Using RIVPACS for studies on conservation and biodiversity

Invertebrate conservation relies not only on public support and political will, but also on possessing an adequate understanding of the distribution and ecology of invertebrate species and communities. In the UK, RIVPACS is making an important contribution to assessing the conservation importance of river invertebrate assemblages. So far, work has largely centred on using RIVPACS as an integral part of SERCON (System for Evaluating Rivers for Conservation), in which data collected using the standard RIVPACS method are interpreted with reference to conservation criteria such as species richness and representativeness. Applications of RIVPACS to other areas of conservation - whether providing information on the ecological requirements of rare species, monitoring the success of river restoration projects, or making broader assessments of sustainability - are probably more limited, but merit further examination. It is important to develop closer links between RIVPACS and techniques such as SERCON and RHS (River Habitat Survey) in order to maximise the benefit each can bring tostudies on conservation and biodiversity. It should also be recognised that there are limitations in transferring such systems to other countries where approaches to nature conservation may be very different.

Conservation value, biodiversity value and methods of assessment in regenerating and human disturbed tropical forest

Although the value of primary forests for biodiversity conservation is well known, the potential biodiversity and conservation value of regenerating forests remains controversial. Many factors likely contribute to this, including: 1. the variable ages of regenerating forests being studied (often dominated by relatively young regenerating forests); 2. the potential for confounding on-going human disturbance (such as logging and hunting); 3. the relatively low number of multi-taxa studies; 4. the lack of studies that directly compare different historic disturbances within the same location; 5. contrasting patterns from different survey methodologies and the paucity of knowledge on the impacts across different vertical levels of rainforest biodiversity (often due to a lack of suitable methodologies available to assess them). We also know relatively little as to how biodiversity is affected by major current impacts, such as unmarked rainforest roads, which contribute to this degradation of habitat and fragmentation. This thesis explores the potential biodiversity value of regenerating rainforests under the best of scenarios and seeks to understand more about the impact of current human disturbance to biodiversity; data comes from case studies from the Manu and Sumaco Biosphere Reserves in the Western Amazon. Specifically, I compare overall biodiversity and conservation value of a best case regenerating rainforest site with a selection of well-studied primary forest sites and with predicted species lists for the region; including a focus on species of key conservation concern. I then investigate the biodiversity of the same study site in reference to different types of historic anthropogenic disturbance. Following this I investigate the impacts to biodiversity from an unmarked rainforest road. In order to understand more about the differential effects of habitat disturbance on arboreal diversity I directly assess how patterns of butterfly biodiversity vary between three vertical strata. Although assessments within the canopy have been made for birds, invertebrates and bats, very few studies have successfully targeted arboreal mammals. I therefore investigate the potential of camera traps for inventorying arboreal mammal species in comparison with traditional methodologies. Finally, in order to investigate the possibility that different survey methodologies might identify different biodiversity patterns in habitat disturbance assessments, I investigate whether two different but commonly used survey methodologies used to assess amphibians, indicate the same or different responses of amphibian biodiversity to historic habitat change by people. The regenerating rainforest study site contained high levels of species richness; both in terms of alpha diversity found in nearby primary forest areas (87% ±3.5) and in terms of predicted primary forest diversity from the region (83% ±6.7). This included 89% (39 out of 44) of the species of high conservation concern predicted for the Manu region. Faunal species richness in once completely cleared regenerating forest was on average 13% (±9.8) lower than historically selectively logged forest. The presence of the small unmarked road significantly altered levels of faunal biodiversity for three taxa, up to and potentially beyond 350m into the forest interior. Most notably, the impact on biodiversity extended to at least 32% of the whole reserve area. The assessment of butterflies across strata showed that different vertical zones within the same rainforest responded differently in areas with different historic human disturbance. A comparison between forest regenerating after selective logging and forest regenerating after complete clearance, showed that there was a 17% greater reduction in canopy species richness in the historically cleared forest compared with the terrestrial community. Comparing arboreal camera traps with traditional ground-based techniques suggests that camera traps are an effective tool for inventorying secretive arboreal rainforest mammal communities and detect a higher number of cryptic species. Finally, the two survey methodologies used to assess amphibian communities identified contrasting biodiversity patterns in a human modified rainforest; one indicated biodiversity differences between forests with different human disturbance histories, whereas the other suggested no differences between forest disturbance types. Overall, in this thesis I find that the conservation and biodiversity value of regenerating and human disturbed tropical forest can potentially contribute to rainforest biodiversity conservation, particularly in the best of circumstances. I also highlight the importance of utilising appropriate study methodologies that to investigate these three-dimensional habitats, and contribute to the development of methodologies to do so. However, care should be taken when using different survey methodologies, which can provide contrasting biodiversity patterns in response to human disturbance.

