Effect of Phytophthora cinnamomi on the habitat utilization of Antechinus stuartii in a Victorian forest

Phytophthora cinnamomi (Cinnamon fungus) is a pathogenic soil fungus which infects plant communities along the south-eastern coast of Australia, and the south-western corner of Western Australia. The symptoms of this disease include chlorosis, death of branches (ie. ‘dieback’), retarded growth and the eventual death of infected plants. This leads to devastating effects upon plant communities by altering both the structural and floristic characteristics of these communities. Small mammal species are dependent on specific features of their habitat such as vegetation structure and floristics. This thesis investigated alterations to the habitat of the insectivorous marsupial mouse, Antechinus stuartii, due to the presence of P. cinnamomi. The study was undertaken in an area of an open forest in the Brisbane Ranges, Victoria. Significant changes were found in both the floristic composition and structure of the vegetation at study sites infected with P, cinnamomi, compared to uninfected sites. The habitat utilization by A. stuartii of uninfected and infected vegetation was investigated using live trapping and radio-telemetric techniques. Capture rates were higher at sites uninfected by P. cinnamomi, and both male and females selected areas free from infection. Home range areas of males were significantly larger than those of females as assessed by telemetry. Both sexes spent a high proportion of time in areas dominated by Xanthorrhoea australis (Austral grass tree). There were significant relationships between the abundance of A. stuartii and the denseness of vegetation above 1 metre in height, and in particular, the proportion of cover afforded by X. australis. There were no significant differences in the cover of Eucalyptus spp. between uninfected and infected sites, but there were significantly more nest hollows in infected areas. The abundance of invertebrates was examined using pitfall traps. There were no significant differences in the abundance of the larger invertebrate taxa at infected and uninfected sites, but higher abundances of some micro-invertebrate groups in infected areas were recorded. The most likely factors considered to be influential in the habitat selection of A. stuartii were vegetation structure, and the presence of X. australis. To assess whether these factors were important the leaves of X. australis were removed with a brushcutter, to mimic the early effects of infection with P. cinnamomi. Animals did not respond to the alteration of vegetation structure in the short term (3-4 days). Longer-term experiments are required to assess the habitat utilization of A. stuartii at different periods following habitat manipulation. The implications of the presence of P. cinnamomi on the conservation of fauna are discussed. The destructive nature of the pathogen, and the slow rate of recovery from the disease, means that P. cinnamomi can be considered a threatening process to plant communities and the fauna that reside within that habitat. Future management of this disease within natural areas must therefore be cognisant of the potential of P. cinnamomi to significantly affect faunal as well as vegetative communities.

