Effects of hook and bait on targeted and bycatch fishes in an equatorial atlantic pelagic longline fishery

We examined the effects of different hook style and bait type combinations on the catches of targeted, bycatch, and discarded fishes in equatorial Atlantic waters. In total, 221 longline sets (>305,000 hooks) were deployed from Portuguese pelagic longline vessels (SELECT -PAL Project) during the February–October fishing season. Three different hook styles and two bait types were tested: the traditional J-hook was compared to two circle hooks (one non-offset and one with 10° offset), and squid bait was compared to mackerel. Catch per unit effort (CPU Es) were calculated and compared between the different hook style and bait type combinations, which indicated that the effects of hook style and bait on the CPU Es were species-specific. For example, swordfish CPU Es were higher with J-hooks baited with squid, while for targeted tunas and blue shark only the bait effect was significant, but with opposite effect (i.e., higher catches of tuna with squid bait and higher catches of blue shark with mackerel bait). For the discarded species, at-haulback mortality was also species-specific. Proportions of alive vs dead specimens at time of fishing gear retrieval did not vary significantly by hook style or bait type combinations. The total retained catch was analyzed in value per unit effort (VPU E), and indicated losses in fishery revenue when mackerel was used instead of squid, but not when circle hooks were used instead of J-hooks.

The consequences of phenotypic plasticity on postglacial fishes

Phenotypic differences within a species significantly contribute to the variation we see among plants and animals. Plasticity as a concept helps us to understand some of this variation. Phenotypic plasticity plays a significant role in multiple ecological and evolutionary processes. Because plasticity can be driven by the environment it is more likely to produce beneficial alternative phenotypes than rare and often deleterious genetic mutations. Furthermore, differences in phenotypes that arise in response to the environment can affect multiple individuals from the same population (or entire populations) simultaneously and are therefore of greater evolutionary significance. This allows similar, beneficial alternative phenotypes to increase quickly within a single generation and allow new environments to produce and select for new phenotypes instantly. The direction of the present thesis is to increase our understanding of how phenotypic plasticity, coupled with contrasting environmental conditions, can produce alternative phenotypes within a population. Plasticity provides a source of variation for natural selection to act upon, and may lead to genetic isolation as a by-product. For example, there are multiple cases of polymorphic populations of fish, where groups belonging to multiple isolated gene pools, have arisen in sympatry. Here it is shown that although plasticity is important in sympatric speciation events, plasticity alone is not responsible for the frequency in which sympatric polymorphic populations occur. The most frequently observed differences among sympatric polymorphic populations are morphological differences associated with parts of the anatomy used in the detection, handling and capture of prey. Moreover, it is shown here that there are physiological effects associated with foraging on alternative prey that may significantly contribute towards ecological speciation. It is also shown in this study that anthropogenic abiotic factors can disrupt developmental processes during early ontogeny, significantly influencing morphology, and therefore having ecological consequences. Phenotypic structuring in postglacial fish is most frequently based around a divergence towards either pelagic or littoral benthic foraging specialisms. Divergences that deviate from this pattern are of greater scientific interest as they increase our understanding of how evolutionary processes and selection pressures work. Here we describe a rare divergence not based around the typical pelagic/littoral benthic foraging specialisms. Finally, in this study, the effectiveness of local level conservation policy shows that species of fish which are highly variable in their life history strategies are harder to effectively manage and often poorly represented at a local level.

Flower animals

The coral reefs around the world may be likened to canaries down the mineshaft of global warming. These sensitive plant-like animals have evolved for life in tropical seas. Their needs are quite specific – not too cold, not too hot. A rise of as little as one degree Celsius is enough to cause some bleaching of these colourful jewels of the sea. Many climate models indicate we can expect sea temperature increases of between two and six degrees Celsius. Research - such as that detailed in a 2004 report by the University of Queensland’s Centre for Marine Studies – indicates that by the year 2050 most of the worlds major reef systems will be dead. Many of us have heard this kind of information, but it remains difficult to comprehend. It’s almost impossible to imagine the death of the Great Barrier Reef. Some six to nine thousand years old and visible from space, it is the world’s largest structure created by living organisms. Yet whilst it is hard to believe, this gentle, sensitive giant is at grave risk because it cannot adapt quickly enough to the changes in the environment. This cluster of fluffy felt brain coral sculptures are connected in real time to temperature data collected by monitoring stations within the Great Barrier Reef, that form part of the Australian Institute of Marine Science’s Great Barrier Reed Ocean Observing System. These corals display illumination patterns showing changes in sea temperature at Heron Reef, one of the 2,900 reefs that comprise the Great Barrier Reef. Their spectrum of colour ranges from cool hues, through warm tones to bright white when temperatures exceed those that tropical corals are able to tolerate over sustained periods. The Flower Animals also blush in colour and make sound when people come within close proximity. In a reef, fishes and other creatures generate significant amounts of sound. These cacophonies are considered an indicator of reef health, and are used by reef fish to determine where they can best live and forage.

