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.

A candidate gene association study for growth performance in an improved Giant Freshwater Prawn (Macrobrachium rosenbergii) culture line

A candidate gene approach using type I single nucleotide polymorphism (SNP) markers can provide an effective method for detecting genes and gene regions that underlie phenotypic variation in adaptively significant traits. In the absence of available genomic data resources, transcriptomes were recently generated in Macrobrachium rosenbergii to identify candidate genes and markers potentially associated with growth. The characterisation of 47 candidate loci by ABI re-sequencing of four cultured and eight wild samples revealed 342 putative SNPs. Among these, 28 SNPs were selected in 23 growth-related candidate genes to genotype in 200 animals selected for improved growth performance in an experimental GFP culture line in Vietnam. The associations between SNP markers and individual growth performance were then examined. For additive and dominant effects, a total of three exonic SNPs in glycogen phosphorylase (additive), heat shock protein 90 (additive and dominant) and peroxidasin (additive), and a total of six intronic SNPs in ankyrin repeats-like protein (additive and dominant), rolling pebbles (dominant), transforming growth factor-β induced precursor (dominant), and UTP-glucose-1-phosphate uridylyltransferase 2 (dominant) genes showed significant associations with the estimated breeding values in the experimental animals (P =0.001−0.031). Individually, they explained 2.6−4.8 % of the genetic variance (R2=0.026−0.048). This is the first large set of SNP markers reported for M. rosenbergii and will be useful for confirmation of associations in other samples or culture lines as well as having applications in marker-assisted selection in future breeding programs.

Conserved gene structure and function of interleukin-10 in teleost fish

Interleukin-10 (IL-10) is an important immunoregulatory cytokine produced by various types of cells. Researchers describe here the isolation and characterization of olive flounder IL-10 (ofIL-10) cDNA and genomic organization. The ofIL-10 gene encodes a 187 amino acid protein and is composed of a five exon/four intron structure, similar to other known IL-10 genes. The ofIL-10 promoter sequence analysis shows a high level of homology in putative binding sites for transcription factors which are sufficient for transcriptional regulation ofIL-10. Important structural residues are maintained in the ofIL-10 protein including the four cysteines responsible for the two intra-chain disulfide bridges reported for human IL-10 and two extra cysteine residues that exist only in fish species. The phylogenetic analysis clustered ofIL-10 with other fish IL-10s and apart from mammalian IL-10 molecules. Quantitative real-time Polymerase Chain Reaction (PCR) analysis demonstrated ubiquitous ofIL-10 gene expression in the 13 tissues examined. Additionally, the induction of ofIL-10 gene expression was observed in the kidney tissue from olive flounder infected with bacteria (Edawardsiella tarda) or virus (Viral Hemorrhagic Septicemia Virus; VHSV). These data indicate that IL-10 is an important immune regulator that is conserved strictly genomic organization and function during the evolution of vertebrate immunity.

Genomic architecture of ecologically divergent body shape in a pair of sympatric crater lake cichlid fishes

Determining the genetic bases of adaptations and their roles in speciation is a prominent issue in evolutionary biology. Cichlid fish species flocks are a prime example of recent rapid radiations, often associated with adaptive phenotypic divergence from a common ancestor within a short period of time. In several radiations of freshwater fishes, divergence in ecomorphological traits - including body shape, colour, lips and jaws - is thought to underlie their ecological differentiation, specialization and, ultimately, speciation. The Midas cichlid species complex (Amphilophus spp.) of Nicaragua provides one of the few known examples of sympatric speciation where species have rapidly evolved different but parallel morphologies in young crater lakes. This study identified significant QTL for body shape using SNPs generated via ddRAD sequencing and geometric morphometric analyses of a cross between two ecologically and morphologically divergent, sympatric cichlid species endemic to crater Lake Apoyo: an elongated limnetic species (Amphilophus zaliosus) and a high-bodied benthic species (Amphilophus astorquii). A total of 453 genome-wide informative SNPs were identified in 240 F-2 hybrids. These markers were used to construct a genetic map in which 25 linkage groups were resolved. Seventy-two segregating SNPs were linked to 11 QTL. By annotating the two most highly supported QTL-linked genomic regions, genes that might contribute to divergence in body shape along the benthic-limnetic axis in Midas cichlid sympatric adaptive radiations were identified. These results suggest that few genomic regions of large effect contribute to early stage divergence in Midas cichlids.

