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Through using different sources, population reintroductions can create genetically diverse populations at low risk of harmful inbreeding and well equipped for adaptation to future environments. Genetic variation from one source can mask locally nonoptimal alleles from another, thereby enhancing adaptive potential and population persistence. We assessed the outcomes in survival, growth and reproduction of using two differentiated sources (genetically diverse Yarra and moderately diverse Dartmouth) for translocations and stocking to reintroduce the endangered Australian freshwater Macquarie perch Macquaria australasica into the Ovens River. For stocking, same- and different-population parents ("cross-types") were used during hatchery production. Genetic samples and data on individual fish were collected over three years of monitoring the Ovens. We genetically assigned Ovens fish to their broodstock parents and tested whether cross-type and genetic dissimilarity between parents are associated with offspring survival, and whether cross-type and parental dissimilarity or individual genetic diversity are associated with somatic growth rates of stocked fish. We genetically identified translocated fish and assessed local recruit ancestry. Of 296 Ovens fish, 31.1% were inferred to be stocked, 1.3% translocated and 67.6% locally born. Cross-type strongly predicted survival of stocked offspring: those with two Yarra parents had the highest survival, followed by offspring with two-population, then Dartmouth, ancestry. Of the Ovens recruits, 59.5% had Yarra, 33.5% two-population and 7.0% Dartmouth ancestry, despite 67% of stocked and 98% of translocated fish originating from Dartmouth. Offspring with two Yarra parents grew faster than offspring of Dartmouth or two-population ancestry. Although Dartmouth fish appear to be less fit in the Ovens compared to Yarra fish, possibly due to deleterious variation or genetic or plastic maladaptation, they contribute to the reintroduced pop

Understanding how environmental change has shaped species evolution can inform predictions of how future climate change might continue to do so. Research of widespread biological systems spanning multiple climates that have been subject to environmental change can yield generalizable inferences about the neutral and adaptive processes driving lineage divergence during periods of environmental change. We contribute to the growing body of multi-locus phylogeographic studies investigating the effect of Pleistocene climate change on species evolution by focusing on a widespread Australo-Papuan songbird with several mitochondrial lineages that diverged during the Pleistocene, the grey shrike-thrush (Colluricincla harmonica). We employed multi-locus phylogenetic, population genetic and coalescent analyses to (1) assess whether nuclear genetic diversity suggests a history congruent with that based on phenotypically defined subspecies ranges, mitochondrial clade boundaries and putative biogeographical barriers, (2) estimate genetic diversity within and genetic differentiation and gene flow among regional populations and (3) estimate population divergence times. The five currently recognized subspecies of grey shrike-thrush are genetically differentiated in nuclear and mitochondrial genomes, but connected by low levels of gene flow. Divergences among these populations are concordant with recognized historical biogeographical barriers and date to the Pleistocene. Discordance in the order of population divergence events based on mitochondrial and nuclear genomes suggests a history of sex-biased gene flow and/or mitochondrial introgression at secondary contacts. This study demonstrates that climate change can impact sexes with different dispersal biology in different ways. Incongruence between population and mitochondrial trees calls for a genome-wide investigation into dispersal, mitochondrial introgression and mitonuclear evolution.

Millions of dollars are spent on wildlife crossing structures intended to reduce the barrier effects of roads on wildlife. However, we know little about the degree to which these structures facilitate dispersal and gene flow. Our study incorporates two elements that are rarely used in the evaluation of wildlife crossing structures: an experimental design including a before and after comparison, and the use of genetic techniques to demonstrate effects on gene flow at both population and individual levels. We evaluated the effect of wildlife crossing structures (canopy bridges and glider poles) on a gliding mammal, the squirrel glider (Petaurus norfolcensis). We genotyped 399 individuals at eight microsatellite markers to analyse population structure, first‐generation migrants and parentage relationships. We found that the freeway was not a complete genetic barrier, with a strong effect evident at only one site. We hypothesise that the presence of corridors alongside the freeway and throughout the surrounding landscape facilitated circuitous detours for squirrel gliders. Installing a crossing structure at the location with a strong barrier effect restored gene flow within just 5 years of mitigation. Synthesis and applications. Our study highlights the importance of using genetic techniques not just to evaluate the success of road‐crossing structures for wildlife, but also to guide their placement within the landscape. Managers wishing to reduce the effects of linear infrastructure on squirrel gliders and other arboreal mammals should aim to preserve and enhance vegetation along roadsides and within centre medians, as well as mitigate large gaps by implementing wildlife crossing structures.

