Karen Firestone

Phylogeographical population structure of tiger quolls Dasyurus maculatus (Dasyuridae: Marsupialia), an endangered carnivorous marsupial

Tiger quolls, Dasyurus maculatus, are the largest carnivorous marsupials still extant on the mainland of Australia, and occupy an important ecological niche as top predators and scavengers. Two allopatric subspecies are recognized, D.m. gracilis in north Queensland, and D.m. maculatus in the southeast of the mainland and Tasmania. D.m. gracilis is considered endangered while D.m. maculatus is listed as vulnerable to extinction; both subspecies are still in decline. Phylogeographical subdivision was examined to determine evolutionarily significant units (ESUs) and management units (MUs) among populations of tiger quolls to assist in the conservation of these taxa. Ninety‐three tiger quolls from nine representative populations were sampled from throughout the species range. Six nuclear microsatellite loci and the mitochondrial DNA (mtDNA) control region (471 bp) were used to examine ESUs and MUs in this species. We demonstrated that Tasmanian tiger quolls are reciprocally monophyletic to those from the mainland using mtDNA analysis, but D.m. gracilis was not monophyletic with respect to mainland D.m. maculatus. Analysis of microsatellite loci also revealed significant differences between the Tasmanian and mainland tiger quolls, and between D.m. gracilis and mainland D.m. maculatus. These results indicate that Tasmanian and mainland tiger quolls form two distinct evolutionary units but that D.m. gracilis and mainland D.m. maculatus are different MUs within the same ESU. The two marker types used in this study revealed different male and female dispersal patterns and indicate that the most appropriate units for short‐term management are local populations. A revised classification and management plan are needed for tiger quolls, particularly in relation to conservation of the Tasmanian and Queensland populations.

Advancement to hair-sampling surveys of a medium-sized mammal: DNA-based individual identification and population estimation of a rare Australian marsupial, the spotted-tailed quoll (Dasyurus maculatus)

Context. Enumeration of cryptic/rare or widely distributed mammal species is exceedingly difficult for wildlife managers using standard survey methods. Individual identification via non-invasive hair-DNA methods offers great promise in extending the information available from hairs collected to survey for presence/absence of a species. However, surprisingly few wildlife studies have attempted this because of potential limitations with the field method and genetic samples. Aim. The applicability of hair DNA to identify individuals and estimate numbers was assessed for a rare, medium-sized Australian marsupial carnivore, the spotted-tailed quoll (Dasyurus maculatus). Methods. Hair samples were obtained remotely in the field with baited hair-sampling devices (known as handi-glaze hair tubes) that permit multiple visitations by individuals and species. A hierarchical approach developed and applied to the DNA extraction and PCR protocol, based on single and four pooled hairs of each collected sample, was used to assess genotype reliability (cross-species DNA mixing, allelic dropout and false allele errors) and enumerate the local study population. These results were compared against a concurrent live-cage trapping survey that was equivalent in scale and trap density to enable a rigorous evaluation of the efficiency and reliability of the DNA-based hair-sampling technique. Key results. Of the 288 hair devices deployed, 52 (18%) captured spotted-tailed quoll hair and the majority (90%) of these samples provided adequate DNA to genetically profile individuals at 10 microsatellite loci and a sexing marker. The hierarchical approach provided a feasible way to verify whether cross-species DNA mixing had occurred in the pooled-hair DNA extracts by comparing the results against the independent single-hair DNA extract, and assess genotyping reliability of both DNA concentrations. Fewer individuals were detected using hair-sampling (n = 16) than live-trapping (n = 21), despite hair-sampling occurring over a longer period (40 cf. 26 nights). Conclusions. The population-level information gained by the DNA-based technologies adds considerable value to the remote hair-sampling method which up until the present study had been used to detect the presence of medium-sized mammals. Our study demonstrated the utility of the DNA-based hair-sampling method to identify spotted-tailed quoll individuals and for surveying local populations. However, improvements to the hair-sampling method, such as increasing the density of stations or the provision of a food reward, should be considered to enhance sampling efficiency to allow the enumeration of local populations. Implications. The use of remote hair-sampling devices that permit multiple visitations and do not require daily collection can be feasible and reliable to genetically identify individuals when coupled with appropriate strategies. By combining single- and pooled-hair DNA extracts, a good compromise between laboratory efficiency and data integrity is afforded.