Body shape variation and colour change during growth in a protogynous fish

Protogynous sequential hermaphroditism is very common in marine fish. Despite a large number of studies on various aspects of sequential hermaphroditism in fish, the relationship between body shape and colour during growth in dichromatic species has not been assessed. Using geometric morphometrics, the present study explores the relationship between growth, body shape and colouration in Coris julis (L. 1758), a small protogynous labrid species with distinct colour phases. Results show that body shape change during growth is independent of change in colour phase, a result which can be explained by the biology of the species and by the social control of sex change. Also, during growth the body grows deeper and the head has a steeper profile. It is hypothesized that a deeper body and a steeper profile might have a function in agonistic interactions between terminal phase males and that the marked chromatic difference between colour phases allows the lack of strict interdependence of body shape and colour during growth.

The gut microbial community of midas cichlid fish in repeatedly evolved limnetic-benthic species pairs

Gut bacterial communities are now known to influence a range of fitness related aspects of organisms. But how different the microbial community is in closely related species, and if these differences can be interpreted as adaptive is still unclear. In this study we compared microbial communities in two sets of closely related sympatric crater lake cichlid fish species pairs that show similar adaptations along the limnetic-benthic axis. The gut microbial community composition differs in the species pair inhabiting the older of two crater lakes. One major difference, relative to other fish, is that in these cichlids that live in hypersaline crater lakes, the microbial community is largely made up of Oceanospirillales (52.28%) which are halotolerant or halophilic bacteria. This analysis opens up further avenues to identify candidate symbiotic or co-evolved bacteria playing a role in adaptation to similar diets and life-styles or even have a role in speciation. Future functional and phylosymbiotic analyses might help to address these issues.

Identification of bacterial community composition in freshwater aquaculture system farming of Litopenaeus vannamei reveals distinct temperature-driven patterns

Change in temperature is often a major environmental factor in triggering waterborne disease outbreaks. Previous research has revealed temporal and spatial patterns of bacterial population in several aquatic ecosystems. To date, very little information is available on aquaculture environment. Here, we assessed environmental temperature effects on bacterial community composition in freshwater aquaculture system farming of Litopenaeus vannamei (FASFL). Water samples were collected over a one-year period, and aquatic bacteria were characterized by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and 16S rDNA pyrosequencing. Resulting DGGE fingerprints revealed a specific and dynamic bacterial population structure with considerable variation over the seasonal change, suggesting that environmental temperature was a key driver of bacterial population in the FASFL. Pyrosequencing data further demonstrated substantial difference in bacterial community composition between the water at higher (WHT) and at lower (WLT) temperatures in the FASFL. Actinobacteria, Proteobacteria and Bacteroidetes were the highest abundant phyla in the FASFL, however, a large number of unclassified bacteria contributed the most to the observed variation in phylogenetic diversity. The WHT harbored remarkably higher diversity and richness in bacterial composition at genus and species levels when compared to the WLT. Some potential pathogenenic species were identified in both WHT and WLT, providing data in support of aquatic animal health management in the aquaculture industry.

Does size matter? An assessment of quota market evolution and performance in the Great Barrier Reef fin-fish fishery

In fisheries managed using individual transferable quotas (ITQs) it is generally assumed that quota markets are well-functioning, allowing quota to flow on either a temporary or permanent basis to those able to make best use of it. However, despite an increasing number of fisheries being managed under ITQs, empirical assessments of the quota markets that have actually evolved in these fisheries remain scarce. The Queensland Coral Reef Fin-Fish Fishery (CRFFF) on the Great Barrier Reef has been managed under a system of ITQs since 2004. Data on individual quota holdings and trades for the period 2004-2012 were used to assess the CRFFF quota market and its evolution through time. Network analysis was applied to assess market structure and the nature of lease-trading relationships. An assessment of market participants’ abilities to balance their quota accounts, i.e., gap analysis, provided insights into market functionality and how this may have changed in the period observed. Trends in ownership and trade were determined, and market participants were identified as belonging to one out of a set of seven generalized types. The emergence of groups such as investors and lease-dependent fishers is clear. In 2011-2012, 41% of coral trout quota was owned by participants that did not fish it, and 64% of total coral trout landings were made by fishers that owned only 10% of the quota. Quota brokers emerged whose influence on the market varied with the bioeconomic conditions of the fishery. Throughout the study period some quota was found to remain inactive, implying potential market inefficiencies. Contribution to this inactivity appeared asymmetrical, with most residing in the hands of smaller quota holders. The importance of transaction costs in the operation of the quota market and the inequalities that may result are discussed in light of these findings

