Population persistence and evolutionary potential in the management of threatened wildlife

Genetic diversity is vital for the persistence and evolutionary potential of populations, but is often compromised in taxa of conservation concern. Although promoting evolutionarily resilient species is increasingly recognised as a conservation necessity, evolutionary processes are still often neglected in management strategies. Effective management strategies to promote persistence under environmental change will benefit from knowledge about the effects of environment on genetic diversity and on the neutral and adaptive processes that shape genetic diversity in natural systems. The core theme of this thesis is the application of genetics and evolutionary biology to the management of wildlife populations affected by human-driven environmental change. My thesis addresses five key general and system-specific knowledge gaps: 1) estimating evolutionary potential from genetic data in natural populations; 2) effects of environment on gene flow across landscapes; 3) effectiveness of human-assisted gene flow in conservation management; 4) effects of environment on intra-specific genetic variation across landscapes; and 5) effects of environment on adaptive processes across landscapes. To address these knowledge gaps I apply genetic approaches to several management case studies of threatened Australian passerine bird and freshwater fish species to explore the effects of environment on genetic diversity and on the neutral and adaptive processes that shape genetic diversity. In addressing key knowledge gaps, I: 1) reviewed the strengths and limitations of genomics as a tool for characterising evolutionary potential and argue that for most typical conservation scenarios, genome-wide variation represents a generalised measure of evolutionary potential that is robust to uncertainties surrounding the genetic basis of adaptation; 2) highlighted the complexities of species’ responses to habitat fragmentation, finding evidence of species- and sex- specific effects of fragmentation on genetic connectivity in natural populations of three honeyeater species; 3) used population viability analysis to demonstrate introduction of gene flow from a neighbouring closely related subspecies as a viable conservation strategy for boosting genetic diversity, reducing inbreeding and promoting population growth in a critically endangered subspecies, the helmeted honeyeater; 4) demonstrated a modelling approach that can identify environmental factors associated with range-wide intra-specific genetic variation and applied this approach to range-wide genetic data for a socially, culturally and economically important freshwater fish species, the Murray cod; and 5) detected potentially functionally relevant fixed amino acid differences between the mitochondrial genomes of inland and coastal species of Maccullochella cod, potentially as a result of adaptation to different climate and thermal regimes. Results presented in this thesis provide support for stronger integration of genetics and evolutionary processes in conservation. Effective conservation strategies that promote population persistence will be those that are informed by both broad and taxon-specific knowledge of the effects of environment on genetic diversity and on the neutral and adaptive processes that shape genetic diversity in natural systems. While challenges concerning the genetic basis of adaptation remain, the measurement of genome-wide variation has great scope for generating new insights into adaptive processes occurring across landscapes in natural populations.

Awards: Winner of the Mollie Holman Doctoral Medal for Excellence, Faculty of Science, 2016.