Field-based evaluation of scat DNA methods to estimate population abundance of the spotted-tailed quoll (Dasyurus maculatus), a rare Australian marsupial

Context. DNA extracted non-invasively from remotely collected scat samples has been used successfully to enumerate populations of a few endangered mammal species. However, scat DNA surveys relying on scent-marking behaviours need to identify if age- or sex-specific variations or seasonal changes in scat scent-marking patterns affect population estimates. Furthermore, owing to the low quantity and quality of scat DNA, a thorough assessment of the technique is needed when it is applied to different species to ensure that individual identification is reliable. Aims. In the current study, microsatellite genetic profiles derived from 208 remotely collected scats of the spotted-tailed quoll (Dasyurus maculatus), a rare Australian marsupial carnivore, were compared with DNA profiles from tissue of 22 live-trapped individuals from the same study area to critically assess the reliability of the non-invasive method to estimate population abundance. Methods. Scat samples were collected at scent-marking sites over 4 consecutive months (April–July 2005), 7 weeks of which overlapped with the trapping program to allow direct comparisons of population estimates. Key results. Combining a multiple-tubes approach with error checking analyses provided reliable genetic tags and resulted in the detection of the majority of the live-trapped population (18 of 22 individuals). Ten additional individuals not known from trapping were also observed from scat DNA. A longer-term sampling regime was required for scats than for trapping to allow direct detection of a large proportion of the population and to provide a comparable population estimate. Critically, the 4-month scat collection period highlighted the importance of performing scat surveys during the mating season when scat scent marking is more frequent, and to avoid sex and age biases in scat marking patterns. Implications. Non-invasive scat DNA sampling methods that rely on scent-marking behaviours need to consider the duration of the sampling period and temporal differences in behaviours by the sexes and age groups to ensure that meaningful population estimates are achieved.

Variability and differentiation of microsatellites in the genus Dasyurus and conservation implications for the large Australian carnivorous marsupials

All four species of Australian quolls (Dasyurusspecies) have declined since European settlement in terms of bothrange and population numbers. Six highly polymorphic simplesequence repeats (CAn microsatellites) were used to estimate thegenetic variability and population differentiation within andamong twenty populations (including museum specimens from sixpopulations), as a preliminary means of assessing populationconservation status and relative levels of variability withinmembers of the genus. Overall mean expected heterozygosity (HE)and corrected allelic diversity (A′) were highest among westernquolls. Northern quolls, eastern quolls, and tiger quolls werenot significantly different from each other in either measure. There were also significant differences in diversity amongpopulations within species. Genetic differentiation wasestimated by a number of methods and showed that themicrosatellites used here were useful for defining differencesboth among species and populations. Allele frequency data weresummarised by two-dimensional MDS, which was able to partitionpopulations into distinct species clusters. Similarly, theassignment test was able to assign most individuals to both thecorrect species and population levels. Results of MDS and theassignment test may prove useful in forensic applications. Genetic distance and subdivision between pairs of populationswere assessed by two means based on different mutation models formicrosatellites: infinite alleles model (Neis D, FST) andstepwise mutation model (Goldsteins δ mu;2, RST). Pairwisemeasures of population subdivision indicate that most populationsshould be conserved as separate management units. We discussresults of these analyses in terms of applications toconservation for each of the four Australian species of quoll andprovide a genetic basis for future population monitoring in thesespecies.

Genetic monitoring reveals significant population structure in eastern quolls: implications for the conservation of a threatened carnivorous marsupial

The eastern quoll (Dasyurus viverrinus), while still relatively abundant in Tasmania, is now threatened by the recently introduced European red fox (Vulpes vulpes). Due to a lack of demographic information on eastern quolls, molecular data become a crucial surrogate to inform the management of the species. The aim of this study was to acquire baseline genetic data for use in current and future conservation strategies. Genetic variation, at seven microsatellite loci, was lower in Tasmanian eastern quolls than in quoll species from the Australian mainland. Within Tasmania, genetic variation was greater in central than peripheral populations, with the lowest levels detected on Bruny Island. Significant genetic population structure, consistent with regional differentiation, appears related to geographic distance among populations. Levels of gene flow appeared moderate, with genetic admixture greatest among central populations. Therefore, eastern quolls from genetically diverse central Tasmanian populations will become an important source for conservation initiatives if widespread declines begin to occur. Ongoing genetic monitoring of existing populations will allow conservation strategies to be adaptive. However, in order for translocations to be successful, managers must not only consider the genetic composition of founding individuals, but also habitat-specific adaptations, disease and threatening processes at translocation sites.