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Obtaining reliable estimates of the effective number of breeders (Nb) and generational effective population size (Ne) 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 Nb and Ne 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 Nb and Ne 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 Nb and Ne 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. [ABSTRACT FROM AUTHOR]

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

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. [ABSTRACT FROM AUTHOR]

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

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

Population genomic data sets have enhanced power to detect cryptic and complex population structure and generate valuable information for the conservation and management of wildlife species. Globally, killer whales (Orcinus orca) are considered to have a complex population structure due to their ability to specialize in a variety of ecological niches. In the Australasian region, they are found year round in New Zealand waters and are sighted in all Australian waters, with seasonal aggregations in the northwest (NWA) and southwest (SWA). Regionally, there is some knowledge regarding killer whale abundance, diet, acoustics, and social structure, but limited information about their population structure. Here, we present a population structure assessment of Australasian killer whales using 17,491 high quality genome‐wide single nucleotide polymorphisms (SNPs), combined with sequences of the mitochondrial DNA control region. The results indicate a minimum of three populations: New Zealand, NWA, and SWA. These populations present moderate levels of genomic diversity, negligible levels of inbreeding, small effective population sizes, and low contemporary migration rates among them. Mitochondrial DNA analysis elucidated five closely related haplotypes, suggestive of matrilineal societies, consistent with killer whales elsewhere. This information will assist conservation management of killer whales in the Australasian region. [ABSTRACT FROM AUTHOR]

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

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

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. [ABSTRACT FROM AUTHOR]

Aim: During ecological speciation, reproductive isolation is predicted to evolve between populations adapted to different biotic or abiotic environments despite the absence of geographical isolation. Regions of oceanographic heterogeneity (e.g. current interfaces, habitat transition zones, ecological gradients) are strong candidates for the presence of ecologically divergent natural selection, but their role in the radiation of elasmobranch species is yet to be tested. We used an integrative framework to assess the relative influence of oceanographic heterogeneity and geological history on the diversification of an elasmobranch genus. Location: Gulf of California (GC) and Baja California Peninsula (BCP), Mexico. Taxon: Shovelnose guitarfish (genus Pseudobatos). Methods: We sampled 210 Pseudobatos specimens from four distinct but physically connected oceanographic regions within the GC and in the BCP. We used genetic (mtDNA sequences and AFLP genotypes) and environmental (six oceanographic variables) datasets to clarify phylogenetic relationships, demographic history and evolutionary divergence among populations, and to test for associations between ecologically driven selection and reproductive isolation. Results: Phylogenetic and population genetic evidence exposed five distinct lineages of Pseudobatos in the region, including four cryptic lineages in the GC. Phylogeographic analyses indicate a recent history of ecologically driven diversification associated with the Gulf's young oceanographic environment and its four ecologically discrete regions. This hypothesis was supported by seascape genetics, ecological niche modelling and by tests of selection. Main conclusions: We propose an adaptive radiation for the genus Pseudobatos linked with habitat heterogeneity of the GC. Our study likely represents the first assessment of an ecological radiation in the highly diverse elasmobranch group. It capitalizes on the environmental and biogeographic settings of the GC to offer a new perspective about the application of integrative approaches to study divergent natural selection and diversification in the sea. [ABSTRACT FROM AUTHOR]

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

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. [ABSTRACT FROM AUTHOR]

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 patternwas 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. [ABSTRACT FROM AUTHOR]

Abstract: 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. [ABSTRACT FROM AUTHOR]

Abstract: 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. [ABSTRACT FROM AUTHOR]

Defining species boundaries is important not only for the appropriate attribution of life history and ecological traits but also for sustainable fishery management and for the conservation of biodiversity. Problems arise from taxonomic uncertainty and incorrect species delineation leading to historical misidentification. This is the case of Pacific guitarfishes in the genus Zapteryx. We use a molecular phylogenetic approach combining mitochondrial and nuclear loci to investigate genetic variation in fish along the Mexican Pacific coast. Our analyses reveal a lack of nuclear and mitochondrial distinction between rays identified morphologically as banded guitarfish Z. exasperata and as southern banded guitarfish Z. xyster, casting doubts on the validity of their current systematics. However, we detected two mitochondrial lineages in accordance with the number of species described for the Pacific: a "northern" lineage corresponding to Z. exasperata and a "southern" lineage possibly attributable to Z. xyster. The poorly understood phenotypic plasticity in coloration and size of the evolutionary lineage of Z. exasperata and its apparently wider than currently thought geographic distribution (at least to Oaxaca) are the major sources of confusion regarding the taxonomic and geographic delineation of these nominal species. In light of our findings, eastern Pacific guitarfishes in the genus Zapteryx require a thorough taxonomic revision using morphological and genetic data to unveil what appears to be a complex pattern of diversification. [ABSTRACT FROM AUTHOR]

