Detection of dugongs from unmanned aerial vehicles

Monitoring and estimation of marine populations is of paramount importance for the conservation and management of sea species. Regular surveys are used to this purpose followed often by a manual counting process. This paper proposes an algorithm for automatic detection of dugongs from imagery taken in aerial surveys. Our algorithm exploits the fact that dugongs are rare in most images, therefore we determine regions of interest partially based on color rarity. This simple observation makes the system robust to changes in illumination. We also show that by applying the extended-maxima transform on red-ratio images, submerged dugongs with very fuzzy edges can be detected. Performance figures obtained here are promising in terms of degree of confidence in the detection of marine species, but more importantly our approach represents a significant step in automating this type of surveys.

Comparative analysis and distribution of Omega-3 lcPUFA Biosynthesis genes in marine molluscs

Recent research has identified marine molluscs as an excellent source of omega-3 long-chain polyunsaturated fatty acids (lcPUFAs), based on their potential for endogenous synthesis of lcPUFAs. In this study we generated a representative list of fatty acyl desaturase (Fad) and elongation of very long-chain fatty acid (Elovl) genes from major orders of Phylum Mollusca, through the interrogation of transcriptome and genome sequences, and various publicly available databases. We have identified novel and uncharacterised Fad and Elovl sequences in the following species: Anadara trapezia, Nerita albicilla, Nerita melanotragus, Crassostrea gigas, Lottia gigantea, Aplysia californica, Loligo pealeii and Chlamys farreri. Based on alignments of translated protein sequences of Fad and Elovl genes, the haeme binding motif and histidine boxes of Fad proteins, and the histidine box and seventeen important amino acids in Elovl proteins, were highly conserved. Phylogenetic analysis of aligned reference sequences was used to reconstruct the evolutionary relationships for Fad and Elovl genes separately. Multiple, well resolved clades for both the Fad and Elovl sequences were observed, suggesting that repeated rounds of gene duplication best explain the distribution of Fad and Elovl proteins across the major orders of molluscs. For Elovl sequences, one clade contained the functionally characterised Elovl5 proteins, while another clade contained proteins hypothesised to have Elovl4 function. Additional well resolved clades consisted only of uncharacterised Elovl sequences. One clade from the Fad phylogeny contained only uncharacterised proteins, while the other clade contained functionally characterised delta-5 desaturase proteins. The discovery of an uncharacterised Fad clade is particularly interesting as these divergent proteins may have novel functions. Overall, this paper presents a number of novel Fad and Elovl genes suggesting that many mollusc groups possess most of the required enzymes for the synthesis of lcPUFAs.

Geographical and morphological variation within and between colour phases in Coris julis (L. 1758), a protogynous marine fish

The possible differences between sexes in patterns of morphological variation in geographical space have been explored only in gonochorist freshwater species. We explored patterns of body shape variation in geographical space in a marine sequential hermaphrodite species, Coris julis (L. 1758), analyzing variation both within and between colour phases, through the use of geometric morphometrics and spatially-explicit statistical analyses. We also tested for the association of body shape with two environmental variables: temperature and chlorophyll a concentration, as obtained from time-series of satellite-derived data. Both colour phases showed a significant morphological variation in geographical space and patterns of variation divergent between phases. Although the morphological variation was qualitatively similar, individuals in the initial colour phase showed a more marked variation than individuals in the terminal phase. Body shape showed a weak but significant correlation with environmental variables, which was more pronounced in primary specimens.

