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...

Biochemical and evolutionary interactions between mitochondrial and nuclear genomes (‘mitonuclear interactions’) are proposed to underpin fundamental aspects of biology including evolution of sexual reproduction, adaptation and speciation. We investigated the role of pre‐mating isolation in maintaining functional mitonuclear interactions in wild populations bearing diverged, putatively co‐adapted mitonuclear genotypes. Two lin...

Restoring levels of genetic diversity in small and declining populations is increasingly being considered in biodiversity conservation. Evidence-based genetic management requires assessment of risks and benefits of crossing populations. Because risks are challenging to assess experimentally, e.g. through multi-generational crosses, decision-support approaches utilize proxy risk factors such as time since separation of lineages...

Characterizing inbreeding depression in wildlife populations can be critical to their conservation. Coefficients of individual inbreeding can be estimated from genome‐wide marker data. The degree to which sensitivity of inbreeding coefficients to population genetic substructure alters estimates of inbreeding depression in wild populations is not well understood. Using generalized linear models, we tested the power of two frequ...

Diversifying selection between populations that inhabit different environments can promote lineage divergence within species and ultimately drive speciation. The mitochondrial genome (mitogenome) encodes essential proteins of the oxidative phosphorylation (OXPHOS) system and can be a strong target for climate‐driven selection (i.e., associated with inhabiting different climates). We investigated whether Pleistocene climate cha...

Adaptive differences across species’ ranges can have important implications for population persistence and conservation management decisions. Despite advances in genomic technologies, detecting adaptive variation in natural populations remains challenging. Key challenges in gene–environment association studies involve distinguishing the effects of drift from those of selection and identifying subtle signatures of polygenic ada...

Differential introgression of mitochondrial vs. nuclear DNA generates discordant patterns of geographic variation and can promote population divergence and speciation. We examined a potential case of mitochondrial introgression leading to two perpendicular axes of differentiation. The Eastern Yellow Robin Eopsaltria australis , a widespread Australian bird, shows a deep mitochondrial split that is perpendicular to north–south...

Aim Rump plumage coloration of the Eastern Yellow Robin ( Eopsaltria australis ), a widespread Australian songbird, varies from bright yellow in the tropical north to olive‐green in the temperate south. Here, we test whether colour variation: (1) correlates most strongly with neutral genetic variation and so is best explained by historical processes, (2) reflects selection associated with different visual environments (dense v...

Genetic diversity is positively linked to the viability and evolutionary potential of species but is often compromised in threatened taxa. Genetic rescue by gene flow from a more diverse or differentiated source population of the same species can be an effective strategy for alleviating inbreeding depression and boosting evolutionary potential. The helmeted honeyeater Lichenostomus melanops cassidix is a critically endangered...

Diversifying selection on metabolic pathways can reduce intraspecific gene flow and promote population divergence. An opportunity to explore this arises from mitonuclear discordance observed in an Australian bird E opsaltria australis . Across >1500 km, nuclear differentiation is low and latitudinally structured by isolation by distance, whereas two highly divergent, parapatric mitochondrial lineages (>6.6% in ND 2) show a dis...

Loss of functional connectivity following habitat loss and fragmentation could drive species declines. A comprehensive understanding of fragmentation effects on functional connectivity of an ecological assemblage requires investigation of multiple species with different mobilities, at different spatial scales, for each sex, and in different landscapes. Based on published data on mobility and ecological responses to fragmentati...

Refugia have been suggested as priority sites for conservation under climate change because of their ability to facilitate survival of biota under adverse conditions. Here, we review the likely role of refugial habitats in conserving freshwater biota in arid Australian aquatic systems where the major long‐term climatic influence has been aridification. We introduce a conceptual model that characterizes evolutionary refugia and...

Understanding the processes leading to population declines in fragmented landscapes is essential for successful conservation management. However, isolating the influence of disparate processes, and dispersal in particular, is challenging. The Grey Shrike‐thrush, Colluricincla harmonica , is a sedentary woodland‐dependent songbird, with learned vocalizations whose incidence in suitable habitat patches falls disproportionally wi...

Comparative phylogeographic studies of animals with low mobility and/or high habitat specificity remain rare, yet such organisms may hold fine‐grained palaeoecological signal. Comparisons of multiple, codistributed species can elucidate major historical events. As part of a multitaxon programme, mitochondrial cytochrome oxidase I (COI) variation was analysed in two species of terrestrial flatworm, Artioposthia lucasi and Caeno...