Shorebird population decreases are increasingly evident worldwide, especially in the East Asian-Australasian Flyway (EAAF). To arrest these declines, it is important to understand the scale of both the problem and the solution. We analysed an expansive Australian citizen science data set spanning the years from 1973 to 2014 to explore factors related to differences in trends among shorebird populations in wetlands throughout Australia. Of seven resident Australian shorebird species, the four inland species exhibited continental decreases, while the three coastal species did not. Decreases in inland resident shorebirds were related to changes in water availability at nontidal wetlands, suggesting that degradation of wetlands in Australia's interior is playing a role in these declines. The analyses also revealed continental decreases in abundance in 12 of 19 migratory shorebird species, and decreases in 17 of 19 migratory species in the southern half of Australia over the past 15 years. Many trends were most strongly associated with continental gradients in latitude 2 or longitude, suggesting some large-scale patterns in the decreases with steeper declines often evident in the south of Australia. After accounting for this effect, local variables did not explain variation in migratory shorebird trends between sites. Our results are consistent with other studies indicating that migratory shorebird population decreases in the EAAF are most likely being driven primarily by factors outside Australia. This reinforces the need for urgent overseas conservation actions. However, substantially heterogeneous trends within Australia, combined with inland resident shorebird declines indicate effective management of Australian shorebird habitat remains important.

Genetic identification of individual animals from remotely collected DNA samples provides an alternative approach for the collection of data on populations of elusive or rare species. In this study we used DNA isolated from field-collected faecal samples to estimate the size of a population of common wombats (Vombatus ursinus) surviving in suburban Melbourne parkland. A pilot study revealed that microsatellite genotypes obtained from DNA in faeces were often incorrect, but that by carrying out three replicate polymerase chain reactions (PCRs) for each sample, we were able to reliably identify individuals. We conducted a mark-recapture study using the Mh-jackknife model to estimate the size of the wombat population at Mt Lofty Reserve, and identified 17 individuals - 10 males and seven females. The interpolated population size estimate was 19 with a 95% confidence interval of 18-32. The distribution of individual wombats' scats provided information on ranging behaviour. The genotypic database obtained was used to identify five of the individuals as putative immigrants, suggesting that the population is not isolated from others in a series of reserves along the Yarra River. However, the lack of a detectable female bias in immigration differs from our previous findings in continuous populations of this species. The level of genetic variation at the five loci analysed was also inconsistent with long-term isolation of the population.

Since European colonization, Leadbeater's possum (Gymnobelideus leadbeateri) has declined across its range to the point where it is now only patchily distributed within the montane ash forests of the Central Highlands of Victoria. The loss of large hollowbearing trees coupled with inadequate recruitment of mature ash forest has been predicted to result in a reduction in population size of up to 90% by 2020. Furthermore, bioclimatic analyses have suggested additional reductions in the species' distribution under a variety of climate change scenarios. Using a panel of 15 highly resolving microsatellite markers and mitochondrial control region sequence data, we infer past and present gene flow. Populations in the northern part of the core range were highly admixed, and showed no signs of either current or historical barriers to gene flow. A marginal, isolated and inbred population at Yellingbo was highly genetically differentiated, both in terms of current and historic genetic structure. Sequence data confirmed the conclusions from earlier genetic simulation studies that the Yellingbo population has been isolated from the rest of the species range since before European-induced changes to the montane landscape, and formed part of a larger genetic unit that is now otherwise extinct. Historic loss of maternal lineages in the Central Highlands of Victoria was detected despite signals of immigration, indicating population declines that most probably coincided with changes in climate at the end of the Pleistocene. Given ongoing habitat loss and the recent (February 2009) wildfire in the Central Highlands, we forecast (potentially extensive) demographic declines, in line with predicted range reductions under climate change scenarios.

Effective conservation management requires that genetically divergent populations potentially harbouring important local adaptations be identified and maintained as separate management units. In the case of the endangered Australian Leadbeater's possum (Gymnobelideus leadbeateri), an arboreal marsupial endemic to Victoria, uncertainty over the evolutionary origin of a potentially important extant wild population recently discovered in atypical habitat (lowland swamp) at Yellingbo is hampering such efforts. The population is rumoured to be a recent introduction. Microsatellite allele frequencies at Yellingbo differed substantially from those in sampled populations in montane ash forest (F(ST) between 0.23 and 0.36), and Bayesian clustering analyses of genotypes strongly separated them (K = 2). We conducted a suite of bottlenecking tests which all indicated that Yellingbo had undergone a recent reduction in size. The extent to which the distinctiveness of Yellingbo animals might be expected solely through bottlenecking associated with a recent introduction, was tested by simulating population-history scenarios seeded with genotypes from candidate wild and captive sources. No bottleneck scenario reproduced anything approaching the genetic distinction of the Yellingbo population, with all STRUCTURE analyses placing Yellingbo in a separate cluster to simulated populations (K = 2, minimum F(ST) = 0.13). These results suggest that Yellingbo does not share recent ancestry with other extant populations and instead may be a remnant of an otherwise extinct gene pool. Importantly, this may include genes involved in adaptation to a lowland swamp environment, substantially adding to the conservation importance of this population, and suggesting that separate management may be prudent until evidence suggests otherwise.

Worldwide, local extinctions and severe declines in waterbird densities are being reported from many important waterbird sites.Waterbird sites often exist as a network, collectively providing crucial habitat for different life history stages of different species. Therefore, population changes at one site may strongly influence others. In Australia, many waterbird species are highly mobile, and move rapidly over long distances in response to rainfall. Large tidal wetlands often serve as drought refugia or alternative breeding habitat for these species. These sites are also the migration terminus of many species of shorebirds that spend their non-breeding season in Australia. One such site in south-eastern Australia is Western Port, a Ramsar-listed tidal embayment forming part of the East Asian-Australasian Shorebird Site Network. We measured waterbird population trends over nearly 40 years in Western Port to see whether changes showed consistent trends over time across multiple species.Thirty-nine species were recorded often enough to allow an analysis of trends over time using dynamic linear models and, where appropriate, piecewise linear regression. Twenty-two species had declined, including four species of duck, five species of fish-eating bird (cormorants, terns and pelicans), one species each of grebe, gull and heron, and 10 species of shorebird. Only two species (Australian pied oystercatcher Haematopus longirostris and straw-necked ibis Threskiornis spinicollis) increased significantly over the same time period. Patterns of decline in non-migratory waterbirds may reflect diminishing wetland availability, local reductions in fish prey, increased predation pressure and changes in inland wetland resources. Declines in migratory shorebirds are most likely related to loss of habitat elsewhere in their trans-equatorial migration routes. These trends in waterbirds that use Western Port reflect widespread impacts on populations elsewhere in Australia and overseas, necessitating more than simply local management of this tidal embayment.