Atlantic-Mediterranean and within-Mediterranean molecular variation in Coris julis (L. 1758) (Teleostei, Labridae)

Sequence variation in the mitochondrial control region was studied in the Mediterranean rainbow wrasse (Coris julis), a species with pronounced pelagic larval phase inhabiting the Mediterranean Sea and the adjacent coastal eastern Atlantic Ocean. A total of 309 specimens from 19 sampling sites were analysed with the aim of elucidating patterns of molecular variation between the Atlantic and the Mediterranean as well as within the Mediterranean Sea. Phylogeographic analyses revealed a pronounced structuring into a Mediterranean and an Atlantic group. Samples from a site at the Moroccan Mediterranean coast in the Alboran Sea showed intermediate frequencies of “Mediterranean” and “Atlantic” haplotypes. We recognised a departure from molecular neutrality and a star-like genealogy for samples from the Mediterranean Sea, which we propose to have happened due to a recent demographic expansion. The results are discussed in the light of previous studies on molecular variation in fish species between the Atlantic and the Mediterranean and within the Mediterranean.

Traditional and geometric morphometrics detect morphological variation of lower pharyngeal jaw inCoris julis(Teleostei, Labridae)

In the present study, variation in the morphology of the lower pharyngeal element between two Sicilian populations of the rainbow wrasse Coris julis has been explored by the means of traditional morphometrics for size and geometric morphometrics for shape. Despite close geographical distance and probable high genetic flow between the populations, statistically significant differences have been found both for size and shape. In fact, one population shows a larger lower pharyngeal element that has a larger central tooth. Compared to the other population, this population also has medially enlarged lower pharyngeal jaws with a more pronounced convexity of the medial-posterior margin. The results are discussed in the light of a possible more pronounced durophagy of this population.

Dynamic Bayesian network inferencing for non-homogeneous complex systems

Dynamic Bayesian Networks (DBNs) provide a versatile platform for predicting and analysing the behaviour of complex systems. As such, they are well suited to the prediction of complex ecosystem population trajectories under anthropogenic disturbances such as the dredging of marine seagrass ecosystems. However, DBNs assume a homogeneous Markov chain whereas a key characteristics of complex ecosystems is the presence of feedback loops, path dependencies and regime changes whereby the behaviour of the system can vary based on past states. This paper develops a method based on the small world structure of complex systems networks to modularise a non-homogeneous DBN and enable the computation of posterior marginal probabilities given evidence in forwards inference. It also provides an approach for an approximate solution for backwards inference as convergence is not guaranteed for a path dependent system. When applied to the seagrass dredging problem, the incorporation of path dependency can implement conditional absorption and allows release from the zero state in line with environmental and ecological observations. As dredging has a marked global impact on seagrass and other marine ecosystems of high environmental and economic value, using such a complex systems model to develop practical ways to meet the needs of conservation and industry through enhancing resistance and/or recovery is of paramount importance.

Predicting the temporal response of seagrass meadows to dredging using Dynamic Bayesian Networks

Predicting temporal responses of ecosystems to disturbances associated with industrial activities is critical for their management and conservation. However, prediction of ecosystem responses is challenging due to the complexity and potential non-linearities stemming from interactions between system components and multiple environmental drivers. Prediction is particularly difficult for marine ecosystems due to their often highly variable and complex natures and large uncertainties surrounding their dynamic responses. Consequently, current management of such systems often rely on expert judgement and/or complex quantitative models that consider only a subset of the relevant ecological processes. Hence there exists an urgent need for the development of whole-of-systems predictive models to support decision and policy makers in managing complex marine systems in the context of industry based disturbances. This paper presents Dynamic Bayesian Networks (DBNs) for predicting the temporal response of a marine ecosystem to anthropogenic disturbances. The DBN provides a visual representation of the problem domain in terms of factors (parts of the ecosystem) and their relationships. These relationships are quantified via Conditional Probability Tables (CPTs), which estimate the variability and uncertainty in the distribution of each factor. The combination of qualitative visual and quantitative elements in a DBN facilitates the integration of a wide array of data, published and expert knowledge and other models. Such multiple sources are often essential as one single source of information is rarely sufficient to cover the diverse range of factors relevant to a management task. Here, a DBN model is developed for tropical, annual Halophila and temperate, persistent Amphibolis seagrass meadows to inform dredging management and help meet environmental guidelines. Specifically, the impacts of capital (e.g. new port development) and maintenance (e.g. maintaining channel depths in established ports) dredging is evaluated with respect to the risk of permanent loss, defined as no recovery within 5 years (Environmental Protection Agency guidelines). The model is developed using expert knowledge, existing literature, statistical models of environmental light, and experimental data. The model is then demonstrated in a case study through the analysis of a variety of dredging, environmental and seagrass ecosystem recovery scenarios. In spatial zones significantly affected by dredging, such as the zone of moderate impact, shoot density has a very high probability of being driven to zero by capital dredging due to the duration of such dredging. Here, fast growing Halophila species can recover, however, the probability of recovery depends on the presence of seed banks. On the other hand, slow growing Amphibolis meadows have a high probability of suffering permanent loss. However, in the maintenance dredging scenario, due to the shorter duration of dredging, Amphibolis is better able to resist the impacts of dredging. For both types of seagrass meadows, the probability of loss was strongly dependent on the biological and ecological status of the meadow, as well as environmental conditions post-dredging. The ability to predict the ecosystem response under cumulative, non-linear interactions across a complex ecosystem highlights the utility of DBNs for decision support and environmental management.