Ecology of arboreal marsupials in a network of remnant linear habitats

Linear strips of vegetation set within a less-hospitable matrix are common features of landscapes throughout the world. Depending on location, form and function, these linear landscape elements include hedgerows, fencerows, shelterbelts, roadside or streamside strips and wildlife corridors. In many anthropogenically-modified landscapes, linear strips are important components for conservation because they provide a large proportion of the remaining wooded or shrubby habitat for fauna. They may also function to provide connectivity across the landscape. In some districts, the linear strips form an interconnected network of habitat. The spatial configuration of remnant habitat (size, shape and arrangement) may influence habitat suitability, and hence survival, of many species of plant and animal in modified landscapes. Near Euroa in south-eastern Australia, the clearing and fragmentation of temperate woodlands for agriculture has been extensive and, at present, less than 5% tree cover remains, most of which (83%) occurs as linear strips along roads and streams. The remainder of the woodland occurs as relatively small patches and single isolated trees scattered across the landscape. As an assemblage, arboreal marsupials are woodland dependent and vary in their sensitivity to habitat loss and fragmentation. This thesis focusses on determining the conservation status of arboreal marsupials in the linear network and understanding how they utilise the landscape mosaic. Specifically, the topics examined in this thesis are: (1) the composition of the arboreal marsupial assemblage in linear and non-linear woodland remnants; (2) the status and habitat preferences of species of arboreal marsupial within linear remnants; and (3) the ecology of a population of the Squirrel Glider Petaurus norfolcensis in the linear network, focusing on population dynamics, spatial organisation, and use of den trees. The arboreal marsupial fauna in the linear network was diverse, and comprised seven out of eight species known to occur in the district. The species detected within the strips were P. norfolcensis, the Sugar Glider Petaurus breviceps, Common Brushtail Possum Trichosums vulpecula, Common Ringtail Possum Pseudocheirus peregrinus, Brush-tailed Phascogale Phascogale tapoatafa, Koala Phascolarctos cinereus and Yellow-footed Antechinus Antechinus flavipes. The species not detected was the Feathertail Glider Acrabates pygmaeus. Survey sites in linear remnants (strips of woodland along roads and streams) supported a similar richness and density of arboreal mammals to sites in non-linear remnants (large patches or continuous tracts of woodland nearby). Furthermore, the combined abundance of all species of arboreal marsupials was significantly greater in sites in the linear remnants than in the non-linear remnants. This initial phase of the study provided no evidence that linear woodland remnants support a degraded or impoverished arboreal marsupial fauna in comparison with the nonlinear remnants surveyed. Intensive trapping of arboreal marsupials within a 15 km linear network between February 1997 and June 1998 showed that all species of arboreal marsupial (except A. pygmaeus) were present within the linear strips. Further analyses related trap-based abundance estimates to measures of habitat quality and landscape structure. Width of the linear habitat was significantly positively correlated with the combined abundance of all arboreal marsupials, as well as with the abundance of P. norfolcensis and T. vulpecula. The abundance of T. vulpecula was also significantly positively correlated with variation in overstorey species composition, Acacia density and the number of hollow-bearing trees. The abundance of P. norfolcensis was positively correlated with Acacia density and canopy width, and negatively correlated with distance to the nearest intersection with another linear remnant. No significant variables were identified to explain the abundance of P. tapoatafa, and there were insufficient captures of the remaining species to investigate habitat preferences. Petaurus norfolcensis were resident within the linear network and their density (0.95 -1.54 ha-1) was equal to the maximum densities recorded for this species in continuous forest elsewhere in south-eastern Australia. Rates of reproduction were also similar to those in continuous forest, with births occurring between May and December, a mean natality rate of 1.9, and a mean litter size of 1.7. Sex ratios never differed significantly from parity. Overall, the population dynamics of P. norfolcensis were comparable with published results for the species in contiguous forest, clearly suggesting that the linear remnants currently support a self-sustaining, viable population. Fifty-one P. norfolcensis were fitted with radio transmitters and tracked intermittently between December 1997 and November 1998. Home ranges were small (1.3 - 2.8 ha), narrow (20 - 40 m) and elongated (322 - 839 m). Home ranges were mostly confined to the linear remnants, although 80% of gliders also utilised small clumps of adjacent woodland within farm paddocks for foraging or denning. Home range size was significantly larger at intersections between two or more linear remnants than within straight sections of linear remnants. Intersections appeared to be important sites for social interaction because the overlap of home ranges of members of adjacent social groups was significantly greater at intersections than straight sections. Intersections provided the only opportunity for members of three or more social groups to interact, while still maintaining their territories. The 51 gliders were radiotracked to 143 different hollow-bearing trees on 2081 occasions. On average, gliders used 5.3 den trees during the study (range 1-15), and changed den trees every 4.9 days. The number of den trees used by each glider is likely to be conservative because the cumulative number of den trees continued to increase over the full duration of the study. When gliders shifted between den trees, the mean distance between consecutive den sites was 247 m. Den trees were located throughout a glider's home range, thereby reducing the need to return to a central den site and potentially minimising energy expenditure. Dens were usually located in large trees (mean diameter 88.5 cm) and were selected significantly more often than expected based on their occurrence within the landscape. The overall conclusion of this thesis is that the linear network I studied provides high quality habitat for resident populations of arboreal marsupials. Important factors influencing the suitability of the linear remnants appear to be the high level of network connectivity, the location on soils of high nutrient status, the high density of large trees and an acacia understorey. In highly fragmented landscapes, linear habitats as part of the remaining woodland mosaic have the potential to be an integral component in the conservation of woodland-dependent fauna. The habitat value of linear strips of vegetation should not be underestimated.

No evidence of expression of two classes of natural antibiotics (cathelicidins and defensins) in a sample of platypus milk

Marsupial neonates are born without a fully functioning immune system, and are known to be protected in part by natural antimicrobial peptides present in their mother's milk. Monotreme neonates hatch at a similar stage in development, and it has been hypothesised that their survival in a non-sterile burrow also relies on the presence of natural antibiotics in their mother's milk. Here we review the field of monotreme lactation and the antimicrobial peptide complement of the platypus (Ornithorhynchus anatinus). Using reverse transcriptasepolymerase chain reaction of milk cell RNA from a sample of platypus milk, we found no evidence for the expression of cathelicidins or defensins in the milk. This was unexpected. We hypothesise that these natural antibiotics may instead be produced by the young platypuses themselves.