Floral structure, breeding system and fruit-set in the threatened sub-shrub Tetratheca juncea Smith (Tremandraceae)

Tetratheca juncea Smith (Tremandraceae) has undergone a range contraction of approx. 50 km in the last 100 years and is now listed as a vulnerable sub-shrub restricted to the central and north coast regions of New South Wales, Australia. There are approx. 250 populations in a 110 km north-south distribution and populations are usually small with fewer than 50 plants/clumps. The reproductive ecology of the species was studied to determine why seed-set is reportedly rare. Flowers are bisexual, odourless and nectarless. Flowers are presented dependentally and there are eight stamens recurved around the pistil. Anthers are poricidal, contain viable pollen and basally contain a deep-red tapetal fluid that is slightly oily. Thus flowers are presented for buzz pollinators, although none were observed at flowers during our study. The species was found to be facultatively xenogamous with only one in 50 glasshouse flowers setting seed autogamously, i.e. without pollinator assistance. Field studies revealed fertile fruit in 24 populations but production varied significantly across sites from exceedingly low (0.6 fruits per plant clump) to low (17 fruits per plant clump). Fruit-set ranged from 0 to 65%, suggesting that pollen vectors exist or that autogamy levels in the field are variable and higher than glasshouse results. Fruit production did not vary with population size, although in three of the five populations in the south-west region more than twice as much fruit was produced as in populations elsewhere. A moderately strong relationship between foliage volume and fruit : flower ratios suggests that bigger plants may be more attractive than smaller plants to pollinators. A review of Tetratheca pollination ecology revealed that several species are poorly fecund and pollinators are rare. The habitat requirements for Tetratheca, a genus of many rare and threatened species, is discussed. (C) 2003 Annals of Botany Company.

Change in abundance of dugongs in Shark Bay, Ningaloo and Exmouth Gulf, Western Australia: evidence for large-scale migration

The third in a series of five-yearly aerial surveys for dugongs in Shark Bay, Ningaloo Reef and Exmouth Gulf was conducted in July 1999. The first two surveys provided evidence of an apparently stable population of dugongs, with similar to 1000 animals in each of Exmouth Gulf and Ningaloo Reef, and 10000 in Shark Bay. We report estimates of less than 200 for each of Exmouth Gulf and Ningaloo Reef and similar to 14000 for Shark Bay. This is an apparent overall increase in the dugong population over this whole region, but with a distributional shift of animals to the south. The most plausible hypothesis to account for a large component of this apparent population shift is that animals in Exmouth Gulf and Ningaloo Reef moved to Shark Bay, most likely after Tropical Cyclone Vance impacted available dugong forage in the northern habitat. Bias associated with survey estimate methodology, and normal changes in population demographics may also have contributed to the change. The movement of large numbers of dugongs over the scale we suggest has important management implications. First, such habitat-driven shifts in regional abundance will need to be incorporated in assessing the effectiveness of marine protected areas that aim to protect dugongs and their habitat. Second, in circumstances where aerial surveys are used to estimate relative trends in abundance of dugongs, animal movements of the type we propose could lead to errors in interpretation.

Mate choice in the brown thornbill (Acanthiza pusilla): are settlement decisions, divorce and extrapair mating complementary strategies?

In socially monogamous birds, females may express mate preferences when they first select a breeding partner, through divorce and subsequent breeding dispersal to a new partner and through extrapair mating. We examined settlement patterns, divorce and breeding dispersal in a sedentary Australian passerine, the brown thornbill (Acanthiza pusilla), in relation to two traits known to influence extrapair paternity (male age and male size). Settlement decisions, divorce and territory switching behaviour were all female strategies that reduced their likelihood of breeding with 1-year-old males. Females preferred to settle in territories with 2+ -year-old males, were more likely to divorce 1-year-old males, and only switched territories if they had an opportunity to form a new pair bond with an old male. In contrast, female settlement and divorce decisions were not influenced by male size. Female thornbills obtain a direct benefit from preferring older males as social mates because breeding success improves with male age in brown thornbills. Nevertheless, divorce rates in this species were low (14% of pair bonds were terminated by divorce), and individuals rarely switched territories following the death of a mate. Both of these mating strategies appeared to be primarily constrained by the distance adults moved to initiate a new pair bond (1-2 territories) and by the limited availability of unpaired older males in the immediate neighbourhood.