The ecological condition of estuaries in the Gulf of Mexico

This document is intended for use by scientists and other citizens concerned with the ecological condition of estuaries, as well as by managers and lawmakers interested in the sustained use of estuaries for commercial and recreational purposes. It also addresses public concerns about the aesthetic quality of coastal areas vital to tourism and recreation. By producing this report on the ecological condition of estuaries in the Gulf of Mexico, we have taken one step in assessing the health of this environmental resource. We have produced an environmental report card to be used as a guide in the evaluation of management decisions and research directions. This report is organized in three parts: (1) an introduction that gives background information on the Gulf of Mexico, estuarine ecology, and the factors that impact estuaries in the gulf, (2) the main section on priority ecological indicators used to measure the condition of estuaries in the gulf and (3) an ecological report card that summarizes the data on ecological indicators and provides a rating of the condition of estuaries in each gulf state and for gulf estuaries overall. Many of the ratings were based on the percent area of estuaries in each state exhibiting degraded or adverse levels of an indicator.

Seasonal and interannual variation in juvenile salmonids and associated fish assemblage in open waters of the lower Columbia River estuary

The transition between freshwater and marine environments is associated with high mortality for juvenile anadromous salmonids, yet little is known about this critical period in many large rivers. To address this deficiency, we investigated the estuarine ecology of juvenile salmonids and their associated fish assemblage in open-water habitats of the lower Columbia River estuary during spring of 2007–10. For coho (Oncorhynchus kisutch), sockeye (O. nerka), chum (O. keta), and yearling (age 1.0) Chinook (O. tshawytscha) salmon, and steelhead (O. mykiss), we observed a consistent seasonal pattern characterized by extremely low abundances in mid-April, maximum abundances in May, and near absence by late June. Subyearling (age 0.0) Chinook salmon were most abundant in late June. Although we observed interannual variation in the presence, abundance, and size of juvenile salmonids, no single year was exceptional across all species-and-age classes. We estimated that >90% of juvenile Chinook and coho salmon and steelhead were of hatchery origin, a rate higher than previously reported. In contrast to juvenile salmonids, the abundance and composition of the greater estuarine fish assemblage, of which juvenile salmon were minor members, were extremely variable and likely responding to dynamic physical conditions in the estuary. Comparisons with studies conducted 3 decades earlier suggest striking changes in the estuarine fish assemblage—changes that have unknown but potentially important consequences for juvenile salmon in the Columbia River estuary.

