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Collaborative approaches to conservation management are critical to respond to the ongoing biodiversity crisis. However, local community involvement in many conservation actions is lacking, especially within translocation and reintroduction programs. Similarly, rapid integration of genetic information into collaborative programs with local communities is rarely conducted. Here, we describe a community‐based and collaborative reintroduction program for a threatened Australian freshwater fish, the southern pygmy perch (Nannoperca australis). We integrate on‐the‐ground translocation efforts by volunteers from local communities, captive breeding by a private aquarium business, and genetic analyses done by a research institution to provide a holistic framework for the reintroduction of southern pygmy perch. We evaluated genetic diversity, population structure, relatedness, and inbreeding across the duration of the reintroduction program using data from neutral and adaptive genomic markers. This allowed us to assess the ability of such a program to minimize inbreeding and retain genomic variation, and to promote adaptive potential of the reintroduced population. While genetic variation for the source populations was very low, we found no decrease in genetic diversity or increase in inbreeding across the program. These genetic findings support the efforts made by local communities and will further inform future reintroductions as part of a collaborative conservation framework. We expand on our empirical case study by describing a theoretical framework for integrating conservation genomics research with community‐led conservation management programs and identifying the benefits of such a collaboration. Our study highlights the importance of multifaceted and integrated conservation management approaches to effectively protect and manage threatened species. [ABSTRACT FROM AUTHOR]

The translocation of species outside their natural range is a threat to aquatic biodiversity globally, especially freshwater fishes, as most are not only susceptible to predation and competition but readily hybridize with congeners.Running River rainbowfish (RRR, Melanotaenia sp.) is a narrow‐ranged, small‐bodied freshwater fish that recently became threatened and was subsequently listed as Critically Endangered, owing to introgressive hybridization and competition following the translocation of a congeneric species, the eastern rainbowfish (Melanotaenia splendida).To conserve RRR, wild fish were taken into captivity, genetically confirmed as pure representatives, and successfully bred. As the threat of introgression with translocated eastern rainbowfish could not be mitigated, a plan was devised to translocate captive raised RRR into unoccupied habitats within their native catchment, upstream of natural barriers. The translocation plan involved careful site selection and habitat assessment, predator training (exposure to predators prior to release), soft release (with a gradual transition from captivity to nature), and post‐release monitoring, and this approach was ultimately successful.Two populations of RRR were established in two previously unoccupied streams above waterfalls with a combined stream length of 18 km. Post‐release monitoring was affected by floods and low sample sizes, but suggested that predation and time of release are important factors to consider in similar conservation recovery programmes for small‐bodied, short‐lived fishes. [ABSTRACT FROM AUTHOR]

Climatic changes have caused major environmental restructuring throughout the world's oceans. Marine organisms have responded to novel conditions through various biological systems, including genomic adaptation. Growing accessibility of next-generation DNA sequencing methods to study nonmodel species has recently allowed genomic changes underlying environmental adaptations to be investigated. This study used double-digest restriction-site associated DNA (ddRAD) sequence data to investigate the genomic basis of ecotype formation across currently recognized species and subspecies of bottlenose dolphins (genus Tursiops) in the Southern Hemisphere. Subspecies-level genomic divergence was confirmed between the offshore common bottlenose dolphin (T. truncatus truncatus) and the inshore Lahille's bottlenose dolphin (T. t. gephyreus) from the southwestern Atlantic Ocean (SWAO). Similarly, subspecies-level divergence is suggested between inshore (eastern Australia) Indo-Pacific bottlenose dolphin (T. aduncus) and the proposed Burrunan dolphin (T. australis) from southern Australia. Inshore bottlenose dolphin lineages generally had lower genomic diversity than offshore lineages, a pattern particularly evident for T. t. gephyreus , which showed exceptionally low diversity. Genomic regions associated with cardiovascular, musculoskeletal, and energy production systems appear to have undergone repeated adaptive evolution in inshore lineages across the Southern Hemisphere. We hypothesize that comparable selective pressures in the inshore environment drove similar adaptive responses in each lineage, supporting parallel evolution of inshore bottlenose dolphins. With climate change altering marine ecosystems worldwide, it is crucial to gain an understanding of the adaptive capacity of local species and populations. Our study provides insights into key adaptive pathways that may be important for the long-term survival of cetaceans and other organisms in a changing marine environment. [ABSTRACT FROM AUTHOR]

Aim: Major knowledge gaps exist regarding the evolution of arid zone organisms. For freshwater species with high dispersal potential, little is known if historical aridification influenced connectivity across drainage divides and impacted on their divergence and diversification. We tested the hypothesis that the historical aridification of Australia promoted the isolation and influenced the demographic histories and evolutionary divergence of a migratory group of freshwater obligates. Location: Central and eastern Australia; Murray–Darling Basin (MDB), Lake Eyre Basin (LEB), Fitzroy Basin (FIT). Taxon Three lineages of golden perch (Macquaria ambigua), a widespread fishery resource from inland Australia. Methods: We obtained genome‐wide data for golden perch sampled throughout their range. Phylogenetic relationships were reconstructed using maximum likelihood. Species distribution modelling was used to predict contemporary and past distributions for the three lineages and to develop hypotheses regarding their biogeographic and demographic histories. Hypotheses were independently tested using coalescent simulations in fastsimcoal and DIYABC with the genomic dataset. Results: We found evidence for three reciprocally monophyletic lineages that have experienced little to nil genetic connectivity since divergence. Coalescent models suggest that the coastal (FIT) and inland (MDB and LEB) lineages diverged ~103 thousand years ago (ka), followed by the split of MDB and LEB lineages ~58 ka. These timings agree with reductions of large freshwater environments in Australia during the late Pleistocene. Species distribution models show an extreme decrease in habitat during the Last Glacial Maximum ~21 ka, consistent with inferred demographic contractions in coalescent tests. Main conclusions We reveal that aridification of Australia during the late Pleistocene has driven and reinforced the divergence of a migratory freshwater obligate. Our findings are important for informing the conservation management of aquatic organisms under climate change. This work further demonstrates the value of using species distribution modelling to formulate diversification hypotheses and to improve interpretation of coalescent analyses. [ABSTRACT FROM AUTHOR]

