MDB shows a steep spatial hydroclimatic gradient, which is hypothesised to drive adaptive divergence among populations and produce intraspecific variability in genomic vulnerability. This thesis aims to investigate spatial variation in population structure, genetic diversity, and genomic vulnerability to climate change for three iconic freshwater fishes native to the MDB: the golden perch (Macquaria ambigua), the Murray cod (Maccullochella peelii) and the southern pygmy perch (Nannoperca australis). These species encompass a range of life history (migratory vs. non-migratory), ecological (generalist vs. specialist), and demographic (abundant populations with basin wide gene flow vs. small and fragmented populations) characteristics. This is one of the first studies to examine genomic vulnerability within and among codistributed species. For the genomic analyses, I compiled an extensive single nucleotide polymorphism (SNP) data set covering populations across the distribution of each species in the MDB. Golden perch are a large-bodied and highly mobile species, for which we confirmed range-wide gene flow yet detected signs of adaptive divergence among populations inhabiting climatically varied regions. For this species, genomic vulnerability was highest at the warm range edges, however, a population with arid-adapted diversity showed lower genomic vulnerability. Murray cod are known to exhibit stronger site fidelity than golden perch, and we observed moderate population structure along with spatially variable genomic vulnerability. Notably, we found that these patterns show both concordance and discordance with habitat suitability changes as inferred through ecological niche models. The small-bodied southern pygmy perch, which typically inhabits smaller streams and wetlands, exhibited high levels of population structure and isolation. Genomic vulnerability was greatest in small and isolated upland populations, whereas the more genetically diverse lowland populations appeared less vulnerable. We also found that a formerly extinct population in the Lower Lakes of the MDB has maintained evolutionary potential throughout a captive breeding and reintroduction program. Overall, this thesis contributes to our understanding of how spatial environmental variation and species-specific differences in ecology and population demography influence vulnerability to climate change. These results have direct implications for the management of MDB fishes and provide novel insights for the conservation of freshwater species elsewhere in the world.
Keywords: Murray–Darling Basin, climate change, population genomics, ecological genomics, conservation management, genomic vulnerability, freshwater fish
Subject: Environmental Science thesis
Thesis type: Doctor of Philosophy
Completed: 2025
School: College of Science and Engineering
Supervisor: Luciano Beheregaray