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Anthropogenic climate change is forecast to drive regional climate disruption and instability across the globe. These impacts are likely to be exacerbated within biodiversity hotspots, both due to the greater potential for species loss but also to the possibility that endemic lineages might not have experienced significant climatic variation in the past, limiting their evolutionary potential to respond to rapid climate change. We assessed the role of climatic stability on the accumulation and persistence of lineages in an obligate freshwater fish group endemic to the southwest Western Australia (SWWA) biodiversity hotspot. Using 19,426 genomic (ddRAD-seq) markers and species distribution modelling, we explored the phylogeographic history of western (Nannoperca vittata) and little (Nannoperca pygmaea) pygmy perches, assessing population divergence and phylogenetic relationships, delimiting species and estimating changes in species distributions from the Pliocene to 2100. We identified two deep phylogroups comprising three divergent clusters, which showed no historical connectivity since the Pliocene. We conservatively suggest these represent three isolated species with additional intraspecific structure within one widespread species. All lineages showed long-term patterns of isolation and persistence owing to climatic stability but with significant range contractions likely under future climate change. Our results highlighted the role of climatic stability in allowing the persistence of isolated lineages in the SWWA. This biodiversity hotspot is under compounding threat from ongoing climate change and habitat modification, which may further threaten previously undetected cryptic diversity across the region., (© 2024. The Author(s).)

Obtaining reliable estimates of the effective number of breeders ( N b ) and generational effective population size ( N e ) for fishery-important species is challenging because they are often iteroparous and highly abundant, which can lead to bias and imprecision. However, recent advances in understanding of these parameters, as well as the development of bias correction methods, have improved the capacity to generate reliable estimates. We utilized samples of both single-cohort young of the year and mixed-age adults from two geographically and genetically isolated stocks of the Australasian snapper ( Chrysophrys auratus ) to investigate the feasibility of generating reliable N b and N e estimates for a fishery species. Snapper is an abundant, iteroparous broadcast spawning teleost that is heavily exploited by recreational and commercial fisheries. Employing neutral genome-wide SNPs and the linkage-disequilibrium method, we determined that the most reliable N b and N e estimates could be derived by genotyping at least 200 individuals from a single cohort. Although our estimates made from the mixed-age adult samples were generally lower and less precise than those based on a single cohort, they still proved useful for understanding relative differences in genetic effective size between stocks. The correction formulas applied to adjust for biases due to physical linkage of loci and age structure resulted in substantial upward modifications of our estimates, demonstrating the importance of applying these bias corrections. Our findings provide important guidelines for estimating N b and N e for iteroparous species with large populations. This work also highlights the utility of samples originally collected for stock structure and stock assessment work for investigating genetic effective size in fishery-important species., Competing Interests: The authors declare no conflict of interest., (© 2024 The Author(s). Evolutionary Applications published by John Wiley & Sons Ltd.)

Marine ecosystems are ideal for studying evolutionary adaptations involved in lineage diversification due to few physical barriers and reduced opportunities for strict allopatry compared to terrestrial ecosystems. Cetaceans (whales, dolphins, and porpoises) are a diverse group of mammals that successfully adapted to various habitats within the aquatic environment around 50 million years ago. While the overall adaptive transition from terrestrial to fully aquatic species is relatively well understood, the radiation of modern whales is still unclear. Here high-quality genomes derived from previously published data were used to identify genomic regions that potentially underpinned the diversification of baleen whales (Balaenopteridae). A robust molecular phylogeny was reconstructed based on 10,159 single copy and complete genes for eight mysticetes, seven odontocetes and two cetacean outgroups. Analysis of positive selection across 3,150 genes revealed that balaenopterids have undergone numerous idiosyncratic and convergent genomic variations that may explain their diversification. Genes associated with aging, survival and homeostasis were enriched in all species. Additionally, positive selection on genes involved in the immune system were disclosed for the two largest species, blue and fin whales. Such genes can potentially be ascribed to their morphological evolution, allowing them to attain greater length and increased cell number. Further evidence is presented about gene regions that might have contributed to the extensive anatomical changes shown by cetaceans, including adaptation to distinct environments and diets. This study contributes to our understanding of the genomic basis of diversification in baleen whales and the molecular changes linked to their adaptive radiation, thereby enhancing our understanding of cetacean evolution., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

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., (© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

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).)

Restoration programs in the form of ex-situ breeding combined with reintroductions are becoming critical to counteract demographic declines and species losses. Such programs are increasingly using genetic management to improve conservation outcomes. However, the lack of long-term monitoring of genetic indicators following reintroduction prevents assessments of the trajectory and persistence of reintroduced populations. We carried out an extensive monitoring program in the wild for a threatened small-bodied fish (southern pygmy perch, Nannoperca australis) to assess the long-term genomic effects of its captive breeding and reintroduction. The species was rescued prior to its extirpation from the terminal lakes of Australia's Murray-Darling Basin, and then used for genetically informed captive breeding and reintroductions. Subsequent annual or biannual monitoring of abundance, fitness, and occupancy over a period of 11 years, combined with postreintroduction genetic sampling, revealed survival and recruitment of reintroduced fish. Genomic analyses based on data from the original wild rescued, captive born, and reintroduced cohorts revealed low inbreeding and strong maintenance of neutral and candidate adaptive genomic diversity across multiple generations. An increasing trend in the effective population size of the reintroduced population was consistent with field monitoring data in demonstrating successful re-establishment of the species. This provides a rare empirical example that the adaptive potential of a locally extinct population can be maintained during genetically informed ex-situ conservation breeding and reintroduction into the wild. Strategies to improve biodiversity restoration via ex-situ conservation should include genetic-based captive breeding and longitudinal monitoring of standing genomic variation in reintroduced populations., (© 2022 Society for Conservation Biology.)