Identifying the spatial scale of land use that most strongly influences overall river ecosystem health score

Catchment and riparian degradation has resulted in declining ecosystem health of streams worldwide. With restoration a priority in many regions, there is an increasing interest in the scale at which land use influences stream ecosystem health. Our goal was to use a substantial data set collected as part of a monitoring program (the Southeast Queensland, Australia, Ecological Health Monitoring Program data set, collected at 116 sites over six years) to identify the spatial scale of land use, or the combination of spatial scales, that most strongly influences overall ecosystem health. In addition, we aimed to determine whether the most influential scale differed for different aspects of ecosystem health. We used linear-mixed models and a Bayesian model-averaging approach to generate models for the overall aggregated ecosystem health score and for each of the five component indicators (fish, macroinvertebrates, water quality, nutrients, and ecosystem processes) that make up the score. Dense forest close to the survey site, mid-dense forest in the hydrologically active nearstream areas of the catchment, urbanization in the riparian buffer, and tree cover at the reach scale were all significant in explaining ecosystem health, suggesting an overriding influence of forest cover, particularly close to the stream. Season and antecedent rainfall were also important explanatory variables, with some land-use variables showing significant seasonal interactions. There were also differential influences of land use for each of the component indicators. Our approach is useful given that restoring general ecosystem health is the focus of many stream restoration projects; it allowed us to predict the scale and catchment position of restoration that would result in the greatest improvement of ecosystem health in the regions streams and rivers. The models we generated suggested that good ecosystem health can be maintained in catchments where 80% of hydrologically active areas in close proximity to the stream have mid-dense forest cover and moderate health can be obtained with 60% cover.

An evaluation of potential candidate genes involved in salinity tolerance in striped catfish (Pangasianodon hypopthalmus) using an RNA-SEQ approach

The project investigated the molecular response of Tra catfish (Pangasianodon hypophthalmus) to elevated salinity conditions. We employed Next generation sequencing platform to evaluate differential gene expression profiles of key genes under two salinity conditions. Results of the current project can form the basis for further studies to confirm the functional roles of specific genes that influence salinity tolerance in the target species and more broadly in other freshwater teleost fishes. Ultimately, the approach can contribute to developing superior culture stocks of the target species.

Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus)

Striped catfish (Pangasianodon hypophthalmus) is a commercially important freshwater fish used in inland aquaculture in the Mekong Delta, Vietnam. The culture industry is facing a significant challenge however from saltwater intrusion into many low topographical coastal provinces across the Mekong Delta as a result of predicted climate change impacts. Developing genomic resources for this species can facilitate the production of improved culture lines that can withstand raised salinity conditions, and so we have applied high-throughput Ion Torrent sequencing of transcriptome libraries from six target osmoregulatory organs from striped catfish as a genomic resource for use in future selection strategies. We obtained 12,177,770 reads after trimming and processing with an average length of 97 bp. De novo assemblies were generated using CLC Genomic Workbench, Trinity and Velvet/Oases with the best overall contig performance resulting from the CLC assembly. De novo assembly using CLC yielded 66,451 contigs with an average length of 478 bp and N50 length of 506 bp. A total of 37,969 contigs (57%) possessed significant similarity with proteins in the non-redundant database. Comparative analyses revealed that a significant number of contigs matched sequences reported in other teleost fishes, ranging in similarity from 45.2% with Atlantic cod to 52% with zebrafish. In addition, 28,879 simple sequence repeats (SSRs) and 55,721 single nucleotide polymorphisms (SNPs) were detected in the striped catfish transcriptome. The sequence collection generated in the current study represents the most comprehensive genomic resource for P. hypophthalmus available to date. Our results illustrate the utility of next-generation sequencing as an efficient tool for constructing a large genomic database for marker development in non-model species.