Species composition and hybridisation of mussel species (Bivalvia: Mytilidae) in Australia

Mussels belonging to the Mytilus edulis species complex have been the focus of numerous studies exploring the systematics and origin of this commercially and ecologically important genus. Species have wide geographical ranges and hybridise where their distributions overlap, making identification difficult. Several molecular markers have been used to distinguish between the species within the M. edulis species complex; however, no single marker system has been found to be completely diagnostic, and a combination of markers are used. Here, we used a combination of three nuclear genes and a mitochondrial gene region to assess the species composition of Mytilus mussels collected across its geographical range in Australia. Our results show that the majority (98.5%) of individuals sampled from Australian populations are Mytilus galloprovincialis, with 56.2% of them displaying a southern hemisphere haplotype, 10.3% displaying a putatively northern hemisphere haplotype, and 32% having M. galloprovincialis genotypes consistent with either northern or southern hemisphere M. galloprovincialis lineages. The taxonomic origin of the remaining 1.5% of samples (n ¼ 3) could not be conclusively determined. Our results suggest that there have been significant introductions of non-native M. galloprovincialis lineages into both southern and northern hemisphere populations.

Population genetic structure of serotine bats (Eptesicus serotinus) across Europe and implications for the potential spread of bat rabies (European bat lyssavirus EBLV-1).

Understanding of the movements of species at multiple scales is essential to appreciate patterns of population connectivity and in some cases, the potential for pathogen transmission. The serotine bat (Eptesicus serotinus) is a common and widely distributed species in Europe where it frequently harbours European bat lyssavirus type 1 (EBLV-1), a virus causing rabies and transmissible to humans. In the United Kingdom, it is rare, with a distribution restricted to south of the country and so far the virus has never been found there. We investigated the genetic structure and gene flow of E. serotinus across the England and continental Europe. Greater genetic structuring was found in England compared with continental Europe. Nuclear data suggest a single population on the continent, although further work with more intensive sampling is required to confirm this, while mitochondrial sequences indicate an east-west substructure. In contrast, three distinct populations were found in England using microsatellite markers, and mitochondrial diversity was very low. Evidence of nuclear admixture indicated strong male-mediated gene flow among populations. Differences in connectivity could contribute to the high viral prevalence on the continent in contrast with the United Kingdom. Although the English Channel was previously thought to restrict gene flow, our data indicate relatively frequent movement from the continent to England highlighting the potential for movement of EBLV-1 into the United Kingdom.

Population genetic structure of the red fox (Vulpes vulpes) in the UK

The red fox (Vulpes vulpes) is common and widely distributed within the UK. It is a carrier or potential carrier of numerous zoonotic diseases. Despite this, there are no published reports on the population genetics of foxes in Britain. In this study, we aim to provide an insight into recent historical movement of foxes within Britain, as well as a current assessment of the genetic diversity and gene flow within British populations. We used 14 microsatellite markers to analyse 501 red fox samples originating from England, southern Scotland and northern France. High genetic diversity was evident within the sample set as a whole and limited population genetic structure was present in British samples analysed. Notably, STRUCTURE analysis found support of four population clusters, one of which grouped two southern England sampling areas with the nearby French samples from Calais, indicating recent (post-formation of the Channel) mixing of British and French populations. This may coincide with reports of large-scale translocations of foxes into Britain during the nineteenth century for sport hunting. Other STRUCTURE populations may be related to geographic features or to cultural practices such as fox hunting. In addition, the two British urban populations analysed showed some degree of differentiation from their local rural counterparts.

An endangered arboreal specialist, the western ringtail possum (Pseudocheirus occidentalis), shows a greater genetic divergence across a narrow artificial waterway than a major road

The fragmentation of habitats by roads and other artificial linear structures can have a profound effect on the movement of arboreal species due to their strong fidelity to canopies. Here, we used 12 microsatellite DNA loci to investigate the fine-scale spatial genetic structure and the effects of a major road and a narrow artificial waterway on a population of the endangered western ringtail possum (Pseudocheirus occidentalis) in Busselton, Western Australia. Using spatial autocorrelation analysis, we found positive genetic structure in continuous habitat over distances up to 600 m. These patterns are consistent with the sedentary nature of P. occidentalis and highlight their vulnerability to the effects of habitat fragmentation. Pairwise relatedness values and Bayesian cluster analysis also revealed significant genetic divergences across an artificial waterway, suggesting that it was a barrier to gene flow. By contrast, no genetic divergences were detected across the major road. While studies often focus on roads when assessing the effects of artificial linear structures on wildlife, this study provides an example of an often overlooked artificial linear structure other than a road that has a significant impact on wildlife dispersal leading to genetic subdivision.