Background: High levels of standing genomic variation in wide-ranging marine species may enhance prospects for their long-term persistence. Patterns of connectivity and adaptation in such species are often thought to be influenced by spatial factors, environmental heterogeneity, and oceanographic and geomorphological features. Population-level studies that analytically integrate genome-wide data with environmental information (i.e., seascape genomics) have the potential to inform the spatial distribution of adaptive diversity in wide-ranging marine species, such as many marine mammals. We assessed genotype-environment associations (GEAs) in 214 common dolphins (Delphinus delphis) along > 3000 km of the southern coast of Australia., Results: We identified 747 candidate adaptive SNPs out of a filtered panel of 17,327 SNPs, and five putatively locally-adapted populations with high levels of standing genomic variation were disclosed along environmentally heterogeneous coasts. Current velocity, sea surface temperature, salinity, and primary productivity were the key environmental variables associated with genomic variation. These environmental variables are in turn related to three main oceanographic phenomena that are likely affecting the dispersal of common dolphins: (1) regional oceanographic circulation, (2) localised and seasonal upwellings, and (3) seasonal on-shelf circulation in protected coastal habitats. Signals of selection at exonic gene regions suggest that adaptive divergence is related to important metabolic traits., Conclusion: To the best of our knowledge, this represents the first seascape genomics study for common dolphins (genus Delphinus). Information from the associations between populations and their environment can assist population management in forecasting the adaptive capacity of common dolphins to climate change and other anthropogenic impacts., (© 2022. The Author(s).)

The efficacy of fisheries management strategies depends on stock assessment and management actions being carried out at appropriate spatial scales. This requires understanding of spatial and temporal population structure and connectivity, which is challenging in weakly structured and highly connected marine populations. We carried out a population genomics study of the heavily exploited snapper ( Chrysophrys auratus ) along ~2600 km of the Australian coastline, with a focus on Western Australia (WA). We used 10,903 filtered SNPs in 341 individuals from eight sampling locations to characterize population structure and connectivity in snapper across WA and to assess if current spatial scales of stock assessment and management agree with evidence from population genomics. Our dataset also enabled us to investigate temporal stability in population structure as well as connectivity between WA and its nearest, eastern jurisdictional neighbour. As expected for a species influenced by the extensive ocean boundary current in the region, low genetic differentiation and high connectivity were uncovered across WA. However, we did detect strong isolation by distance and genetic discontinuities in the mid-west and south-east. The discontinuities correlate with boundaries between biogeographic regions, influenced by on-shelf oceanography, and the sites of important spawning aggregations. We also detected temporal instability in genetic structure at one of our sites, possibly due to interannual variability in recruitment in adjacent regions. Our results partly contrast with the current spatial management of snapper in WA, indicating the likely benefits of a review. This study supports the value of population genomic surveys in informing the management of weakly structured and wide-ranging marine fishery resources., Competing Interests: The authors declare no conflict of interest., (© 2022 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

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., (© 2022 John Wiley & Sons Ltd.)

Background: Understanding how species biology may facilitate resilience to climate change remains a critical factor in detecting and protecting species at risk of extinction. Many studies have focused on the role of particular ecological traits in driving species responses, but less so on demographic history and levels of standing genetic variation. Additionally, spatial variation in the interaction of demographic and adaptive factors may further complicate prediction of species responses to environmental change. We used environmental and genomic datasets to reconstruct the phylogeographic histories of two ecologically similar and largely co-distributed freshwater fishes, the southern (Nannoperca australis) and Yarra (N. obscura) pygmy perches, to assess the degree of concordance in their responses to Plio-Pleistocene climatic changes. We described contemporary genetic diversity, phylogenetic histories, demographic histories, and historical species distributions across both species, and statistically evaluated the degree of concordance in co-occurring populations., Results: Marked differences in contemporary genetic diversity, historical distribution changes and historical migration were observed across the species, with a distinct lack of genetic diversity and historical range expansion suggested for N. obscura. Although several co-occurring populations within a shared climatic refugium demonstrated concordant demographic histories, idiosyncratic population size changes were found at the range edges of the more spatially restricted species. Discordant responses between species were associated with low standing genetic variation in peripheral populations. This might have hindered adaptive potential, as documented in recent demographic declines and population extinctions for the two species., Conclusion: Our results highlight both the role of spatial scale in the degree of concordance in species responses to climate change, and the importance of standing genetic variation in facilitating range shifts. Even when ecological traits are similar between species, long-term genetic diversity and historical population demography may lead to discordant responses to ongoing and future climate change., (© 2022. 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.)