Characterisation of monotreme caseins reveals lineage-specific expansion of an ancestral casein locus in mammals

Using a milk-cell cDNA sequencing approach we characterised milk-protein sequences from two monotreme species, platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus) and found a full set of caseins and casein variants. The genomic organisation of the platypus casein locus is compared with other mammalian genomes, including the marsupial opossum and several eutherians. Physical linkage of casein genes has been seen in the casein loci of all mammalian genomes examined and we confirm that this is also observed in platypus. However, we show that a recent duplication of β-casein occurred in the monotreme lineage, as opposed to more ancient duplications of α-casein in the eutherian lineage, while marsupials possess only single copies of α- and β-caseins. Despite this variability, the close proximity of the main α- and β-casein genes in an inverted tail-tail orientation and the relative orientation of the more distant kappa-casein genes are similar in all mammalian genome sequences so far available. Overall, the conservation of the genomic organisation of the caseins indicates the early, pre-monotreme development of the fundamental role of caseins during lactation. In contrast, the lineage-specific gene duplications that have occurred within the casein locus of monotremes and eutherians but not marsupials, which may have lost part of the ancestral casein locus, emphasises the independent selection on milk provision strategies to the young, most likely linked to different developmental strategies. The monotremes therefore provide insight into the ancestral drivers for lactation and how these have adapted in different lineages.

Responsible aquaculture and trophic level implications to global fish supply

Hunger and malnutrition remain among the most devastating problems facing the world’s poor and needy, and continue to dominate the health and well-being of the world’s poorest nations. Moreover, there are growing doubts as to the long-term sustainability of many existing food production systems, including capture fisheries and aquaculture, to meet the future increasing global demands.Of the different agricultural food production systems, aquaculture (the farming of aquatic animals and plants) is widely viewed as an important weapon in the global fight against malnutrition and poverty, particularly within developing countries where over 93% of global production is currently produced, providing in most instances an affordable and a much needed source of high quality animal protein, lipids, and other essential nutrients. The current article compares for the first time the development and growth of the aquaculture sector and capture fisheries by analyzing production by mean trophic level. Whereas marine capture fisheries have been feeding the world on high trophic level carnivorous fish species since mankind has been fishing the oceans, aquaculture production within developing countries has focused, by and large, on the production of lower trophic level species. However, like capture fisheries, aquaculture focus within economically developed countries has been essentially on the culture of high value-, high trophic level-carnivorous species. The long term sustainability of these production systems is questionable unless the industry can reduce its dependence upon capture fisheries for sourcing raw materials for feed formulation and seed inputs. In line with above, the article calls for the urgent need for all countries to adopt and adhere to the principles and guidelines for responsible aquaculture of the FAO Code of Conduct for Responsible Fisheries.

Comparative genomics and transcriptomics of lactation

Lactation is an important characteristic of mammalian reproduction sometimes referred to as the quintessence of mammals. Comparative genomics and transcriptomics experiments are allowing a more in-depth molecular analysis of the evolution of lactation throughout the mammalian kingdom and these recent results are reviewed here. Milk cell and mammary gland gene expression analysis with sequencing methodology have started to reveal conserved or specific milk protein and components of the lactation system of monotreme, marsupial and eutherian lineages. These experiments have confirmed the ancient origin of the complex lactation system and provided useful insight into the function of specific milk proteins in the control of the lactation programme or the role of milk in the regulation of growth and development of the young beyond simple nutritive aspects.

Evolution of lactation : ancient origin and extreme adaptations of the lactation system

Lactation, an important characteristic of mammalian reproduction, has evolved by exploiting a diversity of strategies across mammals. Comparative genomics and transcriptomics experiments have now allowed a more in-depth analysis of the molecular evolution of lactation. Milk cell and mammary gland genomic studies have started to reveal conserved milk proteins and other components of the lactation system of monotreme, marsupial, and eutherian lineages. These analyses confirm the ancient origin of the lactation system and provide useful insight into the function of specific milk proteins in the control of lactation. These studies also illuminate the role of milk in the regulation of growth and development of the young beyond simple nutritive aspects.

