Environment Institute Leaders publications

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Browsing Environment Institute Leaders publications by Advisors "Cooper, Steven John Baynard"

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    The effect of habitat fragmentation and population isolation on the genetic diversity, reproductive status and population viability of the southern hairy-nosed wombat (Lasiorhinus latifrons) in South Australia.
    (2010) Sparrow, Elisa; Taggart, David Augustine; Breed, William Godfrey; Cooper, Steven John Baynard; School of Earth and Environmental Sciences : Ecology and Evolutionary Biology
    A range of negative consequences associated with habitat fragmentation and population isolation have been demonstrated in a variety of animal species. Such consequences include inbreeding, reduced genetic diversity, increased mortality of young, reduced fecundity and compromised male fertility. Since the time of European settlement, many populations of the southern hairy-nosed wombat (Lasiorhinus latifrons) have become fragmented and isolated throughout South Australia, particularly on the Yorke Peninsula. This study aimed to examine the impact of habitat fragmentation and population isolation on the genetic diversity, seminal quality and reproductive success of the southern hairy-nosed wombat. The results showed there were very few wombats remaining on the Yorke Peninsula, with a total of 643 individuals estimated within 24 colonies all of which were geographically isolated by cleared agricultural land. Of these 24 colonies, 21 were estimated to have < 20 animals. Southern hairy-nosed wombats from two of these small isolated Yorke Peninsula colonies, namely Urania and Kulpara, were found to be genetically differentiated from one another, suggesting minimal current migration between these two colonies. These wombats were also genetically differentiated from wombats within the large population at Swan Reach, which is part of a continuous population in the Murraylands. High mean observed heterozygosity values were found in wombats from Urania and Kulpara (0.69 and 0.74 respectively), and these values did not differ significantly from that of the Swan Reach population (0.71). Allelic diversity was slightly lower in the colonies on the Yorke Peninsula; but this was not statistically significant from the population in the Murraylands. Inbreeding was not detected in any population. Despite this, wombats from the Yorke Peninsula were found to be smaller in body morphology and have larger testes. These animals also had significantly lower ejaculate volumes, with greater numbers of sperm morphological abnormalities in the ejaculate. A trend for lower sperm concentration and sperm motility in wombats from the Yorke Peninsula was also observed. The lower seminal quality in Yorke Peninsula male wombats was not reflected in a reduction in the reproductive success of the population, with all three populations examined exhibiting a similar number of females with pouch young, and in late lactation. There was, however, an unequal sex ratio within the Urania population, with a lower number of adult females in the population during the breeding season. The results from this study suggest that colonies of southern hairy-nosed wombats on the Yorke Peninsula are in danger of localised extinction if not appropriately managed and conserved. Future study directions and possible management techniques are discussed in order to minimise localised extinctions and maintain the viability of southern hairy-nosed wombats on the Yorke Peninsula and throughout South Australia.
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    Modes of speciation in subterranean diving beetles from a single calcrete aquifer in Central Western Australia.
    (2010) Bradford, Tessa Margaret; Cooper, Steven John Baynard; Austin, Andrew Donald; School of Earth and Environmental Sciences : Ecology and Evolutionary Biology
    Calcrete aquifers from the Yilgarn region in central Western Australia‘s arid zone contain a highly diverse range of obligate groundwater invertebrate species (stygofauna), with many endemic to single calcretes. Phylogenetic studies on the diving beetles from the Yilgarn calcretes suggest a scenario of invasion of the subterranean environment by several surface dwelling ancestors during aridification of the region since the Miocene. This system is ideal for examining modes of speciation within a closed calcrete body and in particular the relative roles of allopatric, parapatric and sympatric speciation in the generation of diving beetle (Dytiscidae) species diversity. Previous phylogenetic analyses have identified 13 independent cases of sympatric sister species pairs of large and small diving beetles in separate calcretes, suggesting the potential for their speciation in sympatry as a result of ecological niche partitioning. A single calcrete at Sturt Meadows contains a sympatric sister triplet of large and small diving beetles (Paroster macrosturtensis, P. mesosturtensis, P microsturtensis), and can be accessed by an extensive grid of mineral exploration bores (3.5km², 115 bores), allowing intensive sampling for population genetic studies and biodiversity assessment. Comparative phylogeographic analyses by others on these Paroster beetle species found no evidence for long term allopatric processes operating within the calcrete, although any fragmentation event that could have led to the