Comparison of the Distribution, Abundance, and Diversity of Zooplankton in Trevor Channel and Alberni Inlet, Barkley Sound, Vancouver Island, Canada

Senior thesis written for Oceanography 444

Melbourne's indigenous plants movement : the return of the natives

This thesis examines Greater Melbourne’s indigenous plants movement from the 1930s to the early twenty first century. It demonstrates the important scientific and educational role of the public intellectual, Professor John Turner, and of the Melbourne University Botany School which he led for thirty five years. The case study of the movement within the City of Sandringham and its successor the City of Bayside reveals how the inhabitants of an urbanised are responded to threats to the indigenous trees and wildflowers of their neighbourhood, stimulating botanists to assist them and using political means in order to achieve their conservation objectives. The thesis draws upon a range of local archives, conservation literature and private papers.

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.

Effects of phytophthora cinnamomi on heathland flora and fauna of the Eastern Otway Ranges

The plant pathogen, Phytophthora dnnamomi, is a cause of dieback disease observed in sclerophyll vegetation in Australia, The effects of P. dnnamomi on flora and fauna were studied at two locations in heathland vegetation near the coastal town of Anglesea, Victoria. The pathogen was isolated from soils beneath diseased heathland plants. The extent of diseased vegetation was assessed by the presence and absence of highly sensitive indicator species, Xanthorrhoea australis and hopogon ceratophyllus. The characteristics of heathland vegetation exhibiting dieback disease associated with the presence of P. dnnamomi were investigated. Plant species richness was similar between diseased and non-diseased areas however diseased areas were characterised by significant declines in the cover and frequency of susceptible species, increases in resistant species and increases in percent cover of open ground. Compared to non-diseased areas, diseased areas exhibited fewer shrub species and decreased shrub cover. The percentage cover and number of species of sedges, lilies and grasses were higher in diseased areas. Structural differences were significant between 0-0.6 m with decreased cover of vegetation in diseased areas. Differences in structure between diseased and non-diseased areas were not as great as expected due to increases in the cover of resistant species. A number of regenerating X australis were observed in post-disease areas. Cluster analysis of floristic data could clearly separate diseased and non-diseased trap stations. The population dynamics and habitat use of eight small mammal species present were compared in diseased and non-diseased areas using trapping and radio-tracking techniques. The number of small mammal species captured in post-disease areas was significantly lower than non-diseased areas. Mean captures of Antechinus stuartii and Rattus fiisdpes were significantly lower in diseased areas on Grid B. Mean captures of Rattus lutreolus were significantly lower in diseased areas on both study grids. Significant differences were not observed in every season over the two year study period. Radio tracking revealed more observations of Sminthopsis leucopus in non-diseased vegetation than in diseased. Cercartetus nanus was frequently observed to utilise the disease susceptible X. australis for nesting. At one location, the recovery of vegetation and small mammal communities in non-diseased and diseased vegetation after fuel reduction burning was monitored for three years post-fire. Return of plant species after fire in both disease classes were similar, reaching 75% of pre-fire richness after three years. Vegetation cover was slower to return after fire in diseased areas. Of the seven small mammal species captured pre-fire, five were regularly captured in the three years after fire. General linear model analysis revealed a significant influence of disease on capture rates for total small mammals before fire and a significant influence of fire on capture rates for total small mammals after fire. After three years, the influence of fire on capture rates was reduced no significant difference was detected between disease classes. Measurements of microclimate indicate that diseased, burnt heathland was likely to experience greater extremes of temperature and wind speed. Seeding of diseased heathland with X. australis resulted in the establishment of seedlings of this sensitive species. The reported distributions of the mamma] species in Victoria were analysed to determine which species were associated with the reported distribution of dieback disease. Twenty-two species have more than 20% of their known distribution in diseased areas. Five of these species, Pseudomys novaehollandiae, Pseudomys fumeust Pseudomys shortridgei, Potorous longipes and Petrogale pencillata are rare or endangered in Victoria. Four of the twenty-two species, Sminthopsis leucopus, Isoodon obesulus, Cercartetus nanus and Rottus lutreolus am observed in Victorian heathlands. Phytophthora cinnamomi changes both the structure and floristics of heathland vegetation in the eastern Qtway Ranges. Small mammals respond to these changes through decreased utilisation of diseased heathland. The pathogen threatens the diversity of species present and future research efforts should be directed towards limiting its spread and rehabilitating diseased areas.