Heterogeneous seascapes and strong environmental gradients in coastal waters are expected to influence adaptive divergence, particularly in species with large population sizes where selection is expected to be highly efficient. However, these influences might also extend to species characterized by strong social structure, natal philopatry and small home ranges. We implemented a seascape genomic study to test this hypothesis in Indo‐Pacific bottlenose dolphins (Tursiops aduncus) distributed along the environmentally heterogeneous coast of southern Australia. The data sets included oceanographic and environmental variables thought to be good predictors of local adaptation in dolphins and 8081 filtered single nucleotide polymorphisms (SNPs) genotyped for individuals sampled from seven different bioregions. From a neutral perspective, population structure and connectivity of the dolphins were generally influenced by habitat type and social structuring. Genotype‐environment association analysis identified 241 candidate adaptive loci and revealed that sea surface temperature and salinity gradients influenced adaptive divergence in these animals at both large‐ (1000 km) and fine‐scales (<100 km). Enrichment analysis and annotation of candidate genes revealed functions related to sodium‐activated ion transport, kidney development, adipogenesis and thermogenesis. The findings of spatial adaptive divergence and inferences of putative physiological adaptations challenge previous suggestions that marine megafauna is most likely to be affected by environmental and climatic changes via indirect, trophic effects. Our work contributes to conservation management of coastal bottlenose dolphins subjected to anthropogenic disturbance and to efforts of clarifying how seascape heterogeneity influences adaptive diversity and evolution in small cetaceans. [ABSTRACT FROM AUTHOR]

Hatchery production and fisheries stocking is a widespread and high profile management practice because it allows recreational fisheries to continue in threatened species. Human-mediated transfer of fish across the geographic boundaries of intraspecies lineages or closely related species can cause introgression and occasionally outbreeding depression. Hybridization can be difficult to detect due to limited morphological differences among close lineages and the relatively low power of traditional genetic datasets. Here we showcase the use of genomic techniques to detect admixture of the economically important and threatened golden perch (Macquaria ambigua) in the Murray-Darling Basin, southeast Australia. We detected admixture through a genome-wide dataset of 6,862 single nucleotide polymorphisms (SNPs) across 174 Murray-Darling sourced fish and 15 fish from each of two neighbouring basins: the Lake Eyre and Fitzroy basins. Individuals with partial ancestry from both neighboring basins were detected using genomics throughout the Murray-Darling, suggesting the release of individuals and introgression into the Murray-Darling Basin. Importantly, a traditional microsatellite dataset was unreliable for identifying admixed individuals. The SNP-detected admixed individuals were also found in Murray-Darling impoundments, where fish are solely sourced from government-managed hatcheries, suggesting that some broodstock in hatcheries might have non-endemic ancestry. Stocking programs for golden perch release over one million fingerlings each year, and so could impact the genetic variation in the wild. We advocate for using genomics to check the ancestry of broodstock and for increasing collaboration between managers and academics—as done here—to better integrate the power of genomics into biodiversity management and conservation. [ABSTRACT FROM AUTHOR]

How populations of aquatic fauna persist in extreme desert environments is an enigma. Individuals often breed and disperse during favorable conditions. Theory predicts that adaptive capacity should be low in small populations, such as in desert fishes. We integrated satellite‐derived surface water data and population genomic diversity from 20,294 single‐nucleotide polymorphisms across 344 individuals to understand metapopulation persistence of the desert rainbowfish (Melanotaenia splendida tatei) in central Australia. Desert rainbowfish showed very small effective population sizes, especially at peripheral populations, and low connectivity between river catchments. Yet, there was no evidence of population‐level inbreeding and a signal of possible adaptive divergence associated with aridity was detected. Candidate genes for local adaptation included functions related to environmental cues and stressful conditions. Eco‐evolutionary modeling showed that positive selection in refugial subpopulations combined with connectivity during flood periods can enable retention of adaptive diversity. Our study suggests that adaptive variation can be maintained in small populations and integrate with neutral metapopulation processes to allow persistence in the desert. [ABSTRACT FROM AUTHOR]

Wildlife species are challenged by various infectious diseases that act as important demographic drivers of populations and have become a great conservation concern particularly under growing environmental changes. The new era of whole genome sequencing provides new opportunities and avenues to explore the role of genetic variants in the plasticity of immune responses, particularly in non‐model systems. Cetacean morbillivirus (CeMV) has emerged as a major viral threat to cetacean populations worldwide, contributing to the death of thousands of individuals of multiple dolphin and whale species. To understand the genomic basis of immune responses to CeMV, we generated and analysed whole genomes of 53 Indo‐Pacific bottlenose dolphins (Tursiops aduncus) exposed to Australia's largest known CeMV‐related mortality event that killed at least 50 dolphins from three different species. The genomic data set consisted of 10,168,981 SNPs anchored onto 23 chromosome‐length scaffolds and 77 short scaffolds. Whole genome analysis indicated that levels of inbreeding in the dolphin population did not influence the outcome of an individual. Allele frequency estimates between survivors and nonsurvivors of the outbreak revealed 15,769 candidate SNPs, of which 689 were annotated to 295 protein coding genes. These included 50 genes with functions related to innate and adaptive immune responses, and cytokine signalling pathways and genes thought to be involved in immune responses to other morbilliviruses. Our study characterised genomic regions and pathways that may contribute to CeMV immune responses in dolphins. This represents a stride towards clarifying the complex interactions of the cetacean immune system and emphasises the value of whole genome data sets in understanding genetic elements that are essential for species conservation, including disease susceptibility and adaptation. [ABSTRACT FROM AUTHOR]