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., (© 2021 The Authors. Evolution © 2021 The Society for the Study of Evolution.)

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., (© 2021 John Wiley & Sons Ltd.)

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., (© 2021 John Wiley & Sons Ltd.)

The KwaZulu-Natal sardine run, popularly known as the “greatest shoal on Earth,” is a mass migration of South African sardines from their temperate core range into the subtropical Indian Ocean. It has been suggested that this represents the spawning migration of a distinct subtropical stock. Using genomic and transcriptomic data from sardines collected around the South African coast, we identified two stocks, one cool temperate (Atlantic) and the other warm temperate (Indian Ocean). Unexpectedly, we found that sardines participating in the sardine run are primarily of Atlantic origin and thus prefer colder water. These sardines separate from the warm-temperate stock and move into temporarily favorable Indian Ocean habitat during brief cold-water upwelling periods. Once the upwelling ends, they find themselves trapped in physiologically challenging subtropical habitat and subject to intense predation pressure. This makes the sardine run a rare example of a mass migration that has no apparent fitness benefits.

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., Competing Interests: The authors declare no competing interest.

The ecological impacts of increasing global temperatures are evident in most ecosystems on Earth, but our understanding of how climatic variation influences natural selection and adaptive resilience across latitudes remains largely unknown. Latitudinal gradients allow testing general ecosystem-level theories relevant to climatic adaptation. We assessed differences in adaptive diversity of populations along a latitudinal region spanning highly variable temperate to subtropical climates. We generated and integrated information from environmental mapping, phenotypic variation and genome-wide data from across the geographical range of the rainbowfish Melanotaenia duboulayi, an emerging aquatic system for studies of climate change. We detected, after controlling for spatial population structure, strong interactions between genotypes and environment associated with variation in stream flow and temperature. Some of these hydroclimate-associated genes were found to interact within functional protein networks that contain genes of adaptive significance for projected future climates in rainbowfish. Hydroclimatic selection was also associated with variation in phenotypic traits, including traits known to affect fitness of rainbowfish exposed to different flow environments. Consistent with predictions from the "climatic variability hypothesis," populations exposed to extremes of important environmental variables showed stronger adaptive divergence and less variation in climate-associated genes compared to populations at the centre of the environmental gradient. Our findings suggest that populations that evolved at environmental range margins and at geographical range edges may be more vulnerable to changing climates, a finding with implications for predicting adaptive resilience and managing biodiversity under climate change., (© 2020 John Wiley & Sons Ltd.)

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., Competing Interests: None declared., (© 2020 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

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.)

Hybridization poses a major challenge for species conservation because it threatens both genetic integrity and adaptive potential. Yet, hybridization can occasionally offer unprecedented opportunity for species recovery if the genome of an extinct taxon is present among living hybrids such that selective breeding could recapture it. We explored the design elements for establishing a captive-breeding program for Galapagos tortoises (Chelonoidis spp.) built around individuals with admixed ancestry involving an extinct species. The target individuals were hybrids between the extinct species from Floreana Island, C. niger, and an extant species, C. becki, which were recently found in the endemic range of C. becki, from Wolf Volcano on Isabela Island. We combined genotypic data from 35 tortoises with high ancestry from C. niger with forward-in-time simulations to explore captive breeding strategies that maximized overall genetic diversity and ancestry from C. niger while accommodating resource constraints, species biology, and the urgency to return tortoises to Floreana Island for facilitating ecosystem restoration. Overall genetic diversity was maximized when in the simulation tortoises were organized in relatively small breeding groups. Substantial amounts of the C. niger genome were captured despite limited resources available for selectively breeding tortoises in captivity. Genetic diversity was maximized when captive-bred offspring were released to the wild rather than being used as additional breeders. Our results provide genetic-based and practical guidance on the inclusion of hybrids with genomic representation from extinct taxa into species restoration programs and informs the ongoing debate on the value of hybrids in biodiversity conservation., (© 2019 Society for Conservation Biology.)

Aquatic species represent a vast diversity of metazoans, provide humans with the most abundant animal protein source, and are of increasing conservation concern, yet landscape genomics is dominated by research in terrestrial systems. We provide researchers with a roadmap to plan aquatic landscape genomics projects by aggregating spatial and software resources and offering recommendations from sampling to data production and analyses, while cautioning against analytical pitfalls. Given the unique properties of water, we discuss the importance of considering freshwater system structure and marine abiotic properties when assessing genetic diversity, population connectivity, and signals of natural selection. When possible, genomic datasets should be parsed into neutral, adaptive, and sex-linked datasets to generate the most accurate inferences of eco-evolutionary processes., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Intraspecific genetic structure in widely distributed marine species often mirrors the boundaries between temperature-defined bioregions. This suggests that the same thermal gradients that maintain distinct species assemblages also drive the evolution of new biodiversity. Ecological speciation scenarios are often invoked to explain such patterns, but the fact that adaptation is usually only identified when phylogenetic splits are already evident makes it impossible to rule out the alternative scenario of allopatric speciation with subsequent adaptation. We integrated large-scale genomic and environmental datasets along one of the world's best-defined marine thermal gradients (the South African coastline) to test the hypothesis that incipient ecological speciation is a result of divergence linked to the thermal environment. We identified temperature-associated gene regions in a coastal fish species that is spatially homogeneous throughout several temperature-defined biogeographic regions based on selectively neutral markers. Based on these gene regions, the species is divided into geographically distinct regional populations. Importantly, the ranges of these populations are delimited by the same ecological boundaries that define distinct infraspecific genetic lineages in co-distributed marine species, and biogeographic disjunctions in species assemblages. Our results indicate that temperature-mediated selection represents an early stage of marine ecological speciation in coastal regions that lack physical dispersal barriers.

