Source population of dispersing rock-wallabies (Petrogale lateralis) identified by assignment tests on multilocus genotypic data

Understanding Historical Demographic Processes to Inform Contemporary Conservation of an Arid zone Specialist: The Yellow-Footed Rock-Wallaby

Little genetic research has been undertaken on mammals across the vast expanse of the arid biome in Australia, despite continuing species decline and need for conservation management. Here, we evaluate the contemporary and historical genetic connectivity of the yellow-footed rock-wallaby, Petrogalexanthopusxanthopus, a threatened macropodid which inhabits rocky outcrops across the disconnected mountain range systems of the southern arid biome. We use 17 microsatellite loci together with mitochondrial control region data to determine the genetic diversity of populations and the evolutionary processes shaping contemporary population dynamics on which to base conservation recommendations. Our results indicate the highly fragmented populations have reduced diversity and limited contemporary gene flow, with most populations having been through population bottlenecks. Despite limited contemporary gene flow, the phylogeographic relationships of the mitochondrial control region indicate a lack of structure and suggests greater historical connectivity. This is an emerging outcome for mammals across this arid region. On the basis of our results, we recommend augmentation of populations of P. x.xanthopus, mixing populations from disjunct mountain range systems to reduce the chance of continued diversity loss and inbreeding depression, and therefore maximize the potential for populations to adapt and survive into the future.

Identification of a remnant population of the black-flanked rock-wallaby (Petrogale lateralis lateralis) in Kalbarri National Park, Western Australia, and implications for its management

Black-flanked rock-wallabies (Petrogale lateralis lateralis) were thought to be locally extinct in Kalbarri National Park, Western Australia, until 2015 when a pair were photographed in the Murchison River gorge. Subsequent searches failed to locate any other populations and, in combination with previous surveys, suggest that these animals were the sole survivors of a formerly abundant population. Efforts to capture the rock-wallabies to obtain tissue samples and ascertain their genetic affinities were unsuccessful. However, fresh faecal material was collected and a ~600-bp fragment of DNA sequence data was obtained from a mitochondrial DNA gene. The Kalbarri rock-wallabies were found to be genetically distinct from all other sampled populations of P. l. lateralis. They were genetically most similar to rock-wallabies in the Calvert Range, 950km to the north-east in the Little Sandy Desert. Nearer populations in Cape Range (600km north) and the Western Australian Wheatbelt (500km south-east) were less closely related. Following evaluation of a variety of factors, including population size, genetics, demography, ecology, environment and logistics, a decision was made to supplement the Kalbarri National Park population with females sourced from the Western Australian Wheatbelt. In May 2016 three females were released at the same site as the Kalbarri pair to try to ensure the survival of the population whilst still preserving unique Kalbarri alleles.

Genetic affinities of a remnant population of the brush-tailed rock-wallaby (Petrogale penicillata) in Mt Kaputar National Park, northern New South Wales

The brush-tailed rock-wallaby (Petrogale penicillata) is now extinct west of the Great Dividing Range, apart from remnant populations in the Warrumbungles and at Mt Kaputar. Previous genetic analysis has identified deep genetic subdivisions within P. penicillata, but samples from Mt Kaputar were not included. Mitochondrial DNA sequences obtained from Mt Kaputar and the Warrumbungles clustered within the Central ESU, extending its distribution north of the Hunter River onto the north-western slopes adjacent to populations of the Northern ESU. These highly threatened western populations are the only P. penicillata persisting in semiarid conditions. This makes them of particular value to the long-term survival of the species and their conservation should be a priority.

