The ecology of free-living nematodes in nearshore marine and estuarine sediments of the microtidal lower west coast of Australia.

The overarching aim of this thesis was to describe the ecology of the assemblages of free-living nematodes in the sediments of nearshore marine and estuarine waters on the microtidal lower west coast of Australia. The thesis also provides descriptions of ten previously undescribed species as well as develops and tests a habitat classification scheme for the Swan River Estuary using these biotic assemblages. The first section of my thesis has determined the ways in which the characteristics of the nematode assemblages in nearshore marine waters along the microtidal lower west coast of Australia are related to habitat type, time of year and shore-perpendicular zones. Three habitat types, which had previously been identified on the basis of a suite of enduring environmental characteristics, could be broadly described as highly sheltered from wave activity and containing dense seagrass (habitat type 1), moderately sheltered from wave activity and with sparse seagrass (habitat type 2) and relatively exposed to wave activity and with no seagrass (habitat type 6). Sampling in five consecutive seasons yielded > 15 000 nematodes, representing 75 species. The number of species and densities in habitat type 1, and particularly those in its subtidal zone, were far greater than those in the other two habitat types. Both of these biotic variables underwent marked seasonal changes, declining to low levels during winter. The compositions of the assemblages differed significantly among the three habitat types, with the differences between habitat types 1 and 6 being particularly marked. Paracomesoma sipho, Dichromadora sp., Marylynnia annae and Pomponema sp., which, on the basis of their buccal cavity morphology, are assumed to feed primarily on benthic diatoms, were particularly abundant at the most sheltered habitat type, whereas Gonionchus australis, Theristus sp. and Bathylaimus australis, which are assumed to be deposit feeders, were relatively abundant at the most highly exposed habitat type. The compositions of the assemblages differed among seasons and were most discrete in spring, due to marked increases in the densities of certain species. However, differences in the compositions in the different zones of each habitat type were relatively small, presumably reflecting the influence of the small tidal regime of this region. The second component of this thesis has determined the ways in which the density, number of species, species composition and trophic structure of free-living nematode assemblages in the subtidal waters of a large microtidal estuary change spatially and temporally, and has explored whether those four biotic characteristics are related to certain environmental factors. Based on data derived from samples collected seasonally at 12 sites throughout the estuary, the densities and number of species of nematodes decreased progressively with distance from estuary mouth, to reach a minimum at sites where salinities were most variable, and then increased slightly in the uppermost part of the estuary where salinities were least. Densities were also generally greatest in spring, due largely to increases in the abundance of epistrate-grazing species at the time when the amount of primary food (microphytobenthos) peaked. The spatial distribution of the composition of the nematode assemblages was closely correlated with salinity and, to a lesser extent, grain-size composition and amount of particulate organic material in the sediment (%POM). Although species composition changed sequentially along the estuary, the change was particularly pronounced between sites above and below the area where salinities started to decline markedly and become more variable and %POM increased markedly. This reflected, in particular, far greater abundances of Spirinia parasitifera at the six downstream sites, and of Theristus sp. 1 at the six sites further upstream. Species composition underwent pronounced seasonal cyclical changes at all sites, presumably reflecting interspecific differences in the timing of peak reproduction and thus of recruitment. The trophic structure of the nematode assemblages changed both spatially and temporally in relation to the relative abundance of different food sources. Thus, for example, non-selective deposit feeders, such as Theristus sp. 1, dominated samples in the upper estuary, where %POM was by far the greatest, and was rare or absent at downstream sites. Conversely, epistrate grazers, such as species of the Chromadoridae, were most abundant at downstream sites in spring, when the density of the microphytobenthos reached its maximum. The data for the nematode assemblages in nearshore subtidal marine sediments of the lower west coast of Australia were compared with those in nearshore subtidal sediments in the upper and lower regions of the Swan River Estuary. The densities and average species richness in cores from the marine environment were much lower than in cores from both estuarine regions. However, the total number of species found in the marine environment was much greater than in the estuary. The compositions of the nematode assemblages were more variable in marine than estuarine sediments. The assemblages from the two estuarine regions were far more similar to each other than to those from the marine region at a species level, and also, but to a lesser extent, at the generic and family levels. While the trophic compositions of the nematode assemblages in the upper estuarine region was dominated by non-selective deposit feeding species and those of the lower estuarine region were dominated by epistrate grazing species during spring and non-selective deposit feeding species in other seasons, the dominant functional feeding groups varied among the sites representing the marine region. That variability presumably reflects differences in the relative contributions of the different potential food sources. Surprisingly, the trophic composition in the upper estuarine region, i.e. comprising predominantly non-selective deposit feeders, was similar to that at the very different environment of the most exposed marine site. The dominance of this feeding group at the marine site is assumed to be attributable to the fact that the only food source of any note is POM and, even then, it occurs in only small amounts. Taxonomic descriptions have been produced for ten new species of nematodes found during the ecological studies of the free-living aquatic nematofaunas of south-western Australia. These species were chosen because they were members of families for which the other species had been described and, in a number of cases, were important for distinguishing between the compositions of a priori groups. They comprised four species of Axonolaimidae, representing the genera Ascolaimus, Parascolaimus, Odontophora and Parodontophora, and six species of Desmodoridae, representing single species of Bolbonema, Eubostrichus, Catanema and Leptonemella and two species of Onyx. As a complement to the nematological study of the Swan River Estuary, a novel habitat classification system was developed and then applied in this environment. This system was based on enduring environmental characteristics and employed the relatively new multivariate statistical routines SIMPROF and LINKTREE. The applicability of habitat types produced by this classification system to biotic assemblages was tested using the data for the estuarine nematode assemblages described above. The results demonstrate that the compositions of the assemblages differed significantly among each of the habitat types defined by the classification system. While there were also significant differences between the compositions of the nematofaunas at sites belonging to the same habitat type, the extent of these differences were generally less than those between habitat types. A significant and strong correlation was also found between the spatial pattern exhibited by the environmental characteristics used to define habitat types, and that of the nematofauna