Giant tortoises are among the longest-lived vertebrate animals and, as such, provide an excellent model to study traits like longevity and age-related diseases. However, genomic and molecular evolutionary information on giant tortoises is scarce. Here, we describe a global analysis of the genomes of Lonesome George-the iconic last member of Chelonoidis abingdonii-and the Aldabra giant tortoise (Aldabrachelys gigantea). Comparison of these genomes with those of related species, using both unsupervised and supervised analyses, led us to detect lineage-specific variants affecting DNA repair genes, inflammatory mediators and genes related to cancer development. Our study also hints at specific evolutionary strategies linked to increased lifespan, and expands our understanding of the genomic determinants of ageing. These new genome sequences also provide important resources to help the efforts for restoration of giant tortoise populations.

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., Competing Interests: None declared.

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.)

Pygmy perches (Percichthyidae) are a group of poorly dispersing freshwater fishes that have a puzzling biogeographic disjunction across southern Australia. Current understanding of pygmy perch phylogenetic relationships suggests past east-west migrations across a vast expanse of now arid habitat in central southern Australia, a region lacking contemporary rivers. Pygmy perches also represent a threatened group with confusing taxonomy and potentially cryptic species diversity. Here, we present the first study of the evolutionary history of pygmy perches based on genome-wide information. Data from 13 991 ddRAD loci and a concatenated sequence of 1 075 734 bp were generated for all currently described and potentially cryptic species. Phylogenetic relationships, biogeographic history and cryptic diversification were inferred using a framework that combines phylogenomics, species delimitation and estimation of divergence times. The genome-wide phylogeny clarified the biogeographic history of pygmy perches, demonstrating multiple east-west events of divergence within the group across the Australian continent. These results also resolved discordance between nuclear and mitochondrial data from a previous study. In addition, we propose three cryptic species within a southwestern species complex. The finding of potentially new species demonstrates that pygmy perches may be even more susceptible to ecological and demographic threats than previously thought. Our results have substantial implications for improving conservation legislation of pygmy perch lineages, especially in southwestern Western Australia., Competing Interests: The authors declare no competing interests.

Tests for isolation by distance (IBD) are the most commonly used method of assessing spatial genetic structure. Many studies have exclusively used mitochondrial DNA (mtDNA) sequences to test for IBD, but this marker is often in conflict with multilocus markers. Here, we report a review of the literature on IBD, with the aims of determining (a) whether significant IBD is primarily a result of lumping spatially discrete populations, and (b) whether microsatellite datasets are more likely to detect IBD when mtDNA does not. We also provide empirical data from four species in which mtDNA failed to detect IBD by comparing these with microsatellite and SNP data. Our results confirm that IBD is mostly found when distinct regional populations are pooled, and this trend disappears when each is analysed separately. Discrepancies between markers were found in almost half of the studies reviewed, and microsatellites were more likely to detect IBD when mtDNA did not. Our empirical data rejected the lack of IBD in the four species studied, and support for IBD was particularly strong for the SNP data. We conclude that mtDNA sequence data are often not suitable to test for IBD, and can be misleading about species' true dispersal potential. The observed failure of mtDNA to reliably detect IBD, in addition to being a single-locus marker, is likely a result of a selection-driven reduction in genetic diversity obscuring spatial genetic differentiation.

Spatial and temporal scales at which processes modulate genetic diversity over the landscape are usually overlooked, impacting the design of conservation management practices for widely distributed species. We examine processes shaping population divergence in highly mobile species by re-assessing the case of panmixia in the iconic olive ridley turtle from the eastern Pacific. We implemented a biophysical model of connectivity and a seascape genetic analysis based on nuclear DNA variation of 634 samples collected from 27 nesting areas. Two genetically distinct populations largely isolated during reproductive migrations and mating were detected, each composed of multiple nesting sites linked by high connectivity. This pattern was strongly associated with a steep environmental gradient and also influenced by ocean currents. These findings relate to meso-scale features of a dynamic oceanographic interface in the eastern tropical Pacific (ETP) region, a scenario that possibly provides different cost-benefit solutions and selective pressures for sea turtles during both the mating and migration periods. We reject panmixia and propose a new paradigm for olive ridley turtles where reproductive isolation due to assortative mating is linked to its environment. Our study demonstrates the relevance of integrative approaches for assessing the role of environmental gradients and oceanographic currents as drivers of genetic differentiation in widely distributed marine species. This is relevant for the conservation management of species of highly mobile behaviour, and assists the planning and development of large-scale conservation strategies for the threatened olive ridley turtles in the ETP., (© 2018 The Author(s).)

