Characterisation of the complete mitochondrial genome and 13 microsatellite loci through next-generation sequencing for the New Caledonian spider-ant Leptomyrmex pallens.

The complete mitochondrial genome and a set of polymorphic microsatellite markers were identified by 454 pyrosequencing (1/16th of a plate) for the New Caledonian rainforest spider-ant Leptomyrmex pallens. De novo genome assembly recovered the entire mitochondrial genome with mean coverage of 8.9-fold (range 1-27). The mitogenome consists of 15,591 base pairs including 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The genome arrangement is typical of insect taxa and very similar to the only other published ant mitogenome from the Solenopsis genus, with the main differences consisting of translocations and inversions of tRNAs. A total of 13 polymorphic loci were also characterized using 41 individuals from a single population in the Aoupinié region, corresponding to workers from 21 nests and 16 foraging workers. We observed moderate genetic variation across most loci (mean number of alleles per locus = 4.50; mean expected heterozygosity = 0.53) with evidence of only two loci deviating significantly from Hardy-Weinberg equilibrium due to null alleles. Marker independence was confirmed with tests for linkage disequilibrium. Most loci cross amplified for three additional Leptomyrmex species. The annotation of the mitogenome and characterization of microsatellite markers will provide useful tools for assessing the colony structure, population genetic patterns, and dispersal strategy of L. pallens in the context of rainforest fragmentation in New Caledonia. Furthermore, this paper confirms a recent line of evidence that comprehensive mitochondrial data can be obtained relatively easily from small next-generation sequencing analyses. Greater synthesis of next-generation sequencing data will play a significant role in expanding the taxonomic representation of mitochondrial genome sequences.

Assessment and monitoring of nutrient loading in the sediments of tidal creeks receiving shrimp farm effluent in Quang Ninh, Vietnam.

Coastal shrimp farming may lead to the contamination of sediments of surrounding estuarine and marine ecosystems as shrimp farm effluent often contains high levels of pollutants including a range of organic compounds (from uneaten feed, shrimp feces, and living and dead organisms) which can accumulate in the sediments of receiving waterways. The assessment and monitoring of sediment quality in tidal creeks receiving shrimp farm effluent can support environmental protection and decision making for sustainable development in coastal areas since sediment quality often shows essential information on long-term aquatic ecosystem health. Within this context, this paper investigates nutrient loadings in the sediments of tidal creeks receiving shrimp farm effluent in Quang Ninh, Vietnam, which now have a high concentration of intensive and semi-intensive shrimp farms. Sediment samples taken from inside creek sections directly receiving effluent from concentrated shrimp farms (IEC), from main creeks adjacent to points of effluent discharge outside concentrated shrimp farms (OEC), and few kilometers away from shrimp farms (ASF) as reference sites were collected and analyzed before and after shrimp crops to investigate spatial and temporal variation. The results showed that there were statistically significant differences in the concentrations of total nitrogen, total phosphorus, and total organic carbon among IEC, OEC, and ASF sites while the seasonal variation being limited over study times. A sediment nutrient index (SNI) computed from coefficient scores of the factor analysis efficiently summarizes sediment nutrient loads, which are high, albeit quite variable, in canals directly receiving effluents from farms but then decline sharply with distance from shrimp farms. The visualization and monitoring of sediment quality data including SNI on maps can strongly support managers to manage eutrophication at concentrated shrimp farming areas, contributing to sustainable development and management at coastal zones.

Identification of rays through DNA barcoding: an application for ecologists.

DNA barcoding potentially offers scientists who are not expert taxonomists a powerful tool to support the accuracy of field studies involving taxa that are diverse and difficult to identify. The taxonomy of rays has received reasonable attention in Australia, although the fauna in remote locations such as Ningaloo Reef, Western Australia is poorly studied and the identification of some species in the field is problematic. Here, we report an application of DNA-barcoding to the identification of 16 species (from 10 genera) of tropical rays as part of an ecological study. Analysis of the dataset combined across all samples grouped sequences into clearly defined operational taxonomic units, with two conspicuous exceptions: the Neotrygon kuhlii species complex and the Aetobatus species complex. In the field, the group that presented the most difficulties for identification was the spotted whiptail rays, referred to as the 'uarnak' complex. Two sets of problems limited the successful application of DNA barcoding: (1) the presence of cryptic species, species complexes with unresolved taxonomic status and intra-specific geographical variation, and (2) insufficient numbers of entries in online databases that have been verified taxonomically, and the presence of lodged sequences in databases with inconsistent names. Nevertheless, we demonstrate the potential of the DNA barcoding approach to confirm field identifications and to highlight species complexes where taxonomic uncertainty might confound ecological data.