Academic literature on the topic 'Conservation genetics; southern brown bandicoot; Isoodon obesulus'

Southern brown (Isoodon obesulus) and golden (Isoodon auratus) bandicoots are iconic Australian marsupials that have experienced dramatic declines since European settlement. Conservation management programs seek to protect the remaining populations; however, these programs are impeded by major taxonomic uncertainties. We investigated the history of population connectivity to inform subspecies and species boundaries through a broad-scale phylogeographic and population genetic analysis of Isoodon taxa. Our analyses reveal a major east–west phylogeographic split within I. obesulus/I. auratus, supported by both mtDNA and nuclear gene analyses, which is not coincident with the current species or subspecies taxonomy. In the eastern lineage, all Tasmanian samples formed a distinct monophyletic haplotype group to the exclusion of all mainland samples, indicative of long-term isolation of this population from mainland Australia and providing support for retention of the subspecific status of the Tasmanian population (I. o. affinis). Analyses further suggest that I. o. obesulus is limited to south-eastern mainland Australia, representing a significant reduction in known range. However, the analyses provide no clear consensus on the taxonomic status of bandicoot populations within the western lineage, with further analyses required, ideally incorporating data from historical museum specimens to fill distributional gaps.

Conservation programs for threatened species are greatly benefiting from genetic data, for their power in providing knowledge of dispersal/gene flow across fragmented landscapes and for identifying populations of high conservation value. The endangered southern brown bandicoot (Isoodon obesulus obesulus) has a disjunct distribution range in South Australia, raising the possibility that populations of the subspecies may represent distinct conservation units. In the current study, we used a combination of 14 microsatellite and two mitochondrial sequence markers to investigate the phylogeography and population structure of I. o. obesulus in South Australia and south-western Victoria, with the aim of identifying any potential evolutionarily significant units and management units relevant to conservation management. Our phylogenetic/population analyses supported the presence of two distinct evolutionary lineages of I. o. obesulus. The first lineage comprised individuals from the Mount Lofty Ranges, Fleurieu Peninsula and Kangaroo Island. A second lineage comprised individuals from the south-east of South Australia and south-western Victoria. We propose that these two lineages represent distinct evolutionarily significant units and should be managed separately for conservation purposes. The findings also raise significant issues for the national conservation status of I. o. obesulus and suggest that the current subspecies classification needs further investigation.

Geographic variation in body size and shape was examined among populations of the southern brown bandicoot, Isoodon obesulus, in the south-west of Western Australia, with a view to determining the possible presence of adaptive divergence. Analysis of variance and canonical variate analysis were employed to examine the variation in body weight, head length, pes length and ear length among six locations. Significant sexual dimorphism was detected for these morphological variables, with males being larger than females. Significant geographic variation in overall body size and shape was found for both males and females. Correlations between body size and shape and each of five environmental variables (mean annual rainfall, mean maximum summer temperature, mean minimum winter temperature, relative humidity and latitude) were tested. Neither body size nor shape was correlated with any of the five variables, but both were related to habitat structure, with larger bandicoots being found in open forest habitats, while smaller bandicoots were found among swamp reeds. If the above variation has a genetic basis, these differences between locations may represent adaptive divergence and thus be of importance when formulating a conservation strategy for this species.

This paper describes the South Australian distribution of the southern brown bandicoot (Isoodon obesulus obesulus) on the basis of records of its past occurrence and field surveys undertaken to determine its present distribution. Since European settlement I. o. obesulus has been recorded from four separate regions of the state: the Mount Lofty Ranges, the South East, Kangaroo Island and Eyre Peninsula. Subfossil remains show that I. o. obesulus also once occurred on Yorke Peninsula but there is no evidence that it has existed there in modem times. Field surveys conducted between 1986 and 1993 confirmed that I. o. obesulus still exists in the Mount Lofty Ranges, the South East and on Kangaroo Island. Its status on Eyre Peninsula is uncertain. Isoodon o. obesulus is vulnerable in the South East and Mount Lofty Ranges because of habitat fragmentation and predation by feral carnivores. The Kangaroo Island population is less threatened as large areas of habitat have been preserved and the fox (Vulpes vulpes) has not been introduced. The area of potential bandicoot habitat remaining in these three regions totals approximately 190 000 ha, most of which is already managed for nature conservation. This habitat is highly fragmented, occurring as small remnant patches of native vegetation separated by extensive tracts of cleared and modified land cover. The implications of this habitat configuration for the long-term survival of I. o. obesulus are discussed.