There has been remarkably little attention to using the high resolution provided by genotyping-by-sequencing (i.e., RADseq and similar methods) for assessing relatedness in wildlife populations. A major hurdle is the genotyping error, especially allelic dropout, often found in this type of data that could lead to downward-biased, yet precise, estimates of relatedness. Here, we assess the applicability of genotyping-by-sequencing for relatedness inferences given its relatively high genotyping error rate. Individuals of known relatedness were simulated under genotyping error, allelic dropout and missing data scenarios based on an empirical ddRAD data set, and their true relatedness was compared to that estimated by seven relatedness estimators. We found that an estimator chosen through such analyses can circumvent the influence of genotyping error, with the estimator of Ritland (Genetics Research, 67, 175) shown to be unaffected by allelic dropout and to be the most accurate when there is genotyping error. We also found that the choice of estimator should not rely solely on the strength of correlation between estimated and true relatedness as a strong correlation does not necessarily mean estimates are close to true relatedness. We also demonstrated how even a large SNP data set with genotyping error (allelic dropout or otherwise) or missing data still performs better than a perfectly genotyped microsatellite data set of tens of markers. The simulation-based approach used here can be easily implemented by others on their own genotyping-by-sequencing data sets to confirm the most appropriate and powerful estimator for their data., (© 2017 John Wiley & Sons Ltd.)

Populations of broadcast spawning marine organisms often have large sizes and are exposed to reduced genetic drift. Under such scenarios, strong selection associated with spatial environmental heterogeneity is expected to drive localized adaptive divergence, even in the face of connectivity. We tested this hypothesis using a seascape genomics approach in the commercially important greenlip abalone (Haliotis laevigata). We assessed how its population structure has been influenced by environmental heterogeneity along a zonal coastal boundary in southern Australia linked by strong oceanographic connectivity. Our data sets include 9,109 filtered SNPs for 371 abalones from 13 localities and environmental mapping across ~800 km. Genotype-environment association analyses and outlier tests defined 8,786 putatively neutral and 323 candidate adaptive loci. From a neutral perspective, the species is better represented by a metapopulation with very low differentiation (global F ST  = 0.0081) and weak isolation by distance following a stepping-stone model. For the candidate adaptive loci, however, model-based and model-free approaches indicated five divergent population clusters. After controlling for spatial distance, the distribution of putatively adaptive variation was strongly correlated to selection linked to minimum sea surface temperature and oxygen concentration. Around 80 candidates were annotated to genes with functions related to high temperature and/or low oxygen tolerance, including genes that influence the resilience of abalone species found in other biogeographic regions. Our study includes a documented example about the uptake of genomic information in fisheries management and supports the hypothesis of adaptive divergence due to coastal environmental heterogeneity in a connected metapopulation of a broadcast spawner., (© 2018 John Wiley & Sons Ltd.)

Genetic datasets of tens of markers have been superseded through next-generation sequencing technology with genome-wide datasets of thousands of markers. Genomic datasets improve our power to detect low population structure and identify adaptive divergence. The increased population-level knowledge can inform the conservation management of endangered species, such as the blue whale ( Balaenoptera musculus ). In Australia, there are two known feeding aggregations of the pygmy blue whale ( B. m. brevicauda ) which have shown no evidence of genetic structure based on a small dataset of 10 microsatellites and mtDNA. Here, we develop and implement a high-resolution dataset of 8294 genome-wide filtered single nucleotide polymorphisms, the first of its kind for blue whales. We use these data to assess whether the Australian feeding aggregations constitute one population and to test for the first time whether there is adaptive divergence between the feeding aggregations. We found no evidence of neutral population structure and negligible evidence of adaptive divergence. We propose that individuals likely travel widely between feeding areas and to breeding areas, which would require them to be adapted to a wide range of environmental conditions. This has important implications for their conservation as this blue whale population is likely vulnerable to a range of anthropogenic threats both off Australia and elsewhere., Competing Interests: The authors declare no competing interests.

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.)

High-throughput DNA sequencing allows efficient discovery of thousands of single nucleotide polymorphisms (SNPs) in nonmodel species. Population genetic theory predicts that this large number of independent markers should provide detailed insights into population structure, even when only a few individuals are sampled. Still, sampling design can have a strong impact on such inferences. Here, we use simulations and empirical SNP data to investigate the impacts of sampling design on estimating genetic differentiation among populations that represent three species of Galápagos giant tortoises ( Chelonoidis spp.). Though microsatellite and mitochondrial DNA analyses have supported the distinctiveness of these species, a recent study called into question how well these markers matched with data from genomic SNPs, thereby questioning decades of studies in nonmodel organisms. Using >20,000 genomewide SNPs from 30 individuals from three Galápagos giant tortoise species, we find distinct structure that matches the relationships described by the traditional genetic markers. Furthermore, we confirm that accurate estimates of genetic differentiation in highly structured natural populations can be obtained using thousands of SNPs and 2-5 individuals, or hundreds of SNPs and 10 individuals, but only if the units of analysis are delineated in a way that is consistent with evolutionary history. We show that the lack of structure in the recent SNP-based study was likely due to unnatural grouping of individuals and erroneous genotype filtering. Our study demonstrates that genomic data enable patterns of genetic differentiation among populations to be elucidated even with few samples per population, and underscores the importance of sampling design. These results have specific implications for studies of population structure in endangered species and subsequent management decisions.

