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The Australian gummy shark Mustelus antarcticus is distributed across southern and eastern Australian waters and is the main target of a large shark fishery. Commercial harvest of the species is considered sustainable based on biomass estimates that show recovery from past overexploitation. However, the effective population size and genetic-based assessments of stock structure remain unresolved. We evaluated the genetic structure and effective population size (Ne) of the gummy shark using genome-wide single nucleotide polymorphisms. We found genetic divergence between individuals from the east coast and those along the south coast, resulting in 2 discrete populations with signatures of adaptive divergence. Spatial analyses revealed widespread gene flow within each of these populations, with some evidence for mild isolation-by-distance observed using individual-based tests. Demographic modelling of each population showed a comparatively rapid decline of Ne in the most recent past compared to more historical projections, with evidence that such declines have occurred to the point where genetic variation could be at risk. The identification of 2 divergent populations of gummy shark suggests that management should consider each individually to ensure the long-term sustainability of the species.

Widespread degradation across Australia’s inland wetland network has contributed to severe declines for many waterbird species. In contrast, breeding colonies of the Australian white ibis (Threskiornis molucca) have increased in urbanised areas along the coast, but the level of dispersal and gene flow between inland and coastal areas remain unknown. This study uses single nucleotide polymorphisms (SNPs) to ascertain the variables influencing genetic connectivity among several inland and urban colonies of white ibis across south-eastern Australia between 2015 and 2018. The contemporary effective population size was estimated, and this value was used in simulations to evaluate the impact of various management scenarios on future genetic diversity. We found no significant differences in allele frequencies between localities, or robust evidence of site fidelity, therefore suggesting widespread dispersal and gene flow between inland and urban colonies. Furthermore, effective sizes were large enough to maintain genetic diversity into the future under various realistic management scenarios. However, the lack of genetic partitioning found suggests that urban management of the ibis should not be undertaken in isolation of the conservation requirements of inland colonies.

This work was supported by the Australian Research Council (ARC DP130102998 grant to MJW and RWB), Natural Sciences and Engineering Research Council of Canada (scholarship to JLR), the Australasian Society for the Study of Animal Behavior, the Australian Museum, and Macquarie University (scholarship to JLR). The ability to produce viable offspring without recently mating, either through sperm storage or parthenogenesis, can provide fitness advantages under a suite of challenging ecological scenarios. Using genetic analysis, we demonstrate that three wild-caught female Tree Skinks (Egernia striolata) reproduced in captivity with no access to males for over a year, and that this is best explained by sperm storage. To the best of our knowledge, this is the first time female sperm storage has been documented in any monogamous family-living reptile, including social Australian egerniine skinks (from the subfamily Egerniinae). Furthermore, by using paternal reconstruction of genotypes we show that captive-born offspring produced by the same females in the preceding year, presumably without sperm storage, were sired by different males. We qualitatively compared aspects of these females' mates and offspring between years. The parents of each litter were unrelated, but paternal and offspring genotypes from litters resulting from stored sperm were more heterozygous than those inferred to be from recent matings. Family-living egerniine skinks generally have low rates of multiple paternity, yet our study suggests that female sperm storage, potentially from outside social partners, offers the real possibility of benefits. Possible benefits include increasing genetic compatibility of mates and avoiding inbreeding depression via cryptic female choice. Sperm storage in Tree Skinks, a family-living lizard with a monogamous mating system, suggests that females may bet-hedge through extra-pair copulation with more heterozygous males, reinforcing the idea that females could have more control on reproductive outcomes than previously thought. Postprint

Oyster reef habitats are critical to coastal biodiversity and their decline has prompted restoration efforts in Australia. Knowledge gaps exist regarding the population structure and diversity of key species in these habitats. This may be critical information for the design of effective restoration programs. Sydney rock oysters (Saccostrea glomerata) are the dominant reef-forming bivalve in eastern Australia. Wild populations of S. glomerata have declined due to overharvesting, disease outbreaks, coastal development and reduced water quality. Here, we use genetic markers identified by genome-wide sequencing to investigate the genetic structure and diversity of wild Sydney rock oysters throughout their distribution in eastern Australia. We examine evidence for past population bottlenecks and spatial genetic structure associated with the East Australian Current. Analysis of 3, 400 neutral single-nucleotide polymorphisms (SNPs) revealed a single population, and an overlap with two other Saccostrea sp. at the northernmost boundary of the distribution. We detected signals of asymmetric gene flow consistent with the direction of the East Australian Current, and spatial structure patterns of limited genetic isolation by distance and spatial autocorrelation in the northern region (which experiences stronger effects of the East Australian Current) but not in the southern region of the distribution. We found no evidence of significant recent bottlenecks, with high effective population size throughout the species’ range. This information will provide a baseline against which to assess the impact of restoration projects, and guide strategies for sourcing stock for the enhancement of wild oyster populations. Our results provide a positive outlook for the resilience and adaptive capacity of Sydney rock oysters, and highlight wild populations as valuable resources for aquaculture and restoration initiatives.

Local adaptation can occur at small spatial scales relative to the dispersal capacity of species. Alpine ecosystems have sharp environmental clines that offer an opportunity to investigate the effects of fine-scale shifts in species' niche breadth on adaptive genetic processes. Here we examine two grasshopper species endemic to the Australian Alps (Kosciuscola spp.) that differ in elevational niche breadth: one broader, K. usitatus (1400-2200 m), and one narrower, K. tristis (1600-2000 m). We examine signatures of selection with respect to environmental and morphological variables in two mountain regions using FST outlier tests and environmental association analyses (EAAs) applied to single nucleotide polymorphism (SNP) data (K. usitatus: 9017 SNPs, n = 130; K. tristis: 7363 SNPs, n = 135). Stronger genetic structure was found in the more narrowly distributed K. tristis, which showed almost twice the number of SNPs under putative selection (10.8%) compared with K. usitatus (5.3%). When examining SNPs in common across species (n = 3058), 260 SNPs (8.5%) were outliers shared across species, and these were mostly associated with elevation, a proxy for temperature, suggesting parallel adaptive processes in response to climatic drivers. Additive polygenic scores (an estimate of the cumulative signal of selection across all candidate loci) were nonlinearly and positively correlated with elevation in both species. However, a steeper correlation in K. tristis indicated a stronger signal of spatially varying selection towards higher elevations. Our study illustrates that the niche breadth of co-occurring and related species distributed along the same environmental cline is associated with differences in patterns of microgeographical adaptation.