Isoodon obesulus exhibits geographic variation in body size and shape, which appears to be adaptive. The geographic range of this species is declining, so the presence of adaptive divergence is of concern for the conservation of this species, both in the long term (loss of diversity decreasing evolutionary potential) and short term (choice of source populations for translocations). In this study, skulls of I. obesulus, both recent (animals alive within the last 100 years) and fossil (a few thousand years old), were examined and a range of measurements obtained. Comparisons were made between the two data sets to see whether skull morphology has changed over this relatively short period. Such a change may indicate rapid evolution of these characters and therefore the potential for fast regeneration of any lost geographic variation. Fossil skulls were smaller than their recent counterparts, had shorter ‘snouts’ relative to skull width and depth, and displayed no geographic variation in size and shape, whereas recent skulls were geographically differentiated. Because of the apparent rapid evolution in these characters, the implications of adaptive variation in size and shape inI. obesulus with regard to its conservation may be strictly short term, since any geographic variation lost may be quickly recovered if suitable conditions exist.

The number, distribution, maturation, motility and ultrastructure of spermatozoa from both northern (Isoodon macrourus) and southern (Isoodon obesulus) brown bandicoots were examined. One epididymidis per animal was fixed for light microscopy and transmission electron microscopy, and the contralateral side was used for the determination of sperm number, distribution and motility. Sperm form was similar between the two species. Approximately 56 x 10(6) testicular sperm and 100 x 10(6) epididymal sperm per side were present in I. macrourus, about 60% of which were in the caudal region. Initiation of sperm nuclear rotation and loss of the cytoplasmic droplet was first observed in distal caput or proximal corpus segments along with slow progressive motility. In these sperm, dislocation and anterior movement of the sperm neck from the implantation fossa and the modification of the distal margins of the sperm acrosome were evident. Motility of cauda epididymidal spermatozoa was rapid and coordinated, movement was restricted to one plane, and lateral head displacement was marked. As media viscosity increased, sperm velocity decreased, as did the amplitude of the tail beat, its frequency, and lateral head displacement but, in viscous mineral oil and mixtures of media and prostatic exudate, extremely rapid sinusoidal motility occurred. This study has detailed unusual morphological changes in bandicoot sperm during epididymal maturation and has shown that, although bandicoot sperm differ morphologically from those of the dasyurids, particularly in relation to head-tail orientation and tail ultrastructure, they exhibit similar motility.

Microhabitat use by the long-nosed potoroo, Potorous tridactylus, and six other species of small mammal was studied in remnant forest vegetation in south-western Victoria, Australia. Throughout its geographic range, P. tridactylus is consistently associated with dense vegetation in the ground and shrub strata. However, at a local scale, captures of P. tridactylus were not clearly associated with a particular floristic group, and were not strongly correlated with any structural feature of the vegetation. Rather, individuals utilised a range of sites of differing floristic composition and vegetation density. Dense cover provided diurnal shelter and protection from predators, whereas food resources were most abundant in adjacent more open areas. The use of vegetation mosaics or ecotones that allow the inclusion of contrasting microhabitats within an individual home range appears to be characteristic of potoroids in temperate environments. Such mosaics may result from topographic or edaphic variation, or from sera1 successional stages in vegetation following disturbance. Of the other small mammals, the bush rat, Rattus fuscipes, and the brown antechinus, Antechinus stuartii, favoured floristic groups that provided dense low cover. Captures of the swamp rat, Rattus lutreolus, were clumped, and centred on several sites along the forest edge on impeded drainage where potential foods were common. The long-nosed bandicoot, Perameles nasuta, and the southern brown bandicoot, Isoodon obesulus, were uncommon and clear microhabitat preferences were not displayed. The house mouse, Mus musculus, was of transient occurrence, mostly during autumn, and no obvious habitat preference was apparent. The quality and availability of microhabitats in remnant vegetation, together with landscape structure, are important in ensuring the persistence and conservation of small mammals in fragmented landscapes.

