Understanding population structure is important for predicting the outcomes of anthropogenic development, harvest, and environmental change on the abundance of fisheries species. Logically, the use of several data sources is best for delineating population structure, but combining across data types adds extra challenges as results can be incongruent. Here, genetic and environmental markers were used to test hypotheses about population structure in a collection of 523 tropical inshore finfish (Lutjanus johnii) across northern Australia from 20 locations. Redundancy analyses (RDA) were used to statistically test for correlations among data sources providing a basis for reconciliation and insights into ecological and evolutionary processes. Genomic data (10349 SNP loci) revealed low, but significant genetic divergence (max FST 0.0402) between 16 locations. A total of 12 putative contiguous biological stocks were proposed whose distributions were correlated with IMCRA bioregions but not to existing regions used for management of the fishery. RDA showed a significant correlation between environmental markers (otolith chemistry and parasite abundances) and SNP genotype in two of three region-wide analyses supporting the proposed stock structure, and suggesting that L. johnii may be locally adapted to the heterogeneous environment. These findings are significant for the conservation of the commercially and recreationally important L. johnii and can be used to guide future fisheries management actions.

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. Species boundaries and distribution patterns were discordant with those previously reported, most notably for the tank goby Glossogobius giuris, which included a cryptic species. Genetic divergence was matched with accompanying unique visual characters that aid field identification. Additional taxonomic complexity was also evident, by comparison with DNA barcodes from international locations, suggesting that the specific names applicable for two of the candidate species in Australia remain unresolved due to confusion surrounding type specimens. Although flathead gobies are assumed to be widespread and common, this study demonstrates that unrealised taxonomic and ecological complexity is evident, and this will influence assessments of tropical biodiversity and species conservation. This study supports the need for taxonomic studies of freshwater fishes to underpin management in areas subject to significant environmental change.

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. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20–40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the sequence quickly generates a powerful multi-allelic haplotype-based genotypic dataset, calling to new theoretical and analytical frameworks to extract more information from multi-nucleotide polymorphism marker systems.

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 Alosa alosa (Linnaeus, 1758) and twaite shad Alosa fallax (Lacépède, 1803), two clupeids sister species, have been severely impacted by human activities across Europe. The shrinkage of A. alosa distribution range along with the decline of the remaining populations' abundance threatens its persistence. The main objective was to evaluate the extent of hybridization and introgression between those interacting species. We developed a set of 77 species‐specific SNP loci that allowed a better resolution than morphological traits as they enabled the detection of hybrids up to the third generation. Variable rates of contemporary hybridization and introgression patterns were detected in 12 studied sites across the French Atlantic coast. Mitochondrial markers revealed a cyto‐nuclear discordance almost invariably involving A. alosa individuals with an A. fallax mitochondrial DNA and provided evidence of historical asymmetric introgression. Overall, contemporary and historical introgression revealed by nuclear and mitochondrial markers strongly suggests that a transfer of genes occurs from A. fallax toward A. alosa genome since at least four generations. Moreover, the outcomes of introgression greatly depend on the catchments where local processes are thought to occur. Undoubtedly, interspecific interaction and gene flow should not be overlooked when considering the management of those species.

The grass emperor Lethrinus laticaudis is a conspicuous element of the commercial and recreational catch from nearshore reef systems across northern Australia. The nearshore reef systems across northern Australia are exposed to increasing levels of fishing pressure from commercial and recreational fishers. To inform ongoing management of this species, the present study examined the stock structure of L. laticaudis across northern Australia using a combination of complementary techniques. In all, 342 L. laticaudis samples were collected from 13 locations in the coastal waters of northern Australia ranging from the Pilbara region of Western Australia to Moreton Bay in south-east Queensland. Population genetic analyses using microsatellite markers demonstrated that there were at least four genetically distinct populations across northern Australia with gene flow between management jurisdictions (with significantly more separation between Western Australian and Northern Territory locations than between Northern Territory and Queensland locations). An isolation by distance effect was evident (genetic differences increasing linearly with distance). Otolith microchemistry and parasitology analyses indicated some spatial structuring of populations within broader regions. These findings of restricted connectivity at small spatial scales suggest that L. laticaudis is vulnerable to localised depletion in areas where fishing effort is concentrated. This conclusion is consistent with recent observations of fishery declines in heavily fished locations.

This file contains the individual otolith microchemistry data used for the paper entitled Strong population structure deduced from genetics, otolith chemistry and parasite abundances explains vulnerability to localised fishery collapse in a large Sciaenid fish, Protonibea diacanthus

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, Protonibea diacanthus , 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. Localized declines in the abundance of this species have been observed, highlighting the urgent requirement by managers for information on fine‐ and broad‐scale population connectivity. This study examined the population structure of P. diacanthus across north‐western Australia using three complementary methods: genetic variation in microsatellite markers, otolith elemental composition and parasite assemblage composition. The genetic analyses demonstrated that there were at least five genetically distinct populations across the study region, with gene flow most likely restricted by inshore biogeographic barriers such as the Dampier Peninsula. The otolith chemistry and parasite analyses also revealed strong spatial variation among locations within broad‐scale regions, suggesting fine‐scale location fidelity within the lifetimes of individual fish. The complementarity of the three techniques elucidated patterns of connectivity over a range of spatial and temporal scales. We conclude that fisheries stock assessments and management are required at fine scales (100 s of km) to account for the restricted exchange among populations (stocks) and to prevent localized extirpations of this species. Realistic management arrangements may involve the successive closure and opening of fishing areas to reduce fishing pressure.