While the influence of Pleistocene climatic changes on divergence and speciation has been well‐documented across the globe, complex spatial interactions between hydrology and eustatics over longer timeframes may also determine species evolutionary trajectories. Within the Australian continent, glacial cycles were not associated with changes in ice cover and instead largely resulted in fluctuations from moist to arid conditions across the landscape. We investigated the role of hydrological and coastal topographic changes brought about by Plio‐Pleistocene climatic changes on the biogeographic history of a small Australian freshwater fish, the southern pygmy perch Nannoperca australis. Using 7958 ddRAD‐seq (double digest restriction‐site associated DNA) loci and 45,104 filtered SNPs, we combined phylogenetic, coalescent and species distribution analyses to assess the various roles of aridification, sea level and tectonics and associated biogeographic changes across southeast Australia. Sea‐level changes since the Pliocene and reduction or disappearance of large waterbodies throughout the Pleistocene were determining factors in strong divergence across the clade, including the initial formation and maintenance of a cryptic species, N. 'flindersi'. Isolated climatic refugia and fragmentation due to lack of connected waterways maintained the identity and divergence of inter‐ and intraspecific lineages. Our historical findings suggest that predicted increases in aridification and sea level due to anthropogenic climate change might result in markedly different demographic impacts, both spatially and across different landscape types. [ABSTRACT FROM AUTHOR]

Explaining why some species are widespread, while others are not, is fundamental to biogeography, ecology, and evolutionary biology. A unique way to study evolutionary and ecological mechanisms that either limit species’ spread or facilitate range expansions is to conduct research on species that have restricted distributions. Nonindigenous species, particularly those that are highly invasive but have not yet spread beyond the introduced site, represent ideal systems to study range size changes. Here, we used species distribution modeling and genomic data to study the restricted range of a highly invasive Australian marine species, the ascidian Pyura praeputialis. This species is an aggressive space occupier in its introduced range (Chile), where it has fundamentally altered the coastal community. We found high genomic diversity in Chile, indicating high adaptive potential. In addition, genomic data clearly showed that a single region from Australia was the only donor of genotypes to the introduced range. We identified over 3,500 km of suitable habitat adjacent to its current introduced range that has so far not been occupied, and importantly species distribution models were only accurate when genomic data were considered. Our results suggest that a slight change in currents, or a change in shipping routes, may lead to an expansion of the species’ introduced range that will encompass a vast portion of the South American coast. Our study shows how the use of population genomics and species distribution modeling in combination can unravel mechanisms shaping range sizes and forecast future range shifts of invasive species. [ABSTRACT FROM AUTHOR]

Understanding the factors driving population structure in marine mammals is needed to evaluate the impacts of previous exploitation, current anthropogenic threats, conservation status, and success of population recovery efforts.Sperm whales are characterized by a worldwide distribution, low genetic diversity, complex patterns of social and genetic structure that differ significantly within and between ocean basins, and a long history of being commercially whaled. In Australia, sperm whales from the (International Whaling Commission assigned) southern hemisphere 'Division 5' stock were very heavily exploited by whaling.The present study assessed the potential effects of whaling on the genetic diversity of sperm whales in Australia and the population genetic structure of these whales within a global context. A combination of historical and contemporary sperm whale samples (n = 157) were analysed across six regions, from south‐eastern Australia ('Division 6' stock in the Pacific Ocean) to south‐western Australia ('Division 5' stock in the Indian Ocean).Sperm whales sampled from the 'Division 5' and 'Division 6' stocks belong to the same population based on nuclear and mitochondrial DNA (mtDNA) analyses. Four novel sperm whale mtDNA haplotypes were identified in animals from Australian waters. Levels of genetic diversity were low in Australian sperm whales but were similar to those previously reported for populations in the Indian and Pacific Oceans.Given the genetic distinctiveness of sperm whales in Australian waters from other regions in the Pacific and Indian Oceans, and the lack of recovery in population numbers, further scientific studies are needed to increase our understanding of population dynamics and the effectiveness of threat management strategies in this species. [ABSTRACT FROM AUTHOR]

Anthropogenic habitat fragmentation is often implicated as driving the current global extinction crisis, particularly in freshwater ecosystems. The genetic signal of recent population isolation can be confounded by the complex spatial arrangement of dendritic river systems. Consequently, many populations may presently be managed separately based on an incorrect assumption that they have evolved in isolation. Integrating landscape genomics data with models of connectivity that account for landscape structure, we show that the cumulative effects of multiple in‐stream barriers have contributed to the recent decline of a freshwater fish from the Murray–Darling Basin, Australia. In addition, individual‐based eco‐evolutionary simulations further demonstrate that contemporary inferences about population isolation are consistent with the 160‐year time frame since construction of in‐stream barriers began in the region. Our findings suggest that the impact of very recent fragmentation may be often underestimated for freshwater biodiversity. We argue that proactive conservation measures to reconnect many riverine populations are urgently needed. [ABSTRACT FROM AUTHOR]