A remarkably quick habituation and high use of a rope bridge by an endangered marsupial, the western ringtail possum

Rope bridges are being increasingly installed worldwide to mitigate the negative impacts of roads on arboreal animals. However, monitoring of these structures is still limited and an assessment of factors influencing the crossing behaviours is lacking. We monitored the use of a rope bridge near Busselton, Western Australia by the endangered western ringtail possums (Pseudocheirus occidentalis) in order to identify the patterns of use and factors influencing the crossings. We installed motion sensor cameras and microchip readers on the bridge to record the crossings made by individual animals, and analysed these crossing data using generalised linear models that included factors such as days since the installation of the bridge, breeding season, wind speed, minimum temperature and moonlight. Possums started investigating the bridge even before the installation was completed, and the first complete crossing was recorded only 36 days after the installation, which is remarkably sooner than arboreal species studied in other parts of Australia. The possums crossed the bridge increasingly over 270 days of monitoring at a much higher rate than we expected (8.87 ± 0.59 complete crossings per night). Possums crossed the bridge less on windy nights and warm nights probably due to the risk of being blown away and heat stress on warmer days. Crossings also decreased slightly on brighter nights probably due to the higher risk of predation. Breeding season did not influence the crossings. Pseudocheirus occidentalis habituated to the bridge very quickly, and our results demonstrate that rope bridges have a potential as an effective mitigation measure against the negative impacts of roads on this species. More studies and longer monitoring, as well as investigating whether crossing results in the restoration of gene flow are then needed in order to further assess the true conservation value of these crossing structures.

Multiple dispersal vectors drive range expansion in an invasive marine species

The establishment and subsequent spread of invasive species is widely recognised as one of the most threatening processes contributing to global biodiversity loss. This is especially true for marine and estuarine ecosystems, which have experienced significant increases in the number of invasive species with the increase in global maritime trade. Understanding the rate and mechanisms of range expansion is therefore of significant interest to ecologists and conservation managers alike. Using a combination of population genetic surveys, eDNA plankton sampling and hydrodynamic modelling we examined the patterns of introduction of the predatory Northern Pacific seastar (Asterias amurensis) and pathways of secondary spread within southeast Australia. Genetic surveys across the invasive range reveal some genetic divergence between the two main invasive regions and no evidence of ongoing gene flow; a pattern that is consistent with the establishment of the second invasive region via a human-mediated translocation event. In contrast hydrodynamic modelling combined with eDNA plankton sampling demonstrated that the establishment of range expansion populations within a region is consistent with natural larval dispersal and recruitment. Our results suggest that both anthropogenic and natural dispersal vectors have played an important role in the range expansion of this species in Australia. The multiple modes of spread combined with high levels of fecundity and a long larval duration in A. amurensis suggests it is likely to continue its range expansion and significantly impact Australian marine ecosystems.

Contrasting patterns of population connectivity between regions in a commercially important mollusc Haliotis rubra: integrating population genetics, genomics and marine LiDAR data

Estimating contemporary genetic structure and population connectivity in marine species is challenging, often compromised by genetic markers that lack adequate sensitivity, and unstructured sampling regimes. We show how these limitations can be overcome via the integration of modern genotyping methods and sampling designs guided by LIDAR and SONAR datasets. Here we explore patterns of gene flow and local genetic structure in a commercially harvested abalone species (Haliotis rubra) from South Eastern Australia, where the viability of fishing stocks is believed to be dictated by recruitment from local sources. Using a panel of microsatellite and genome-wide SNP markers we compare allele frequencies across a replicated hierarchical sampling area guided by bathymetric LIDAR imagery. Results indicate high levels of gene flow and no significant genetic structure within or between benthic reef habitats across 1400 km of coastline. These findings differ to those reported for other regions of the fishery indicating that larval supply is likely to be spatially variable, with implications for management and long-term recovery from stock depletion. The study highlights the utility of suitably designed genetic markers and spatially informed sampling strategies for gaining insights into recruitment patterns in benthic marine species, assisting in conservation planning and sustainable management of fisheries.

Dispersal responses override density effects on genetic diversity during post-disturbance succession.