Biogeographic barriers such as rivers have been shown to shape spatial patterns of biodiversity in the Amazon basin, yet relatively little is known about the distribution of genetic variation across continuous rainforest. Here, we characterize the genetic structure of the brilliant-thighed poison frog (Allobates femoralis) across an 880-km-long transect along the Purus-Madeira interfluve south of the Amazon river, based on 64 individuals genotyped at 7609 single-nucleotide polymorphism (SNP) loci. A population tree and clustering analyses revealed 4 distinct genetic groups, one of which was strongly divergent. These genetic groups were concomitant with femoral spot coloration differences, which was intermediate within a zone of admixture between two of the groups. The location of these genetic groups did not consistently correspond to current ecological transitions between major forest types. A multimodel approach to quantify the relative influence of isolation-by-geographic distance (IBD) and isolation-by-environmental resistance (IBR) nevertheless revealed that, in addition to a strong signal of IBD, spatial genetic differentiation was explained by IBR primarily linked to dry season intensity (r2 = 8.4%) and canopy cover (r2 = 6.4%). We show significant phylogenetic divergence in the absence of obvious biogeographical barriers and that finer-scaled measures of genetic structure are associated with environmental variables also known to predict the density of A. femoralis.

While intraspecific variation in aposematic signals can be selected for by different predatory responses, their evolution is also contingent on other processes shaping genetic variation. We evaluate the relative contributions of selection, geographic isolation, and random genetic drift to the evolution of aposematic color polymorphism in the poison frog Adelphobates galactonotus, distributed throughout eastern Brazilian Amazonia. Dorsal coloration was measured for 111 individuals and genetic data were obtained from 220 individuals at two mitochondrial genes (mtDNA) and 7963 Single Nucleotide Polymorphisms (SNPs). Four color categories were described (brown, blue, yellow, orange) and our models of frog and bird visual systems indicated that each color was distinguishable for these taxa. Using outlier and correlative analyses we found no compelling genetic evidence for color being under divergent selection. A time-calibrated mtDNA tree suggests that the present distribution of dorsal coloration resulted from processes occurring during the Pleistocene. Separate phylogenies based on SNPs and mtDNA resolved the same well supported clades, each containing different colored populations. Ancestral character state analysis provided some evidence for evolutionary transitions in color type. Genetic structure was more strongly associated with geographic features, than color category, suggesting that the distribution of color is explained by localized processes. Evidence for geographic isolation together with estimates of low effective population size implicates drift as playing a key role in color diversification. Our results highlight the relevance of considering the neutral processes involved with the evolution of traits with important fitness consequences.

Our knowledge of the conservation status of reptiles, the most diverse class of terrestrial vertebrates, has improved dramatically over the past decade, but still lags behind that of the other tetrapod groups. Here, we conduct the first comprehensive evaluation (~92% of the world’s ~1,714 described species) of the conservation status of skinks (Scincidae), a speciose reptile family with a worldwide distribution. Using International Union for Conservation of Nature (IUCN) criteria, we report that ~20% of species are threatened with extinction, and nine species are Extinct or Extinct in the Wild. The highest levels of threat are evident in Madagascar and the Neotropics, and in the subfamilies Mabuyinae, Eugongylinae and Scincinae. The vast majority of threatened skink species were listed based primarily on their small geographic ranges (Criterion B, 83%; Criterion D2, 13%). Although the population trend of 42% of species was stable, 14% have declining populations. The key threats to skinks are habitat loss due to agriculture, invasive species, and biological resource use (e.g., hunting, timber harvesting). The distributions of 61% of species do not overlap with protected areas. Despite our improved knowledge of the conservation status of the world’s skinks, 8% of species remain to be assessed, and 14% are listed as Data Deficient. The conservation status of almost a quarter of the world’s skink species thus remains unknown. We use our updated knowledge of the conservation status of the group to develop and outline the priorities for the conservation assessment and management of the world’s skink species.

Habitat modification and invasive species are among the most important contemporary drivers of biodiversity loss. These two threatening processes are often studied independently and few studies have focused on how they interact to influence species declines. Here we assess the predation pressure placed on the threatened great desert skink (Liopholis kintorei) and how this interacts with fire‐induced habitat modifications. We collected daily track data of potential predators for 1 month at 30 great desert skink burrow‐systems where vegetation cover varied significantly after experimental burns. We used these data to evaluate potential predation pressure at the burrow‐system and assess whether fire influenced predator pressure. We supplemented this analysis by documenting predation via the inspection of large mammalian predator scats collected from great desert skink habitat. The level of feral cat activity at a burrow‐system entrance was significantly higher than that of any other potential predator, however fire had no effect on the visitation rates of feral cats, dingoes or large snakes to great desert skink burrow‐systems. The remains of great desert skink were found significantly more frequently in feral cat scats, compared to fox and dingo scats. We provide the first direct evidence that feral cats are a significant predator for great desert skink, thus supporting the hypothesis that feral cat predation is a key threatening process. Feral cat activity was not influenced by small‐scale experimental burns, however, this does not preclude an effect of larger scale fires and we recommend further research exploring this possible interaction.