evolution of the three beetle species may not have persisted post-speciation, and thus would not been seen in their gene genealogies. The aim of this study was to investigate the possibility that the three beetle species at Sturt Meadows may have evolved by sympatric speciation due to trophic niche partitioning. Two main approaches were used to achieve this aim. First, whether the different beetle species have different trophic niches was determined and, second, whether micro-allopatric processes, such as fragmentation events, may have led to the evolution of the three beetle species was investigated. To detect evidence for such fragmentation events, a comparative phylogeography of chiltoniid amphipods in the Sturt Meadows calcrete was undertaken. A DNA barcoding framework was established for the macro-invertebrates in the Sturt Meadows calcrete, in order to obtain sequence information on potential prey groups for the diving beetles. A 623-bp fragment of the mitochondrial cytochrome c oxidase 1 (COI) gene was amplified from stygofauna plus terrestrial organisms that were found in the calcrete. Phylogenetic analyses revealed the existence of 12 divergent monophyletic groups of haplotypes, including three unrelated lineages of chiltoniid amphipod that are morphologically cryptic. Allozyme analyses on the amphipods showed them to be three species that can be separated at multiple allozyme loci. Spatial variation in genetic diversity was assessed for the chiltoniid amphipods, enabling a comparative phylogeography of the three species across the bore field. There was no common pattern in the gene trees of the amphipod species, so no evidence for three isolation events in the diversification of the diving beetles at this site. However, high haplotype diversity coupled with low nucleotide diversity, plus signatures of population expansion and isolation by distance in two out of three species, match previous findings for diving beetles at the same site and indicate the potential for micro-allopatric evolutionary processes to have operated within the calcrete. Isolation of populations in pockets of favourable habitat (refugia) within the calcrete followed by expansion events, are proposed as the most likely generator of population genetic diversity, and are thought to be related to water level changes in the aquifer. Trophic niche partitioning in the sister triplet of large and small Paroster diving beetles and their larvae was investigated by molecular amplification of small fragments of the COI gene identified by the barcode. Amphipods (Chiltoniidae) and copepods (Harpacticoida, Cyclopoidea) were chosen for the analysis as they were the most abundant potential prey items in the calcrete. There was not complete trophic partitioning in the adult beetles, with all three species feeding on amphipods and copepods. As the trophic analysis was molecular, differences in size of the prey were not tested for. There was some evidence for preferential feeding on particular prey species by the adult beetle species, however, small sample sizes precluded making comparisons between their larvae. It is thought that in the impoverished environment of the aquifer, the adult beetles are scavengers and opportunistic feeders, as well as active predators. Stable isotope analysis confirmed that the three diving beetle species are feeding on similar food items, and indicated a separate source of carbon and nitrogen to the tree roots as the basis of the food web of the calcrete. In summary, there was no evidence for complete trophic niche partitioning in the adult diving beetles of different sizes that could have led to their speciation in sympatry. Any further investigation of trophic differences needs to concentrate on preferential feeding in the adults, and the trophic niche of the beetle larvae which are active predators. The potential for micro-allopatry in the diversification of the different sized diving beetles at Sturt Meadows has been identified, through congruence in current population genetic patterns for the amphipods and the diving beetles. Stygofauna in the calcrete have high genetic diversity, which is thought to be the result of historical water level fluctuations leading to frequent population bottlenecks, followed by range expansion after aquifer recharge. Identification of at least 12 macro-invertebrate species in a single calcrete increases the total number of stygobytic and troglobytic species discovered in the Yilgarn, and has enabled estimates to be made of possible numbers of subterranean species in the region still to be discovered. The presence of large and small dytiscid beetles in multiple calcretes that are sympatric sister species still points to some common ecological niche differentiation within the calcrete environment. It is hypothesized that there could be depth partitioning in the different sized diving beetles related to their oxygen requirements. The population genetic and ecological data generated at Sturt Meadows provide a baseline for the Yilgarn calcretes. Extending such a study to examine spatial and ecological differentiation in sympatric sister species of subterranean diving beetles across multiple calcretes, would be a powerful approach in the investigation of modes of speciation.
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    Molecular evolution of the carboxy terminal, the putative sperm-ZP binding site, of the zona pellucida 3 glycoprotein in old world murine rodents.
