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.

Life history influences how fire affects genetic diversity in two lizard species

'Fire mosaics' are often maintained in landscapes to promote successional diversity in vegetation with little understanding of how this will affect ecological processes in animal populations such as dispersal, social organization and re-establishment. To investigate these processes, we conducted a replicated, spatiotemporal landscape genetics study of two Australian woodland lizard species [Amphibolurus norrisi (Agamidae) and Ctenotus atlas (Scincidae)]. Agamids have a more complex social and territory structure than skinks, so fire might have a greater impact on their population structure and thus genetic diversity. Genetic diversity increased with time since fire in C. atlas and decreased with time since fire in A. norrisi. For C. atlas, this might reflect its increasing population size after fire, but we could not detect increased gene flow that would reduce the loss of genetic diversity through genetic drift. Using landscape resistance analyses, we found no evidence that postfire habitat succession or topography affected gene flow in either species and we were unable to distinguish between survival and immigration as modes of postfire re-establishment. In A. norrisi, we detected female-biased dispersal, likely reflecting its territorial social structure and polygynous mating system. The increased genetic diversity in A. norrisi in recently burnt habitat might reflect a temporary disruption of its territoriality and increased male dispersal, a hypothesis that was supported with a simulation experiment. Our results suggest that the effects of disturbance on genetic diversity will be stronger for species with territorial social organization.

Genetic analyses reveal limited dispersal and recovery potential in the large freshwater crayfish Euastacus armatus from the southern Murray-Darling Basin

Understanding dispersal traits and adaptive potential is critically important when assessing the vulnerability of freshwater species in highly modified ecosystems. The present study investigates the population genetic structure of the Murray crayfish Euastacus armatus in the southern Murray–Darling Basin. This species has suffered significant population declines in sections of the Murray River in recent years, prompting the need for information on natural recruitment processes to help guide conservation. We assessed allele frequencies from 10 polymorphic microsatellite loci across 20 sites encompassing the majority of the species’ range. Low levels of gene flow were observed throughout hydrologically connected waterways, but significant spatial autocorrelation and low migration rate estimates reflect local genetic structuring and dispersal limitations, with home ranges limited to distances <50-km. Significant genetic differentiation of headwater populations upstream of barriers imposed by impoundments were also observed; however, population simulations demonstrate that these patterns likely reflect historical limitations to gene flow rather than contemporary anthropogenic impacts. Dispersal limitations, coupled with its biological traits, suggest that local populations are vulnerable to environmental disturbance with limited potential for natural recolonisation following population decline. We discuss the implications of these findings in the context of managing the recovery of the species.

Fine-scale effects of habitat loss and fragmentation despite large-scale gene flow for some regionally declining woodland bird species

Habitat loss and associated fragmentation effects are well-recognised threats to biodiversity. Loss of functional connectivity (mobility, gene flow and demographic continuity) could result in population decline in altered habitat, because smaller, isolated populations are more vulnerable to extinction. We tested whether substantial habitat reduction plus fragmentation is associated with reduced gene flow in three 'decliner' woodland-dependent bird species (eastern yellow robin, weebill and spotted pardalote) identified in earlier work to have declined disproportionately in heavily fragmented landscapes in the Box-Ironbark forest region in north-central Victoria, Australia. For these three decliners, and one 'tolerant' species (striated pardalote), we compared patterns of genetic diversity, relatedness, effective population size, sex-ratios and genic (allele frequency) differentiation among landscapes of different total tree cover, identified population subdivision at the regional scale, and explored fine-scale genotypic (individual-based genetic signature) structure. Unexpectedly high genetic connectivity across the study region was detected for 'decliner' and 'tolerant' species. Power analysis simulations suggest that moderate reductions in gene flow should have been detectable. However, there was evidence of local negative effects of reduced habitat extent and structural connectivity: slightly lower effective population sizes, lower genetic diversity, higher within-site relatedness and altered sex-ratios (for weebill and eastern yellow robin) in 10 x 10 km 'landscapes' with low vegetation cover. We conclude that reduced structural connectivity in the Box-Ironbark ecosystem may still allow sufficient gene flow to avoid the harmful effects of inbreeding in our study species. Although there may still be negative consequences of fragmentation for demographic connectivity, the high genetic connectivity of mobile bird species in this system suggests that reconnecting isolated habitat patches may be less important than increasing habitat extent and/or quality if these need to be traded off.