Establishing corridors of connecting habitat has become a mainstay conservation strategy to maintain gene flow and facilitate climate‐driven range shifts. Yet, little attention has been given to ascertaining the extent to which corridors will benefit philopatric species, which might exhibit localized adaptation. Measures of genetic connectivity and adaptive genetic variation across species’ ranges can help fill this knowledge gap. Here, we characterized the spatial genetic structure of Cunningham's skink (Egernia cunninghami), a philopatric species distributed along Australia's Great Dividing Range, and assessed evidence of localized adaptation. Analysis of 4,274 SNPs from 94 individuals sampled at four localities spanning 500 km and 4° of latitude revealed strong genetic structuring at neutral loci (mean F ST ± SD = 0.603 ± 0.237) among the localities. Putatively neutral SNPs and those under divergent selection yielded contrasting spatial patterns, with the latter identifying two genetically distinct clusters. Given low genetic connectivity of the four localities, we suggest that the natural movement rate of this species is insufficient to keep pace with spatial shifts to its climate envelope, irrespective of habitat availability. In addition, our finding of localized adaptation highlights the risk of outbreeding depression should the translocation of individuals be adopted as a conservation management strategy.

Kladothrips (Froggatt) is a genus of gall-inducing thrips that develop broods, and in some species, long-lived colonies within galls they form on phyllodes of Acacia in arid and semi-arid Australia. The gall interior is a stable environment for thrips in an otherwise inhospitable environment, but these conditions may also be favorable for fungal parasites. This fungal threat is corroborated by the observation that Kladothrips produce highly effective antifungal compounds. Here we investigated antifungal production in three Acacia thrips species, two gall-inducers: Kladothrips arotrum and Kladothrips tepperi, and one kleptoparasitic thrips, Koptothrips dyskritus. Using a spectrophotometer, the germination of a suspension of Cordyceps bassiana spores (an entomopathogenic fungus) can be detected by observing an abrupt increase in light absorption by the suspension. The addition of thrips exterior washes to these fungal spore suspensions resulted in significant delays in fungal germination for all three species. Foundresses in both Kladothrips species strongly delay fungal germination before their brood has matured. Young and maturing colonies with less than 50 adult individuals (the remainder of the brood are in juvenile stages of development) produced some antifungal effects but within the range produced by the foundress alone. Mature colonies (>100 adults) delayed germination for the duration of our observational window (48 h), suggesting a possible group size threshold for antifungal effectiveness. Koptothrips dyskritus antifungals were observed to be the strongest of the three species when

Demersal elasmobranchs are ecologically important mesopredators but little is known about their population connectivity or dispersal patterns. Here we use a comparative approach based on mitochondrial DNA and nuclear amplified fragment length polymorphism (AFLP) markers to examine spatial genetic structure and dispersal in three closely related demersal elasmobranchs from eastern Australia: Orectolobus halei, Orectolobus maculatus, and Orectolobus ornatus. We found evidence of significant spatial genetic structure, possibly indicating regional philopatry in wobbegongs. The molecular data also indicate that dispersal in wobbegongs may be sex-biased. This represents the first genetic study of dispersal and population connectivity in codistributed demersal sharks. It provides insights into the ecology of dispersal behaviours with implications for conservation management of demersal species.

Invertebrate pests often show high morphological variation and wide environmental tolerances. Knowledge of how phenotypic variation is associated with environmental heterogeneity can elucidate the processes underpinning these patterns. Here we examine morphological variation and relative abundance along environmental gradients in a widespread agricultural pest, native to Australia, the wingless grasshopper Phaulacridium vittatum (Sjöstedt). We test for correlations between body size, wing presence, and stripe polymorphism with environmental variables. Using multiple regression and mixed-effects modeling, body size and stripe polymorphism were positively associated with solar radiation, and wing presence was positively associated with foliage projective cover (FPC). There were no associations between body size or morphological traits with relative abundance. However, relative abundance was positively associated with latitude, soil moisture, and wind speed, but was negatively associated with FPC. Therefore, sites with low relative abundance and high forest cover were more likely to contain winged individuals. Overall, our results suggest that environmental and climatic conditions strongly influence the relative abundance and the distribution of morphotypes in P. vittatum, which is likely to affect dispersal and fitness in different landscapes. This knowledge is useful for informing how environmental change might influence the future spread and impact of this agricultural pest.

The distribution of biodiversity within the Amazon basin is often structured by sharp environmental boundaries, such as large rivers. The Amazon region is also characterized by subtle environmental clines, but how they might affect the distributions and abundance of organisms has so far received less attention. Here, we test whether soil and forest characteristics are associated with the occurrence and relative abundance of the forest-floor dwelling Aromobatid frog,Allobates femoralis. We applied a structured sampling regime along an 880 km long transect through forest of different density. High detection probabilities were estimated forA. femoralisin each of the sampling modules. Using generalized linear mixed-effects models and simple linear regressions that take detectability into account, we show thatA. femoralisis more abundant in open forests than in dense forests. The presence and relative abundance ofA. femoralisis also positively associated with clay-rich soils, which are poorly drained and therefore likely support the standing water bodies required for reproduction. Taken together, we demonstrate that relatively easy-to-measure environmental features can explain the distribution and abundance of a widespread species at different spatial scales. Such proxies are of clear value to ecologists and conservation managers working in large inaccessible areas such as the Amazon basin.

The lifetime monogamy hypothesis claims that the evolution of permanently unmated worker castes always requires maximal full-sibling relatedness to be established first. The long-lived diploid ambrosia beetle Austroplatypus incompertus (Schedl) is known to be highly social, but whether it has lifetime sterile castes has remained unclear. Here we show that the gallery systems of this beetle inside the heartwood of live Eucalyptus trees are always inhabited by a single core family, consisting of a lifetime-inseminated mother, permanently unmated daughter workers, and immatures that are always full siblings to each other and their adult caretakers. Overall sex ratios are even. Males always disperse and only survive as stored sperm, but female offspring either disperse to mate and found their own colony or assume unmated worker roles, probably surviving for many years without any reproductive potential because tarsal loss precludes later dispersal. A well-supported Platypodinae phylogeny has allowed us to infer that parental monogamy evolved before a lifetime-unmated worker caste emerged, confirming the prediction that monogamy and full-sibling relatedness are necessary conditions for the evolution of such workers. The initially very challenging but ultimately long-term stable nesting habitat in live trees appears to have provided the crucial benefit/cost factor for maintaining selection for permanently sterile workers after strict monogamy and lifetime sperm storage had become established in this curculionid coleopteran lineage.