1.Freshwater ecosystems worldwide harbour disproportionately high numbers of endemic species under threat from human activity, particularly accelerated habitat fragmentation. The Murray–Darling Basin in south‐eastern Australia, one of the country's largest and arguably its most vulnerable freshwater ecosystem, is inhabited by a number of small‐bodied fishes that are threatened with imminent extinction.2.Here an extensive microsatellite dataset was used, supplemented by additional allozyme and mitochondrial DNA analyses, to assess the genetic diversity, population structure and contemporary migration patterns in the Murray hardyhead Craterocephalus fluviatilis, one of Australia's most threatened fishes.3.Genetic diversity estimates, primarily based on 413 fish collected during the latter period of intense drought (1997–2010) from 23 sites and genotyped at 14 microsatellite loci, were higher than those previously detected for other regionally co‐occurring small‐bodied freshwater fishes.4.Population structure analyses identified a subtle primary split between 'lower Murray' (lower river reaches) versus 'upstream Murray' (upper river reaches) and a total of nine genetically similar sub‐populations. This includes unexpected sub‐population differentiation in the Lower Lakes, a region at the terminus of the Murray–Darling Basin that most often has inter‐connected habitat.5.Very low levels of contemporary migration were detected between most inferred populations (<2%) during the drought, with all exceptions involving moderate levels of migration from an upstream sub‐population into an adjacent downstream sub‐population.6.This article describes how these genetic data have guided translocation and reintroduction efforts in recent years. We advocate the use of assisted gene flow as a central component of continuing efforts to rescue this species from imminent extinction. [ABSTRACT FROM AUTHOR]

Infectious diseases are significant demographic and evolutionary drivers of populations, but studies about the genetic basis of disease resistance and susceptibility are scarce in wildlife populations. Cetacean morbillivirus (CeMV) is a highly contagious disease that is increasing in both geographic distribution and incidence, causing unusual mortality events (UME) and killing tens of thousands of individuals across multiple cetacean species worldwide since the late 1980s. The largest CeMV outbreak in the Southern Hemisphere reported to date occurred in Australia in 2013, where it was a major factor in a UME, killing mainly young Indo‐Pacific bottlenose dolphins (Tursiops aduncus). Using cases (nonsurvivors) and controls (putative survivors) from the most affected population, we carried out a genome‐wide association study to identify candidate genes for resistance and susceptibility to CeMV. The genomic data set consisted of 278,147,988 sequence reads and 35,493 high‐quality SNPs genotyped across 38 individuals. Association analyses found highly significant differences in allele and genotype frequencies among cases and controls at 65 SNPs, and Random Forests conservatively identified eight as candidates. Annotation of these SNPs identified five candidate genes (MAPK8, FBXW11, INADL, ANK3 and ACOX3) with functions associated with stress, pain and immune responses. Our findings provide the first insights into the genetic basis of host defence to this highly contagious disease, enabling the development of an applied evolutionary framework to monitor CeMV resistance across cetacean species. Biomarkers could now be established to assess potential risk factors associated with these genes in other CeMV‐affected cetacean populations and species. These results could also possibly aid in the advancement of vaccines against morbilliviruses. [ABSTRACT FROM AUTHOR]

Aim We provide an overview of the location and ages of coastal phylogeographical breaks in southern Australian planktonic dispersers, and test the hypothesis that the absence of such breaks in some species is an artefact of insufficient resolution of genetic markers when such breaks evolved comparatively recently. Location Temperate coastal Australia. Methods We generated a large (> 1500 individuals) data set from rapidly evolving microsatellite markers for two codistributed Australian coastal gastropods, and compared it with mitochondrial DNA data. Both study species, the snail Nerita atramentosa and the limpet Siphonaria diemenensis, have long planktonic dispersal phases, and neither taxon exhibits substantial regional genetic structure on the basis of mitochondrial DNA. We tested for the presence of genetic structure by means of AMOVA, Bayesian clustering ( structure) and iterated realloction ( flock). Results There was no compelling evidence for the existence of more than one evolutionary lineage in either species. Main conclusions Discrepancies in the phylogeographical structuring of co-distributed intertidal taxa cannot be attributed to insufficient marker resolution for the two species considered here, and likely reflect a combination of abiotic and biotic factors that include porous dispersal barriers, life history and species age/history. It appears that contemporary oceanography does not explain the presence of phylogeographical breaks, but may serve to maintain breaks that evolved earlier. Deep genetic divergence in some of the previously studied coastal invertebrates suggests that these could be cryptic species, in which case competitive exclusion may play a role in constraining species biogeography. [ABSTRACT FROM AUTHOR]