    (2007) Swann, Christine A.; Breed, William Godfrey; Cooper, Steven John Baynard; School of Medical Sciences : Anatomical Sciences
    In mammals, before fertilisation can occur, sperm have to bind to, and penetrate, the extracellular coat of the oocyte, the zona pellucida (ZP). In the laboratory mouse, which has been used as a model system for fertilization studies, sperm-ZP binding has been found to be mediated by a region near the carboxy terminal, encoded by exon 7 of the Zp3 gene. This region shows considerable interspecific sequence diversity in North American cricetid rodents, with some evidence of adaptive evolution, suggesting that this may contribute to species specific sperm-ZP binding. However, by contrast, in a preliminary study of three species of Australian murine rodents an identical protein sequence of the region encoded by exon 7 of Zp3 was found to be present. The aim of this present study was to determine the pattern of sequence diversity of this region in the most speciose subfamily of mammals, the murine rodents, and to obtain insight into the selective pressures involved in its evolution. For this, DNA was extracted from murine rodents of Africa, Eurasia, South-east Asia, New Guinea and Australia. The nucleotide and predicted amino acid sequence of exons 6 and 7 of Zp3 in 96 murine species from 14 divisions, as recently defined by Musser and Carleton (2005), was determined and compared. Generally, it was found that closely related species shared a highly similar ZP3 sequence. Maximum likelihood analyses of codon substitution models using representatives from 14 murine divisions, suggested that positive selection had occurred within only a few lineages at several different codon sites adjacent to, or within, the putative combining-site for sperm of ZP3. Positive selection was not evident when the analysis was restricted to the Australian taxa which showed low levels of both intra- and inter-generic sequence divergence. There was no good evidence that this region contributes to species specificity of sperm-ZP binding in these species. These findings thus suggest that the selective forces acting on the Zp3 exon 7 region during the evolution of the murine rodents have varied possibly due to a range of selective pressures not necessarily restricted to the prevention of hybridization. It seems unlikely, therefore, that the amino acid sequence of the exon 7 coding region contributes to species specificity of sperm-ZP binding within most of the lineages from this most speciose subfamily of eutherian mammals.
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    Phylogenetics and biogeography of Australian subterranean Parabathynellidae.
    (2012) Abrams, Kym; Guzik, Michelle Tanya; Austin, Andrew Donald; Cooper, Steven John Baynard; King, Rachael Amy; School of Earth and Environmental Sciences
    The putatively ancient subterranean crustacean family Parabathynellidae has been poorly studied, in part because of the problem of obtaining material from difficult to access subterranean habitats in which they live. Further, the systematics of the group has been complicated by their generally simplified morphology and isolated descriptions of new taxa in the absence of any phylogenetic framework. This thesis provides a comprehensive molecular systematics framework for Australian Parabathynellidae, which is used to explore phylogenetic relationships amongst parabathynellids, their diversity, some aspects of character evolution and their biogeographic history within Australia. In addition, taxonomic descriptions are provided for the first parabathynellid species from South Australia. For the first data chapter molecular sequence data from the mitochondrial cytochrome c oxidase subunit 1 (COI) and 18S rRNA genes were generated in order to examine phylogenetic relationships amongst Australian genera and assess the species diversity of this group within Australia. The resultant phylogenetic framework, in combination with an ancestral state reconstruction analysis, was used to explore the evolution of two key morphological characters previously used to define genera, and assess the oligomerization principle (i.e. serial appendage reduction over time), which is commonly invoked in crustacean systematics. The ancestral state reconstruction analysis was also used to determine whether there has been convergent evolution of appendage numbers during the evolution of Australian parabathynellids. Phylogenetic analyses revealed that species of each known genus, defined by traditional morphological methods, were monophyletic, suggesting that the commonly used generic characters are robust for defining distinct evolutionary lineages. These analyses also revealed a remarkable diversity of parabathynellids. Additionally, ancestral state reconstruction analysis provided evidence for multiple cases of convergent evolution for the two morphological characters evaluated and contradicted the conventional view of parabathynellid evolution, which assumes that more simplified taxa (i.e. those with fewer-segmented appendages and setae) are derived and more complex taxa are primitive. The third chapter focuses on South Australia, where phylogenetic analyses revealed a previously unknown diversity of parabathynellids from South Australia, and a complex set of relationships with the New South Wales and Western Australian fauna. Additionally, the first parabathynellid genus from South Australia, Arkaroolabathynella gen. nov, is described and a key to and checklist of Australian parabathynellid genera is also provided. The final data chapter used an expanded dataset to investigate the geographic distribution, history and evolutionary relationships of extant parabathynellids between subterranean bioregions in Australia. This study found evidence for significant regional biogeographic structuring of parabathynellids at the genus and species levels, indicating a long and complex evolutionary history for these animals in Australia, likely shaped by fluctuating climates throughout the continent’s development. The high incidence of regional endemism for parabathynellids is signifcant because it confirms the poor dispersal capability of these animals, which makes them particularly vulnerable to disturbance or destruction of their subterranean habitats.