The Yucatán Peninsula in Mexico contains some of the largest breeding groups of the globally distributed and critically endangered hawksbill turtle (Eretmochelys imbricata). An improved understanding of the breeding system of this species and how its genetic variation is structured among nesting areas is required before the threats to its survival can be properly evaluated. Here, we genotype 1195 hatchlings and 41 nesting females at 12 microsatellite loci to assess levels of multiple paternity, genetic variation and whether individual levels of homozygosity are associated with reproductive success. Of the 50 clutches analyzed, only 6% have multiple paternity. The distribution of pairwise relatedness among nesting localities (rookeries) was not random with elevated within‐rookery relatedness, and declining relatedness with geographic distance indicating some natal philopatry. Although there was no strong evidence that particular rookeries had lost allelic variation via drift, younger turtles had significantly lower levels of genetic variation than older turtles, suggesting some loss of genetic variation. At present there is no indication that levels of genetic variation are associated with measures of reproductive success such as clutch size, hatching success, and frequency of infertile eggs.

Aposematic colouration deters visually oriented predators because conspicuous signals are easier to detect and associate with unpalatability. Consequently, brightly coloured prey that are novel are predicted to be preyed on more than those with bright but typical colours. Here we evaluated whether predatory bias is associated with the colour differences observed at two different localities for a large, conspicuously coloured and poisonous Amazonian frog, Adelphobates galactonotus. At each locality predation experiments were carried out using frog models of two naturally occurring colours of the study species (blue and orange) and a control (brown). We found no evidence that novel colours were more vulnerable to predation than local colours. These results do not therefore support our hypothesis that predatory bias explains the geographic variation of colour in A. galactonotus.

The ability of species to track their climate niche is dependent on their dispersal potential and the connectivity of the landscape matrix linking current and future suitable habitat. However, studies modeling climate-driven range shifts rarely address the movement of species across landscapes realistically, often assuming “unlimited” or “no” dispersal. Here, we incorporate dispersal rate and landscape connectivity with a species distribution model (Maxent) to assess the extent to which the Cunningham’s skink (Egernia cunninghami) may be capable of tracking spatial shifts in suitable habitat as climate changes. Our model was projected onto four contrasting, but equally plausible, scenarios describing futures that are (relative to now) hot/wet, warm/dry, hot/with similar precipitation and warm/wet, at six time horizons with decadal intervals (2020–2070) and at two spatial resolutions: 1 km and 250 m. The size of suitable habitat was projected to decline 23–63% at 1 km and 26–64% at 250 m, by 2070. Combining Maxent output with the dispersal rate of the species and connectivity of the intervening landscape matrix showed that most current populations in regions projected to become unsuitable in the medium to long term, will be unable to shift the distance necessary to reach suitable habitat. In particular, numerous populations currently inhabiting the trailing edge of the species’ range are highly unlikely to be able to disperse fast enough to track climate change. Unless these populations are capable of adaptation they are likely to be extirpated. We note, however, that the core of the species distribution remains suitable across the broad spectrum of climate scenarios considered. Our findings highlight challenges faced by philopatric species and the importance of adaptation for the persistence of peripheral populations under climate change.

Detecting genetic variants under selection using FST outlier analysis (OA) and environmental association analyses (EAAs) are popular approaches that provide insight into the genetic basis of local adaptation. Despite the frequent use of OA and EAA approaches and their increasing attractiveness for detecting signatures of selection, their application to field-based empirical data have not been synthesized. Here, we review 66 empirical studies that use Single Nucleotide Polymorphisms (SNPs) in OA and EAA. We report trends and biases across biological systems, sequencing methods, approaches, parameters, environmental variables and their influence on detecting signatures of selection. We found striking variability in both the use and reporting of environmental data and statistical parameters. For example, linkage disequilibrium among SNPs and numbers of unique SNP associations identified with EAA were rarely reported. The proportion of putatively adaptive SNPs detected varied widely among studies, and decreased with the number of SNPs analysed. We found that genomic sampling effort had a greater impact than biological sampling effort on the proportion of identified SNPs under selection. OA identified a higher proportion of outliers when more individuals were sampled, but this was not the case for EAA. To facilitate repeatability, interpretation and synthesis of studies detecting selection, we recommend that future studies consistently report geographical coordinates, environmental data, model parameters, linkage disequilibrium, and measures of genetic structure. Identifying standards for how OA and EAA studies are designed and reported will aid future transparency and comparability of SNP-based selection studies and help to progress landscape and evolutionary genomics.

International audience; Vocal characteristics can vary among and within populations. In species with geographic variation in the structure of vocalizations, individuals may have the ability to discriminate between calls from local and non-local individuals. The ability to distinguish differences in acoustic signals is likely to have a significant influence on the outcome of social interactions between individuals, including potentially mate selection and breeding success. Pinnipeds (seals, fur seals, sea lions and walruses) are highly vocal yet the Australian sea lion (Neophoca cinerea) is the only eared seal known to show geographic vocal variation in male barks. Barks are produced in many social interactions and encode sufficient information for both individual and colony identity to be discriminable. Yet until now, whether males could themselves discriminate these bark differences was unclear. We performed playback experiments in four breeding colonies to investigate whether males can discriminate local from non-local barks. Overall, males responded more strongly to barks from their own colony compared to barks from other colonies regardless of whether those other colonies were close or distant. Competition for females is high in Australian sea lions, but mating periods are asynchronous across colonies. The ability to correctly assess whether a male is from the same colony, thus representing a potential competitor for mates, or merely a visitor from elsewhere, may influence how males interact with others. Given the high cost of fighting, the ability to discern competitors may influence the nature of male-male interactions and ultimately influence how they allocate reproductive effort.

