Unravelling the taxonomy and identification of a problematic group of benthic fishes from tropical rivers (Gobiidae: Glossogobius).

Flathead gobies (genus Glossogobius) include c. 40 small- to medium-sized benthic fishes found primarily in freshwater habitats across the Indo-Pacific, having biodiversity value as well as cultural and economic value as food fishes, especially in developing countries. To help resolve considerable confusion regarding the identification of some of the larger-growing Glossogobius species, a systematic framework was established using nuclear genetic markers, mitochondrial DNA barcoding and phenotypic evidence for a geographically widespread collection of individuals from the waterways of tropical northern Australia.

Fast sequence-based microsatellite genotyping development workflow.

Application of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability.

Variable outcomes of hybridization between declining and .

Hybridization dynamics between co-occurring species in environments where human-mediated changes take place are important to quantify for furthering our understanding of human impacts on species evolution and for informing management. The allis shad (Linnaeus, 1758) and twaite shad (Lacépède, 1803), two clupeids sister species, have been severely impacted by human activities across Europe. The shrinkage of distribution range along with the decline of the remaining populations' abundance threatens its persistence.

Strong population structure deduced from genetics, otolith chemistry and parasite abundances explains vulnerability to localized fishery collapse in a large Sciaenid fish, .

As pressure on coastal marine resources is increasing globally, the need to quantitatively assess vulnerable fish stocks is crucial in order to avoid the ecological consequences of stock depletions. Species of Sciaenidae (croakers, drums) are important components of tropical and temperate fisheries and are especially vulnerable to exploitation. The black-spotted croaker, , is the only large sciaenid in coastal waters of northern Australia where it is targeted by commercial, recreational and indigenous fishers due to its food value and predictable aggregating behaviour.

Characterization, development and multiplexing of microsatellite markers in three commercially exploited reef fish and their application for stock identification.

Thirty-four microsatellite loci were isolated from three reef fish species; golden snapper Lutjanus johnii, blackspotted croaker Protonibea diacanthus and grass emperor Lethrinus laticaudis using a next generation sequencing approach. Both IonTorrent single reads and Illumina MiSeq paired-end reads were used, with the latter demonstrating a higher quality of reads than the IonTorrent. From the 1-1.

The complete mitochondrial genome of the grass emperor, (Perciformes: Lethrinidae).

The grass emperor is a coral reef fish that has high value to fisheries and is vulnerable to overharvesting. The complete mitochondrial genome was assembled from approximately 5.5 million reads produced by Illumina MiSeq.

The complete mitochondrial genome of the golden snapper Lutjanus johnii (Perciformes: Lutjanidae).

We describe the complete mitochondrial genome of the golden snapper Lutjanus johnii. It was assembled from approximately 1.4 million reads produced by Ion Torrent next generation sequencing.

The complete mitochondrial genome of the black jewfish Protonibea diacanthus (Perciformes: Sciaenidae).

We describe the complete mitochondrial genome of the black Jewfish Protonibea diacanthus. It was assembled from approximately 1.6 million reads produced by Ion Torrent next generation sequencing.