Population genetics and phylogeography of antilopine wallaroo using degraded dna from scats and museum specimens.

Abstract

The research conducted in this thesis utilises faecal pellets (scats) and museum samples to examine the population genetics of one of Australia’s large macropods, the antilopine wallaroo, Macropus antilopinus, across the monsoonal tropics of northern Australia. The project focussed on populations of antilopine wallaroos and other large sympatric macropods in north-eastern Australia where visual and indirect (scat) surveys were undertaken at 53 sites. Macropod scats were collected from transect points at the same sites where the visual surveys were conducted. Macropod scats are often difficult to identify based only on morphology. Prior to their use in species occurrence and population genetic analyses a simple, rapid DNA-based identification test was developed to positively identify scats from seven species of Macropus that occur in north-eastern Australia. The identified scats were then included in an indirect genetic survey to examine their utility as an alternative to visual surveys to determine species occurrence. The presence and absence data from the survey was used to investigate the ecological determinants of occurrence for each species. The indirect, molecular derived occurrence data, alone, can be used to develop informative ecological models that describe the inter-specific habitat requirements of macropods. The indirect genetic survey of macropods was also cheaper and less time consuming to conduct, and provided more occurrence records (and less false absences), then visual surveys. The non-invasively collected scats also provide an excellent source of genetic material for further genetic analysis including determining the patterns of dispersal and contemporary population structure. Scats from two populations of antilopine wallaroo from the latitudinal extremes of the Cape York distribution were analysed using 15 microsatellite loci. Genetic diversity within the two populations was low compared to the levels reported in other macropod species. Population structure analyses indicated that gene flow between the two populations was restricted. Population structure and the current pattern of gene flow within antilopine wallaroo were examined further to elucidate phylogeographic structure within the species, and explore potential causes of geographic variation from the species entire range. Museum samples, including bone and skin, from the remainder of the species distribution were utilised to determine the historical aspects of the contemporary spatial distributions of gene lineages across the species range. Evidence for significant phylogeographic structuring across northern Australia was found and can be related to know biogeographical barriers in the area. Divergence dates calculated for the major mtDNA clades suggested the environment and climate changes associated with glacial cycles may have facilitated this diversification. The thesis demonstrates some of the many applications of utilising non-invasive sampling for both ecological and evolutionary studies of species. Once an accurate identification of species is made, occurrence, distribution, environmental and genetic data can all be used to create better informed management decisions for antilopine wallaroo.