Biogeographic models of gene flow in two waterfowl of the Australo-Papuan tropics

There are many large, easy-to-observe anseriform birds (ducks, geese, and swans) in northern Australia and New Guinea and they often gather in large numbers. Yet, the structure of their populations and their regional movements are poorly understood. Lack of understanding of population structure limits our capacity to understand source-sink dynamics relevant to their conservation or assess risks associated with avian-borne pathogens, in particular, avian influenza for which waterfowl are the main reservoir species. We set out to assess present-day genetic connectivity between populations of two widely distributed waterfowl in the Australo-Papuan tropics, magpie goose Anseranas semipalmata (Latham, 1798) and wandering whistling-duck Dendrocygna arcuata (Horsfield, 1824). Microsatellite data were obtained from 237 magpie geese and 64 wandering whistling-duck. Samples were collected across northern Australia, and at one site each in New Guinea and Timor Leste. In the wandering whistling-duck, genetic diversity was significantly apportioned by region and sampling location. For this species, the best model of population structure was New Guinea as the source population for all other populations. One remarkable result for this species was genetic separation of two flocks sampled contemporaneously on Cape York Peninsula only a few kilometers apart. In contrast, evidence for population structure was much weaker in the magpie goose, and Cape York as the source population provided the best fit to the observed structure. The fine scale genetic structure observed in wandering whistling-duck and magpie goose is consistent with earlier suggestions that the west-coast of Cape York Peninsula is a flyway for Australo-Papuan anseriforms between Australia and New Guinea across Torres Strait.

Population genetic structure, gene flow and sex-biased dispersal in frillneck lizards (Chlamydosaurus kingii)

By using both mitochondrial and nuclear multiloci markers, we explored population genetic structure, gene flow and sex-specific dispersal of frillneck lizards (Chlamydosaurus kingii) sampled at three locations, separated by 10 to 50 km, in a homogenous savannah woodland in tropical Australia. Apart from a recombinant lizard, the mitochondrial analyses revealed two nonoverlapping haplotypes/populations, while the nuclear markers showed that the frillneck lizards represented three separate clusters/populations. Due to the small population size of the mtDNA, fixation may occur via founder effects and/or drift. We therefore suggest that either of these two processes, or a combination of the two, are the most likely causes of the discordant results obtained from the mitochondrial and the nuclear markers. In contrast to the nonoverlapping mitochondrial haplotypes, in 12 out of 74 lizards, mixed nuclear genotypes were observed, hence revealing a limited nuclear gene flow. Although gene flow should ultimately result in a blending of the populations, we propose that the distinct nuclear population structure is maintained by frequent fires resulting in local bottlenecks, and concomitant spatial separation of the frillneck lizard populations. Limited mark-recapture data and the difference in distribution of the mitochondrial and nuclear markers suggest that the mixed nuclear genotypes were caused by juvenile male-biased dispersal.

Population genetic structuring in Acanthopagrus butcheri (Pisces: Sparidae): does low gene flow among estuaries apply to both sexes?

Acanthopagrus butcheri completes its entire life history within estuaries and coastal lakes of southern Australia, although adults occasionally move between estuaries via the sea. Consequently, it is expected that populations of A. butcheri in different estuaries will be genetically distinct, with the magnitude of genetic divergence increasing with geographic isolation. However, previous genetic studies of A. butcheri from southeast Australia yielded conflicting results; allozyme variation exhibited minimal spatial structuring (θ = 0.012), whereas mitochondrial DNA distinguished the majority of populations analyzed (θ = 0.263) and genetic divergence was positively correlated with geographic isolation. This discrepancy could reflect high male gene flow, which impacts nuclear but not mitochondrial markers. Here we estimated allele frequencies at five nuclear microsatellite loci across 11 southeast Australian populations (595 individuals). Overall structuring of microsatellite variation was weaker (θ = 0.088) than that observed for mitochondrial DNA, but was able to distinguish a greater number of populations and was positively correlated with geographic distance. Therefore, we reject high male gene flow and invoke a stepping-stone model of infrequent gene flow among estuaries for both sexes. Likewise, management of A. butcheri within the study range should be conducted at the scale of individual or geographically proximate estuaries for both sexes. The lack of allozyme structuring in southeast Australia reflects either the large variance in structuring expected among loci under neutral conditions and the low number of allozymes surveyed or a recent colonization of estuaries such that some but not all nuclear loci have approached migration-drift equilibrium.

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.

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.

