Limited population structure, genetic drift and bottlenecks characterise an endangered bird species in a dynamic, fire-prone ecosystem

Fire is a major disturbance process in many ecosystems world-wide, resulting in spatially and temporally dynamic landscapes. For populations occupying such environments, fire-induced landscape change is likely to influence population processes, and genetic patterns and structure among populations. The Mallee Emu-wren Stipiturus mallee is an endangered passerine whose global distribution is confined to fire-prone, semi-arid mallee shrublands in south-eastern Australia. This species, with poor capacity for dispersal, has undergone a precipitous reduction in distribution and numbers in recent decades. We used genetic analyses of 11 length-variable, nuclear loci to examine population structure and processes within this species, across its global range. Populations of the Mallee Emu-wren exhibited a low to moderate level of genetic diversity, and evidence of bottlenecks and genetic drift. Bayesian clustering methods revealed weak genetic population structure across the species' range. The direct effects of large fires, together with associated changes in the spatial and temporal patterns of suitable habitat, have the potential to cause population bottlenecks, serial local extinctions and subsequent recolonisation, all of which may interact to erode and homogenise genetic diversity in this species. Movement among temporally and spatially shifting habitat, appears to maintain long-term genetic connectivity. A plausible explanation for the observed genetic patterns is that, following extensive fires, recolonisation exceeds in-situ survival as the primary driver of population recovery in this species. These findings suggest that dynamic, fire-dominated landscapes can drive genetic homogenisation of populations of species with low-mobility and specialised habitat that otherwise would be expected to show strongly structured populations. Such effects must be considered when formulating management actions to conserve species in fire-prone systems.

Genetic connectivity between trans-oceanic populations of Capreolia implexa (Gelidiales, Rhodophyta) in cool temperate waters of Australasia and Chile.

Capreolia is a monospecific genus of gelidioid red algae and has been considered to be endemic to Australasia. This is the first report on the occurrence of Capreolia implexa outside of Australasian waters, based on investigations of fresh collections in southern Chile as well as Australia and New Zealand. Thalli are prostrate and form entangled turfs, growing on high intertidal rocks at three locations in Chile. Analyses of rbcL and cox1 revealed that C. implexa was of Australasian origin and also distinct from its relatives. Analyses of 1356. bp of cox1 revealed cryptic diversity, consisting of two genealogical groups within C. implexa; one present in Australia and New Zealand, and the other in Chile and Stewart Island, New Zealand. The extremely low genetic diversity found in C. implexa in Chile and the absence of shared haplotypes between Chile and Australasia suggest genetic bottleneck possibly as a result of colonization after dispersal by rafting from Stewart Island, New Zealand to Chile. © 2014 Elsevier B.V.

Differing impact of a major biogeographic barrier on genetic structure in two large kangaroos from the monsoon tropics of Northern Australia

Tropical savannas cover 20-30% of the world's land surface and exhibit high levels of regional endemism, but the evolutionary histories of their biota remain poorly studied. The most extensive and unmodified tropical savannas occur in Northern Australia, and recent studies suggest this region supports high levels of previously undetected genetic diversity. To examine the importance of barriers to gene flow and the environmental history of Northern Australia in influencing patterns of diversity, we investigated the phylogeography of two closely related, large, vagile macropodid marsupials, the antilopine wallaroo (Macropus antilopinus; n = 78), and the common wallaroo (Macropus robustus; n = 21). Both species are widespread across the tropical savannas of Australia except across the Carpentarian Barrier (CB) where there is a break in the distribution of M. antilopinus. We determined sequence variation in the hypervariable Domain I of the mitochondrial DNA control region and genotyped individuals at 12 polymorphic microsatellite loci to assess the historical and contemporary influence of the CB on these species. Surprisingly, we detected only limited differentiation between the disjunct Northern Territory and QueenslandM. antilopinus populations. In contrast, the continuously distributedM. robustus was highly divergent across the CB. Although unexpected, these contrasting responses appear related to minor differences in species biology. Our results suggest that vicariance may not explain well the phylogeographic patterns in Australia's dynamic monsoonal environments. This is because Quaternary environmental changes in this region have been complex, and diverse individual species' biologies have resulted in less predictable and idiosyncratic responses.

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.

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.

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.

Genetic analysis along an invasion pathway reveals endemic cryptic taxa, but a single species with little population structure in the introduced range

The invasion pathways of pest arthropods can be traced using genetic tools to develop an understanding of the processes that have shaped successful invasions and to inform both pest management and conservation strategies in their non-native and native ranges, respectively. The redlegged earth mite, Halotydeus destructor, is a major economic pest in Australia, successfully establishing and spreading after arrival from South Africa more than 100 years ago. Halotydeus destructor has recently expanded its range and evolved resistance to numerous pesticides in Australia, raising questions around its origin and spread. Location: South Africa and Australia. Methods: We sampled H. destructor populations in South Africa and Australia and developed a microsatellite marker library. We then examined genetic variation using mtDNA and microsatellite markers across both native and invasive ranges to determine endemic genetic diversity within South Africa, identify the likely origin of invasive populations and test genetic divergence across Australia. Results: The data show that H. destructor comprises a cryptic species complex in South Africa, with putative climatic/host plant associations that may correspond to regional variation. A lineage similar to that found near Cape Town has spread throughout Western and eastern Australia, where populations remain genetically similar. Main conclusions: Tracing the invasion pathway of this economically important pest revealed cryptic lineages in South Africa which points to the need for a taxonomic revision. The absence of significant genetic structure across the wide invasive range of H. destructor within Australia has implications for the development (and spread) of pesticide resistance and also points to recent local adaptation in physiological traits.