This file contains the individual genotypes used for the paper entitled Strong population structure deduced from genetics, otolith chemistry and parasite abundances explains vulnerability to localised fishery collapse in a large Sciaenid fish, Protonibea diacanthus.

Amphidromous fish are the biggest contributor to the diversity of fish communities in river systems of Caribbean islands. Among them, Sicydium punctatum Perugia, 1896, which is endemic to the West Indies, represents the vast majority of fish in these rivers. The otolith microstructure and the biometry of S. punctatum postlarvae from Guadeloupe were investigated to explore the dispersal modalities of this species through an appreciation of the growth pattern, the pelagic larval duration (PLD) and the size-at-recruitment. The study was made on one cohort of 83 recruited postlarvae, fished at the Capesterre River's mouth on 2 November 2011. The mean (±SD) size-at-recruitment of the postlarvae was 24.6 ± 1.3 mm (range of 20.5–28.1 mm, n = 83). We found a mean (±SD) PLD of 72.2 ± 10.5 days (range of 54–101.5 days, n = 67). The growth rate estimated from the otolith increments showed a globally decreasing pattern during the marine larval phase. Growth rates at the beginning of the larval stage were significantly different between hatching periods, suggesting a relation between the hatching period and the growth rate in S. punctatum. This study adds on to the general understanding of the life cycle of S. punctatum in Guadeloupe that will help implement strategies to manage amphidromous fish populations in the Caribbean region.

Raw sequences of black jewfish Protonibea diacanthus - Single reads obtained from IonTorrent technology

The grass emperor Lethrinus laticaudis 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 16,758 bp consisted of 13 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes (12S and 16S). The genes and RNAs order and orientation on as well as the A + T base content (50.7%) was similar to what is found in other Teleosts. A phylogenetic tree with the most closely related species available in GenBank was built to validate L. laticaudis mitogenome.

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 genome was 16,596bp in length consisting of 13 protein-coding regions, 22 tRNA, 12S and 16S rRNA as well as two non-coding regions. The A+T base content (52.8%) is similar to other teleosts.

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 1-1.5 million raw re ads per species, we successfully obtained 10-13 polymorphic loci for each species, which satisfied stringent design criteria. We developed multiplex panels for the amplification of the golden snapper and the blackspotted croaker loci, as well as post-amplification pooling panels for the grass emperor loci. The microsatellites characterized in this work were tested across three locations of northern Australia. The microsatellites we developed can detect population differentiation across northern Australia and may be used for genetic structure studies and stock identification.

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. The complete genome was 16,521bp in length consisting of 13 protein-coding regions, 22 tRNA, 12S and 16S rRNA as well as two non-coding regions. The A+T base content (52.8%) is similar to other teleosts.

Amphidromous fish species contribute most to the diversity of fish communities in the tropical insular rivers. Hence, their biological life cycle remains poorly known. The otolith elemental composition of three Sicydiinae species Sicyopus zosterophorum, Smilosicyopus chloe, Akihito vanuatu was investigated to describe their biological life cycle for the first time. The otolith analysis using a femtosecond laser ablation - inductively coupled plasma mass spectrometer (fs-LA-ICP-MS) revealed an amphidromous life history for the three species as it suggested a habitat shift from a marine habitat to a freshwater environment. Also, several types of elemental profiles were observed in the adult stage suggesting a diversity of behaviors and/or habitats. Water chemistry analyses would help understanding the origin of the ratios variations in the adult stage and would push forward our general understanding of Sicydiinae life cycle.

– Status and distribution of Smilosicyopus species are unclear, as they are rare, difficult to sample and to distinguish. During thirteen years, many specimens were collected by the MNHN and collaborators in Pacific islands, including samples in all type localities. These specimens were compared and Coigene sequenced. Seven out of the eight species known to date were confirmed, while S.mystax is considered a synonym of S.leprurus. Moreover, Smilosicyopus species have a broader distribution than previously thought and endemicity seems to be not the main rule in this genus. A key to species is provided. Resume . – Statut et distribution des especes du genre Smilosicyopus (teleostei, Gobioidei). Le statut et la distribution des especes de Smilosicyopus ne sont pas clairs. Durant treize ans, des specimens ont ete collectes dans les iles du Pacifique par le MNHN et des collaborateurs, y compris dans toutes les localites types. Ces specimens ont ete compares et le gene Coi a ete sequence. Sept especes sur les huit connues ont ete validees; S.mystax est considere comme synonyme de S.leprurus. Plusieurs especes de Smilosicyopus ont fina-lement une repartition plus large que celle qui etait supposee initialement et l’endemicite n’est donc pas la regle principale chez ce genre. Une cle de determination est donnee.

Even if amphidromous fish species contribute most to the diversity of fish communities in the tropical insular rivers, their biological cycle remain poorly known. For the first time, the otolith elemental composition and microstructure of two ancestral gobioids, Rhyacichthys guilberti and Protogobius attiti, were investigated to describe their biological cycle and pelagic larval duration (PLD). The otolith analysis using a femtosecond laser ablation coupled to an inductively coupled plasma–mass spectrometer (fs-LA-ICP-MS) revealed an amphidromous life history for R. guilberti and it suggested a progressive habitat shift from a marine habitat to a freshwater environment for P. attiti. For the first time, an endemic species, P. attiti, showed longer and more variable PLD (55.2 ± 13.5 days) than did a widespread one (R. guilberti: ~30 days). These results need to be confirmed by analysing more samples but suggest that factors other than the PLD control endemism and dispersal processes. In association with this first description of the biological cycle for both species, such an approach is a prerequisite for the management and conservation of both patrimonial species.