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    Socioecology and phylogeography of the Yellow-bellied Glider (Petaurus australis)
    (2006) Brown, Meredeth; Carthew, Susan Mary; Cooper, Steven John Baynard; School of Earth and Environmental Sciences
    Marsupials have complex and interesting socioecology and life history strategies that differ quite markedly to much - studied eutherian mammals. However, the socioecology and life history strategies of a number of Australian marsupials are most often observed only within the context of a much larger study on their ecology. My aim was to study, using a combination of behavioural observations and molecular DNA techniques, aspects of the socioecology of a population of yellow - bellied gliders ( Petaurus australis ) in Rennick State Forest, south - western Victoria. Petaurid gliders feed on plant and insect exudates, pollen / nectar and arthropods. Yellow - bellied gliders are arboreal, rare, nocturnal and cryptic, have persistent pair bonds, are territorial and exist in low population densities. In particular, I sought to confirm that the Rennick population of yellow - bellied gliders maintained a predominantly monogamous mating system. I also sought to confirm that the timing of reproduction in this population of yellow - bellied gliders would be seasonal, and timed to coincide with peaks in the abundances of two indices of protein food resources ( i.e. flowering and bark shed ). In a more broadscale study, I sought to examine the geographic distribution of mitochondrial haplotyes and morphological variation of the yellowbellied glider throughout its range. Polymorphic microsatellite loci are the choice of genetic marker for fine - scale studies, such as relatedness and paternity. Microsatellite loci had previously only been characterised and optimised for Petaurus norfolcensis ( squirrel gliders ). However, close inspection of the GenBank sequences revealed the presence of replicates differing only by sequencing errors. A panel of seven polymorphic tetranucleotide loci in Petaurus breviceps ( sugar gliders ) and three polymorphic trinucleotide loci in P. australis were isolated and optimised. Five P. breviceps loci were polymorphic in P. norfolcensis and two were polymorphic in P. australis. Only one P. australis locus was variable in P. breviceps and P. norfolcensis. No locus showed a deficit in heterozygotes according to Hardy - Weinberg expectations, and the large number of alleles for some of the loci confirmed their usefulness for studies in relatedness and paternity. A number of Australian arboreal marsupials have been reported to show monogamous and polygynous mating systems in different populations, but previous studies have not included genetic analyses to confirm the observations. My aim was to test the hypothesis that monogamy was the predominant mating system in a population of yellow - bellied gliders ( Petaurus australis ) in south - western Victoria. Home range overlap, cohesiveness of pairs, rates of den site co - occupancy and location of den trees within the home ranges of 13 gliders were determined via radio - tracking. A monogamous social system predominated, demonstrated by extensive home range overlap between cohabiting adult males and females ( 40 - 100 % ) and little home range overlap between adjacent territories ( < 7 % ). Males spent approximately 55 % of their active time within 25m of their female partners and 55 - 85 % of their sleeping time in dens with their female partner. The paternity of all juveniles within the population was analysed using five microsatellite DNA markers. Of 37 individuals genotyped, 12 of 13 juveniles could be attributed to the resident adult male. My results suggest that social monogamy equates with genetic monogamy in this population of yellow - bellied gliders. Mammalian taxa living in seasonal environments usually coincide energy - demanding reproductive activities with the seasonal availability of food resources. However, few studies on arboreal marsupial taxa in Australia have focussed upon the interplay of forest phenology and the timing of breeding. This study examined forest phenology in a temperate environment, and the timing of reproduction the yellow - bellied glider. I captured adult females once per month between August 2001 and August 2003 to determine reproductive condition, and monitored indicators for two key food resources over the same period. Flowering phenology ( as an index of pollen availability ) was assessed in 170 manna gum ( Eucalyptus viminalis ) and brown stringybark ( E. baxteri ) trees, while bark shed ( as an index of arthropod availability ) was assessed in 45 manna gum, the only eucalypt species at this site that sheds it bark. Aseasonal reproduction was indicated within this population of gliders, as distributions of births were not statistically different from random. However, yellow - bellied gliders did exhibit distinct birth peaks in spring, summer and winter, when data were combined for both years. The temporal distributions of flowering for both eucalypt species were statistically different from random, indicating seasonal availability of nectar and pollen. Peak flowering occurred in summer for brown stringybark, and autumn for manna gum in both years, although for manna gum peak abundance of flowers was one month earlier