Transcriptomics via RNA-seq has rapidly emerged as a powerful tool for ecological and evolutionary studies, enabling genome-scale studies of adaptation via regulation of global gene expression. Here we present a de novo transcriptome for the desert rainbowfish (Melanotaenia splendida tatei) based on individuals sampled in the Lake Eyre Basin, Australia's arid zone river system. Recently developed methods in RNA-seq and bioinformatics were used for sequencing, assembling and annotating a high-quality liver transcriptome suitable for studies of ecology and adaptation in desert rainbowfish. Transcript annotation in UniprotKB using BLASTx assigned unique protein matches to ~47% of 116,092 Trinity genes, while BLASTp assigned unique protein matches to ~35% of 62,792 predicted protein-coding regions. A full Trinotate annotation report is provided for predicted genes and their corresponding transcripts. Annotations were compared with previously identified genes for transcriptional regulation and heritable plasticity in future climates in the subtropical rainbowfish (M. duboulayi), finding ~57% of these candidate genes present in the desert rainbowfish transcriptome. We discuss the utility of transcriptomics methods for ecological studies of adaptation, while emphasising a range of methodological considerations for dealing with transcriptome datasets. This newly assembled transcriptome is expected to help elucidate mechanisms for adaptation to high temperatures and a variable climate in desert aquatic fauna., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Due to their worldwide distribution and occupancy of different types of environments, bottlenose dolphins display considerable morphological variation. Despite limited understanding about the taxonomic identity of such forms and connectivity among them at global scale, coastal (or inshore) and offshore (or oceanic) ecotypes have been widely recognized in several ocean regions. In the Southwest Atlantic Ocean (SWA), however, there are scarce records of bottlenose dolphins differing in external morphology according to habitat preferences that resemble the coastal-offshore pattern observed elsewhere. The main aim of this study was to analyze the genetic variability, and test for population structure between coastal ( n  = 127) and offshore ( n  = 45) bottlenose dolphins sampled in the SWA to assess whether their external morphological distinction is consistent with genetic differentiation. We used a combination of mtDNA control region sequences and microsatellite genotypes to infer population structure and levels of genetic diversity. Our results from both molecular marker types were congruent and revealed strong levels of structuring (microsatellites F ST  = 0.385, p  < .001; mtDNA F ST  =  0.183, p  < .001; Φ ST  = 0.385, p  < .001) and much lower genetic diversity in the coastal than the offshore ecotype, supporting patterns found in previous studies elsewhere. Despite the opportunity for gene flow in potential "contact zones", we found minimal current and historical connectivity between ecotypes, suggesting they are following discrete evolutionary trajectories. Based on our molecular findings, which seem to be consistent with morphological differentiations recently described for bottlenose dolphins in our study area, we recommend recognizing the offshore bottlenose dolphin ecotype as an additional Evolutionarily Significant Unit (ESU) in the SWA. Implications of these results for the conservation of bottlenose dolphins in SWA are also discussed.

Species are being lost at an unprecedented rate due to human-driven environmental changes. The cases in which species declared extinct can be revived are rare. However, here we report that a remote volcano in the Galápagos Islands hosts many giant tortoises with high ancestry from a species previously declared as extinct: Chelonoidis elephantopus or the Floreana tortoise. Of 150 individuals with distinctive morphology sampled from the volcano, genetic analyses revealed that 65 had C. elephantopus ancestry and thirty-two were translocated from the volcano's slopes to a captive breeding center. A genetically informed captive breeding program now being initiated will, over the next decades, return C. elephantopus tortoises to Floreana Island to serve as engineers of the island's ecosystems. Ironically, it was the haphazard translocations by mariners killing tortoises for food centuries ago that created the unique opportunity to revive this "lost" species today.

Species range limits often fluctuate in space and time in response to variation in environmental factors and to gradual niche evolution due to changes in adaptive traits. We used genome-wide data to investigate evolutionary divergence and species range limits in a generalist and highly dispersive fish species that shows an unusually wide distribution across arid and semi-arid regions of Australia. We generated ddRAD data (18,979 filtered SNPs and 1.725million bp of sequences) for samples from 27 localities spanning the native range of golden perch, Macquaria ambigua (Teleostei; Percichthyidae). Our analytical framework uses population genomics to assess connectivity and population structure using model-based and model-free approaches, phylogenetics to clarify evolutionary relationships, and a coalescent-based Bayesian species delimitation method to assess statistical support of inferred species boundaries. Addressing uncertainties regarding range limits and taxonomy is particularly relevant for this iconic Australian species because of the intensive stocking activities undertaken to support its recreational fishery and its predicted range shifts associated with ongoing climate change. Strong population genomic, phylogenetic, and coalescent species delimitation support was obtained for three separately evolving metapopulation lineages, each lineage should be considered a distinct cryptic species of golden perch. Their range limits match the climate-determined boundaries of main river basins, despite the ability of golden perch to cross drainage divides. We also identified cases suggestive of anthropogenic hybridization between lineages due to stocking of this recreationally important fish, as well as a potential hybrid zone with a temporally stable pattern of admixture. Our work informs on the consequences of aridification in the evolution of aquatic organisms, a topic poorly represented in the literature. It also shows that genome-scale data can substantially improve and rectify inferences about taxonomy, hybridization and conservation management previously proposed by detailed genetic studies., (Copyright © 2017 Elsevier Inc. All rights reserved.)