Prioritising search effort to locate previously unknown populations of endangered marine reptiles

Strategies aimed to conserve and manage rare species are often hindered by the lack of data needed for their effective design. Incomplete and inaccurate data on habitat associations and current species distributions pose a barrier to effective conservation and management for several species of endemic sea snakes in Western Australia that are thought to be in decline. Here we used a correlative modelling approach to understand habitat associations and identify suitable habitats for five of these species (Aipysurus apraefrontalis, A. foliosquama, A. fuscus, A. l. pooleorum and A. tenuis). We modelled species-specific habitat suitability across 804,244 km(2) of coastal waters along the North-west Shelf of Western Australia, to prioritise future survey regions to locate unknown populations of these rare species. Model projections were also used to quantify the effectiveness of current spatial management strategies (Marine Protected Areas) in conserving important habitats for these species. Species-specific models matched well with the records on which they were trained, and identified additional regions of suitability without records. Subsequent field validation of the model projections uncovered a previously unknown locality for A. fuscus within the mid-shelf shoal region, outside its currently recognised global range. Defining accurate geographic distributions for rare species is a vital first step in defining more robust extent of species occurrence and range overlap with threatening processes

Establishment of a taxonomic and molecular reference collection to support the identification of species regulated by the Western Australian Prevention List for Introduced Marine Pests

Introduced Marine Pests (IMP, = non-indigenous marine species) prevention, early detection and risk-based management strategies have become the priority for biosecurity operations worldwide, in recognition of the fact that, once established, the effective management of marine pests can rapidly become cost prohibitive or impractical. In Western Australia (WA), biosecurity management is guided by the “Western Australian Prevention List for Introduced Marine Pests” which is a policy tool that details species or genera as being of high risk to the region. This list forms the basis of management efforts to prevent introduction of these species, monitoring efforts to detect them at an early stage, and rapid response should they be detected. It is therefore essential that the species listed can be rapid and confidently identified and discriminated from native species by a range of government and industry stakeholders. Recognising that identification of these species requires very specialist expertise which may be in short supply and not readily accessible in a regulatory environment, and the fact that much publicly available data is not verifiable or suitable for regulatory enforcement, the WA government commissioned the current project to collate a reference collection of these marine pest specimens. In this work, we thus established collaboration with researchers worldwide in order to source representative specimens of the species listed. Our main objective was to build a reference collection of taxonomically vouchered specimens and subsequently to generate species-specific DNA barcodes suited to supporting their future identification. To date, we were able to obtain specimens of 75 species (representative of all but four of the pests listed) which have been identified by experts and placed with the WA Government Department of Fisheries and, where possible, in accessible museums and institutions in Australasia. The reference collection supports the fast and reliable taxonomic and molecular identification of marine pests in WA and constitutes a valuable resource for training of stakeholders with interest in IMP recognition in Australia. The reference collection is also useful in supporting the development of a variety of DNA-based detection strategies such as real-time PCR and metabarcoding of complex environmental samples (e.g. biofouling communities). ThePrevention List is under regular review to ensure its continued relevance and that it remains evidence and risk-based. Similarly, its associated reference collection also remains to some extent a work in progress. In recognition of this fact, this report seeks to provide details of this continually evolving information repository publicly available to the biosecurity management community worldwid

A long way from home: Biosecurity lessons learnt from the impact of La Niña on the transportation and establishment of tropical portunid species.