Australia’s savanna herbivores : bioclimatic distributions and an assessment of the potential impact of regional climate change

The future impacts of climate change are predicted to significantly affect the survival of many species. Recent studies indicate that even species that are relatively mobile and/or have large geographic ranges may be at risk of range contractions or extinction. An ecologically and evolutionary significant group of mammals that has been largely overlooked in this research is Australia’s large marsupial herbivores, the macropodids (kangaroos). The aims of our investigation were to define and compare the climatic conditions that influence the current distributions of four sympatric large macropodids in northern Australia (Macropus antilopinus, Macropus robustus, Macropus giganteus, and Macropus rufus) and to predict the potential future impact of climate change on these species. Our results suggest that contemporary distributions of these large macropodids are associated with well‐defined climatic gradients (tropical and temperate conditions) and that climatic seasonality is also important. Bioclimatic modeling predicted an average reduction in northern Australian macropodid distributions of in response to increases of 2.0°C. At this temperature, the distribution of M. antilopinus was reduced by . We predict that increases of 6.0°C may cause severe range reductions for all four macropodids ( ) in northern Australia, and this range reduction may result in the extinction of M. antilopinus.

Large-herbivore distribution and abundance : intra-and interspecific niche variation in the tropics

Determining the biological and environmental factors that limit the distribution and abundance of organisms is central to our understanding of the niche concept and crucial for predicting how species may respond to large-scale environmental change, such as global warming. However, detailed ecological information for the majority of species has been collected only at a local scale, and insufficient consideration has been given to geographical variation in intraspecific niche requirements. To evaluate the influence of environmental and biological factors on patterns of species distribution and abundance, we conducted a detailed, broadscale study across the tropical savannas of northern Australia on the ecology of three large, sympatric marsupial herbivores (family Macropodidae): the antilopine wallaroo (Macropus antilopinus), common wallaroo (M. robustus), and eastern grey kangaroo (M. giganteus). Using information on species abundance, climate, fire history, habitat, and resource availability, we constructed species' habitat models varying from the level of the complete distribution to smaller regional areas. Multiple factors affected macropod abundance, and the importance of these factors was dependent on the spatial scale of analyses. Fire regimes, water availability, geology, and soil type and climate were most important at the large scale, whereas aspects of habitat structure and interspecific species abundance were important at smaller scales. The distribution and abundance of eastern grey kangaroos and common wallaroos were strongly influenced by climate. Our results suggest that interspecific competition between antilopine wallaroos and eastern grey kangaroos may occur. The antilopine wallaroo and eastern grey kangaroo (grazers) preferred more nutrient-rich soils than the common wallaroo (grazer/browser), which we relate to differences in feeding modes. The abundance of antilopine wallaroos was higher on sites that were burned, whereas the abundance of common wallaroos was higher on unburned sites. Future climate change predicted for Australia has the capacity to seriously affect the abundance and conservation of macropod species in tropical savannas. The results of our models suggest that, in particular, the effects of changing climatic conditions on fire regimes, habitat structure, and water availability may lead to species declines and marked changes in macropod communities.