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The estuary perch (Macquaria colonorum) represents an important model for assessing how historical changes in coastal geomorphology and current oceanographic and estuarine conditions may have impacted connectivity in a catadromous fish. A fragment of the mitochondrial control region and six microsatellite DNA markers were used to clarify connectivity in 17 populations (n = 354) of estuary perch from the southeast and southern coasts of Australia. The mtDNA data showed a latitudinal disjunction in haplotype frequencies that divided populations into two groups (ΦST = 0.419), in a pattern suggestive of isolation by geographic distance. However, no marked structure or correlation with distance was apparent within each group, a result consistent with microsatellite data that showed high contemporary population connectivity across large distances. This was contrary to expectations that the species would exhibit moderate to strong genetic structure consistent with a one-dimensional stepping stone pattern. Coalescent phylogeographic and population genetic analyses provided support for a historical divergence probably due to the emergence of the Bassian Isthmus in southern Australia. Current connectivity appears to be maintained by both large- and fine-scale oceanographic currents and processes, highlighting the important role of the marine environment for an estuarine resident species. La perche des estuaires (Macquaria colonorum) constitue un important modèle pour évaluer comment les changements historiques de géomorphologie côtière et les conditions actuelles océaniques et estuariennes affectent la connectivité chez un poisson catadrome. Un fragment de la région de contrôle mitochondriale et six marqueurs microsatellites d'ADN nous ont servi à mettre en évidence la connectivité chez 17 populations (n = 354) de perches des estuaires sur les côtes sud-est et sud de l'Australie. Les données d'ADNmt montrent une disjonction latitudinale dans les fréquences des haplotypes qui sépare les populations en deux groupes (ΦST = 0,419) en un patron qui semble relié à l'isolement par la distance géographique. Cependant, dans chacun des deux groupes, il n'y a pas de structure marquée, ni de corrélation avec la distance, un résultat qui est en accord avec les données des microsatellites qui montrent une forte connectivité actuelle entre les populations sur de grandes distances. Cela est contraire à nos attentes qui étaient que les espèces posséderaient une structure génétique moyenne à forte compatible avec un patron unidimensionnel par étapes. Des analyses génétiques phylogéographiques et démographiques de coalescence appuient l'existence d'une divergence historique probablement due à l'émergence de l'isthme de Bass dans le sud de l'Australie. La connectivité actuelle semble être maintenue par des courants et processus océaniques à la fois à grande échelle et à échelle fine, ce qui souligne le rôle de l'environnement marin chez une espèce résidante des estuaires. [ABSTRACT FROM AUTHOR]

Oceanographic processes play a significant role in shaping the genetic structure of marine populations, but it is less clear whether they affect genetic differentiation of highly mobile vertebrates. We used microsatellite markers and mtDNA control region sequences to investigate the spatial genetic structure of short-beaked common dolphins ( Delphinus delphis) in southeastern Australia, a region characterised by complex oceanographic conditions associated with the East Australian Current (EAC). A total of 115 biopsy samples of dolphins were collected from six localities spanning approximately 1,000 km of the New South Wales (NSW) coastline. We found evidence for contrasting genetic diversity and fine-scale genetic structure, characterised by three genetically differentiated populations with varying levels of admixture. Spatial genetic structure was not explained by a model of isolation by distance, instead it coincides with main patterns of oceanographic variation along the EAC. We propose that common dolphins along the EAC may be adapted to three water masses recently characterised in this region. [ABSTRACT FROM AUTHOR]

Rivers provide an excellent system to study interactions between patterns of biodiversity structure and ecological processes. In these environments, gene flow is restricted by the spatial hierarchy and temporal variation of connectivity within the drainage network. In the Australian arid zone, this variability is high and rivers often exist as isolated waterholes connected during unpredictable floods. These conditions cause boom/bust cycles in the population dynamics of taxa, but their influence on spatial genetic diversity is largely unknown. We used a landscape genetics approach to assess the effect of hydrological variability on gene flow, spatial population structure and genetic diversity in an Australian freshwater fish, Macquaria ambigua. Our analysis is based on microsatellite data of 590 samples from 26 locations across the species range. Despite temporal isolation of populations, the species showed surprisingly high rates of dispersal, with population genetic structure only evident among major drainage basins. Within drainages, hydrological variability was a strong predictor of genetic diversity, being positively correlated with spring-time flow volume. We propose that increases in flow volume during spring stimulate recruitment booms and dispersal, boosting population size and genetic diversity. Although it is uncertain how the hydrological regime in arid Australia may change under future climate scenarios, management strategies for arid-zone fishes should mitigate barriers to dispersal and alterations to the natural flow regime to maintain connectivity and the species' evolutionary potential. This study contributes to our understanding of the influence of spatial and temporal heterogeneity on population and landscape processes. [ABSTRACT FROM AUTHOR]

Aim We conducted a range-wide phylogeographic study of a common Australian freshwater fish, the golden perch ( Macquaria ambigua), to investigate the relationship between environmental processes and evolutionary history in drainage basins. Location Inland [Lake Eyre (LEB), Murray–Darling (MDB) and Bulloo (BULL)] and coastal basins [Fitzroy (FITZ)] of eastern Australia. Methods A total of 590 samples were collected from across the entire species’ distribution and a section of the mitochondrial DNA control region was sequenced. In order to reconstruct the evolutionary history of M. ambigua a comprehensive suite of phylogeographic analyses was conducted, including nested clade phylogeographic analysis, mismatch analysis and isolation-with-migration model simulations. Results Three major lineages corresponding to the major drainage basins, FITZ, MDB and LEB/BULL, were identified (ΦST = 0.92). Lineages from the coastal basin (FITZ) were highly divergent from those of the inland basins (up to 6%). Levels of genetic diversity in the inland basins were relatively low and our analyses indicate that these populations experienced both demographic and range expansions during the Pleistocene. Main conclusions Investigation of the range-wide phylogeography of M. ambigua has revealed new insights into the biogeography of the Australian arid zone, particularly with regard to evolutionary events chronologically associated with cyclical moist and dry conditions. We propose that M. ambigua originated on the east coast (FITZ) and crossed a major geographic barrier, the Great Dividing Range (GDR), to colonize the inland basins (MDB, LEB and BULL). We infer a series of demographic and range expansion events for M. ambigua consistent with a scenario of moister Pleistocene conditions and increased connectivity of freshwater environments, both within and among drainage basins. Major lineages then diversified following isolation of freshwater environments under increasingly arid climate conditions. We suggest that management priorities for M. ambigua should include the resolution of taxonomic uncertainties and the maintenance of genetic diversity of both stocked populations in the MDB and native populations of the LEB that may be at risk of further isolation and reduced gene flow due to increased aridification under future climate change scenarios. [ABSTRACT FROM AUTHOR]