Dispersal fundamentally influences spatial population dynamics but little is known about dispersal variation in landscapes where spatial heterogeneity is generated predominantly by disturbance and succession. We tested the hypothesis that habitat succession following fire inhibits dispersal, leading to declines over time in genetic diversity in the early successional geckoNephrurus stellatus We combined a landscape genetics field study with a spatially explicit simulation experiment to determine whether successional patterns in genetic diversity were driven by habitat-mediated dispersal or demographic effects (declines in population density leading to genetic drift). Initial increases in genetic structure following fire were likely driven by direct mortality and rapid population expansion. Subsequent habitat succession increased resistance to gene flow and decreased dispersal and genetic diversity inN. stellatus Simulated changes in population density alone did not reproduce these results. Habitat-mediated reductions in dispersal, combined with changes in population density, were essential to drive the field-observed patterns. Our study provides a framework for combining demographic, movement and genetic data with simulations to discover the relative influence of demography and dispersal on patterns of landscape genetic structure. Our results suggest that succession can inhibit connectivity among individuals, opening new avenues for understanding how disturbance regimes influence spatial population dynamics.

Genetic structure and sex-biased dispersal of a declining cooperative-breeder, the Grey-crowned Babbler, Pomatostomus temporalis, at the southern edge of its range

Loss and fragmentation of habitat can disrupt genetic exchange between populations, which is reflected in changes to the genetic structure of populations. The Grey-crowned Babbler (Pomatostomus temporalis) is a cooperatively breeding woodland bird, once common and widespread in south-eastern Australia. The species has suffered population declines of >90% across its southern distribution as a result of loss and fragmentation of habitat. We investigated patterns of genetic diversity and population structure of Grey-crowned Babblers in fragmented habitats at the southernmost extent of its range. We sampled blood from 135 individual Babblers from 39 groups stratified into six subpopulations in three regions. Genotypic data were used to estimate genetic diversity, population substructure, local relatedness and dispersal patterns. Individuals showed high heterozygosity within regions, and varying numbers of private alleles among regions suggested differences in levels of connectivity between regions. Four genetic clusters revealed population substructure consistent with treeless landscapes acting as strong barriers to gene flow. In contrast to previous studies,we identified a male-biased dispersal pattern and significant isolation-by-distance patterns for females at fine spatial scales. We recommend that conservation plans for this species incorporate opportunities to increase and enhance corridor areas to facilitate genetic exchange among subpopulations.

Drought survival strategies, dispersal potential and persistence of invertebrate species in an intermittent stream landscape

Intermittent stream systems create a mosaic of aquatic habitat that changes through time, potentially challenging freshwater invertebrate dispersal. Invertebrates inhabiting these mosaics may show stronger dispersal capacity than those in perennial stream systems. To relate different combinations of dispersal and drought survival strategies to species persistence, we compared the distribution and dispersal potential of six invertebrate species across all streams in a montane landscape where drying is becoming increasingly frequent and prolonged. Invertebrates were collected from seventeen streams in the Victoria Range, Grampians National Park, Victoria, Australia. The species analysed were as follows: the caddisflies Lectrides varians Moseley (Leptoceridae) and Agapetus sp. (Glossosomatidae); the mayflies Nousia AV1 and Koorrnonga AV3 (Leptophlebiidae); the water penny beetle Sclerocyphon sp. (Psephenidae); and a freshwater crayfish Geocharax sp. nov. 1 (Parastacidae). These species were widespread in the streams and varied in their dispersal and drought survival strategies. The distribution of each species across the Victoria Range, their drought responses and within-stream habitat associations were determined. Hypotheses of the dispersal capacity and population structure for each species were developed and compared to four models of gene flow: Death Valley Model (DVM), Stream Hierarchy Model (SHM), Headwater Model (HM) or panmixia (PAN). Molecular genetic methods were then used to infer population structure and dispersal capacity for each species. The large caddisfly Lectrides resisted drought through aestivation and was panmictic (PAN) indicating strong dispersal capacity. Conversely, the small caddisfly Agapetus relied on perennially flowing reaches and gene flow was limited to short distances among stream headwaters, resembling the HM. Both mayflies depended on perennial surface water during drying and showed evidence of gene flow among streams: Koorrnonga mainly dispersed along stream channels within catchments, resembling the SHM, whereas Nousia appeared to disperse across land by adult flight. Sclerocyphon relied on perennial water to survive drying and showed an unusual pattern of genetic structure that indicated limited dispersal but did not resemble any of the models. Geocharax survived drought through aestivation or residence in perennial pools, and high levels of genetic structure indicated limited dispersal among streams, resembling the DVM. Despite good knowledge of species' drought survival strategies, the population structure of four species differed from predictions. Dispersal capacity varied strongly among species; most species were poor dispersers and only one species showed panmixia. Therefore, intermittent stream species may not necessarily be better dispersers than those in perennial streams. Species showing strong drought resistance strategies differed in dispersal capacity. Knowledge of life-history characteristics, distribution and refuge use does not necessarily enable successful prediction of invertebrate dispersal pathways or population structure. Dispersal among intermittent streams may be restricted to relatively short distances (km) for most invertebrate species. Thus, frequent drought refuges (perennial water) that provide strong connectivity to subpopulations through stream flow (hydrological dispersal), or continuous terrestrial vegetation (flight dispersal), will be critical to maintain genetic diversity, adaptability and population persistence.

