Conservation Genetics 2: 145–156, 2001. © 2001 Kluwer Academic Publishers. Printed in the Netherlands. 145 Multifaceted genetic analysis of the “Critically Endangered” brush-tailed rock-wallaby Petrogale penicillata in Victoria, Australia: implications for management Teena L. Browning 1 , David A. Taggart 2 , Catherine Rummery 3 , Robert L. Close 4 & Mark D.B. Eldridge 1,∗ 1 Department of Biological Sciences, Division of Environmental and Life Sciences, Macquarie University, New South Wales, 2109, Australia; 2 Department of Zoology, University of Melbourne, Parkville, Victoria 3052, Australia; 3 New South Wales National Parks and Wildlife Service, P.O. Box 1967, Hurstville, NSW 2220; 4 School of Science, Food and Horticulture, University of Western Sydney, Locked Bag 1797, Penrith South DC, NSW 1797, Australia ( ∗ Corresponding author: E-mail: meldridg@rna.bio.mq.edu.au) Received 15 November 2000; accepted 20 February 2001 Key words: chromosomes, control region, genetic divergence microsatellites, mtDNA Abstract The use of molecular genetic techniques can aid wildlife managers in setting priorities and devising management strategies for scattered populations of threatened taxa. In this study, six remnant populations of the “critically endangered” brush-tailed rock-wallaby (Petrogale penicillata) in Victoria, Australia, were examined using karyotypic, microsatellite (11 loci) and mitochondrial DNA (mtDNA) control region sequence analysis. Each remnant population was found to be genetically distinct (unique microsatellite alleles and control region haplotypes), but had low genetic diversity. This distribution of genetic diversity between, rather than within populations, is most likely a consequence of recent severe reductions in population size and dispersal that have occurred since European settlement. The six mtDNA control region haplotypes identified in the Victorian populations were all closely related (average 1.3% sequence divergence), and only 2% divergence separated haplotypes from East Gippsland and the Grampians (550 km to the west). In contrast there was considerable sequence divergence (7.7%) between the Victorian haplotypes and those found in P. penicillata from elsewhere in the species range. In comparison, 8.8% divergence separates P. penicillata from the closely related P. herberti. The Victorian haplotypes also formed a distinct and well supported monophyletic group that excluded haplotypes from other P. penicillata and P. herberti. In light of these data, we recommend that the remnant Victorian populations of P. penicillata be managed separately from remaining populations in New South Wales and Queensland; and that individuals be regularly exchanged amongst the Victorian populations to increase their diversity and reduce the likelihood of inbreeding depression. Introduction Rapid loss of biological diversity is occurring across the globe in all environments and at all levels. From ecosystems to genes, abundance and vari- ation is diminishing. The number of individuals in many species is decreasing and populations are becoming increasingly fragmented. As a result, many species, which were once widespread now exist only in isolated remnants. Management of these widely scattered remnant populations presents difficulties, both practical and financial for wildlife managers. This is especially true when prior knowledge of the species’ population structure is absent. Therefore, the use of highly variable molecular genetic markers to determine population structure (e.g., microsatellite