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 and . [ABSTRACT FROM AUTHOR]

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

Abstract: Genetic methods can be a powerful tool to resolve the native versus introduced status of populations whose taxonomy and biogeography are poorly understood. The genetic study of introduced species is presently dominated by analyses that identify signatures of recent colonization by means of summary statistics. Unfortunately, such approaches cannot be used in low‐dispersal species, in which recently established populations originating from elsewhere in the species' native range also experience periods of low population size because they are founded by few individuals. We tested whether coalescent‐based molecular analyses that provide detailed information about demographic history supported the hypothesis that a sea squirt whose distribution is centered on Tasmania was recently introduced to mainland Australia and New Zealand through human activities. Methods comparing trends in population size (Bayesian Skyline Plots and Approximate Bayesian Computation) were no more informative than summary statistics, likely because of recent intra‐Tasmanian dispersal. However, IMa2 estimates of divergence between putatively native and introduced populations provided information at a temporal scale suitable to differentiate between recent (potentially anthropogenic) introductions and ancient divergence, and indicated that all three non‐Tasmanian populations were founded during the period of European settlement. While this approach can be affected by inaccurate molecular dating, it has considerable (albeit largely unexplored) potential to corroborate nongenetic information in species with limited dispersal capabilities. [ABSTRACT FROM AUTHOR]

The northern Mexican Pacific (NMP), the Gulf of California (GC), and Baja California have been recognized as an ecological and evolutionarily dynamic region having experienced significant tectonic and climatic changes leading to the diversification of terrestrial and marine biotas. Zapteryx exasperata is a predominant ray caught in the artisanal fisheries of the NMP. Morphometric and reproductive differences between rays from the GC and the Pacific coast of Baja California (PCBC) regions suggest the presence of distinct populations. We investigate whether this distinction correlates with differences in genetic diversity and differentiation using sequences of the mitochondrial nicotinamide adenine dinucleotide dehydrogenase subunit 2 (ND2) gene and the noncoding control region (CR) in 63 specimens. Contrary to our expectations, ND2 bore significantly more diversity (h = 0.76) than CR (h = 0.39). Geographic patterns of diversity of CR were opposite to those of ND2, with GC being significantly less (ND2) and more (CR) diverse than PCBC. The diversity of concatenated haplotypes was high (h = 0.84). Low nucleotide diversity suggests the recent coancestry of haplotypes. Marked genetic structure (Φst = 0.23, P < 0.0001) revealed the existence of reproductive isolation and limited matrilineal gene flow between GC and PCBC, which correlates with their phenotypic distinction. These results suggest the influence of factors such as female reproductive philopatry, and ecological or historical vicariant barriers to gene flow. Our results point to the existence of a distinct management unit of banded guitarfish in each region, and add to the increasing evidence attesting to the diversifying nature of this evolutionarily dynamic region. [ABSTRACT FROM PUBLISHER]

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 reaction-restriction 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 (ΦCT = 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 = 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. [ABSTRACT FROM PUBLISHER]

Siphon limpets are an ecologically important component of the intertidal zone of Australia's temperate coast. Using 1/16 of a shotgun pyrosequencing plate, a set of 14 microsatellites was developed for the Van Diemen's siphon limpet ( Siphonaria diemenensis). From 2,744 sequences that contained putative microsatellite motifs, 18 were selected for primer design and tested for amplification. Fourteen microsatellite loci were successfully genotyped in 48 specimens of S. diemenensis from two localities. The number of alleles per locus varied from 5 to 35 (mean = 14.6) and the observed heterozygosity ranged from 0.53 to 0.90 (mean = 0.77). Only one locus showed significant deviation from Hardy-Weinberg equilibrium, probably due to null alleles. No linkage disequilibrium between pairs of loci was detected. Connectivity and seascape genetic studies on siphon limpets using the markers reported here should provide important information for management of temperate Australian marine biodiversity. [ABSTRACT FROM AUTHOR]

Black nerite snails are ecologically important herbivores of the intertidal zone of Australia's temperate marine coast. A set of 13 microsatellites was developed for the black nerite Nerita atramentosa using 1/8 of a shot-gun pyrosequencing reaction. From 46,971 sequences containing putative microsatellite motifs, 18 were selected for primer design. Thirteen microsatellite loci were successfully genotyped using three multiplex reactions in 45 specimens of black nerite from two localities. The number of alleles per locus varied from four to 23 (mean = 12.4) and the observed heterozygosity ranged from 0.40 to 0.96 (mean = 0.72). Only one locus showed significant deviation from Hardy-Weinberg equilibrium probably due to null alleles. No linkage disequilibrium between pairs of loci was detected. These polymorphic markers represent useful tools for connectivity and seascape genetic studies of Australian black nerites. These studies should provide valuable information for the design and assessment of marine protected areas in temperate waters of Australia. [ABSTRACT FROM AUTHOR]