A broad-scale analysis of links between coastal fisheries production and mangrove extent : a case-study for northeastern Australia

The paradigm that mangroves are critical for sustaining production in coastal fisheries is widely accepted, but empirical evidence has been tenuous. This study showed that links between mangrove extent and coastal fisheries production could be detected for some species at a broad regional scale (1000s of kilometres) on the east coast of Queensland, Australia. The relationships between catch-per-unit-effort for different commercially caught species in four fisheries (trawl, line, net and pot fisheries) and mangrove characteristics, estimated from Landsat images were examined using multiple regression analyses. The species were categorised into three groups based on information on their life history characteristics, namely mangrove-related species (banana prawns Penaeus merguiensis, mud crabs Scylla serrata and barramundi Lates calcarifer), estuarine species (tiger prawns Penaeus esculentus and Penaeus semisulcatus, blue swimmer crabs Portunus pelagicus and blue threadfin Eleutheronema tetradactylum) and offshore species (coral trout Plectropomus spp.). For the mangrove-related species, mangrove characteristics such as area and perimeter accounted for most of the variation in the model; for the non-mangrove estuarine species, latitude was the dominant parameter but some mangrove characteristics (e.g. mangrove perimeter) also made significant contributions to the models. In contrast, for the offshore species, latitude was the dominant variable, with no contribution from mangrove characteristics. This study also identified that finer scale spatial data for the fisheries, to enable catch information to be attributed to a particular catchment, would help to improve our understanding of relationships between mangroves and fisheries production.

Taxonomic resolution and quantification of freshwater macroinvertebrate samples from an Australian dryland river : The benefits and costs of using species abundance data

In studies using macroinvertebrates as indicators for monitoring rivers and streams, species level identifications in comparison with lower resolution identifications can have greater information content and result in more reliable site classifications and better capacity to discriminate between sites, yet many such programmes identify specimens to the resolution of family rather than species. This is often because it is cheaper to obtain family level data than species level data. Choice of appropriate taxonomic resolution is a compromise between the cost of obtaining data at high taxonomic resolutions and the loss of information at lower resolutions. Optimum taxonomic resolution should be determined by the information required to address programme objectives. Costs saved in identifying macroinvertebrates to family level may not be justified if family level data can not give the answers required and expending the extra cost to obtain species level data may not be warranted if cheaper family level data retains sufficient information to meet objectives. We investigated the influence of taxonomic resolution and sample quantification (abundance vs. presence/absence) on the representation of aquatic macroinvertebrate species assemblage patterns and species richness estimates. The study was conducted in a physically harsh dryland river system (Condamine-Balonne River system, located in south-western Queensland, Australia), characterised by low macroinvertebrate diversity. Our 29 study sites covered a wide geographic range and a diversity of lotic conditions and this was reflected by differences between sites in macroinvertebrate assemblage composition and richness. The usefulness of expending the extra cost necessary to identify macroinvertebrates to species was quantified via the benefits this higher resolution data offered in its capacity to discriminate between sites and give accurate estimates of site species richness. We found that very little information (<6%) was lost by identifying taxa to family (or genus), as opposed to species, and that quantifying the abundance of taxa provided greater resolution for pattern interpretation than simply noting their presence/absence. Species richness was very well represented by genus, family and order richness, so that each of these could be used as surrogates of species richness if, for example, surveying to identify diversity hot-spots. It is suggested that sharing of common ecological responses among species within higher taxonomic units is the most plausible mechanism for the results. Based on a cost/benefit analysis, family level abundance data is recommended as the best resolution for resolving patterns in macroinvertebrate assemblages in this system. The relevance of these findings are discussed in the context of other low diversity, harsh, dryland river systems.