© 2017 Macmillan Publishers Limited, part of Springer Nature. With overfishing reducing the abundance of marine predators in multiple marine ecosystems, knowledge of genetic structure and local adaptation may provide valuable information to assist sustainable management. Despite recent technological advances, most studies on sharks have used small sets of neutral markers to describe their genetic structure. We used 5517 nuclear single-nucleotide polymorphisms (SNPs) and a mitochondrial DNA (mtDNA) gene to characterize patterns of genetic structure and detect signatures of selection in grey reef sharks (Carcharhinus amblyrhynchos). Using samples from Australia, Indonesia and oceanic reefs in the Indian Ocean, we established that large oceanic distances represent barriers to gene flow, whereas genetic differentiation on continental shelves follows an isolation by distance model. In Australia and Indonesia differentiation at nuclear SNPs was weak, with coral reefs acting as stepping stones maintaining connectivity across large distances. Differentiation of mtDNA was stronger, and more pronounced in females, suggesting sex-biased dispersal. Four independent tests identified a set of loci putatively under selection, indicating that grey reef sharks in eastern Australia are likely under different selective pressures to those in western Australia and Indonesia. Genetic distances averaged across all loci were uncorrelated with genetic distances calculated from outlier loci, supporting the conclusion that different processes underpin genetic divergence in these two data sets. This pattern of heterogeneous genomic differentiation, suggestive of local adaptation, has implications for the conservation of grey reef sharks; furthermore, it highlights that marine species showing little genetic differentiation at neutral loci may exhibit patterns of cryptic genetic structure driven by local selection.Heredity advance online publication, 19 April 2017; doi:10.1038/hdy.2017.21.

For ectotherms such as lizards, the importance of behavioural thermoregulation in avoiding thermal extremes is well-established and is increasingly acknowledged in modern studies of climate warming and its impacts. Less appreciated and understood are the buffering roles of retreat sites and activity phase, in part because of logistical challenges of studying below-ground activity. Burrowing and nocturnal activity are key behavioural adaptations that have enabled a diverse range of reptiles to survive extreme environmental temperatures within hot desert regions. Yet, the direct impact of recent global warming on activity potential has been hypothesised to have caused extinctions in desert lizards, including the Australian arid zone skink Liopholis kintorei. We test the relevance of this hypothesis through a detailed characterisation of the above- and below-ground thermal and hydric microclimates available to, and used by, L. kintorei. We integrate operative temperatures with observed body temperatures to construct daily activity budgets, including the inference of subterranean behaviour. We then assess the likelihood that contemporary and future local extinctions in this species, and those of similar burrowing habits, could be explained by the direct effects of warming on its activity budget and exposure to thermal extremes. We found that L. kintorei spent only 4% of its time active on the surface, primarily at dusk, and that overall potential surface activity will be increased, not restricted, with climate warming. The burrow system provides an exceptional buffer to current and future maximum extremes of temperature (≈40°C reduction from potential surface temperatures), and desiccation (burrows near 100% humidity). Therefore, any climate warming impacts on this species are likely to be indirect. Our findings reflect the general buffering capacity of underground microclimates, therefore, our conclusions for L. kintorei are more generally applicable to nocturnal and crepuscular ectotherms, and highlight the need to consider the buffering properties of retreat sites and activity phase when forecasting climate change impacts.

The European shore crab Carcinus maenas is a highly successful marine invader, and has displayed rapid range expansion following its introduction to many parts of the world. In Australia, it was first reported in Port Phillip Bay, Victoria in the late 1800s. Despite predictions that it would expand its range northward, its distribution has remained limited to the southeast coast of the mainland and to Tasmania. Using microsatellite loci and mitochondrial DNA, we assessed whether low connectivity among southeastern Australian estuaries might be contribut- ing to the limited distribution of this invasive species. Under this hypothesis, we expected that sampling of C. maenas from 6 estuaries, roughly evenly spaced along the southeast coast, would reveal: (1) greater genetic variability among than within estuaries; (2) increasing genetic dissimi- larity with distance from Port Phillip Bay; and (3) in the absence of human-mediated dispersal, declining genetic variation with distance from Port Phillip Bay. Contrary to these predictions, we found that genetic variability was no greater among than within mainland southeast Australian estuaries — indicating significant gene flow. Some slight genetic differentiation was, however, evident between Tasmania and the mainland. Multiple introductions appear to have contributed to the Australian population. The high connectivity of populations among southeast Australian estuaries suggest that management strategies focused on eradication of C. maenas from individ- ual localities will not be effective. Factors other than limited connectivity appear to be responsible for the slow range expansion up the east Australian coast.

SUMMARY 1. Members of the stygofauna are highly specialised invertebrates living within groundwater systems. The hydrographical isolation of groundwater habitats combined with low dispersal abilities of stygofauna has resulted in narrow distributions and high levels of regional endemism. Consequently, stygofauna are particularly vulnerable to disturbance and habitat destruction. Aquifers are under enormous pressure from excessive water extraction, pollution and mining, and the efficient conservation of groundwater ecosystems requires detailed knowledge of dispersal and colonisation capabilities of stygofauna. 2. We investigated fine-scale genetic structure and gene flow in the ancient crustacean Parabathynellidae (Bathynellacea, Syncarida) across a section of the Macquarie River alluvium, New South Wales, Australia. We sampled 175 parabathynellids from eight groundwater monitoring bores at pairwise distances up to 300 m and genotyped each individual at eight microsatellite markers. 3. We found significant intraspecific genetic structuring over short geographical distances (

ABSTBACT The secretion of cuticular antimicrobial compounds is an important defensive mechanism for social insects and recent studies have demonstrated their role in the evolution of sociality. However, the factors that might affect their production and effectiveness are not well understood. For example, natural variation in colony size and genetic diversity are predicted to influence susceptibility to disease and, as a consequence, we hypothesized that colonies adjust by varying antimicrobial production. We examined the effects of colony size and genetic diversity on the antimicrobial properties of cuticular compounds in 10 colonies of the Australian paper wasp, Polistes humilis F. ( Vespidae: Polistinae). The effectiveness of antimicrobial compounds produced by a colony was found to increase with genetic diversity but decrease with colony size. Further, genetic diversity appears to be the stronger factor in determining effectiveness of antimicrobial compounds and may compensate for larger group sizes. These data highlight a possible trade-off between increasing group size for work efficiency and maximizing relatedness for indirect fitness benefits, with disease risk being the underlying driving factor.