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 catchment will help to maintain large effective population sizes and maximize species adaptive potential. The approach proposed here could be readily applicable to genetic management of other threatened species to improve their adaptive potential.

Conflicting results from different molecular datasets have long confounded our ability to characterise species boundaries. Here we use genome-wide SNP data and an expanded allozyme dataset to resolve conflicting systematic hypotheses on an enigmatic group of fishes (Gadopsis, river blackfishes, Percichthyidae) restricted to southeastern Australia. Previous work based on three sets of molecular markers: mtDNA, nuclear intron DNA and 51 allozyme loci was unable to clearly resolve the status of a putative fifth candidate species (SWV) within Gadopsis marmoratus. Resolving the taxonomic status of candidate species SWV is particularly critical as based on IUCN criteria this taxon would be considered Critically Endangered. After all filtering steps we retained a subset of 10,862 putatively unlinked SNP loci for population genetic and phylogenomic analyses. Analyses of SNP loci based on maximum likelihood, fastSTRUCTURE and DAPC were all consistent with the previous and updated allozyme results supporting the validity of the candidate Gadopsis species SWV. Immediate conservation actions should focus on preventing take by anglers, protection of water resources to sustain perennial reaches and drought refuge pools, and aquatic and riparian habitat protection and improvement. In addition, a formal morphological taxonomic review of the genus Gadopsis is urgently required., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Captive breeding programmes are often a necessity for the continued persistence of a population or species. They typically have the goal of maintaining genetic diversity and minimizing inbreeding. However, most captive breeding programmes have been based on the assumption that the founding breeders are unrelated and outbred, even though in situ anthropogenic impacts often mean these founders may have high relatedness and substantial inbreeding. In addition, polygamous group-breeding species in captivity often have uncertain pedigrees, making it difficult to select the group composition for subsequent breeding. Molecular-based estimates of relatedness and inbreeding may instead be used to select breeding groups (≥two individuals) that minimize relatedness and filter out inbred individuals. swinger constructs breeding groups based on molecular estimates of relatedness and inbreeding. The number of possible combinations of breeding groups quickly becomes intractable by hand. swinger was designed to overcome this major issue in ex situ conservation biology. The user can specify parameters within swinger to reach breeding solutions that suit the mating system of the target species and available resources. We provide evidence of the efficiency of the software with an empirical example and using simulations. The only data required are a typical molecular marker data set, such as a microsatellite or SNP data set, from which estimates of inbreeding and pairwise relatedness may be obtained. Such molecular data sets are becoming easier to gather from non-model organisms with next-generation sequencing technology. swinger is an open-source software with a user-friendly interface and is available at http://www.molecularecology.flinders.edu.au/molecular-ecology-lab/software/swinger/swinger/ and https://github.com/Yuma248/Swinger., (© 2016 John Wiley & Sons Ltd.)

The recognition of cryptic diversity within geographically widespread species is gradually becoming a trend in the highly speciose Neotropical biomes. The statistical methods to recognise such cryptic lineages are rapidly advancing, but have rarely been applied to genomic-scale datasets. Herein, we used phylogenomic data to investigate phylogenetic history and cryptic diversity within Tropidurus itambere, a lizard endemic to the Cerrado biodiversity hotspot. We applied a series of phylogenetic methods to reconstruct evolutionary relationships and a coalescent Bayesian species delimitation approach (BPP) to clarify species limits. The BPP results suggest that the widespread nominal taxon comprises a complex of 5 highly supported and geographically structured cryptic species. We highlight and discuss the different topological patterns recovered by concatenated and coalescent species tree methods for these closely related lineages. Finally, we suggest that the existence of cryptic lineages in the Cerrado is much more common than traditionally thought, highlighting the value of using NGS data and coalescent techniques to investigate patterns of species diversity., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Understanding how natural selection generates and maintains adaptive genetic diversity in heterogeneous environments is key to predicting the evolutionary response of populations to rapid environmental change. Detecting selection in complex spatial environments remains challenging, especially for threatened species where the effects of strong genetic drift may overwhelm signatures of selection. We carried out a basinwide riverscape genomic analysis in the threatened southern pygmy perch (Nannoperca australis), an ecological specialist with low dispersal potential. High-resolution environmental data and 5162 high-quality filtered SNPs were used to clarify spatial population structure and to assess footprints of selection associated with a steep hydroclimatic gradient and with human disturbance across the naturally and anthropogenically fragmented Murray-Darling Basin (Australia). Our approach included F ST outlier tests to define neutral loci, and a combination of spatially explicit genotype-environment association analyses to identify candidate adaptive loci while controlling for the effects of landscape structure and shared population history. We found low levels of genetic diversity and strong neutral population structure consistent with expectations based on spatial stream hierarchy and life history. In contrast, variables related to precipitation and temperature appeared as the most important environmental surrogates for putatively adaptive genetic variation at both regional and local scales. Human disturbance also influenced the variation in candidate loci for adaptation, but only at a local scale. Our study contributes to understanding of adaptive evolution along naturally and anthropogenically fragmented ecosystems. It also offers a tangible example of the potential contributions of landscape genomics for informing in situ and ex situ conservation management of biodiversity., (© 2016 John Wiley & Sons Ltd.)