Chlamydial infections of fish: Diverse pathogens and emerging causes of disease in aquaculture species

Chlamydial infections of fish are emerging as an important cause of disease in new and established aquaculture industries. To date, epitheliocystis, a skin and gill disease associated with infection by these obligate intracellular pathogens, has been described in over 90 fish species, including hosts from marine and fresh water environments. Aided by advances in molecular detection and typing, recent years have seen an explosion in the description of these epitheliocystis-related chlamydial pathogens of fish, significantly broadening our knowledge of the genetic diversity of the order Chlamydiales. Remarkably, in most cases, it seems that each new piscine host studied has revealed the presence of a phylogenetically unique and novel chlamydial pathogen, providing researchers with a fascinating opportunity to understand the origin, evolution and adaptation of their traditional terrestrial chlamydial relatives. Despite the advances in this area, much still needs to be learnt about the epidemiology of chlamydial infections in fish if these pathogens are to be controlled in farmed environments. The lack of in vitro methods for culturing of chlamydial pathogens of fish is a major hindrance to this field. This review provides an update on our current knowledge of the taxonomy and diversity of chlamydial pathogens of fish, discusses the impact of these infections on the health, and highlights further areas of research required to understand the biology and epidemiology of this important emerging group of fish pathogens of aquaculture species.

Modeling meat yield based on measurements of body traits in genetically improved giant freshwater prawn (GFP) Macrobrachium rosenbergii

A single-generation dataset consisting of 1,730 records from a selection program for high growth rate in giant freshwater prawn (GFP, Macrobrachium rosenbergii) was used to derive prediction equations for meat weight and meat yield. Models were based on body traits [body weight, total length and abdominal width (AW)] and carcass measurements (tail weight and exoskeleton-off weight). Lengths and width were adjusted for the systematic effects of selection line, male morphotypes and female reproductive status, and for the covariables of age at slaughter within sex and body weight. Body and meat weights adjusted for the same effects (except body weight) were used to calculate meat yield (expressed as percentage of tail weight/body weight and exoskeleton-off weight/body weight). The edible meat weight and yield in this GFP population ranged from 12 to 15 g and 37 to 45 %, respectively. The simple (Pearson) correlation coefficients between body traits (body weight, total length and AW) and meat weight were moderate to very high and positive (0.75–0.94), but the correlations between body traits and meat yield were negative (−0.47 to −0.74). There were strong linear positive relationships between measurements of body traits and meat weight, whereas relationships of body traits with meat yield were moderate and negative. Step-wise multiple regression analysis showed that the best model to predict meat weight included all body traits, with a coefficient of determination (R 2) of 0.99 and a correlation between observed and predicted values of meat weight of 0.99. The corresponding figures for meat yield were 0.91 and 0.95, respectively. Body weight or length was the best predictor of meat weight, explaining 91–94 % of observed variance when it was fitted alone in the model. By contrast, tail width explained a lower proportion (69–82 %) of total variance in the single trait models. It is concluded that in practical breeding programs, improvement of meat weight can be easily made through indirect selection for body trait combinations. The improvement of meat yield, albeit being more difficult, is possible by genetic means, with 91 % of the variation in the trait explained by the body and carcass traits examined in this study.

Prediction of the fate of oxytetracycline and oxolinic acid in a fish pond using simulation model: A preliminary study

The fate of two popular antibiotics, oxytetracycline and oxolinic acid, in a fish pond were simulated using a computational model. The VDC model, which is designed based on a model for predicting pesticide fate and transport in paddy fields, was modified to take into account the differences between the pond and the paddies as well as those between the fish and the rice plant behaviors. The pond conditions were set following the typical practice in South East Asia aquaculture. The two antibiotics were administered to the animal in the pond through medicated feed during a period of 5 days as in actual practice. Concentrations of oxytetracycline in pond water were higher than those of oxolinic acid at the beginning of the simulation. Dissipation rate of oxytetracycline is also higher as it is more readily available for degradation in the water. For the long term, oxolinic acid was present at higher concentration than oxytetracycline in pond water as well as pond sediment. The simulated results were expected to be conservative and can be useful for the lower tier assessment of exposure risk of veterinary medicine in aquaculture industry but more data are needed for the complete validation of the model.