Knowledge of genetic structure, geographic distance and environmental heterogeneity can be used to identify environmental features and natural history traits that influence dispersal and gene flow. Foraging mode is a trait that might predict dispersal capacity in snakes, because actively foragers typically have greater movement rates than ambush predators. Here, we test the hypothesis that 2 actively foraging snakes have higher levels of gene flow than 2 ambush predators. We evaluated these 4 co-distributed species of snakes in the Brazilian Amazon. Snakes were sampled along an 880 km transect from the central to the southwest of the Amazon basin, which covered a mosaic of vegetation types and seasonal differences in climate. We analyzed thousands of single nucleotide polymorphisms to compare patterns of neutral gene flow based on isolation by geographic distance (IBD) and environmental resistance (IBR). We show that IBD and IBR were only evident in ambush predators, implying lower levels of dispersal than the active foragers. Therefore, gene flow was high enough in the active foragers analyzed here to prevent any build-up of spatial genotypic structure with respect to geographic distance and environmental heterogeneity. © The American Genetic Association 2017. All rights reserved.

International audience; Describing patterns of connectivity throughout a species range is critical to conservation management. In common with other mammals, pinnipeds typically display male-biased dispersal. Earlier studies using mitochondrial DNA showed that the endangered Australian sea lion (Neophoca cinerea) exhibits extreme matrilineal structure throughout its range. If male dispersal were similarly restricted, most breeding colonies may not receive sufficient levels of new genetic variation to buffer against risks associated with inbreeding and environmental change. To address these concerns we used 16 microsatellite loci to obtain a more highly resolving measure of genetic structure among colonies and determine whether dispersal is male-biased. We found that both male and female Australian sea lions are highly philopatric with limited dispersal. Within those constraints, when animals disperse between close colonies (

The shark genus Mustelus is speciose, commercially important and systematically troublesome. We use a molecular approach combining inter and intra-specific data to investigate Mustelus species in the central Indo-Pacific and Australasia. Our analysis supports two Mustelus clades, one comprising species with no white spots and a placental reproductive mode and a second clade of white spotted, aplacental species. Levels of genetic divergence are low, especially among species in the white spotted, aplacental clade and this should be taken into account when employing molecular data to delineate species. Our data support the hypothesis of a radiation following dispersal from a northern hemisphere ancestor. Molecular dating suggests that localised speciation in Australasia may have occurred during the Pleistocene. We propose that some of the difficulties associated with Mustelus systematics relate to a recent radiation, particularly in the Australasian region.

It has been proposed that limits on habitat availability and the risk of dispersal may have been a driver for the evolution of social behavior in the Egernia group of lizards. To test this hypothesis we sampled 46 individual Egernia striolata from trees in the Pilliga National Park, Australia, where retreat sites appeared abundant and often unoccupied. We collected genetic data at seven microsatellite loci from each individual and show that individuals within the same aggregation were highly related to each other, and that this was significantly different from random (mean 0.208 ± 0.400 SD, P = 0.002). From the geographic distribution of relatedness and parentage analysis we infer that adults can show high levels of site fidelity, and their offspring delayed dispersal from their natal tree. We have therefore provided evidence for kin-based sociality in habitat with abundant retreat sites, thus indicating that limitations on habitat availability are not necessary for social aggregations in this species.

The Australian sea lion, Neophoca cinerea, one of the world’s rarest otariids, is notable for an asynchronous, aseasonal breeding chronology. Determining the ecological features that shape the genetic structure of marine predators such as Australian sea lions is challenging because their demersal foraging habitat is difficult to observe and quantify. Recent developments in stable isotope screening techniques using milk-dependent pups as proxies for maternal isotope signatures identified temporally stable, alternative (inshore and offshore) foraging ecotypes in adult female Australian sea lions. We combined this technique with mitochondrial DNA (mtDNA) analysis of samples of 40–60% of all pups produced at 17 of the largest South Australian colonies to determine whether ecological specialization in foraging ecotype within and between colonies has shaped maternal population structure within the species. Genetic isolation by distance was apparent at very fine geographical scales with three distinct clusters of colonies that share multiple haplotypes being interspersed with isolated breeding sites. There was no congruence between mtDNA haplotype distribution and foraging ecotypes suggesting that observed behavioural specialization was not maintained along matrilines. We propose that foraging specialization within discrete fine-scale foraging areas and habitats at the individual level limits the dispersive capacity of adult female Australian sea lions which in turn drives population structure. Given this species’ vulnerability to anthropogenic impacts and the high degree of female population structure, determining the extent of male-mediated gene flow in this species is critical. Only then can breeding colony connectivity be established and appropriate management units identified for the species.

Rock boulders or ‘bush-rocks’ provide essential habitat for many organisms and there has been interest in rehabilitating areas denuded of rock with artificial substitutes. We examine whether the density and size of bush rock influences the density of the coppertail skink (Ctenotus taeniolatus). The success of habitat rehabilitation is contingent on dispersal of rock-dwelling organisms into areas that have been remediated. To gauge the likelihood of this we characterize geneflow of coppertail skinks among discrete patches of rocky habitat associated with ridge tops. We genotyped 154 individuals from seven localities at six microsatellite DNA loci and from a subset of these individuals we obtained sequence data from the mitochondrial ND4 region. Our field survey established that lizard density was positively associated with the availability of suitably sized bush-rock (P

Estimating paternity patterns provides insights into the importance of competing evolutionary forces on mating systems. The number of sires contributing to a female’s offspring is mostly influenced by her relative promiscuity. However, in a postcopulatory context, it will also be affected by sperm competition and cryptic female choice. Here, we describe the paternity patterns of two species of praying mantis from the genus Ciulfina, the agile praying mantid. This study is the first to describe patterns of paternity in the Mantodea. We found a variation in paternity in these two closely related species. Ciulfina rentzi exhibited single paternity, with a single male siring all offspring within a clutch. By contrast, Ciulfina klassi displayed multiple paternity, with the minimum number of fathers contributing to a clutch ranging from one to four. Differences in copulation duration and reproductive output between these two species may help to explain these paternity patterns.