Population monitoring of small and declining brush-tailed rock wallaby (Petrogale penicillata) colonies at the extreme of their range using faecal DNA sampling

Obtaining much-needed information on population parameters such as abundance and genetic diversity can be difficult for small and declining populations. The brush-tailed rock-wallaby (Petrogale penicillata) is an endangered and cryptic species with many colonies in decline. The Warrumbungle National Park (NP) in New South Wales contains a declining metapopulation of P. penicillata at the western (inland) extreme of the species’ current range. Loss of these colonies would cause substantial range contraction and probable loss of regional genetic diversity in the Central Evolutionary Significance Unit (ESU). We used non-invasive genetic methods to identify individuals from faecal DNA from five colonies in the Warrumbungle NP. We identified a minimum of 21 individuals, with the largest colony containing seven individuals. The Warrumbungle NP colonies showed significant intercolony structuring and we were able to detect a single dispersal event. Comparison of genetic diversity to other Central ESU colonies shows that loss of the Warrumbungle NP population will result in loss of unique diversity from this region. The minimum number of animals and genetic diversity information obtained in this study was used to support management actions of herbivore control and translocation in the Warrumbungle NP population.

Fox control and 1080 baiting conundrums: time to prepare for a CRISPR solution

For many years, managing rock-wallaby colonies (Petrogale lateralis lateralis) in the Western Australian Wheatbelt seemed to be a matter of routinely exposing foxes (Vulpes vulpes) to toxic baits (sodium fluoroacetate, 1080®) laid around their rocky outcrops. Recent research has revealed that 1080 baitings are no longer a viable management option. Baiting is flawed over the long term because it does not erase the wallabies’ pervasive fear of being depredated by foxes, which can still make their menacing presence felt before succumbing to poison bait. Accordingly, a ‘landscape of fear’ exists on all rock-wallaby sites, creating a ‘virtual boundary’ beyond which they fear to forage. Severe overgrazing occurs, ultimately causing population crashes, leaving behind devastated outcrops greatly diminished in carrying capacity. The fallout from this scenario produces a management conundrum. Rock-wallaby populations are unstable in the absence of fox control, and conversely, they are also unstable under long-term fox control. Management is now left with few options, and the future of the colonies remains open. Other conundrums involving bait interference and mesopredator release are described. An alternative to 1080 baiting is clearly needed. Recent developments in gene engineering (CRISPR technology) offer a solution in the foreseeable future.

Monitoring for adaptive management in a trial reintroduction of the black-footed rock-wallabyPetrogale lateralis

Reintroduction practitioners must often make critical decisions about reintroduction protocols despite having little understanding of the reintroduction biology of the focal species. To enhance the available knowledge on the reintroduction biology of the warru, or black-footed rock-wallabyPetrogale lateralisMacDonnell Ranges race, we conducted a trial reintroduction of 16 captive individuals into a fenced predator and competitor exclosure on the An̲angu Pitjantjatjara Yankunytjatjara Lands in South Australia. We conducted seven trapping sessions and used radio-tracking and camera traps to monitor survival, reproduction and recruitment to the population over 36 months. Blood samples were collected pre-release and during two trapping sessions post-release to assess nutritional health. The survival rate of founders was 63%, with all losses occurring within 10 weeks of release. Post-release blood biochemistry indicated that surviving warru adapted to their new environment and food sources. Female warru conceived within 6 months of release; 28 births were recorded during the study period and 52% of births successfully recruited to the population. Our results suggest that captive-bred warru are capable of establishing and persisting in the absence of introduced predators. However, the high mortality rate immediately post-release, with only a modest recruitment rate, suggests that future releases into areas where predators and competitors are present should use a trial approach to determine the viability of reintroduction. We recommend that future releases of warru into unfenced areas include an intensive monitoring period in the first 3 months post-release followed by a comprehensive long-term monitoring schedule to facilitate effective adaptive management.

Three divergent lineages within an Australian marsupial (Petrogale penicillata) suggest multiple major refugia for mesic taxa in southeast Australia