The life-history strategies of some species make them strong candidates for rapid exploitation of novel habitat under new climate regimes. Some early-responding species may be considered invasive, and negatively impact on ‘naïve’ ecosystems. The barrens-forming sea urchin Centrostephanus rodgersii is one such species, having a high dispersal capability and a high-latitude range margin limited only by a developmental temperature threshold. Within this species’ range in eastern Australian waters, sea temperatures have increased at greater than double the global average rate. The coinciding poleward range extension of C. rodgersii has caused major ecological changes, threatening reef biodiversity and fisheries productivity. We investigated microsatellite diversity and population structure associated with range expansion by this species. Generalized linear model analyses revealed no reduction in genetic diversity in the newly colonized region. A ‘seascape genetics’ analysis of genetic distances found no spatial genetic structure associated with the range extension. The distinctive genetic characteristic of the extension zone populations was reduced population-specific FST, consistent with very rapid population expansion. Demographic and genetic simulations support our inference of high connectivity between pre- and post-extension zones. Thus, the range shift appears to be a poleward extension of the highly-connected rangewide population of C. rodgersii. This is consistent with advection of larvae by the intensified warm water East Australian current, which has also increased Tasmanian Sea temperatures above the species’ lower developmental threshold. Thus, ocean circulation changes have improved the climatic suitability of novel habitat for C. rodgersii and provided the supply of recruits necessary for colonization. [ABSTRACT FROM AUTHOR]

Abstract: Crabs of the family Hymenosomatidae are common in coastal and shelf regions throughout much of the southern hemisphere. One of the genera in the family, Hymenosoma, is represented in Africa and the South Pacific (Australia and New Zealand). This distribution can be explained either by vicariance (presence of the genus on the Gondwanan supercontinent and divergence following its break-up) or more recent transoceanic dispersal from one region to the other. We tested these hypotheses by reconstructing phylogenetic relationships among the seven presently-accepted species in the genus, as well as examining their placement among other hymenosomatid crabs, using sequence data from two nuclear markers (Adenine Nucleotide Transporter [ANT] exon 2 and 18S rDNA) and three mitochondrial markers (COI, 12S and 16S rDNA). The five southern African representatives of the genus were recovered as a monophyletic lineage, and another southern African species, Neorhynchoplax bovis, was identified as their sister taxon. The two species of Hymenosoma from the South Pacific neither clustered with their African congeners, nor with each other, and should therefore both be placed into different genera. Molecular dating supports a post-Gondwanan origin of the Hymenosomatidae. While long-distance dispersal cannot be ruled out to explain the presence of the family Hymenosomatidae on the former Gondwanan land-masses and beyond, the evolutionary history of the African species of Hymenosoma indicates that a third means of speciation may be important in this group: gradual along-coast dispersal from tropical towards temperate regions, with range expansions into formerly inhospitable habitat during warm climatic phases, followed by adaptation and speciation during subsequent cooler phases. [Copyright &y& Elsevier]

To conserve the high functional and genetic variation in hotspots such as tropical rainforests, it is essential to understand the forces driving and maintaining biodiversity. We asked to what extent environmental gradients and terrain structure affect morphological and genomic variation across the wet tropical distribution of an Australian rainbowfish, Melanotaenia splendida splendida. We used an integrative riverscape genomics and morphometrics framework to assess the influence of these factors on both putative adaptive and non-adaptive spatial divergence. We found that neutral genetic population structure was largely explainable by restricted gene flow among drainages. However, environmental associations revealed that ecological variables had a similar power to explain overall genetic variation, and greater power to explain body shape variation, than the included neutral covariables. Hydrological and thermal variables were the strongest environmental predictors and were correlated with traits previously linked to heritable habitat-associated dimorphism in rainbowfishes. In addition, climate-associated genetic variation was significantly associated with morphology, supporting heritability of shape variation. These results support the inference of evolved functional differences among localities, and the importance of hydroclimate in early stages of diversification. We expect that substantial evolutionary responses will be required in tropical rainforest endemics to mitigate local fitness losses due to changing climates., (© 2023. The Author(s).)

Growth is one of the most important traits of an organism. For exploited species, this trait has ecological and evolutionary consequences as well as economical and conservation significance. Rapid changes in growth rate associated with anthropogenic stressors have been reported for several marine fishes, but little is known about the genetic basis of growth traits in teleosts. We used reduced genome representation data and genome-wide association approaches to identify growth-related genetic variation in the commercially, recreationally, and culturally important Australian snapper (Chrysophrys auratus, Sparidae). Based on 17,490 high-quality single-nucleotide polymorphisms and 363 individuals representing extreme growth phenotypes from 15,000 fish of the same age and reared under identical conditions in a sea pen, we identified 100 unique candidates that were annotated to 51 proteins. We documented a complex polygenic nature of growth in the species that included several loci with small effects and a few loci with larger effects. Overall heritability was high (75.7%), reflected in the high accuracy of the genomic prediction for the phenotype (small vs large). Although the single-nucleotide polymorphisms were distributed across the genome, most candidates (60%) clustered on chromosome 16, which also explains the largest proportion of heritability (16.4%). This study demonstrates that reduced genome representation single-nucleotide polymorphisms and the right bioinformatic tools provide a cost-efficient approach to identify growth-related loci and to describe genomic architectures of complex quantitative traits. Our results help to inform captive aquaculture breeding programs and are of relevance to monitor growth-related evolutionary shifts in wild populations in response to anthropogenic pressures., (© The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America.)