Grey reef sharks (Carcharhinus amblyrhynchos) are important apex predators on coral reefs, and their numbers have declined dramatically as a result of overfishing. Knowledge of environmental factors that shape gene flow is essential for developing appropriate management strategies, but the lack of suitable genetic markers has hindered research on this species. Here, we characterised 15 polymorphic microsatellite loci for grey reef sharks. None of the loci deviated significantly from Hardy–Weinberg equilibrium and there was no evidence of Linkage Disequilibrium. Several loci cross-amplified in other carcharhinid species, and will be useful in future studies of this family.

We hypothesize that aggregations of animals are likely to attract pathogenic micro-organisms and that this is especially the case for semisocial and eusocial insects where selection ultimately led to group sizes in the thousands or even millions, attracting the epithet ‘superorganism’. Here, we analyse antimicrobial strength, per individual, in eight thrips species (Insecta: Thysanoptera) that present increasing innate group sizes and show that species with the largest group size (100–700) had the strongest antimicrobials, those with smaller groups (10–80) had lower antimicrobial activity, while solitary species showed none. Species with large innate group sizes showed strong antimicrobial activity while the semisocial species showed no activity until group size increased sufficiently to make activity detectable. The eusocial species behaved in a similar way, with detectable activity appearing once group size exceeded 120. These analyses show that antimicrobial strength is determined by innate group size. This suggests that the evolution of sociality that, by definition, increases group size, may have had particular requirements for defences against microbial pathogens. Thus, increase in group size, accompanied by increased antibiotic strength, may have been a critical factor determining the ‘point of no return’, early in the evolution of social insects, beyond which the evolution of social anatomical and morphological traits was irreversible. Our data suggest that traits that increase group size in general are accompanied by increased antimicrobial strength and that this was critical for transitions from solitary to social and eusocial organization.

This study shows a range extension for the Australian blacktip shark Carcharhinus tilstoni, which was believed to be restricted to Australia's tropical waters, of >1000 km into temperate waters, revealing its vulnerability to a wider commercial fishery.

Microbial pathogens were important in the evolution of insect societies and remain a major cause of colony death. The differential effects are reported of antimicrobial compounds extracted from six species of Australian native bees on the spores and hyphae of the entomopathogenic fungus Cordyceps bassiana. The bee species were: Amegilla bombiformis, A. asserta, Exoneura robusta, E. nigrescens, Exoneurella tridentata and Trigona carbonaria. The fungus was isolated from E. robusta and it was this species that showed the greatest activity against both Cordyceps spore germination and hyphal growth. One explanation is that anti-Cordyceps activity may have been under greatest selection in this bee species, but its congener, E. nigrescens, showed only slightly weaker activity against the pathogen. In contrast, A. bombiformis, A. asserta, E. tridentata and T. carbonaria showed considerable variation in anti-Cordyceps activity. Nevertheless, there was a trend of greater activity against Cordyceps spore germination than hyphal growth. On the basis of this result, a mechanism whereby fungal pathogens may have been important drivers of social evolution is suggested.

Loss of sharks and other upper-trophic marine predators has sparked worldwide concern for the stability of ocean ecosystems. The grey nurse (ragged-tooth or sand tiger) shark (Carcharias taurus) is Vulnerable on a global scale, Critically Endangered in Australia and presumed extinct in parts of its historical range. We used 193 muscle and fin samples collected from six extant populations to assess global mtDNA and microsatellite diversity and the degree of global population genetic structure. Control region mtDNA diversity was low in every population, and two populations (eastern Australia and Japan) contained only a single mtDNA haplotype. Genetic signatures of recent losses of genetic variation were not yet apparent at microsatellite loci, indicating that this low mtDNA variation is not a result of anthropogenic population declines. Population differentiation was substantial between each population pair except Brazil and South Africa, F(ST) values ranged from 0.050 to 0.699 and 0.100 to 1.00 for microsatellite and mitochondrial data respectively. Bayesian analysis clearly partitioned individuals into five of the populations from which they were sampled. Our data imply a low frequency of immigrant exchange among each of these regions and we suggest that each be recognized as a distinct evolutionary significant unit. In contrast to pelagic species such as whale shark and white shark that may cross ocean basins and where cooperative international efforts are necessary for conservation, grey nurse shark, like many coastal species, need to be managed regionally.

In the hymenopterans, haplodiploidy, leading to high-genetic relatedness amongst full sisters has been regarded as critical to kin selection and inclusive fitness hypotheses that explain the evolution of eusociality and altruistic behaviours. Recent evidence for independent origins of eusociality in phylogenetically diverse taxa has led to the controversy regarding the general importance of relatedness to eusociality and its evolution. Here, we developed a highly polymorphic microsatellite marker to test whether the eusocial ambrosia beetle Austroplatypus incompertus (Schedl) is haplodiploid or diplodiploid. We found that both males and females of A. incompertus are diploid, signifying that altruistic behaviour resulting from relatedness asymmetries did not play a role in the evolution of eusocialty in this species. This provides additional evidence against the haplodiploidy hypothesis and implicates alternative hypotheses for the evolution of eusociality.