One of the most iconic Australian fish is the Murray cod, Maccullochella peelii (Mitchell 1838), a freshwater species that can grow to ∼1.8 metres in length and live to age ≥48 years. The Murray cod is of a conservation concern as a result of strong population contractions, but it is also popular for recreational fishing and is of growing aquaculture interest. In this study, we report the whole genome sequence of the Murray cod to support ongoing population genetics, conservation, and management research, as well as to better understand the evolutionary ecology and history of the species. A draft Murray cod genome of 633 Mbp (N50 = 109 974bp; BUSCO and CEGMA completeness of 94.2% and 91.9%, respectively) with an estimated 148 Mbp of putative repetitive sequences was assembled from the combined sequencing data of 2 fish individuals with an identical maternal lineage; 47.2 Gb of Illumina HiSeq data and 804 Mb of Nanopore data were generated from the first individual while 23.2 Gb of Illumina MiSeq data were generated from the second individual. The inclusion of Nanopore reads for scaffolding followed by subsequent gap-closing using Illumina data led to a 29% reduction in the number of scaffolds and a 55% and 54% increase in the scaffold and contig N50, respectively. We also report the first transcriptome of Murray cod that was subsequently used to annotate the Murray cod genome, leading to the identification of 26 539 protein-coding genes. We present the whole genome of the Murray cod and anticipate this will be a catalyst for a range of genetic, genomic, and phylogenetic studies of the Murray cod and more generally other fish species of the Percichthydae family.

Genetic rescue is an under‐utilised conservation strategy used to boost the genetic diversity and/or fitness of small, isolated populations through the introduction of novel genes. Effective implementation of genetic rescue requires an understanding of the evolutionary history and genetic distinctiveness of populations. The Eltham copper butterfly (ECB) is an endangered subspecies that exists as small, isolated populations across four disjunct regions in Victoria, Australia. Mitochondrial and nuclear sequence data were used to assess the genetic distinctiveness of ECB from its nearest relative: the fiery dull copper butterfly (FDC), explore the evolutionary history and population structure of ECB across its contemporary distribution, and assess the scope for genetic rescue of the most‐threatened ECB population in Eltham‐Greensborough. Findings support the current status of ECB and FDC as distinct evolutionary units, which should continue to be managed separately given current knowledge. Modest population genetic structure across the range of ECB was detected. However, low levels of historical gene flow and shared haplotypes between Eltham‐Greensborough and the northern regions suggest relatively recent divergence. Given relatively recent divergence, low population numbers and low genetic diversity, the population located in the Eltham‐Greensborough region is a strong candidate for genetic rescue. Using established criteria, explicit recommendations are made for the implementation of genetic rescue via translocations. Genetic rescue, together with ongoing habitat management, should improve genetic diversity, fitness and persistence of the ECB in the region most threatened by urban disturbance. Any risks associated with genetic rescue in conservation should be weighed against extinction risk as a result of inaction.

Genetic diversity underpins the ability of populations to persist and adapt to environmental changes. Substantial empirical data show that genetic diversity rapidly deteriorates in small and isolated populations due to genetic drift, leading to reduction in adaptive potential and fitness and increase in inbreeding. Assisted gene flow (e.g. via translocations) can reverse these trends, but lack of data on fitness loss and fear of impairing population "uniqueness" often prevents managers from acting. Here, we use population genetic and riverscape genetic analyses and simulations to explore the consequences of extensive habitat loss and fragmentation on population genetic diversity and future population trajectories of an endangered Australian freshwater fish, Macquarie perch Macquaria australasica. Using guidelines to assess the risk of outbreeding depression under admixture, we develop recommendations for population management, identify populations requiring genetic rescue and/or genetic restoration and potential donor sources. We found that most remaining populations of Macquarie perch have low genetic diversity, and effective population sizes below the threshold required to retain adaptive potential. Our simulations showed that under management inaction, smaller populations of Macquarie perch will face inbreeding depression within a few decades, but regular small-scale translocations will rapidly rescue populations from inbreeding depression and increase adaptive potential through genetic restoration. Despite the lack of data on fitness loss, based on our genetic data for Macquarie perch populations, simulations and empirical results from other systems, we recommend regular and frequent translocations among remnant populations within catchments. These translocations will emulate the effect of historical gene flow and improve population persistence through decrease in demographic and genetic stochasticity. Increasing population genetic connectivity within each catch

