Molecular Ecology (2007) 16, 75–87 doi: 10.1111/j.1365-294X.2006.03125.x © 2006 The Authors Journal compilation © 2006 Blackwell Publishing Ltd Blackwell Publishing Ltd High levels of variation despite genetic fragmentation in populations of the endangered mountain pygmy-possum, Burramys parvus, in alpine Australia P. MITROVSKI,* D. A. HEINZE,† L. BROOME,‡ A. A. HOFFMANN * and A. R. WEEKS * *Centre for Environmental Stress and Adaptation Research, Departments of Genetics and Zoology, The University of Melbourne, Parkville, Victoria 3010, Australia, †Department of Environmental Management and Ecology, La Trobe University, Albury-Wodonga 3689, Australia, ‡New South Wales National Parks and Wildlife Services, Queanbeyan, New South Wales 2620, Australia Abstract In endangered mammals, levels of genetic variation are often low and this is accompanied by genetic divergence among populations. The mountain pygmy-possum (Burramys parvus) is an endangered marsupial restricted to the alpine region of Victoria and New South Wales, Australia. By scoring variation at eight microsatellite loci, we found that B. parvus populations exhibit high levels of genetic divergence and fall into three distinct groups from the northern, central and southern areas of the distribution of this species, consistent with previous assessments of mitochondrial DNA variation. F ST values between popula- tions from these regions ranged from 0.19 to 0.54. Within the central area, there was further genetic fragmentation, and a linear association between genetic and geographical distance. This pattern is likely to reflect limited dispersal across barriers despite the fact that individual B. parvus can move several kilometres. Levels of genetic variation within populations were high with the exception of a southern population where there was evidence of inbreeding. From a conservation perspective, all three areas where B. parvus are found should be considered as separate gene pools; management of populations within these areas needs to take into account the low gene flow between populations, as well as threats posed by roads, resorts and other developments in the alpine region. The low genetic variability and inbreeding in the southern population is of particular concern given the high levels of variability in other B. parvus populations. Keywords: Burramys parvus, endangered, fragmentation, gene flow, microsatellites, population genetics Received 21 May 2006; revision accepted 7 August 2006 Introduction Genetic analyses of endangered mammal populations often indicate that these populations have reduced levels of genetic variability (Taylor et al. 1994; Menotti-Raymond & O’Brien 1995; Houlden et al. 1996; Eldridge et al. 1999; Jones et al. 2004), and there is often also evidence for genetic divergence among remnant populations (Houlden et al. 1996; Jones et al. 2004). In marsupials, the advent of European settlement in Australia has drastically reduced and modified the habitat of many species (Short & Smith 1994; Maxwell et al. 1996). The fragmentation of habitats has resulted in reduced, disparate populations that are prone to the effects of genetic bottlenecks resulting in a loss of genetic diversity. Such a loss of diversity over the last 100 years has been found in both the northern hairy-nosed wombat (Taylor et al. 1994) and the black-footed rock wallaby (Eldridge et al. 1999). Other marsupial species that are not considered endangered, including the Tasmanian devil ( Jones et al. 2004) and the southeastern Australian koala (Houlden et al. 1996), can also exhibit a loss of genetic diversity and genetic evidence of fragmentation even though these species persist at relatively large census sizes. Correspondence: Andrew Weeks, Fax: +61 383447089; E-mail: aweeks@unimelb.edu.au