An investigation of functional diversity of endogenous cellulase and expression of other digestive enzyme genes in freshwater crayfish (Cherax) species

The project evaluated potential of soluble cellulose as a cheap feed ingredient for major farmed Australian freshwater crayfish species testing their growth performance, digestive enzyme activity and digestive enzyme gene expression patterns. Test animals showed an innate capacity to utilise a range of carbohydrate sources including complex structural polysaccharides. Results suggest that more plant-derived ingredient can be incorporated in formulated low-cost feeds for the culture industry.

Separating resource rents from intra-marginal rents in fisheries economics survey data

Economic surveys of fisheries are undertaken in several countries as a means of assessing the economic performance of their fisheries. The level of economic profits accruing in the fishery can be estimated from the average economic profits of the boats surveyed. Economic profits consist of two components—resource rent and intra-marginal rent. From a fisheries management perspective, the key indicator of performance is the level of resource rent being generated in the fishery. Consequently, these different components need to be separated out. In this paper, a means of separating out the rent components is identified for a heterogeneous fishery. This is applied to the multi-purpose fleet operating in the English Channel. The paper demonstrates that failing to separate out these two components may result in a misrepresentation of the economic performance of the fishery.

Diversity of New Zealand's Terrestrial and Freshwater Fauna

As a large, isolated and relatively ancient landmass, New Zealand occupies a unique place in the biological world, with distinctive terrestrial biota and a high proportion of primitive endemic forms. Biology Aotearoa covers the origins, evolution and conservation of the New Zealand flora, fauna and fungi. Each chapter is written by specialists in the field, often working from different perspectives to build up a comprehensive picture. Topics include: the geological history of our land origins, and evolution of our plants, animals and fungi current status of rare and threatened species past, present and future management of native species the effect of human immigration on the native biota.

Corporate-cooperative management of fisheries: A potential alternative governance structure for low value small fisheries?

While the economic and environmental benefits of fisheries management are well accepted, the costs of effective management in low value fisheries, including the research necessary to underpin such management, may be considerable relative to the total economic benefits they may generate. Co-management is often seen as a panacea in low value fisheries. Increasing fisher participation increases legitimacy of management decision in the absence of detailed scientific input. However, where only a small number of operators exist, the potential benefits of co-management are negated by the high transaction cost to the individual fishers engaging in the management process. From an economic perspective, sole ownership has been identified as the management structure which can best achieve biological and economic sustainability. Moving low value fisheries with a small number of participants to a corporate-cooperative management model may come close to achieving these sole ownership benefits, with lower transaction costs. In this paper we look at the applicability of different management models with industry involvement to low value fisheries with a small number of participants. We provide an illustration as to how a fishery could be transitioned to a corporate-cooperative management model that captures the key benefits of sole management at a low cost and is consistent with societal objectives.

Appendix 8: Quantifying the effects of environmental factors on catch rates in South-East fisheries: 1986-2006

The collection of basic environmental data by industry members was successful and offers a way of overcoming the problems associated with differences in scale between the environment and fisheries datasets. A simple method of collecting environmental data was developed that was only a small time burden on skippers, yet has the potential to provide very useful information on the same scale as the catch and effort data recorded in the logbooks. The success of this trial was aided by the natural interest of fishers to learn more about the environment in which they fish. The archival temperature-depth tags chosen proved robust, reliable and easy to use. While the use of large scale environmental data may not yield significant improvements in stock assessments for most SESSF species, fine-scale data collected from selected vessels using methods developed during this project may, in the longer term, be useful for incorporation into CPUE standardisations in the future...