The application of high-resolution genetic data has revealed that oceanographic connectivity in marine species with planktonic larvae can be surprisingly limited, even in the absence of major barriers to dispersal. Australia's southern coast represents a particularly interesting system for studying planktonic larval dispersal, as the hydrodynamic regime of the wide continental shelf has potential to facilitate onshore retention of larvae. We used a seascape genetics approach (the joint analysis of genetic data and oceanographic connectivity simulations) to assess population genetic structure and self-recruitment in a broadcast-spawning marine gastropod that exists as a single meta-population throughout its temperate Australian range. Levels of self-recruitment were surprisingly high, and oceanographic connectivity simulations indicated that this was a result of low-velocity nearshore currents promoting the retention of planktonic larvae in the vicinity of natal sites. Even though the model applied here is comparatively simple and assumes that the dispersal of planktonic larvae is passive, we find that oceanography alone is sufficient to explain the high levels of genetic structure and self-recruitment. Our study contributes to growing evidence that sophisticated larval behaviour is not a prerequisite for larval retention in the nearshore region in planktonic-developing species.

Population-level conservation is required to prevent biodiversity loss within a species, but it first necessitates determining the number and distribution of populations. Many whale populations are still depleted due to 20th century whaling. Whales are one of the most logistically difficult and expensive animals to study because of their mobility, pelagic lifestyle and often remote habitat. We tackle the question of population structure in the Antarctic blue whale (Balaenoptera musculus intermedia) - a critically endangered subspecies and the largest extant animal - by capitalizing on the largest genetic dataset to date for Antarctic blue whales. We found evidence of three populations that are sympatric in the Antarctic feeding grounds and likely occupy separate breeding grounds. Our study adds to knowledge of population structure in the Antarctic blue whale. Future research should invest in locating the breeding grounds and migratory routes of Antarctic blue whales through satellite telemetry to confirm their population structure and allow population-level conservation.

Whilst adaptation and phenotypic plasticity might buffer species against habitat degradation associated with global climate change, few studies making such claims also possess the necessary and sufficient data to support them. Doing so requires demonstration of heritable variation in traits affecting fitness under new environmental conditions. We address this issue using an emerging aquatic system to study adaptation to climate change, the crimson-spotted rainbowfish (Melanotaenia duboulayi), a freshwater species from a region of eastern Australia projected to be affected by marked temperature increases. Captive born M. duboulayi of known pedigree were used to assess the long-term effects of contemporary and 2070-projected summer temperatures on the expression of genes previously identified in a climate change transcriptomics (RNA-Seq) experiment. Nearly all genes responded to increasing temperature. Significant additive genetic variance explained a moderate proportion of transcriptional variation for all genes. Most genes also showed broad-sense genetic variation in transcriptional plasticity. Additionally, molecular pathways of candidate genes co-occur with genes inferred to be under climate-mediated selection in wild M. duboulayi populations. Together, these results indicate the presence of existing variation in important physiological traits, and the potential for adaptive responses to a changing thermal environment.

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.)

Background: The smooth marron, Cherax cainii is an important freshwater crustacean species for aquaculture and for a local wild fishery. C. tenuimanus, commonly known as the hairy marron is under threat from environmental impacts and genetic introgression from C. cainii that is hampering the survival of wild C. tenuimanus stocks. Marron are endemic to the south-west of Western Australia and C. tenuimanus is restricted to only the Margaret River., Results: To isolate microsatellite sequences, shotgun 454 pyrosequencing was performed resulting in 184,981 DNA sequence reads. Following screening for microsatellites, 8799 putative microsatellite loci were detected and PCR primers were designed for 968 of these. Ten microsatellite loci were screened in 30 captive C. cainii individuals with eight loci producing unambiguous results. The average number of alleles per locus was 4.7 and average H e was 0.474. Following an analysis of relatedness, 79% of captive dyads were assigned as unrelated. Utilising C. quadricarinatus and C. destructor, cross-species amplification tests were conducted and amplification was achieved at four of the eight loci., Conclusions: Using next-generation sequencing methods, eight polymorphic microsatellite loci were developed from C. cainii, with potential for cross amplification in other Cherax species. The markers can be utilised for studies of natural genetic stock structure and for monitoring relatedness levels and genetic variation in both wild and captive populations.

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.)