Social structure and landscape genetics of the endemic New Caledonian ant Leptomyrmex pallens Emery, 1883 (Hymenoptera: Formicidae: Dolichoderinae), in the context of fire-induced rainforest fragmentation

Habitat fragmentation is a major threat to biodiversity, as it can alter ecological processes at various spatial and trophic scales. At the species level, fragmentation leading to the isolation of populations can trigger reductions in genetic diversity, potentially having detrimental effects on population fitness, adaptability and ultimately population persistence. Leptomyrmex pallens is a widespread rainforest ant endemic to New Caledonia but now confined to habitat patches that have been fragmented by anthropogenic fire regimes over the last 200 years. We investigated the social structure of L. pallens in the Aoupinié region (c.a. 4900 ha), and assessed the impacts of habitat fragmentation on its population genetic structure. Allele frequencies at 13 polymorphic microsatellite loci were compared among 411 worker ants from 21 nests distributed across the region. High within-nest relatedness (r = 0.70 ± 0.02), and a single queen found in 38 % of the nests by pedigree analysis indicate that the species is monogynous to weakly polygynous. Estimates of gene flow and genetic structure across the region were subsequently determined using a combined dataset of single workers per nest and of unrelated foraging workers. These estimates coupled with a comprehensive landscape genetic analysis revealed no evidence of significant population structure or habitat effects, suggesting that the Aoupinié region harbours a single panmictic population. In contrast, analyses of mitochondrial DNA sequence data revealed a high degree of genetic structuring, indicating limited maternal gene flow and suggesting that gene flow among nests is driven primarily by winged males. Overall these findings suggest that fire-induced habitat fragmentation has had little impact on the population dynamics of L. pallens. Additional studies of less mobile species should therefore be conducted to gain further insights into fire related disturbances on the unique biodiversity and function of New Caledonian ecosystems.

Comparative phylogeography of alpine invertebrates indicates deep lineage diversification and historical refugia in the Australian Alps

Aim: Comparative phylogeographic analyses of alpine biota from the Northern Hemisphere have linked patterns of genetic diversification to glacial expansion and contraction events in the Pliocene and Pleistocene. Furthermore, the extent of diversification across species groups appears to be associated with vagility. In this study we test whether these patterns apply to a geologically stable system from eastern Australia with comparatively shallow elevational gradients and minimal influence from historical glacial activity. Location: The Australian Alps, Victoria, eastern Australia. Methods: We considered phylogeographic patterns across five alpine invertebrate species based on mitochondrial and nuclear DNA sequence data. Bayesian inference methods were used to estimate species phylogenies and divergence times among lineages. GIS tools were used to map interpopulation genetic divergence and intrapopulation genetic diversity estimates and to visualize spatial patterns across species, providing insights into patterns of endemism and demographic history. Results: Phylogeographic patterns and the timing of lineage diversification were consistent across taxonomic groups. Mountain summits harbour highly differentiated haplogroups, including summits connected by high-elevational plateaus, pointing to diversifications being maintained since the early to mid-Pleistocene. These findings are consistent with previous studies of alpine mammals and reptiles, demonstrating a high degree of endemism in this region, regardless of species vagility. Main conclusions: The fine spatial scales at which deep genetic differentiation among alpine communities was observed in this study are unprecedented. This suggests that glacial periods have had less of an impact on species distributions and genetic diversity than they have in alpine systems in the Northern Hemisphere. Historical gene flow among sky-island populations has been limited despite connecting snowlines during glacial periods, suggesting that factors other than snow cover have influenced patterns of gene flow in this region. These findings emphasize the unique phylogeographic history affecting Victorian alpine biodiversity, and the importance of conserving biodiversity from multiple mountain summits in this region of high endemism.