Invasive organisms can have major impacts on the environment. Some invasive organisms are parthenogenetic in their invasive range and, therefore, exist as a number of asexual lineages (=clones). Determining the reproductive mode of invasive species has important implications for understanding the evolutionary genetics of such species, more especially, for management-relevant traits. The willow sawfly Nematus oligospilus Förster (Hymenoptera: Tenthredinidae) has been introduced unintentionally into several countries in the Southern Hemisphere where it has subsequently become invasive. To assess the population expansion, reproductive mode and host-plant relationships of this insect, microsatellite markers were developed and applied to natural populations sampled from the native and expanded range, along with sequencing of the cytochrome-oxidase I mitochondrial DNA (mtDNA) region. Other tenthredinids across a spectrum of taxonomic similarity to N. oligospilus and having a range of life strategies were also tested. Strict parthenogenesis was apparent within invasive N. oligospilus populations throughout the Southern Hemisphere, which comprised only a small number of genotypes. Sequences of mtDNA were identical for all individuals tested in the invasive range. The microsatellite markers were used successfully in several sawfly species, especially Nematus spp. and other genera of the Nematini tribe, with the degree of success inversely related to genetic divergence as estimated from COI sequences. The confirmation of parthenogenetic reproduction in N. oligospilus and the fact that it has a very limited pool of genotypes have important implications for understanding and managing this species and its biology, including in terms of phenotypic diversity, host relationships, implications for spread and future adaptive change. It would appear to be an excellent model study system for understanding evolution of invasive parthenogens that diverge without sexual reproduction and g

Major prehistoric forces, such as the climatic shifts of the Pleistocene, can remain visible in a species' population genetics. Inference of refuges via genetic tools is useful for conservation management as it can identify populations whose preservation may help retain a species' adaptive potential. Such investigation is needed for Australia's southern hairy-nosed wombat (Lasiorhinus latifrons), whose conservation status has recently deteriorated, and whose phylogeographic history during the Pleistocene may be atypical compared to other species. Its contemporary range spans approximately 2000 km of diverse habitat on either side of the Spencer Gulf, which was a land bridge during periods of Pleistocene aridity that may have allowed for migration circumventing the arid Eyrean barrier. We sampled from animals in nearly all known sites within the species' current distribution, mainly using non-invasive methods, and employed nuclear and mitochondrial DNA analyses to assess alternative scenarios for Pleistocene impacts on population structure. We found evidence for mildly differentiated populations at the range extremes on either side of Spencer Gulf, with secondary contact between locations neighbouring each side of the barrier. These extreme western and eastern regions, and four other regions in between, were genetically distinct in genotypic clustering analyses. Estimates indicate modest, but complex gene flow patterns among some of these regions, in some cases possibly restricted for several thousand years. Prior to this study there was little information to aid risk assessment and prioritization of conservation interventions facilitating gene flow among populations of this species. The contributions of this study to that issue are outlined.

Major prehistoric forces, such as the climatic shifts of the Pleistocene, can remain visible in a species' population genetics. Inference of refuges via genetic tools is useful for conservation management as it can identify populations whose preservation may help retain a species' adaptive potential. Such investigation is needed for Australia's southern hairy-nosed wombat (Lasiorhinus latifrons), whose conservation status has recently deteriorated, and whose phylogeographic history during the Pleistocene may be atypical compared to other species. Its contemporary range spans approximately 2000 km of diverse habitat on either side of the Spencer Gulf, which was a land bridge during periods of Pleistocene aridity that may have allowed for migration circumventing the arid Eyrean barrier. We sampled from animals in nearly all known sites within the species' current distribution, mainly using non-invasive methods, and employed nuclear and mitochondrial DNA analyses to assess alternative scenarios for Pleistocene impacts on population structure. We found evidence for mildly differentiated populations at the range extremes on either side of Spencer Gulf, with secondary contact between locations neighbouring each side of the barrier. These extreme western and eastern regions, and four other regions in between, were genetically distinct in genotypic clustering analyses. Estimates indicate modest, but complex gene flow patterns among some of these regions, in some cases possibly restricted for several thousand years. Prior to this study there was little information to aid risk assessment and prioritization of conservation interventions facilitating gene flow among populations of this species. The contributions of this study to that issue are outlined.