Habitat loss and fragmentation are major threats to the world’s biodiversity. Throughout Australia, land has been extensively cleared and modified through agriculture, forestry and urbanisation. In South Australia, less than 20% of native forests and woodlands remain and many of these have been severely fragmented into smaller and isolated patches. Species inhabiting fragmented habitats can suffer from decreased population size, reduced or inhibited dispersal and a series of genetic risks, including inbreeding, reduced genetic diversity, increased genetic differentiation among populations and potentially increased extinction risk. The southern brown bandicoot (Isoodon obesulus), the focus of the current thesis, is a rabbit-sized ground-dwelling marsupial, which has declined in number dramatically over the last 220 years. The subspecies I. o. obesulus is listed as nationally endangered under the Australian Environment Protection and Biodiversity Conservation Act 1999. Habitat loss and fragmentation has become one of the main processes threatening the survival of I. obesulus, leading to a contracted distribution and local population extinctions throughout Australia. In this thesis, a combination of microsatellite, nuclear and mitochondrial markers have been applied to investigate several questions relating to population genetic structure, gene flow, dispersal and genetic distinctiveness of populations of I. o. obesulus in southern Australia. The results obtained in this thesis have increased our knowledge of the genetic connectivity of I. o. obesulus populations in fragmented landscapes and provided valuable baseline genetic information for the conservation management of the species. This thesis was structured into four distinct data chapters as explained below. Chapter Two comprises a published primer note, in which nine polymorphic microsatellite markers were developed using a next generation sequencing approach. The markers were genotyped in 59 individuals from two distinct locations (the Mount Burr Range and the Mount Lofty Ranges) in South Australia. These markers, in addition to six microsatellite markers from a previous study, were used for the following thesis chapters and provide a valuable resource for future molecular ecological studies of I. obesulus. In Chapter Three, I investigate population structure and gene flow/dispersal of I. o. obesulus within a fragmented forest system in south-east South Australia – the Mount Burr Range. In this fragmented habitat, native forest patches are surrounded by matrices of either Pinus radiate plantations or cleared agricultural land. A total of 147 samples from 14 native forest patches were genotyped at 15 microsatellite loci. The results showed significant population genetic structuring at a fine spatial scale, with strong genetic differentiation among patches. Gene flow and dispersal was limited and generally only among neighbouring patches. The findings contribute valuable information on the positioning of habitat corridors in this area, and enable the effectiveness of these corridors to be assessed in the future. In the fourth chapter I utilise 14 microsatellite markers to genotype 284 individuals from 15 sites in a heavily modified peri-urban landscape in South Australia – the Mount Lofty Ranges. The results showed significant genetic differentiation among sites. Sites in the central Mount Lofty Ranges were also more genetically differentiated than sites distributed over a similar spatial scale in the Mount Burr Range, with evidence for a dispersal threshold of 1km (the Mount Burr populations had a ~2.5 km dispersal threshold), and with two sites appearing to be genetically isolated. These analyses suggested that gene flow/dispersal was limited to a higher degree in the Mount Lofty Ranges compared to Mount Burr, possibly due to the heavily modified landscape in the former area (e.g. a mixture of matrix of urban constructs and agricultural land). The final data chapter (Chapter Five) investigates the phylogeography and population structure of the I. o. obesulus populations in South Australia and south-western Victoria using a combination of 14 microsatellite markers, two mitochondrial sequence markers (control region and ND2) and three nuclear sequence markers (BRCA1, RAG1, and vWF). This chapter aimed to identify any potential evolutionarily significant units (ESUs) in the study region. All markers supported two distinct genetic lineages of I. o. obesulus in South Australia and south-western Victoria. The first lineage consisted of individuals from the Mount Lofty Ranges and Kangaroo Island. Samples from the lower south-east of South Australia and south-western Victoria (the Grampians and Lower Glenelg) represented the second lineage. These two lineages should be considered as separate evolutionarily significant units and managed separately for conservation purposes. An expanded phylogenetic analysis was conducted using additional samples of I. obesulus from other regions in Australia and samples of I. auratus (the golden bandicoot, distributed in the Northern Territory and Western Australia). The results raise the issue of the taxonomic status of the two lineages and also suggest that current subspecies and species classification within I. obesulus/I. auratus may not adequately reflect the existing major genetic lineages.
Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2014