GIS and remote sensing-based spatial models for commercial fisheries assessment

By applying a novel set of multidisciplinary GIS, remote sensing and spatial modelling approaches, research presented in this thesis advances our knowledge of the distribution patterns, fishery and ecological status of an important commercial benthic macro-invertebrate, blacklip abalone, in south-east Australia.

The evolutionary ecology of transmissible cancers.

Transmissible tumours, while rare, present a fascinating opportunity to examine the evolutionary dynamics of cancer as both an infectious agent and an exotic, invasive species. Only three naturally-occurring transmissible cancers have been observed so far in the wild: Tasmanian devil facial tumour diseases, canine transmissible venereal tumour, and clam leukaemia. Here, we define four conditions that are necessary and sufficient for direct passage of cancer cells between either vertebrate or invertebrate hosts. Successful transmission requires environment and behaviours that facilitate transfer of tumour cells between hosts including: tumour tissue properties that promote shedding of large numbers of malignant cells, tumour cell plasticity that permits their survival during transmission and growth in a new host, and a 'permissible' host or host tissue. This rare confluence of multiple host- and tumour cell-traits both explains the rarity of tumour cell transmission and provides novel insights into the dynamics that both promote and constrain their growth.

A citizen science approach: a detailed ecological assessment of subtropical Reefs at Point Lookout, Australia.

Subtropical reefs provide an important habitat for flora and fauna, and proper monitoring is required for conservation. Monitoring these exposed and submerged reefs is challenging and available resources are limited. Citizen science is increasing in momentum, as an applied research tool and in the variety of monitoring approaches adopted. This paper aims to demonstrate an ecological assessment and mapping approach that incorporates both top-down (volunteer marine scientists) and bottom-up (divers/community) engagement aspects of citizen science, applied at a subtropical reef at Point Lookout, Southeast Queensland, Australia. Marine scientists trained fifty citizen scientists in survey techniques that included mapping of habitat features, recording of substrate, fish and invertebrate composition, and quantifying impacts (e.g., occurrence of substrate damage, presence of litter). In 2014 these volunteers conducted four seasonal surveys along semi-permanent transects, at five sites, across three reefs. The project presented is a model on how citizen science can be conducted in a marine environment through collaboration of volunteer researchers, non-researchers and local marine authorities. Significant differences in coral and algal cover were observed among the three sites, while fluctuations in algal cover were also observed seasonally. Differences in fish assemblages were apparent among sites and seasons, with subtropical fish groups observed more commonly in colder seasons. The least physical damage occurred in the most exposed sites (Flat Rock) within the highly protected marine park zones. The broad range of data collected through this top-down/bottom-up approach to citizen science exemplifies the projects' value and application for identifying ecosystem trends or patterns. The results of the project support natural resource and marine park management, providing a valuable contribution to existing scientific knowledge and the conservation of local reefs.

Assemblage, size and abundance bias in a novel sandy shore macro-infaunal sampling technique

Sampling sandy shore macro-invertebrate fauna is critical in enhancing our understanding of beach ecology and conservation, and is a common monitoring approach. The traditional, and almost universal, method of sampling involves sieving sand to locate infauna, but here we describe a novel Hydraulic Sampling Device (HSD), a candidate method for future macro-invertebrate sampling, which has the potential to be faster and more effective at sampling invertebrates. We compared the results obtained by these two methods. Macro-invertebrate fauna of six beaches on Phillip Island, southern Victoria, Australia were sampled in the upper and lower beach. On average, the HSD sampled a smaller size range of fauna than the sieving method, perhaps because of longer handling times and escape of larger individuals. The sieving method found more individuals and a higher species richness. The methods we describe do not produce directly comparable results. On balance, the sieving method is simpler, apparently not as prone to ‘escape bias’, and reports higher abundances and richness of beach infauna.

Biodiversidad estacional del macrozoobentos mesolitoral de fondos blandos en la playa de Salaverry, La Libertad – Perú

La biodiversidad del macrozoobentos en el mesolitoral de la playa de Salaverry se determinó durante setiembre 2015 a marzo 2016. Se establecieron cuatro transectos (A, B, C y D) y se fijaron tres estaciones. Además se determinó la biodiversidad estacional a través de los índices de Shannon - Wiener (H'), Margalef (d'), Equidad de Pielou (J'), Simpson (λ) y de Similitud de Bray- Curtis. Las muestras fueron colectadas quincenalmente, utilizando un cilindro de Penchaszadeh de 0,028 m2. Asi también se tomaron datos de temperatura, salinidad y granulometría. Las especies se identificaron utilizando claves taxonómicas de invertebrados marinos. Se registraron especies de las clases Polychaeta, Nemertea, Gastropoda, Bivalvia y Malacostraca (Subphylum Crustacea). La biodiversidad del macrozoobentos para primavera fue de 2,51 bits/ind y para verano de 1,91 bits/ind con una riqueza de 22 especies.

DNA barcoding: an effective tool to overcome morphological identification constraints in the assessment of the ecological quality

DNA barcoding has the potential to overcome taxonomic challenges in biological community assessments. However, fulfilling that potential requires successful amplification of a large and unbiased portion of the community. In this study, we attempted to identify mitochondrial gene cytochrome c oxidase I (COI) barcodes from 1024 benthic invertebrate specimens belonging to 54 taxa from low salinity environments of the Mira estuary and Torgal riverside (SW Portugal). Up to 17 primer pairs and several reaction conditions were attempted among specimens from all taxa, with amplification success defined as a single band of approximately 658 bp visualized on a pre-cast agarose gel, starting near the 5' end of the COI gene and suitable for sequencing. Amplification success was achieved for 99.6% of the 54 taxa, though no single primer was successful for more than 88.9% of the taxa. However, only 68.5% of the specimens within these taxa successfully amplified. Inhibition factors resulting from a non-purified DNA extracted and inexistence of species-specific primers for COI were pointed as the main reasons for an unsuccessful amplification. These results suggest that DNA barcoding can be an effective tool for application in low salinity environments where taxa such as chironomids and oligochaetes are challenging for morphological identification. Nevertheless, its implementation is not simple, as methods are still being standardized and multiple species