Mesic southeastern Australia represents the continent's ancestral biome and is highly biodiverse, yet its phylogeographic history remains poorly understood. Here, we examine mitochondrial DNA (mtDNA) control region and microsatellite diversity in the brush-tailed rock-wallaby (Petrogale penicillata;n = 279 from 31 sites), to assess historic evolutionary and biogeographic processes in southeastern Australia. Our results (mtDNA, microsatellites) confirmed three geographically discrete and genetically divergent lineages within brush-tailed rock-wallabies, whose divergence appears to date to the mid-Pleistocene. These three lineages had been hypothesized previously but data were limited. While the Northern and Central lineages were separated by a known biogeographic barrier (Hunter Valley), the boundary between the Central and Southern lineages was not. We propose that during particularly cool glacial cycles, the high peaks of the Great Dividing Range and the narrow adjacent coastal plain resulted in a more significant north-south barrier for mesic taxa in southeastern Australia than has been previously appreciated. Similarly, located phylogeographic breaks in codistributed species highlight the importance of these regions in shaping the distribution of biodiversity in southeastern Australia and suggest the existence of three major refuge areas during the Pleistocene. Substructuring within the northern lineage also suggests the occurrence of multiple local refugia during some glacial cycles. Within the three major lineages, most brush-tailed rock-wallaby populations were locally highly structured, indicating limited dispersal by both sexes. The three identified lineages represent evolutionarily significant units and should be managed to maximize the retention of genetic diversity within this threatened species.

Divergence with gene flow as facilitated by ecological differences: within-island variation in Darwin's finches

Divergence and speciation can sometimes proceed in the face of, and even be enhanced by, ongoing gene flow. We here study divergence with gene flow in Darwin's finches, focusing on the role of ecological/adaptive differences in maintaining/promoting divergence and reproductive isolation. To this end, we survey allelic variation at 10 microsatellite loci for 989 medium ground finches (Geospiza fortis) on Santa Cruz Island, Galápagos. We find only small genetic differences among G. fortis from different sites. We instead find noteworthy genetic differences associated with beak. Moreover, G. fortis at the site with the greatest divergence in beak size also showed the greatest divergence at neutral markers; i.e. the lowest gene flow. Finally, morphological and genetic differentiation between the G. fortis beak-size morphs was intermediate to that between G. fortis and its smaller (Geospiza fuliginosa) and larger (Geospiza magnirostris) congeners. We conclude that ecological differences associated with beak size (i.e. foraging) influence patterns of gene flow within G. fortis on a single island, providing additional support for ecological speciation in the face of gene flow. Patterns of genetic similarity within and between species also suggest that interspecific hybridization might contribute to the formation of beak-size morphs within G. fortis.

High levels of mitochondrial DNA divergence within short-eared rock-wallaby (Petrogale brachyotis) populations in northern Australia

Most population genetics studies of rock-wallabies conducted to date have examined remnant colonies of threatened species inhabiting southern Australia. In this study we examined the natural pattern of contemporary and long-term gene flow among colonies of the widespread and abundant short-eared rock-wallaby, Petrogale brachyotis, in the relatively unmodified landscapes of Australia’s tropical north. We sampled 105 wallabies from seven colonies 1.2 km to 250 km apart. Mitochondrial DNA (mtDNA) control region sequence analysis was conducted on samples from all colonies and microsatellite analysis (10 loci) on samples from the three largest colonies. The microsatellite data revealed no evidence of inbreeding within colonies, but higher levels of genetic diversity were found in the Kakadu National Park population compared with the smaller, more isolated colonies at Litchfield National Park. Both the mtDNA and microsatellite results showed that populations of P. brachyotis are naturally highly structured even within this relatively intact landscape, with only limited contemporary and long-term gene flow between colonies more than 1.2 km apart. Nine mtDNA control region haplotypes were identified within the seven colonies. There were unusually high levels of sequence divergence (up to 6.9%) within colonies at Litchfield NP. This divergence suggests that multiple taxa may exist within what is currently recognised as P. brachyotis. Alternatively, if current taxonomy is correct, the high levels of divergence raise the possibility of ancestral isolation and divergence of populations in allopatry with subsequent admixture at a secondary contact zone. The possibility that these unusually divergent haplotypes result from introgressive interspecific hybridisation with the sympatric P. concinna appears unlikely.