Resource use by the Eastern Grey Kangaroo and the Black Wallaby in a managed remnant woodland community

This work studies the interactions and relationships that exist between Eastern Grey Kangaroos and Black Wallabies in their utilisation of spatial and trophic resources in a managed remnant woodland community. The thesis provides a closer understanding of the way in which these species impact upon their habitats. The Coranderrk Reserve, near Healesville in eastern Victoria, Australia was the study site. A floristic analysis of the communities of the study site was conducted. This consisted of plant biomass measurements, estimates of plant abundance and cover determination. Faecal pellets from Eastern Grey Kangaroos and Black Wallabies were collected from ten vegetation communities during three different plant productivity periods. The spatial and temporal distribution of the animals was identified by analysing the frequency of occurrence of faecal pellets in the various communities. The use of faecal pellet density as a measure of habitat utilisation was examined. Eastern Grey Kangaroos utilised communities which were characterised by the presence of a dense grassy statum. Black Wallabies were able to utilise all of the communities of the study site regardless of their floristic composition. A reference herbarium of the leaf epidermis of 233 possible forage plant species was accumulated. These epidermal specimens were prepared for Confocal Scanning Laser Microscopy. The information gained was enhanced and stored digitally. Diagnostic information critical for the identification of plant epidermal fragments was assembled into a computer database. This was used to assist in the recognition of unknown epidermal fragments in macropodid faeces. These epidermal plant recognition techniques enabled a list of the contents of Eastern Grey Kangaroo and Black Wallaby faeces during the sampling periods in the individual communities, to be accumulated. Eastern Grey Kangaroos utilised forage which consisted largely of grass and their diets were similar regardless of their feeding sites or the time of the year. Black Wallaby diets were heterogenous with wide variations over space and time observed. The implications of these findings for current wildlife management practices were considered. Black Wallaby and Eastern Grey Kangaroo herbivory have significant impacts on ecosystem integrity. Management strategies should seek to establish ecologically sustainable populations of both species in remnant woodlands where conservation values are important.

Impact of stresses imposed on macroinvertebrate communities in two suburban streams

The aim of the project was to determine factors which explain the distribution of macroinvertebrates in two Melbourne streams both drastically affected by urbanisation. A detailed description is given of Dandenong Creek, flowing through the south-eastern suburbs, and Darebin Creek, in the northern suburbs, emphasising stream features likely, or known, to influence the drift and benthic fauna. Faunal sampling was carried out in Dandenong Creek from June 1992 until July 1993, and in Darebin Creek from February 1995 until March 1998. Physicochemical parameters were also recorded. The collected data, together with previously existing data, were analysed using multivariate analyses: non-metric multi-dimensional scaling (NMDS); analysis of similarities (ANOSIM); matching biotic and abiotic variables using BIOENV, and principal component analysis (PCA). Various biotic and diversity indices were calculated in an attempt to identify the major factors responsible for the failure of the fauna to recover from previously more seriously degraded water quality. The contribution of drift to the colonisation potential in Dandenong Creek appeared to be impacted by retarding basins, underground barrel-draining and channelization. Results also indicated that increased conductivity adversely affected the fauna in the lower reaches of Dandenong Creek. It was concluded that in Darebin Creek, high nutrient levels, as well as other pollutants, had resulted in low macroinvertebrate diversity in both the drift and benthos. If, as this study suggests, faunal diversity is a valid measure of stream health, the following factors need to be addressed for catchment-wide, stream management: lack of riparian zone vegetation (increasing bank erosion and making the benthic habitat unstable, with greater temperature variability); control of stormwater runoff (flow variability, increased conductivity, nutrient levels, sediment loads, sewage effluent, industrial discharges and heavy metals), and to modify retarding basins to increase stream continuity.