Marine ecosystems can be modified and shaped by irregular interannual variations in oceanic current patterns and temperatures, such as El Niño and La Niña. These large scale oceanic events have also been shown to influence environmental stressors such as invasive marine species (IMS). Our study indicates that there is a causative link between these climatic events, and atypical detections of native and IMS. Significant La Niña events between 1970 and 2014 were associated with sightings of tropical crab species in temperate waters following a lag period of 18-24 months from the onset of the event. We identified a total of 72 records of six tropical portunid crabs species (from both Charybdis and Scylla) in temperate waters of south-western Australia following these La Niña events, based on reports in published scientific literature, grey literature and museum records, as well as citizen science networks such as FishWatch and PestWatch apps. We suggest that La Niña conditions facilitated transportation and temporary establishment of crab larvae from their native tropical habitat to temperate regions. As the strength of La Niña events is likely to increase into the future due to the escalating effects of climate change, it is likely that there will be a growth in associated atypical establishment events of IMS. Consequently, biosecurity managers will need to reprioritise resources in order to accommodate the potential impacts of these large scale oceanic events as part of their surveillance programmes

Nitschke_etal_BiolLetters

Mitochondrial cytochrome b alignmen

Data from: Rates of population differentiation and speciation are decoupled in sea snakes

Comparative phylogeography can inform many macroevolutionary questions, such as whether species diversification is limited by rates of geographic population differentiation. We examined the link between population genetic structure and species diversification in the fully aquatic sea snakes (Hydrophiinae) by comparing mitochondrial phylogeography in 16 species from two closely related clades that show contrasting diversification dynamics across northern Australia. Contrary to expectations from theory and several empirical studies, our results show that, at the geographic scale studied here, rates of population differentiation and speciation are not positively linked in sea snakes. The eight species sampled from the rapidly speciating Hydrophis clade have weak population differentiation that lacks geographic structure. In contrast, all eight sampled Aipysurus-Emydocephalus species show clear geographical patterns and many deep intraspecific splits, but have three-fold slower speciation rates. Alternative factors, such as ecological specialisation, species duration, and geographic range size, may underlie rapid speciation in sea snakes

Developing novel remote camera approaches to assess and monitor the population status of Australian sea lions

This project trialled the use of remote cameras to monitor the relative abundance of Australian sea lions (ASLs, Neophoca cinerea) at three Western Australian (WA) breeding colonies. The research was undertaken by the Department of Primary Industries and Regional Development (DPIRD) to assess whether the analysis of camera footage could be used to estimate ASL relative abundance, providing an alternative to the traditional “boots on the ground” approach (hereon in “BoG”) of visiting colonies to count animals. This report outlines the strengths and limitations of this novel approach rather than providing an update on the population status of ASLs. Remote cameras and associated infrastructure were installed at Buller Island, Haul Off Rock and Wickham Island in the second half of 2018, after which camera images were manually interpreted with the intention of capturing data over an 18-month period (i.e., approximately one reproductive cycle). Overall, counts of ASLs were obtained from the analysis of 563 days (~6,700 hours) of camera footage. These data comprised the number of ASLs identified within the field of view (FoV) of each camera which represented relative abundance estimates for each colony. Day to day variations in the relative abundance of ASLs were estimated for Buller Island and Wickham Island, with limited data on ASL abundance collected for Haul Off Rock due to camera outages. The time series analysis applied to the Buller Island data provides the most detailed information within a single reproductive cycle at a WA colony. To ‘value-add’ from the original aims of the study, remote piloted aircraft (RPA) operations were also conducted within the Recherche Archipelago to provide a greater understanding of the potential application of both methods for on-going monitoring. In summary, the diversity and remoteness of ASL colonies in WA means that no single survey method is likely to be appropriate for the monitoring of all colonies. Installing and maintaining remote cameras at 32 known ASL breeding colonies would be cost-prohibitive and logistically impractical. Instead, camera monitoring at strategic ASL colonies would provide a realistic prospect of collecting long-term abundance data for hard-to-reach Western Australian colonies which remains a challenging prospect using BoG surveys. The ability to view live camera footage could assist with the scheduling of BoG surveys so that on-site surveys can be conducted regularly and safely. Such an approach would require more formal research arrangements to be established between the various state agencies responsible for managing wildlife and fisheries. This project has provided an extensive permanent digital library of camera images that can be made available for use in subsequent ecological and fisheries-related studies