Predator-baiting experiments for the conservation of rock-wallabies in Western Australia: a 25-year review with recent advances

Predation is widely believed to be the main threatening process for many native vertebrates in Australia. For 25 years, predator-baiting experiments have been used in the Western Australian Central Wheatbelt to control red fox predation on rock-wallabies and other endangered marsupial prey elsewhere. We review here the history of a series of baiting experiments designed to protect rock-wallaby colonies by controlling red foxes with 1080 poison baits. We continue to support the conclusion that red foxes can reduce or exterminate rock-wallaby populations in Western Australia. Research trials from 1990 to 2008 have uniformly shown a dramatic recovery of rock-wallaby populations once red foxes are baited. Baiting experiments are often black boxes and their success should not blind us to their weaknesses. Ideally, what we would like to measure are the functional responses of predators to prey abundance directly. As a contribution towards this goal, we describe new technology that enables one to determine which predator killed which prey, at exactly what time, with improved research and management outcomes.

The tales of two geckos: does dispersal prevent extinction in recently fragmented populations?

Although habitat loss and fragmentation threaten species throughout the world and are a major threat to biodiversity, it is apparent that some species are at greater risk of extinction in fragmented landscapes than others. Identification of these species and the characteristics that make them sensitive to habitat fragmentation has important implications for conservation management. Here, we present a comparative study of the population genetic structure of two arboreal gecko species (Oedura reticulata and Gehyra variegata) in fragmented and continuous woodlands. The species differ in their level of persistence in remnant vegetation patches (the former exhibiting a higher extinction rate than the latter). Previous demographic and modelling studies of these two species have suggested that their difference in persistence levels may be due, in part, to differences in dispersal abilities with G. variegata expected to have higher dispersal rates than O. reticulata. We tested this hypothesis and genotyped a total of 345 O. reticulata from 12 sites and 353 G. variegata from 13 sites at nine microsatellite loci. We showed that O. reticulata exhibits elevated levels of structure (FST=0.102 vs. 0.044), lower levels of genetic diversity (HE=0.79 vs. 0.88), and fewer misassignments (20% vs. 30%) than similarly fragmented populations of G. variegata, while all these parameters were fairly similar for the two species in the continuous forest populations (FST=0.003 vs. 0.004, HE=0.89 vs. 0.89, misassignments: 58% vs. 53%, respectively). For both species, genetic structure was higher and genetic diversity was lower among fragmented populations than among those in the nature reserves. In addition, assignment tests and spatial autocorrelation revealed that small distances of about 500 m through fragmented landscapes are a barrier to O. reticulata but not for G. variegata. These data support our hypothesis that G. variegata disperse more readily and more frequently than O. reticulata and that dispersal and habitat specialization are critical factors in the persistence of species in habitat remnants.

Can assignment tests measure dispersal?

Individual-based assignment tests are now standard tools in molecular ecology and have several applications, including the study of dispersal. The measurement of natal dispersal is vital to understanding the ecology of many species, yet the accuracy of assignment tests in situations where natal dispersal is common remains untested in the field. We studied a metapopulation of the grand skink, Oligosoma grande, a large territorial lizard from southern New Zealand. Skink populations occur on isolated, regularly spaced rock outcrops and are characterized by frequent interpopulation dispersal. We examined the accuracy of assignment tests at four replicate sites by comparing long-term mark-and-recapture records of natal dispersal with the results of assignment tests based on microsatellite DNA data. Assignment tests correctly identified the natal population of most individuals (65-100%, depending on the method of assignment), even when interpopulation dispersal was common (5-20% dispersers). They also provided similar estimates of the proportions of skinks dispersing to those estimated by the long-term mark-and-recapture data. Fully and partially Bayesian assignment methods were equally accurate but their accuracy depended on the stringency applied, the degree of genetic differentiation between populations, and the number of loci used. In addition, when assignments required high confidence, the method of assignment (fully or partially Bayesian) had a large bearing on the number of individuals that could be assigned. Because assignment tests require significantly less fieldwork than traditional mark-and-recapture approaches (in this study < 3 months vs. > 7 years), they will provide useful dispersal data in many applied and theoretical situations.

Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power

Genetic assignment methods use genotype likelihoods to draw inference about where individuals were or were not born, potentially allowing direct, real-time estimates of dispersal. We used simulated data sets to test the power and accuracy of Monte Carlo resampling methods in generating statistical thresholds for identifying F0 immigrants in populations with ongoing gene flow, and hence for providing direct, real-time estimates of migration rates. The identification of accurate critical values required that resampling methods preserved the linkage disequilibrium deriving from recent generations of immigrants and reflected the sampling variance present in the data set being analysed. A novel Monte Carlo resampling method taking into account these aspects was proposed and its efficiency was evaluated. Power and error were relatively insensitive to the frequency assumed for missing alleles. Power to identify F0 immigrants was improved by using large sample size (up to about 50 individuals) and by sampling all populations from which migrants may have originated. A combination of plotting genotype likelihoods and calculating mean genotype likelihood ratios (DLR) appeared to be an effective way to predict whether F0 immigrants could be identified for a particular pair of populations using a given set of markers.

Assessing population structure and gene flow in Montana wolverines (Gulo gulo) using assignment‐based approaches

In North America, wolverines once occupied a continuous range from Alaska southward to New Mexico. In the lower 48 states, small remnant populations remain only in the northwestern United States. Among these remnant populations, the Montana population has the highest probability of long-term persistence given its size and proximity to healthy populations in Canada. In this study, we evaluate population genetic structure and gene flow among Montana wolverines using 10 polymorphic microsatellite loci. Bayesian and frequency-based assignment tests revealed significant population substructure and provide support for at least three subpopulations in Montana. FST values between subpopulations ranged from 0.08 to 0.10 and provide evidence for male-biased dispersal. The high degree of population substructure and low levels of gene flow contrast results from wolverine population genetic studies in less fragmented landscapes of Alaska and Canada. This study provides additional support for the hypothesis that large carnivore populations of Montana are becoming increasingly fragmented due to human development and disturbance.

AFLP utility for population assignment studies: analytical investigation and empirical comparison with microsatellites

Individual-based population assignment tests have thus far mainly relied on the use of microsatellite loci. However, the logistic difficulty of screening large numbers of loci required to reach sufficient statistical power hampers the usefulness of microsatellites in situations of weak population structuring. Amplified fragment length polymorphisms (AFLP) represents an alternative for overcoming this logistical issue as the technique allows the user to characterize a much larger number of loci with a comparable analytical effort. In this study, an assignment test based on maximum likelihood for dominant markers was used to investigate the potential usefulness of AFLP for population assignment. We also compared assignment success achieved with AFLP with that obtained using microsatellites in a case study of low population differentiation involving whitefish (Coregonus clupeaformis) sympatric ecotypes. The analytical investigation showed that the minimum number of AFLP loci required to reach an assignment success of 95% stood within values that are easily achievable in many situations. This also showed how assignment success varied according to the number of AFLP loci used, their absolute frequency and their frequency differential and sampling errors, as well as the number of putative source populations. The case study showed that given a comparable analytical effort in the laboratory, AFLP were much more efficient than the microsatellite loci in discriminating the source of an individual among putative populations. AFLP resulted in higher assignment success at all levels of stringency and the log-likelihood differences between populations obtained with AFLP for each individual were much larger than those obtained with microsatellites. These results indicate that research involving individual-based population assignment methods should benefit importantly from the use of AFLP markers, especially in systems characterized by weak population structuring.

Three Clonal Lineages of Phytophthora cinnamomi in Australia Revealed by Microsatellites

ABSTRACT The genetic structure of populations of Phytophthora cinnamomi, a pathogen of an enormous variety of woody plants, was investigated using microsatellites. Three intensively sampled disease sites in southwest Australia were analyzed along with a large culture collection of Austra-lian isolates and some isolates from elsewhere in the world. The mutation in the four microsatellite loci analyzed revealed spatial patterns at the disease sites that correlated with the age of the infestation. Only three clonal lineages were identified in Australian populations and these same clonal lineages were present in worldwide populations, where it is suggested that a limited number of clonal lineages have spread in most regions. No evidence for sexual reproduction between these clonal lineages in Australia has been found even though the pathogen has the opportunity. Instead, mitotic recombination is frequent within the clonal lineages. The implications of this are discussed.