Genetic diversity and translocation in the marron, Cherax tenuimanus (Smith): implications for management and conservation

Approximately 440 base pairs (bp) of the mitochondrial 16S ribosomal ribose nucleic acid (rRNA) coding region were sequenced from 13 marron, Cherax tenuimanus (Smith), samples from six locations and samples of two additional Cherax species from Western Australia. The results indicated that, with the exception of the Margaret River, no variation was found within or between marron populations. In contrast, marron from the Margaret River were found to be polymorphic for two divergent haplotypes (2.76% divergence). These findings were consistent with allozyme data that highlight the general lack of genetic variability within and between populations of this species apart from the Margaret River stocks. The genetic polymorphisms in the Margaret River stocks contrasted with earlier studies and indicated the recent translocation and mixing of genetically differentiated stocks within this river system. The implications of these findings for the conservation and management of genetic diversity within marron are discussed.

Genetic diversity of brown and rainbow trout in Australia

Australian rainbow and brown trout were analysed using molecular genetic techniques to determine the effect translocation has had on the existing gene pool. There was some indication of loss of diversity associated with their translocation however no differences in genetic diversity between Australian hatchery and wild populations were apparent.

Conservation of genetic diversity in British populations of the diploid endemic Coincya monensis ssp monensis (Isle of Man Cabbage): the risk of hybridisation with the tetraploid alien, Coincya monensis ssp cheiranthos

Coincya monensis is represented in the British flora by two, cytologically distinct subspecies. Coincya monensis ssp monensis is an endemic diploid with a coastal sand dune distribution that includes a number of isolated populations. Coincya monensis ssp cheiranthos is a tetraploid alien, well established in South Wales in early successional habitats. Both subspecies share similar life form traits, flowering times and pollinators. Cluster analysis and phylogenetic reconstruction based on sequences of the mitochondrial nad4 gene confirmed the distinction between alien and endemic taxa. Tetraploid populations carry more polymorphic RAPDs loci and their genetic diversity is partitioned more within than among populations. In contrast, C. monensis ssp monensis has a distinct population genetic structure. Analysis of the multilocus genetic data confirmed a structure of genetically isolated, endemic population clusters in Scotland, Arran, the Isle of Man and South Wales. Experimental hybridisation showed the two subspecies are interfertile. Multivariate analysis of RAPDs data resolved hybrids between alien and endemic clusters and hybrids contained a proportion of alien-specific polymorphic loci. Hybrids of alien maternal parentage contained the mitochondrial nad4 sequence characteristic of the alien subspecies. Since the alien subspecies can invade mobile sand dune communities from urban sites and compete for pollinators, there is a risk that alien and endemic populations will mix and introgress. Conservation of endemic genetic diversity in Britain will require protection for all C. monensis ssp monensis populations. Currently, the most disjunct endemic population in South Wales is most at risk from introgression.

High genetic diversity is not essential for successful introduction

Some introduced populations thrive and evolve despite the presumed loss of diversity at introduction. We aimed to quantify the amount of genetic diversity retained at introduction in species that have shown evidence of adaptation to their introduced environments. Samples were taken from native and introduced ranges of Arctotheca populifolia and Petrorhagia nanteuilii. Using microsatellite data, we identified the source for each introduction, estimated genetic diversity in native and introduced populations and calculated the amount of diversity retained in introduced populations. These values were compared to those from a literature review of diversity in native, confamilial populations and to estimates of genetic diversity retained at introduction. Gene diversity in the native range of both species was significantly lower than for confamilials. We found that, on average, introduced populations showing evidence of adaptation to their new environments retained 81% of the genetic diversity from the native range. Introduced populations of P. nanteuilii had higher genetic diversity than found in the native source populations, whereas introduced populations of A. populifolia retained only 14% of its native diversity in one introduction and 1% in another. Our literature review has shown that most introductions demonstrating adaptive ability have lost diversity upon introduction. The two species studied here had exceptionally low native range genetic diversity. Further, the two introductions of A. populifolia represent the largest percentage loss of genetic diversity in a species showing evidence of substantial morphological change in the introduced range. While high genetic diversity may increase the likelihood of invasion success, the species examined here adapted to their new environments with very little neutral genetic diversity. This finding suggests that even introductions founded by small numbers of individuals have the potential to become invasive.

Gene flow in east antarctic echinoderms and resilience to climate change

The spatial scales of population genetic structure in three species of Antarctic echinoderm, Sterechinus neumayeri, Abatus nimrodi and Abatus ingens was quantified using mitochondrial sequences and a novel set of microsatellite markers. Reduced fertilisation success in S. neumayeri resulting from increasing temperature and decreasing salinity was also identified.