Climate change impacts : challenges for aquaculture

In spite of all the debates and controversies, a global consensus has been reached that climate change is a reality and that it will impact, in diverse manifestations that may include increased global temperature, sea level rise, more frequent occurrence of extreme weather events, change in weather patterns, etc., on food production systems, global biodiversity and overall human well being. Aquaculture is no exception. The sector is characterized by the fact that the organisms cultured, the most diverse of all farming systems and in the number of taxa farmed, are all poikilotherms. It occurs in fresh, brackish and marine waters, and in all climatic regimes from temperate to tropical. Consequently, there are bound to be many direct impacts on aquatic farming systems brought about by climate change. The situation is further exacerbated by the fact that certain aquaculture systems are dependent, to varying degrees, on products such as fishmeal and fish oil, which are derived from wild-caught resources that are subjected to reduction processes. All of the above factors will impact on aquaculture in the decades to come and accordingly, the aquatic farming systems will begin to encounter new challenges to maintain sustainability and continue to contribute to the human food basket. The challenges will vary significantly between climatic regimes. In the tropics, the main challenges will be to those farming activities that occur in deltaic regions, which also happen to be hubs of aquaculture activity, such as in the Mekong and Red River deltas in Viet Nam and the Ganges-Brahamaputra Delta in Bangladesh. Aquaculture in tropical deltaic areas will be mostly impacted by sea level rise, and hence increased saline water intrusion and reduced water flows, among others. Elsewhere in the tropics, inland cage culture and other aquaculture activities could be impacted by extreme weather conditions, increased upwelling of deoxygenated waters in reservoirs, etc., requiring greater vigilance and monitoring, and even perhaps readiness to move operations to more conducive areas in a waterbody. Indirect impacts of climate change on tropical aquaculture could be manifold but are perhaps largely unknown. The reproductive cycles of a great majority of tropical species are dependent on monsoonal rain patterns, which are predicted to change. Consequently, irrespective of whether cultured species are artificially propagated or not, changes in reproductive cycles will impact on seed production and thereby the whole grow-out cycle and modus operandi of farm activities. Equally, such impacts will be felt on the culture of those species that are based on natural spat collection, such as that of many cultured molluscs. In the temperate region, global warming could raise temperatures to the upper tolerance limits of some cultured species, thereby making such culture systems vulnerable to high temperatures. New or hitherto non-pathogenic organisms may become virulent with increases in water temperature, confronting the sector with new, hitherto unmanifested and/or little known diseases. One of the most important indirect effects of climate change will be driven by impacts on production of those fish species that are used for reduction, and which in turn form the basis for aquaculture feeds, particularly for carnivorous species. These indirect effects are likely to have a major impact on some key aquaculture practices in all climatic regimes. Limitations of supplies of fishmeal and fish oil and resulting exorbitant price hikes of these commodities will lead to more innovative and pragmatic solutions on ingredient substitution for aquatic feeds, which perhaps will be a positive result arising from a dire need to sustain a major sector. Aquaculture has to be proactive and start addressing the need for adaptive and mitigative measures. Such measures will entail both technological and socio-economic approaches. The latter will be more applicable to small-scale farmers, who happen to be the great bulk of producers in developing countries, which in turn constitute the “backbone’ of global aquaculture. The sociological approaches will entail the challenge of addressing the potential climate change impacts on small farming communities in the most vulnerable areas, such as in deltaic regions, weighing the most feasible adaptive options and bringing about the policy changes required to implement these adaptive measures economically and effectively. Global food habits have changed over the years. We are currently in an era where food safety and quality, backed up by ecolabelling, are paramount; it was not so 20 years ago. In the foreseeable future, we will move into an era where consumer consciousness will demand that farmed foods of every form will have to include in their labeled products the green house gas (GHG) emissions per unit of produce. Clearly, aquaculture offers an opportunity to meet these aspirations. Considering that about 70 percent of all finfish and almost 100 percent of all molluscs and seaweeds are minimally GHG emitting, it is possible to drive aquaculture as the most GHG-friendly food source. The sector could conform to such demands and continue to meet the need for an increasing global food fish supply. However, to achieve this, a paradigm shift in our seafood consumption preferences will be needed.

Trophic status drives interannual variability in nesting numbers of marine turtles

Large annual fluctuations are seen in breeding numbers in many populations of non–annual breeders. We examined the interannual variation in nesting numbers of populations of green (Chelonia mydas) (n = 16 populations), loggerhead (Caretta caretta) (n =10 populations), leatherback (Dermochelys coriacea) (n = 9 populations) and hawksbill turtles (Eretmochelys imbricata) (n = 10 populations). Interannual variation was greatest in the green turtle. When comparing green and loggerhead turtles nesting in Cyprus we found that green turtles were more likely to change the interval between laying seasons and showed greater variation in the number of clutches laid in a season. We suggest that these differences are driven by the varying trophic statuses of the different species. Green turtles are herbivorous, feeding on sea grasses and macro–algae, and this primary production will be more tightly coupled with prevailing environmental conditions than the carnivorous diet of the loggerhead turtle.

Zooplankton abundance and community structure over a 4000 km transect in the North-east Atlantic

Zooplankton samples were collected by a high speed sampler, the U-Tow, in the north-east Atlantic between 61.6 and 36.7°N during June and July 1996, and were used to examine the causality of spatial distributions along a 4000 km transect. Peak zooplankton abundance and biovolume estimations were associated with a frontal system at 48–52°N, which separated hydrographically distinct water masses. The zooplankton assemblage was dominated by herbivorous/omnivorous taxa in the northern regions, and by carnivorous taxa in the southern regions. Arguments are developed to suggest that the switch in both the zooplankton size structure and trophic status, centred within the frontal region, are consistent with ‘bottom-up’ control of zooplankton size structure in this region of the Atlantic.