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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.

An understanding of population structure and connectivity at multiple spatial scales is required to assist wildlife conservation and management. This is particularly critical for widely distributed and highly mobile marine mammals subject to fisheries by-catch. Here, we present a population genomic assessment of a near-top predator, the common dolphin (Delphinus delphis), which is incidentally caught in multiple fisheries across the Australasian region. The study was carried out using 14,799 ddRAD sequenced genome-wide markers genotyped for 478 individuals sampled at multiple spatial scales across Australasia. A complex hierarchical metapopulation structure was identified, with three highly distinct and genetically diverse regional populations at large spatial scales (>1,500 km). The populations inhabit the southern coast of Australia, the eastern coast of Australia, New Zealand, and Tasmania, with the latter also showing a considerable level of admixture to Australia's east coast. Each of these regional populations contained two to four nested local populations (i.e., subpopulations) at finer spatial scales, with most of the gene flow occurring within distances of 50 to 400 km. Estimates of contemporary migration rates between adjacent subpopulations ranged from 6 to 25%. Overall, our findings identified complex common dolphin population structure and connectivity across state and international jurisdictions, including migration and gene flow across the Tasman Sea. The results indicate that inter-jurisdictional collaboration is required to implement conservation management strategies and mitigate fisheries interactions of common dolphins across multiple spatial scales in the Australasian region.

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.

Significance Adaptation to climate change is expected to be influenced by thermal conditions experienced by species during their evolutionary history. We studied plastic capacity as a target of climatic selection, hypothesizing that populations that evolved under warmer climates have greater plastic adaptive resilience to climate change. This was tested experimentally by comparing upper thermal tolerance and gene expression in fish populations from desert, temperate, and subtropical regions of Australia. Divergent adaptive plastic responses to future climates were found across different bioregions, including in key heat stress genes. The greatest adaptive resilience was shown by the subtropical ecotype, followed by the desert and temperate ecotypes. These results have implications for large-scale assessments of climate impacts and for predictions of species distribution changes., 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.

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.

Resilience to environmental stressors due to climate warming is influenced by local adaptations, including the capacity for plastic responses. The recent literature has focussed on genomic signatures of climatic adaptation, however little work has been done to address how plastic capacity may be influenced by biogeographic history and evolutionary processes. Here, we investigate phenotypic plasticity as a target of climatic selection, hypothesising that lineages that evolved under warmer climate will exhibit greater plastic adaptive resilience to thermal stress. This was tested using common garden experiments to compare gene expression regulation within and among a temperate, a subtropical and a desert ecotype of Australian rainbowfish. Individuals from each ecotype were subjected to contemporary and projected summer thermal conditions for 2070, and their global patterns of gene expression were characterized using liver transcriptomes. Critical thermal maximums were also determined for each ecotype to assess thermal tolerance. A comparative phylogenetic expression variance and evolution model framework was used to assess plastic and evolved changes in gene expression. Similar changes in both the direction and the magnitude of expressed genes were found within ecotypes. Although most expressed genes were identified in all ecotypes, 532 genes were identified as candidates subject to ecotype-specific directional selection. Twenty-three of those genes showed signal of adaptive (i.e. genetic-based) plastic response to future increases in temperature. Network analyses demonstrated centrality of these genes in thermal response pathways, along with several highly conserved hub genes thought to be integral for heat stress responses. The greatest adaptive resilience to warming 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, and we stress the need for integrative assessments of climatic adaptive traits for accurate estimations of population and ecosystem responses.

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.

Species that disperse by means of planktonic larvae are typically not genetically structured along environmentally homogeneous coastlines. In contrast, those that lack a planktonic dispersal phase, or species with a short (

The identification of historical, environmental and biological factors influencing metapopulation connectivity is important for informing management policies and for designing conservation areas to protect biodiversity. The brown smooth-hound shark Mustelus henlei is a key component of the Mexican commercial shark fisheries, one of the largest in the world. However, Mexico lacks conservation management policies for this heavily exploited species. We conducted phylogeographic and population genetic analyses using data from mitochondrial and nuclear DNA markers and from oceanographic variables to assess metapopulation connectivity in M. henlei from the Gulf of California and the Pacific coast of Baja California. We report on historical range expansion during the Pleistocene, probably associated with the last stages of formation of the Gulf of California. From a contemporary perspective, there is significant population structure explained by spatial distance (but not by environmental factors), which contrasts with expectations of high dispersal capacity for this shark. Populationand individual-based genetic analyses suggest that both female philopatry and male-biased dispersal impact on metapopulation structure. These results highlight the importance of protecting nursery areas and habitat connectivity for the conservation management of the species. Our study clarifies important biological aspects of the brown smooth-hound shark that have implications for the design of shark management policies and marine protected areas in the Gulf of California, an iconic marine ecosystem of global significance.

Broadcast-spawning marine organisms with long pelagic larval duration are often expected to be genetically homogeneous throughout their ranges. When genetic structure is found in such taxa, it may be in the form of chaotic genetic patchiness: i.e. patterns that might seem independent of any un- derlying environmental variation. The joint analysis of population genetic data and marine environmental data can elucidate factors driving such spatial genetic diversity patterns. Using meso-scale sampling (at a scale of 10s to 100s of km), microsatellite data and advection connectivity simulations, we studied the effect of temperate southern Australian ocean circu - lation on the genetic structure of the snail Nerita atramentosa. This species has a long pelagic larval duration and is represented as a single metapopula- tion throughout its ~3000 km range, but even so, we found that its dispersal potential is lower than ex- pected. Connectivity simulations indicate that this is a result of the larvae that remain on the continental shelf (where currents are erratic and often shoreward) re- turning to the coast in much larger numbers than lar- vae that become entrained in the region's shelf-edge boundary currents. Our study contributes to the growing evidence that departures from the expecta- tions of panmixia along continuous and environ - mentally homogeneous coastlines are not limited to low-dispersal species, and it identifies on-shelf larval retention as an important factor limiting dispersal.

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 FST = 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.

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.

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/, 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.

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.

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.

Assessing the realized effect of dispersal in the genetic makeup of a species has significant evolutionary, ecological, and economical consequences. Here, we investigate the genetic diversity and population differentiation in the aquilopelagic golden cownose ray Rhinoptera steindachneri from the Gulf of California (GC) and the Pacific coast of Baja California (PCBC) using the mitochondrial NADH2 gene. Low levels of genetic diversity were found with only 4 polymerase chain reactionrestriction fragment length polymorphism haplotypes among 76 specimens. Pacific coast organisms were fixed for a unique haplotype not shared with rays from the gulf; 92% of GC rays possessed a single NADH2 haplotype not found in the Pacific. This produced significant differentiation between the GC and the PCBC (UCT 5 0.972, P , 0.001). A pronounced phylogeographic pattern was found in which GC haplotypes were reciprocally monophyletic relative to a very divergent Pacific lineage (d 5 10%). Our results indicate that despite high dispersal potential, GC and PCBC golden cownose ray populations are characterized by highly divergent mitochondrial lineages. Although more evidence is needed to corroborate the genetic isolation and systematic status of PCBC and GC golden cownose rays, our results suggest a possible cryptic species in the region.