Climatic differences across a taxon's range may be associated with specific bioenergetic demands and may result in genetics-based metabolic adaptation, particularly in aquatic ectothermic organisms that rely on heat exchange with the environment to regulate key physiological processes. Extending down the east coast of Australia, the Great Dividing Range (GDR) has a strong influence on climate and the evolutionary history of freshwater fish species. Despite the GDR acting as a strong contemporary barrier to fish movement, many species, and species with shared ancestries, are found on both sides of the GDR, indicative of historical dispersal events. We sequenced complete mitogenomes from the four extant species of the freshwater cod genus Maccullochella, two of which occur on the semi-arid, inland side of the GDR, and two on the mesic coastal side. We constructed a dated phylogeny and explored the relative influences of purifying and positive selection in the evolution of mitogenome divergence among species. Results supported mid- to late-Pleistocene divergence of Maccullochella across the GDR (220-710 thousand years ago), bringing forward previously reported dates. Against a background of pervasive purifying selection, we detected potentially functionally relevant fixed amino acid differences across the GDR. Although many amino acid differences between inland and coastal species may have become fixed under relaxed purifying selection in coastal environments rather than positive selection, there was evidence of episodic positive selection acting on specific codons in the Mary River coastal lineage, which has consistently experienced the warmest and least extreme climate in the genus.

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 subspecies of the common yellow-tufted honeyeater. Cassidix has declined to a single wild population of ~130 birds, despite being subject to intensive population management over recent decades. We assessed changes in microsatellite diversity in cassidix over the last four decades and used population viability analysis to explore whether genetic rescue through hybridization with the neighbouring Lichenostomus melanops gippslandicus subspecies constitutes a viable conservation strategy. The contemporary cassidix population is characterized by low genetic diversity and effective population size (N(e) < 50), suggesting it is vulnerable to inbreeding depression and will have limited capacity to evolve to changing environments. We find that gene flow from gippslandicus to cassidix has declined substantially relative to pre-1990 levels and argue that natural levels of gene flow between the two subspecies should be restored. Allowing gene flow (~4 migrants per generation) from gippslandicus into cassidix (i.e. genetic rescue), in combination with continued annual release of captive-bred cassidix (i.e. demographic rescue), should lead to positive demographic and genetic outcomes. Although we consider the risk of outbreeding depression to be low, we recommend that genetic rescue be managed within the context of the captive breeding programme, with monitoring of outcomes.

Clonality is a common characteristic of successful invasive species, but general principles underpinning the success of clonal invaders are not established. A number of mechanisms could contribute to invasion success including clones with broad tolerances and preferences, specialist clones and adaptation in situ. The majority of studies to date have been of plants and some invertebrate parthenogens, particularly aphids, and have not necessarily caught invasion at very early stages. Here we describe the early stages of an invasion by a Northern Hemisphere Hymenopteran model in three different land masses in the Southern Hemisphere. Nematus oligospilus Förster (Hymenoptera: Tenthredinidae), a sawfly feeding on willows (Salix spp.), was recently introduced to the Southern Hemisphere where it has become invasive and is strictly parthenogenetic. In this study, the number of N. oligospilus clones, their distribution in the landscape and on different willow hosts in South Africa, New Zealand and Australia were assessed using 25 microsatellite markers. Evidence is presented for the presence of two very common and widespread multilocus genotypes (MLGs) or 'superclones' dominating in the three countries. Rarer MLGs were closely related to the most widespread superclone; it is plausible that all N. oligospilus individuals were derived from a single clone. A few initial introductions to Australia and New Zealand seemed to have occurred. Our results point towards a separate introduction in Western Australia, potentially from South Africa. Rarer clones that were dominant locally putatively arose in situ, and might be locally favoured, or simply have not yet had time to spread. Data presented represent rare baseline data early in the invasion process for insights into the mechanisms that underlie the success of a global invader, and develop Nematus oligospilus as a valuable model to understand invasion genetics of clonal pests.

Widespread species often show geographic variation in thermally-sensitive traits, providing insight into how species respond to shifts in temperature through time. Such patterns may arise from phenotypic plasticity, genetic adaptation, or their interaction. In some cases, the effects of genotype and temperature may act together to reduce, or to exacerbate, phenotypic variation in fitness-related traits across varying thermal environments. We find evidence for such interactions in life-history traits of Heteronympha merope, a butterfly distributed across a broad latitudinal gradient in south-eastern Australia. We show that body size in this butterfly is negatively related to developmental temperature in the laboratory, in accordance with the temperature-size rule, but not in the field, despite very strong temperature gradients. A common garden experiment on larval thermal responses, spanning the environmental extremes of H. merope's distribution, revealed that butterflies from low latitude (warmer climate) populations have relatively fast intrinsic growth and development rates compared to those from cooler climates. These synergistic effects of genotype and temperature across the landscape (co-gradient variation) are likely to accentuate phenotypic variation in these traits, and this interaction must be accounted for when predicting how H. merope will respond to temperature change through time. These results highlight the importance of understanding how variation in life-history traits may arise in response to environmental change. Without this knowledge, we may fail to detect whether organisms are tracking environmental change, and if they are, whether it is by plasticity, adaptation or both.