The colonies of ants, bees, wasps and termites, the social insects, consist of large numbers of closely related individuals; circumstances ideal for contagious diseases. Antimicrobial assays of these animals have demonstrated a wide variety of chemical defenses against both bacteria and fungi that can be broadly classified as either external antiseptic compounds or internal immune molecules. Reducing the disease risks inherent in colonies of social insects is also achieved by behaviors, such as multiple mating or dispersal, that lower genetic relatedness both within- and among colonies. The interactions between social insects and their pathogens are complex, as illustrated by some ants that require antimicrobial and behavioral defenses against highly specialized fungi, such as those in the genus Cordyceps that attack larvae and adults and species in the genus Escovopsis that attack their food supplies. Studies of these defenses, especially in ants, have revealed remarkably sophisticated immune systems, including peptides induced by, and specific to, individual bacterial strains. The latter may be the result of the recruitment by the ants of antibiotic-producing bacteria but the extent of such three-way interactions remains unknown. There is strong experimental evidence that the evolution of sociality required dramatic increases in antimicrobial defenses and that microbes have been powerful selective agents. The antimicrobial chemicals and the insect-killing fungi may be useful in medicine and agriculture, respectively.

Declines in shark populations worldwide are of particular concern to fishery managers and conservation biologists. Molecular-based technologies provide an efficient means to collect basic life-history information and estimates of dispersal that are critical to management. A novel method for obtaining high quality mtDNA from shark jaws and teeth for shark population genetic studies is described.

Despite the extensive literature describing the impacts of habitat fragmentation on the distribution and abundance of species, fragmentation effects on life-history strategies have been relatively understudied. Social interactions are important life-history attributes that have fitness consequences for individuals and have been observed to differ among populations in relation to geographic and demographic variability. Therefore, habitat fragmentation is expected to affect social interactions, and these social impacts or responses may contribute to population viability and broad-scale patterns of distribution and abundance in fragmented landscapes. Here we review the emerging literature on this issue. We focus on the impacts of habitat fragmentation that are expected to, or have been observed to, affect social strategies. These include altered resource distribution (e.g., habitat quality, spatial configuration of patches), interspecific interactions (e.g., predator–prey and host–parasite dynamics, human disturbance), and sex (mate availability and inbreeding risk). The studies we cite identified altered social interactions in response to these influences, including changes to home-range overlap, territoriality, group size, and mating systems. The observed changes to social interactions include passive responses, whereby social interactions are affected by constraints introduced by habitat fragmentation, and adaptive social responses to a modified environment. We suggest that future research could focus on individual fitness benefits and on consequences for population viability of altered social interactions in fragmented environments.

Grey reef sharks (Carcharhinus amblyrhynchos) can be one of the numerically dominant high order predators on pristine coral reefs, yet their numbers have declined even in the highly regulated Australian Great Barrier Reef (GBR) Marine Park. Knowledge of both large scale and fine scale genetic connectivity of grey reef sharks is essential for their effective management, but no genetic data are yet available. We investigated grey reef shark genetic structure in the GBR across a 1200 km latitudinal gradient, comparing empirical data with models simulating different levels of migration. The empirical data did not reveal any genetic structuring along the entire latitudinal gradient sampled, suggesting regular widespread dispersal and gene flow of the species throughout most of the GBR. Our simulated datasets indicate that even with substantial migrations (up to 25% of individuals migrating between neighboring reefs) both large scale genetic structure and genotypic spatial autocorrelation at the reef scale were maintained. We suggest that present migration rates therefore exceed this level. These findings have important implications regarding the effectiveness of networks of spatially discontinuous Marine Protected Areas to protect reef sharks.

Despite the role of Australian native bees in important ecological processes, surprisingly little is known of their population structuring. In this study five microsatellite loci were used to investigate genetic structuring of the allodapine bee Exoneura robusta sampled from four locations (maximum pairwise distance c. 35 km) in the Mountain Ash forests of Victoria. Although E. robusta would seem to have high dispersal ability, several analyses show significant population subdivision and a strong pattern of isolation-by-distance from which limited gene flow was inferred. Limited gene flow was not associated with inbreeding at the within-colony level, and within-colony genetic structure implied co-founding, multiple breeding pairs and some degree of reproductive skew. Strong population structure at such fine scales suggests that substantially divergent populations are likely within the extensive distribution currently ascribed to E. robusta.

Anthropogenic impacts are believed to be the primary threats to the eastern Australian population of grey nurse sharks (Carcharias taurus), which is listed as critically endangered, and the most threatened population globally. Analyses of 235 polymorphic amplified fragment length polymorphisms (AFLP) loci and 700 base pairs of mitochondrial DNA control region provide the first account of genetic variation and geographical partitioning (east and west coasts of Australia, South Africa) inC. taurus. Assignment tests, analysis of relatedness andFst values all indicate that the Australian populations are isolated from South Africa, with negligible migration between the east and west Australian coasts. There are significant differences in levels of genetic variation among regions. AustralianC. taurus, particularly the eastern population, has significantly less AFLP variation than the other sampling localities. Further, the eastern Australian sharks possess only a single mitochondrial haplotype, also suggesting a small number of founding individuals. Therefore, historical, rather than anthropogenic processes most likely account for their depauperate genetic variation. These findings have implications for the viability of the eastern Australian population of grey nurse sharks.

Knowledge of processes that lead to genetic erosion for a range of species is important for conservation management. Relatively little work has assessed anthropogenic impacts on genetic variation in lizards. As part of our research program investigating effects of habitat fragmentation on Cunningham’s skink (Egernia cunninghami), allelic diversity at 10 microsatellite loci was assessed in deforested and adjacent naturally vegetated habitats at two locations on the Central tablelands of NSW, Australia. Previously we have shown that deforestation is associated with significantly reduced dispersal, but not increased levels of inbreeding and homozygosity, presumably owing to strong kin avoidance in mate choice. However, in this study, two measures of allelic diversity, allelic richness and the ratio of allele number to size range, indicate that local levels of variability are lower in deforested habitats. Levels of allelic diversity may be expected to decrease more rapidly than levels of heterozygosity, thereby flagging potential longer-term problems, such as inbreeding depression or reduced recruitment because of mate limitation through strong inbreeding avoidance.