Resilience to environmental stressors due to climate warming is influenced by local adaptations, including plastic responses. The recent literature has focused on genomic signatures of climatic adaptation, but little is known about how plastic capacity may be influenced by biogeographic and evolutionary processes. We investigate phenotypic plasticity as a target of climatic selection, hypothesizing that lineages that evolved in warmer climates will exhibit greater plastic adaptive resilience to upper thermal stress. This was experimentally tested by comparing transcriptomic responses within and among temperate, subtropical, and desert ecotypes of Australian rainbowfish subjected to contemporary and projected summer temperatures. Critical thermal maxima were estimated, and ecological niches delineated using bioclimatic modeling. A comparative phylogenetic expression variance and evolution model was used to assess plastic and evolved changes in gene expression. Although 82% of all expressed genes were found in the three ecotypes, they shared expression patterns in only 5 out of 236 genes that responded to the climate change experiment. A total of 532 genes showed signals of adaptive (i.e., genetic-based) plasticity due to ecotype-specific directional selection, and 23 of those responded to projected summer temperatures. Network analyses demonstrated centrality of these genes in thermal response pathways. The greatest adaptive resilience to upper thermal stress was shown by the subtropical ecotype, followed by the desert and temperate ecotypes. Our findings indicate that vulnerability to climate change will be highly influenced by biogeographic factors, emphasizing the value of integrative assessments of climatic adaptive traits for accurate estimation of population and ecosystem responses., Competing Interests: The authors declare no competing interest., (Copyright © 2020 the Author(s). Published by PNAS.)

Dispersal and natural selection are key evolutionary processes shaping the distribution of phenotypic and genetic diversity. For species inhabiting complex spatial environments however, it is unclear how the balance between gene flow and selection may be influenced by landscape heterogeneity and environmental variation. Here, we evaluated the effects of dendritic landscape structure and the selective forces of hydroclimatic variation on population genomic parameters for the Murray River rainbowfish, Melanotaenia fluviatilis across the Murray-Darling Basin, Australia. We genotyped 249 rainbowfish at 17,503 high-quality SNP loci and integrated these with models of network connectivity and high-resolution environmental data within a riverscape genomics framework. We tested competing models of gene flow before using multivariate genotype-environment association (GEA) analysis to test for signals of adaptive divergence associated with hydroclimatic variation. Patterns of neutral genetic variation were consistent with expectations based on the stream hierarchy model and M. fluviatilis' moderate dispersal ability. Models incorporating dendritic network structure suggested that landscape heterogeneity is a more important factor determining connectivity and gene flow than waterway distance. Extending these results, we also introduce a novel approach to controlling for the unique effects of dendritic network structure in GEA analyses of populations of aquatic species. We identified 146 candidate loci potentially underlying a polygenic adaptive response to seasonal fluctuations in stream flow and variation in the relative timing of temperature and precipitation extremes. Our findings underscore an emerging predominant role for seasonal variation in hydroclimatic conditions driving local adaptation and are relevant for informing proactive conservation management., (© 2018 John Wiley & Sons Ltd.)

Populations that are adaptively divergent but maintain high gene flow may have greater resilience to environmental change as gene flow allows the spread of alleles that have already been tested elsewhere. In addition, populations naturally subjected to ecological disturbance may already hold resilience to future environmental change. Confirming this necessitates ecological genomic studies of high dispersal, generalist species. Here we perform one such study on golden perch (Macquaria ambigua) in the Murray-Darling Basin (MDB), Australia, using a genome-wide SNP data set. The MDB spans across arid to wet and temperate to subtropical environments, with low to high ecological disturbance in the form of low to high hydrological variability. We found high gene flow across the basin and three populations with low neutral differentiation. Genotype-environment association analyses detected adaptive divergence predominantly linked to an arid region with highly variable riverine flow, and candidate loci included functions related to fat storage, stress and molecular or tissue repair. The high connectivity of golden perch in the MDB will likely allow locally adaptive traits in its most arid and hydrologically variable environment to spread and be selected in localities that are predicted to become arid and hydrologically variable in future climates. High connectivity in golden perch is likely due to their generalist life history and efforts of fisheries management. Our study adds to growing evidence of adaptation in the face of gene flow and highlights the importance of considering ecological disturbance and adaptive divergence in biodiversity management., (© 2017 John Wiley & Sons Ltd.)

Understanding whether small populations with low genetic diversity can respond to rapid environmental change via phenotypic plasticity is an outstanding research question in biology. RNA sequencing (RNA-seq) has recently provided the opportunity to examine variation in gene expression, a surrogate for phenotypic variation, in nonmodel species. We used a comparative RNA-seq approach to assess expression variation within and among adaptively divergent populations of a threatened freshwater fish, Nannoperca australis, found across a steep hydroclimatic gradient in the Murray-Darling Basin, Australia. These populations evolved under contrasting selective environments (e.g., dry/hot lowland; wet/cold upland) and represent opposite ends of the species' spectrum of genetic diversity and population size. We tested the hypothesis that environmental variation among isolated populations has driven the evolution of divergent expression at ecologically important genes using differential expression (DE) analysis and an anova-based comparative phylogenetic expression variance and evolution model framework based on 27,425 de novo assembled transcripts. Additionally, we tested whether gene expression variance within populations was correlated with levels of standing genetic diversity. We identified 290 DE candidate transcripts, 33 transcripts with evidence for high expression plasticity, and 50 candidates for divergent selection on gene expression after accounting for phylogenetic structure. Variance in gene expression appeared unrelated to levels of genetic diversity. Functional annotation of the candidate transcripts revealed that variation in water quality is an important factor influencing expression variation for N. australis. Our findings suggest that gene expression variation can contribute to the evolutionary potential of small populations., (© 2017 John Wiley & Sons Ltd.)