Eco-crime and freshwater

The unsustainable and exploitative use of one of the most important but scarce resources on the planet - freshwater - continues to create conflict and human dislocation on a grand scale. Instead of witnessing nation-states adopting more equitable and efficient conservation strategies, powerful corporations are permitted to privatise and monopolise diminishing water reservoirs based on flawed neo-liberal assumptions and market models of the ‘global good’. The commodification of water has enabled corporate monopolies and corrupt states to exploit a fundamental human right, and in the process have created new forms of criminality. In recent years, affluent industrialised nations have experienced violent rioting as protestors express opposition to government ‘freshwater taxes’ and to corporate investors seeking to privatise drinking water. These water conflicts have included unprecedented clashes with police and deaths of innocent civilians in South Africa (BBC News, 2014a); the United Nations intervention in Detroit USA after weeks of public protest (Burns, 2014); and the hundreds of thousands of people protesting in Ireland (BBC News, 2014,b; Irish Times 2015). Subsequently, the commodification of freshwater has become a criminological issue for water-abundant rich states, as well as for the highly indebted water-scarce nations.

Phylogeography of two freshwater prawn species from far-northern Queensland

The distribution of a freshwater species is often dependent on its ability to disperse within the riverine system. Species with high dispersal abilities tend to be widespread, whereas those with restricted dispersal tend to be geographically restricted and are usually given higher conservation priority. Population structure was compared between a widespread freshwater prawn species, Macrobrachium australiense, and a narrow-range endemic freshwater prawn, Macrobrachium koombooloomba. The distribution of M. australiense and M. koombooloomba did not overlap, although suggested historical river-boundary rearrangements indicate that there has been the potential for dispersal into neighbouring catchments. A fragment of the mtDNA CO1 gene was analysed and a Mantel test revealed a significant isolation by distance effect for both species. Significant overall FST values confirmed that both species exhibited low levels of dispersal, a prediction for populations inhabiting a fragmented upland environment. The level of structure in M. australiense is surprising for a widely distributed species. Not all M. australiense populations conformed to the stream-hierarchy model, with results being best explained by historical river realignment or cross-catchment dispersal. The fact that both species show limited dispersal highlights the importance of conservation in highland areas for both endemic and widely spread species.

Analysis, characterisation and expression of gill-expressed carbonic anhydrase genes in the freshwater crayfish Cherax quadricarinatus

Changes in water quality parameters such as pH and salinity can have a significant effect on productivity of aquaculture species. Similarly, relative osmotic pressure influences various physiological processes and regulates expression of a number of osmoregulatory genes. Among those, carbonic anhydrase (CA) plays a key role in systemic acid–base balance and ion regulation. Redclaw crayfish (Cherax quadricarinatus) are unique in their ability to thrive in environments with naturally varied pH levels, suggesting unique adaptation to pH stress. To date, however, no studies have focused on identification and characterisation of CA or other osmoregulatory genes in C. quadricarinatus. Here, we analysed the redclaw gill transcriptome and characterized CA genes along with a number of other key osmoregulatory genes that were identified in the transcriptome. We also examined patterns of gene expression of these CA genes when exposed to three pH treatments. In total, 72,382,710 paired end Illumina reads were assembled into 36,128 contigs with an average length of 800 bp. Approximately 37% of contigs received significant BLAST hits and 22% were assigned gene ontology terms. Three full length CA isoforms; cytoplasmic CA (ChqCAc), glycosyl-phosphatidylinositol-linked CA (ChqCAg), and β-CA (ChqCA-beta) as well as two partial CA gene sequences were identified. Both partial CA genes showed high similarity to ChqCAg and appeared to be duplicated from the ChqCAg. Full length coding sequences of Na+/K+-ATPase, V-type H+-ATPase, sarcoplasmic Ca+-ATPase, arginine kinase, calreticulin and Cl− channel protein 2 were also identified. Only the ChqCAc gene showed significant differences in expression across the three pH treatments. These data provide valuable information on the gill expressed CA genes and their expression patterns in freshwater crayfish. Overall our data suggest an important role for the ChqCAc gene in response to changes in pH and in systemic acid–base balance in freshwater crayfish.