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.

Three molecular markers show no evidence of population genetic structure in the gouldian finch (Erythrura gouldiae)

Assessment of genetic diversity and connectivity between regions can inform conservation managers about risk of inbreeding, potential for adaptation and where population boundaries lie. The Gouldian finch (Erythrura gouldiae) is a threatened species in northern Australia, occupying the savannah woodlands of the biogeographically complex monsoon tropics. We present the most comprehensive population genetic analysis of diversity and structure the Gouldian finch using 16 microsatellite markers, mitochondrial control region and 3,389 SNPs from genotyping-by-sequencing. Mitochondrial diversity is compared across three related, co-distributed finches with different conservation threat-statuses. There was no evidence of genetic differentiation across the western part of the range in any of the molecular markers, and haplotype diversity but not richness was lower than a common co-distributed species. Individuals within the panmictic population in the west may be highly dispersive within this wide area, and we urge caution when interpreting anecdotal observations of changes to the distribution and/or flock sizes of Gouldian finch populations as evidence of overall changes to the population size of this species.

Dasyurid dilemmas: problems and solutions for conserving Australia's small carnivorous marsupials

Dasyurid marsupials are distributed throughout the major terrestrial environments of Australia but since European settlement have suffered local and regional extinctions, range reductions and population declines. In this paper we examine the conservation status of small dasyurids (<500 g) and the threats they face. We also evaluate recovery procedures for threatened taxa and assess their success. Twenty-four percent of smaller dasyurids are classified as vulnerable, endangered or data deficient. Large body size and occupancy of one or two habitat types are correlated strongly with  endangerment species currently considered as 'low risk, near threatened' group closely with vulnerable and endangered species, indicating a risk of further declines. The processes contributing most to declines include habitat loss and fragmentation, altered fire regimes and predation. As of April 200 I, no Recovery Plans had been adopted by the Commonwealth Govemment for any small dasyund species. There is much information on the reproduction and development of smaller dasyurids, making them suitable for captive breeding. However, captive breeding programs have been limited. the  dibbler Paranrechinus apicalis being the only species bred systematically for reintroductions. There is a need for integration between captive breeding programs and recovery planning. as well as for more information on the population viability and metapopulation structures of small dasyurids genetic diversity of populations and inbreeding depression. We suggest a program of survey. research. management and education to Improve conservation outcomes for all small dasyurids.

Microsatellite DNA analysis of southeast Australian Haliotis laevigata (Donovan) populations - implications for ranching in Port Phillip Bay

The genetic composition of greenlip abalone (Haliotis laevigata) from Point Cook in Port Phillip Bay was examined prior to the aggregation of individuals from this site for ranching. The very thinly distributed natural population at Point Cook was believed to be of low genetic diversity, because the animals all originated from a single spawning event 5 y previously. Animals from Point Cook were compared with other H. laevigata from two sampling sites within Port Phillip Bay, and two sites outside the Bay in Bass Strait, to examine their genetic diversity and origin. Variation was assessed at five microsatellite loci. Deviations from Hardy-Weinberg equilibrium (HWE) were observed at some loci in various populations, but the Point Cook population was in HWE at all five loci. Mean heterozygosity and number of alleles was similar in all populations. Hierarchical analysis of molecular variance indicated significant genetic variation among populations, but did not differentiate Port Phillip Bay from Bass Strait populations. Pairwise comparisons of multilocus F_STand R_ST indicated significant genetic differences between Point Cook and some populations, as well as between other populations, but no consistent spatial pattern of differentiation was observed. There was no significant correlation between genetic and geographic distance. The level of genetic variation observed in the Point Cook individuals was similar to that in individuals from the other four sites, and sufficient to support a ranching program. However, this variation should be monitored to maximize genetic potential, and avoid commercially undesirable effects of inbreeding. Implications of this study in relation to the management of a ranching population in Port Phillip Bay are discussed.