Genetic diversity is an essential aspect of species viability, and assessments of neutral genetic diversity are regularly implemented in captive breeding and conservation programs. Despite their importance, information from adaptive markers is rarely included in such programs. A promising marker of significance in fitness and adaptive potential is the major histocompatibility complex (MHC), a key component of the adaptive immune system. Populations of Australian freshwater fishes are generally declining in numbers due to human impacts and the introduction of exotic species, a scenario of particular concern for members of the family Percichthyidae, several of which are listed as nationally vulnerable or endangered, and hence subject to management plans, captive breeding, and restoration plans. We used a next-generation sequencing approach to characterize the MHC IIB locus and provide a conservative description of its levels of diversity in four endangered percichthyids: Gadopsis marmoratus, Macquaria australasica, Nannoperca australis, and Nannoperca obscura. Evidence is presented for a duplicated MHC IIB locus, positively selected sites and recombination of MHC alleles. Relatively moderate levels of diversity were detected in the four species, as well as in different ecotypes within each species. Phylogenetic analyses revealed genus specific clustering of alleles and no allele sharing among species. There were also no shared alleles observed between two ecotypes within G. marmoratus and within M. australasica, which might be indicative of ecologically-driven divergence and/or long divergence times. This represents the first characterization and assessment of MHC diversity for Percichthyidae, and also for Australian freshwater fishes in general, providing key genetic resources for a vertebrate group of increasing conservation concern., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Unusually low genetic diversity can be a warning of an urgent need to mitigate causative anthropogenic activities. However, current low levels of genetic diversity in a population could also be due to natural historical events, including recent evolutionary divergence, or long-term persistence at a small population size. Here, we determine whether the relatively low genetic diversity of pygmy blue whales (Balaenoptera musculus brevicauda) in Australia is due to natural causes or overexploitation. We apply recently developed analytical approaches in the largest genetic dataset ever compiled to study blue whales (297 samples collected after whaling and representing lineages from Australia, Antarctica and Chile). We find that low levels of genetic diversity in Australia are due to a natural founder event from Antarctic blue whales (Balaenoptera musculus intermedia) that occurred around the Last Glacial Maximum, followed by evolutionary divergence. Historical climate change has therefore driven the evolution of blue whales into genetically, phenotypically and behaviourally distinct lineages that will likely be influenced by future climate change., (© 2015 The Author(s) Published by the Royal Society. All rights reserved.)

Habitat fragmentation caused by human activities alters metapopulation dynamics and decreases biological connectivity through reduced migration and gene flow, leading to lowered levels of population genetic diversity and to local extinctions. The threatened Yarra pygmy perch, Nannoperca obscura, is a poor disperser found in small, isolated populations in wetlands and streams of southeastern Australia. Modifications to natural flow regimes in anthropogenically-impacted river systems have recently reduced the amount of habitat for this species and likely further limited its opportunity to disperse. We employed highly resolving microsatellite DNA markers to assess genetic variation, population structure and the spatial scale that dispersal takes place across the distribution of this freshwater fish and used this information to identify conservation units for management. The levels of genetic variation found for N. obscura are amongst the lowest reported for a fish species (mean heterozygosity of 0.318 and mean allelic richness of 1.92). We identified very strong population genetic structure, nil to little evidence of recent migration among demes and a minimum of 11 units for conservation management, hierarchically nested within four major genetic lineages. A combination of spatial analytical methods revealed hierarchical genetic structure corresponding with catchment boundaries and also demonstrated significant isolation by riverine distance. Our findings have implications for the national recovery plan of this species by demonstrating that N. obscura populations should be managed at a catchment level and highlighting the need to restore habitat and avoid further alteration of the natural hydrology.

The elasmobranch fish are an ancient, evolutionarily successful, but under-researched vertebrate group, particularly in regard to their recent evolutionary history. Their lineage has survived four mass extinction events and most present day taxa are thought to be derived from Mesozoic forms. Here we present a molecular phylogenetic analysis of the family Orectolobidae that provides evidence for recent events of diversification in this shark group. Species interrelationships in Orectolobidae were reconstructed based on four mitochondrial and nuclear genes. In line with previous morphological work, our results do not support current taxonomic arrangements in Orectolobidae and indicate that a taxonomic revision of the family is warranted. We propose that the onset of diversification of orectolobid sharks is of Miocene age and occurred within the Indo-Australian region. Surprisingly, we also find evidence for a recent ( approximately last 2 million years) and rapid radiation of wobbegong sharks. Allopatric speciation followed by range expansion seems like the general most likely explanation to account for wobbegong relationships and distributions. We suggest that the evolution of this shark group was mostly influenced by two temporal scenarios of diversification. The oldest relates to major geological changes in the Indo-West Pacific associated with the Miocene collision of the Indo-Australian and Eurasian plates. The most recent scenario was influenced by changes in oceanography and the emergence of biogeographic barriers related to Pleistocene glacial cycles in Australian waters.