Comparative analysis of gill transcriptomes of two freshwater crayfish, Cherax cainii and C. destructor

We undertook deep sequencing of gill transcriptomes from two freshwater crayfish, Cherax cainii and Cherax destructor, in order to generate genomic resources for future genomics research. Over 83 and 100 million high quality (quality score (Q) ≥ 30) paired-end Illumina reads (150 bp) were assembled into 147,101 and 136,622 contigs in C. cainii and C. destructor, respectively. A total of 24,630 and 23,623 contigs received significant BLASTx hits and allowed the identification of multiple gill expressed candidate genes associated with pH and salinity balance. These functionally annotated transcripts will provide a resource to facilitate comparative genomic research in the genus Cherax, and in particular allow insights into respiratory and osmoregulatory physiology of this group of animals.

Molecular data extend Australian Cricotopus midge (Chironomidae) species diversity, and provide a phylogenetic hypothesis for biogeography and freshwater monitoring

Resolving species relationships and confirming diagnostic morphological characters for insect clades that are highly plastic, and/or include morphologically cryptic species, is crucial for both academic and applied reasons. Within the true fly (Diptera) family Chironomidae, a most ubiquitous freshwater insect group, the genera CricotopusWulp, 1874 and ParatrichocladiusSantos-Abreu, 1918 have long been taxonomically confusing. Indeed, until recently the Australian fauna had been examined in just two unpublished theses: most species were known by informal manuscript names only, with no concept of relationships. Understanding species limits, and the associated ecology and evolution, is essential to address taxonomic sufficiency in biomonitoring surveys. Immature stages are collected routinely, but tolerance is generalized at the genus level, despite marked variation among species. Here, we explored this issue using a multilocus molecular phylogenetic approach, including the standard mitochondrial barcode region, and tested explicitly for phylogenetic signal in ecological tolerance of species. Additionally, we addressed biogeographical patterns by conducting Bayesian divergence time estimation. We sampled all but one of the now recognized Australian Cricotopus species and tested monophyly using representatives from other austral and Asian locations. Cricotopus is revealed as paraphyletic by the inclusion of a nested monophyletic Paratrichocladius, with in-group diversification beginning in the Eocene. Previous morphological species concepts are largely corroborated, but some additional cryptic diversity is revealed. No significant relationship was observed between the phylogenetic position of a species and its ecology, implying either that tolerance to deleterious environmental impacts is a convergent trait among many Cricotopus species or that sensitive and restricted taxa have diversified into more narrow niches from a widely tolerant ancestor.

Identification of a putative cellulase gene in the giant freshwater prawn, Macrobrachium rosenbergii (De Man, 1879)

Nutrition plays an important role in the development of all organisms and in particular that of farmed aquatic species where costs associated with feed can often exceed 60% of total production costs. Crustacean species in addition, have the added metabolic requirement for regular moulting to allow normal growth and this requires large amounts of energy in the form of sugars (glucose). The current study explored the capacity of the giant freshwater prawn to produce endogenous cellulose-degrading enzymes capable of extracting nutrients (simple sugars) from plant sources in formulated feeds used in the prawn aquaculture industry. We identified a putative cellulase cDNA fragment in the target organism of 1576 base pairs in length of non-microbial origin that after protein modelling exhibited a TM-score of 0.916 with a described cellulase reported from another crustacean species. The functional role of cellulase enzymes is to hydrolyse cellulose to glucose and the fragment identified in GFP was highly expressed in the hepatopancreas, the site of primary food digestion and absorption in crustaceans. Hepatopancreatic tissue from Macrobrachium rosenbergii also showed active digestion of cellulose to glucose following an endoglucanase assay. Cellulase gene(s) are present in the genomes of many invertebrate taxa and play an active role in the conversion of cellulose to available energy. Identification and characterization of endogenous cellulase gene(s) in giant freshwater prawn can assist development of the culture industry because the findings confirm that potentially greater levels of low-cost plant-material could be included in artificial formulated diets in the future without necessarily compromising individual growth performance. Ultimately, this development may contribute to more efficient, cost-effective production systems for freshwater prawn culture stocks that meet the animal's basic nutritional requirements and that also support good individual growth rates.