Reflecting on ethical and legal issues in wildlife disease

Disease in wildlife raises a number of issues that have not been widely considered in the bioethical literature. However, wildlife disease has major implications for human welfare. The majority of emerging human infectious diseases are zoonotic: that is, they occur in humans by cross-species transmission from animal hosts. Managing these diseases often involves balancing concerns with human health against animal welfare and conservation concerns. Many infectious diseases of domestic animals are shared with wild animals, although it is often unclear whether the infection spills over from wild animals to domestic animals or vice versa. Culling is the standard means of managing such diseases, bringing economic considerations, animal welfare and conservation into conflict. Infectious diseases are also major threatening processes in conservation biology and their appropriate management by culling, vaccination or treatment raises substantial animal ethics issues. One particular issue of great significance in Australia is an ongoing research program to develop genetically modified pathogens to control vertebrate pests including rabbits, foxes and house mice. Release of any self-replicating GMO vertebrate pathogen gives rise to a whole series of ethical questions. We briefly review current Australian legal responses to these problems. Finally, we present two unresolved problems of general importance that are exemplified by wildlife disease. First, to what extent can or should 'bioethics' be broadened beyond direct concerns with human welfare to animal welfare and environmental welfare? Second, how should the irreducible uncertainty of ecological systems be accounted for in ethical decision making?

Real-time reverse transcriptase PCR for the endogenous koala retrovirus reveals an association between plasma viral load and neoplastic disease in koalas

Koala retrovirus (KoRV) is a newly described endogenous retrovirus and is unusual in that inserts comprise a full-length replication competent genome. As koalas are known to suffer from an extremely high incidence of leukaemia/lymphoma, the association between this retrovirus and disease in koalas was examined. Using quantitative real-time reverse transcriptase PCR it was demonstrated that KoRV RNA levels in plasma are significantly increased in animals suffering from leukaemia or lymphoma when compared with healthy animals. Increased levels of KoRV were also seen for animals with clinical chlamydiosis. A significant positive association between viral RNA levels and age was also demonstrated. Real-time PCR demonstrated as much as 5 log variation in KoRV proviral DNA levels in genomic DNA extracted from whole blood from different animals. Taken together these data indicate that KoRV is an active endogenous retrovirus and suggests that it may be causally linked to neoplastic disease in koalas.

Site-directed mutagenesis and kinetic studies of the West Nile virus NS3 protease identify key enzyme-substrate interactions

The flavivirus West Nile virus (WNV) has spread rapidly throughout the world in recent years causing fever, meningitis, encephalitis, and fatalities. Because the viral protease NS2B/NS3 is essential for replication, it is attracting attention as a potential therapeutic target, although there are currently no antiviral inhibitors for any flavivirus. This paper focuses on elucidating interactions between a hexapeptide substrate (Ae-KPGLKR-p-nitroanilide) and residues at S1 and S2 in the active site of WNV protease by comparing the catalytic activities of selected mutant recombinant proteases in vitro. Homology modeling enabled the predictions of key mutations in VWNV NS3 protease at S1 (V115A/F, D129A/ E/N, S135A, Y150A/F, S160A, and S163A) and S2 (N152A) that might influence substrate recognition and catalytic efficiency. Key conclusions are that the substrate P1 Arg strongly interacts with S1 residues Asp-129, Tyr-150, and Ser-163 and, to a lesser extent, Ser-160, and P2 Lys makes an essential interaction with Asn-152 at S2. The inferred substrate-enzyme interactions provide a basis for rational protease inhibitor design and optimization. High sequence conservation within flavivirus proteases means that this study may also be relevant to design of protease inhibitors for other flavivirus proteases.

Efficiency, costs and trade-offs in marine reserve system design

With marine biodiversity conservation the primary goal for reserve planning initiatives, a site's conservation potential is typically evaluated on the basis of the biological and physical features it contains. By comparison, socio-economic information is seldom a formal consideration of the reserve system design problem and generally limited to an assessment of threats, vulnerability or compatibility with surrounding uses. This is perhaps surprising given broad recognition that the success of reserve establishment is highly dependent on widespread stakeholder and community support. Using information on the spatial distribution and intensity of commercial rock lobster catch in South Australia, we demonstrate the capacity of mathematical reserve selection procedures to integrate socio-economic and biophysical information for marine reserve system design. Analyses of trade-offs highlight the opportunities to design representative, efficient and practical marine reserve systems that minimise potential loss to commercial users. We found that the objective of minimising the areal extent of the reserve system was barely compromised by incorporating economic design constraints. With a small increase in area (< 3%) and boundary length (< 10%), the economic impact of marine reserves on the commercial rock lobster fishery was reduced by more than a third. We considered also how a reserve planner might prioritise conservation areas using information on a planning units selection frequency. We found that selection frequencies alone were not a reliable guide for the selection of marine reserve systems, but could be used with approaches such as summed irreplaceability to direct conservation effort for efficient marine reserve design.