Critically low levels of genetic diversity in fragmented populations of the endangered Glenelg spiny freshwater crayfish Euastacus bispinosus

The Glenelg spiny freshwater crayfish Euastacus bispinosus is a large endangered freshwater invertebrate of southeastern Australia that has suffered major population declines over the last century. Disjunct populations in the state of South Australia are in a particularly critical condition, restricted to a few isolated rising-spring habitats and in an ongoing state of decline. We assessed genetic diversity and gene flow within E. bispinosus across its current range using allele frequencies from 11 nuclear microsatellite loci and DNA sequence data from a single mitochon -drial locus (cytochrome oxidase subunit I). Populations were characterized by low levels of genetic diversity and found to be highly structured, with gene flow restricted both within and across catchments, highlighting the species' vulnerability to further habitat fragmentation and the importance of managing environmental threats on local scales across its current natural range. South Australian populations were characterized by critically low levels of genetic diversity generally, highlighting their potential vulnerability to localized extinction. Holistic conservation efforts are necessary to conserve populations, including local habitat management and, potentially, translocations to increase genetic diversity and evolutionary potential, and reduce possible inbreeding effects and the threat of extinction.

A single panmictic population of endemic red crabs, Gecarcoidea natalis, on Christmas Island with high levels of genetic diversity

The red crab, Gecarcoidea natalis, is endemic to Christmas Island in the Indian Ocean and largely responsible for shaping the unique ecosystem found throughout the island's rainforests. However, the introduction and establishment of supercolonies of the highly invasive yellow crazy ant, Anoplolepis gracilipes, has decimated red crab numbers over the last several decades. This poses a significant risk to the future conservation of G. natalis and consequently threatens the integrity of the unique island ecosystem. Here we undertook a population genetic analysis of G. natalis using a combination of 11 microsatellite markers and sequencing of the mitochondrial cytochrome oxidase subunit I gene from samples collected on Christmas Island as well as a single location from North Keeling Island (located approximately 900 km west of Christmas Island). The genetic results indicate that G. natalis is a single panmictic population on Christmas Island, with no spatial genetic structure or restricted gene flow apparent between sampled locations. Further, G. natalis from North Keeling Island are not genetically distinct and are recent immigrants from Christmas Island. The effective population size of G. natalis has likely remained large and stable on Christmas Island throughout its evolutionary history with relatively moderate to high levels of genetic diversity in microsatellite loci and mitochondrial haplotypes assessed in this study. For management purposes G. natalis can be considered a single panmictic population, which should simplify conservation efforts for the genetic management of this iconic island species. © 2014 Springer Science+Business Media Dordrecht.

The development of 10 novel polymorphic microsatellite markers through next generation sequencing and a preliminary population genetic analysis for the endangered Glenelg spiny crayfish, Euastacus bispinosus

The Glenelg spiny crayfish, Euastacus bispinosus, is an iconic freshwater invertebrate of south eastern Australia and listed as 'endangered' under the Environment Protection and Biodiversity Conservation Act 1999, and 'vulnerable' under the International Union for Conservation of Nature's Red List. The species has suffered major population declines as a result of over-fishing, low environmental flows, the introduction of invasive fish species and habitat degradation. In order to develop an effective conservation strategy, patterns of gene flow, genetic structure and genetic diversity across the species distribution need to be clearly understood. In this study we develop a suite of polymorphic microsatellite markers by next generation sequencing. A total of 15 polymorphic loci were identified and 10 characterized using 22 individuals from the lower Glenelg River. We observed low to moderate genetic variation across most loci (mean number of alleles per locus = 2.80; mean expected heterozygosity = 0.36) with no evidence of individual loci deviating significantly from Hardy-Weinberg equilibrium. Marker independence was confirmed with tests for linkage disequilibrium, and analyses indicated no evidence of null alleles across loci. Individuals from two additional sites (Crawford River, Victoria; Ewens Ponds Conservation Park, South Australia) were genotyped at all 10 loci and a preliminary investigation of genetic diversity and population structure was undertaken. Analyses indicate high levels of genetic differentiation among sample locations (F ST = 0.49), while the Ewens Ponds population is genetically homogeneous, indicating a likely small founder group and ongoing inbreeding. Management actions will be needed to restore genetic diversity in this and possibly other at risk populations. These markers will provide a valuable resource for future population genetic assessments so that an effective framework can be developed for implementing conservation strategies for E. bispinosus.