An evaluation of the role and impacts of alien finfish in Asian inland aquaculture

Asia dominates global aquaculture production accounting for over 80% of the total and the mainstay in Asian aquaculture is finfish. Over the years, Asia has experienced a number of inter-continental and intra-continental transfers/introductions/translocation of finfish species, between nations and watersheds, beyond their natural range of distribution, primarily for aquaculture development. In this article all such species are referred to as alien species. An attempt is made to evaluate the importance of the production of alien species in selected Asian nations, using statistics of the Food and Agriculture Organization. Also, negative effects, if any, based on literature surveys, of alien species in relation to displacement of indigenous species, and on biodiversity and/or genetic diversity together with associated pathogen transfers are evaluated. The major alien species, based on their significance to Asian inland aquaculture considered, are the tilapias, catfish, Chinese and Indian major carps and common carp. It is estimated that currently alien species account for nearly 12% of the cultured finfish production (2.6 million tonnes) in Asia, valued at US$ 2.59 billion, and the contribution exceeds 40% when Asian countries excluding China are taken into consideration. Inland finfish aquaculture in some Asian nations, such as Indonesia and the Philippines, is predominated by alien species, and in some others, e.g. Bangladesh and India, the contribution from alien species has been increasing steadily. It is suggested that overall alien finfish species have done little ecological harm to native flora and fauna. However, in the wake of increasing anthropogenic development taking place in watersheds the resulting environments are often made unconducive to indigenous species but not to some alien species, thereby potentially and indirectly making the latter invasive.

The molecular systematics of Leiopotherapon unicolor (Günther, 1859): testing for cryptic speciation in Australia’s most widespread freshwater fish

Leiopotherapon unicolor is the most widespread freshwater fish species in Australia. A comprehensive allozyme and mitochondrial DNA 16S rRNA data set was assembled from 141 specimens of L. unicolor collected Australia-wide in order to test for cryptic speciation in this far-ranging species. Surprisingly, little genetic diversity was observed within L. unicolor and provided no evidence for the existence of cryptic species within this lineage. In contrast, a small sample set of L. aheneus used as the outgroup showed two highly divergent haplotypes strongly suggestive of cryptic speciation. L. unicolor has a number of ecological and life history attributes that may explain the lack of significant genetic divergence over substantial geographical distances. The occurrence of other widespread fish and crustacean species that also display only limited genetic diversity indicate that climate conditions more favourable to dispersal across central and northern Australia than is suggested by the extent of present-day aridity have occurred in the relatively recent geological past.

Aspects of the interaction between Xanthorrhoea australis and Phytophthora cinnamomi in south-western Victoria, Australia

Diseases in natural ecosystems are often assumed to be less severe than those observed in domestic cropping systems due to the extensive biodiversity exhibited in wild vegetation communities. In Australia, it is this natural biodiversity that is now under threat from Phytophthora cinnamomi. The soilborne Oomycete causes severe decline of native vegetation communities in south-western Victoria, Australia, disrupting the ecological balance of native forest and heathland communities. While the effect of disease caused by P. cinnamomi on native vegetation communities in Victoria has been extensively investigated, little work has focused on the Anglesea healthlands in south-western Victoria. Nothing is known about the population structure of P. cinnamomi at Anglesea. This project was divided into two main components to investigate fundamental issues affecting the management of P. cinnamomi in the Anglesea heathlands. The first component examined the phenotypic characteristics of P. cinnamomi isolates sampled from the population at Anglesea, and compared these with isolates from other regions in Victoria, and also from Western Australia. The second component of the project investigated the effect of the fungicide phosphonate on the host response following infection by P. cinnamomi. Following soil sampling in the Anglesea heathlands, a collection of P, cinnamomi isolates was established. Morphological and physiological traits of each isolate were examined. All isolates were found to be of the A2 mating type. Variation was demonstrated among isolates in the following characteristics: radial growth rate on various nutrient media, sporangial production, and sporangial dimensions. Oogonial dimensions did not differ significantly between isolates. Morphological and physiological variation was rarely dependant on isolate origin. To examine the genetic diversity among isolates and to determine whether phenotypic variation observed was genetically based, Random Amplified Polymorphic DNA (RAPD) analyses were conducted. No significant variation was observed among isolates based on an analysis of molecular variance (AMQVA). The results are discussed in relation to population biology, and the effect of genetic variation on population structure and population dynamics. X australis, an arborescent monocotyledon indigenous to Australia, is highly susceptible to infection by P. cinnamomi. It forms an important component of the heathland vegetation community, providing habitat for native flora and fauna, A cell suspension culture system was developed to investigate the effect of the fungicide phosphonate on the host-pathogen interaction between X. australis and P. cinnamomi. This allowed the interaction between the host and the pathogen to be examined at a cellular level. Subsequently, histological studies using X. australis seedlings were undertaken to support the cellular study. Observations in the cell culture system correlated well with those in the plant. The anatomical structure of X australis roots was examined to assist in the interpretation of results of histopathological studies. The infection of single cells and roots of X. australis, and the effect of phosphonate on the interaction are described. Phosphonate application prior to inoculation with P. cinnamomi reduced the infection of cells in culture and of cells in planta. In particular, phosphonate was found to stimulate the production of phenolic material in roots of X australis seedlings and in cells in suspension cultures. In phosphonate-treated roots of X australis seedlings, the deposition of electron dense material, possibly lignin or cellulose, was observed following infection with P. cinnamomi. It is proposed that this is a significant consequence of the stimulation of plant defence pathways by the fungicide. Results of the study are discussed in terms of the implications of the findings on management of the Anglesea heathlands in Victoria, taking into account variation in pathogen morphology, pathogenicity and genotype. The mode of action of phosphonate in the plant is discussed in relation to plant physiology and biochemistry.