in the second year. While the temporal distribution of bark shed on the trunks of trees did not differ from random, it did show seasonality on the main and outer branches, peaking in summer and declining thereafter. Thus, it appears that yellow - bellied gliders breed aseasonally in a predictable, seasonal environment. However, yellow - bellied gliders have a reliance on the complex temporal interplay of different seasonal food resources. Subspecific status has often been used as a surrogate for conservation unit, but does not always reflect intra - specific lineages with different evolutionary histories. One contentious case of subspecific classification occurs in the yellow - bellied glider, a marsupial species showing considerable decline in population size and requiring conservation management. Our aim was to assess the current subspecific status of populations and define units of conservation using a combination of phylogeographical analyses of mitochondrial DNA and morphological analyses. Analyses of the mitochondrial ND4 gene provided evidence for significant phylogeographic structure within yellow - bellied gliders. Isolated populations in north Queensland ( NQ ) and Victoria / South Australia were genetically distinct from populations in New South Wales and southern Queensland. Morphological analyses provided little evidence for discrimination of populations, although NQ specimens were generally smaller in size compared to southern forms. My analyses do not support the classification of subspecies, P. a. reginae, for the original type specimen from southern Queensland. Taking into account other behavioural and ecological data, and the disjunct distribution of NQ populations from southern populations, I propose that the NQ population represents a distinct Evolutionarily Significant Unit, a lineage showing highly restricted gene flow with the rest of the species.
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    Systematics and diversity of Australian pygopodoid geckos (Pygopodoidea, Gekkota, Squamata).
    (2010) Oliver, Paul M.; Lee, Michael Soon Yoong; Cooper, Steven John Baynard; School of Earth and Environmental Sciences
    Lizards and snakes (squamates) are the most diverse endemic component of the Australian terrestrial vertebrate fauna; and three families of Pygopodoid gecko (Carphodactylidae, Diplodactylidae and Pygopodidae) together comprise the third most species rich squamate lineage within Australia. In this thesis I present the results of an analysis of the systematics and species diversity of components of the Australian pygopodoid gecko radation; specifically, I focus on establishing an overall systematic and temporal framework for the evolution of the entire clade, examining estimates of species diversity and interrelationships within three genera, and using the resultant phylogenetic framework to advance our understanding of how the onset and expansion of aridification across Australia may have affected evolution with this lineage. In chapter two the phylogenetic relationships of all Australian pygopodoid genera (except Orraya) are examined, and temporal scale for their diversification is estimated based on Bayesian and Likelihood analyses of two nuclear genes. This work demonstrates that at least five extant lineages within this radiation diverged before the final separation of Australia from Antarctica, and that the clade has a long history within Australia equivalent to famous Gondwanan elements of the fauna, such as the Marsupials. An analysis of systematic relationships within the genus Diplodactylus based on mitochondrial DNA and morphological data indicate that as recognised previously, it comprises two genetically distinct and morphologically diagnosable clades; we resurrect the name Lucasium for one of the these clades. Both genera appear to represent moderately diverse and broadly overlapping radiations of multiple taxa largely restricted to arid and semi-arid Australia, but absent from relatively mesic coastal areas, especially along the east, suggesting semi-arid to arid habitats have a long history within Australia. A multilocus (mitochondrial, alloyme and karyotypic) examination of species boundaries within the newly defined Diplodactylus increases estimates of species diversity from 13 to 29. A similar study of the single recognised species of Crenadactylus, reveals it to comprise a surprisingly ancient radiation of at least ten candidate species. The diversification of Crenadactylus species, some of the oldest cryptic vertebrate taxa yet identified, dates backs to the estimated onset of aridification and has important insights into this process. Together, these two studies demostrate that species diversity in many Australian vertebrates remains significantly underestimated, and that this inadequate taxonomy is masking important conservation and evolutionary information. In chapter five I present a combined mitochondrial and nuclear phylogenetic analysis of the ecologically widespread genus Nephrurus (sensu Bauer 1990). Based on this phylogeny we propose a revised generic arrangment for this clade assigning the two most plesiomorphic and basal lineages to monotypic genera. Molecular dating reveals a strong correlation between the age of a specialised arid-zone clade and independent estimates for the major expansion of the arid zone.