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. 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.

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. 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.

Variable outcomes of hybridization between declining Alosa alosa and Alosa fallax

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.

Strong population structure deduced from genetics, otolith chemistry and parasite abundances explains vulnerability to localized 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.

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 1–1.5 million raw reads 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.

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

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.

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. The complete genome was 16,521 bp 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.

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 genome was 16,596 bp 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.

Contrasting genetic structure among populations of two amphidromous fish species (Sicydiinae) in the Central West Pacific

Both present-day and past processes can shape connectivity of populations. Pleistocene vicariant events and dispersal have shaped the present distribution and connectivity patterns of aquatic species in the Indo-Pacific region. In particular, the processes that have shaped distribution of amphidromous goby species still remain unknown. Previous studies show that phylogeographic breaks are observed between populations in the Indian and Pacific Oceans where the shallow Sunda shelf constituted a geographical barrier to dispersal, or that the large spans of open ocean that isolate the Hawaiian or Polynesian Islands are also barriers for amphidromous species even though they have great dispersal capacity. Here we assess past and present genetic structure of populations of two amphidromous fish (gobies of the Sicydiinae) that are widely distributed in the Central West Pacific and which have similar pelagic larval durations. We analysed sections of mitochondrial COI, Cytb and nuclear Rhodospine genes in individuals sampled from different locations across their entire known range. Similar to other Sicydiinae fish, intraspecific mtDNA genetic diversity was high for all species (haplotype diversity between 0.9–0.96). Spatial analyses of genetic variation in Sicyopus zosterophorum demonstrated strong isolation across the Torres Strait, which was a geologically intermittent land barrier linking Australia to Papua New Guinea. There was a clear genetic break between the northwestern and the southwestern clusters in Si. zosterophorum (φ_ST = 0.67502 for COI) and coalescent analyses revealed that the two populations split at 306 Kyr BP (95% HPD 79–625 Kyr BP), which is consistent with a Pleistocene separation caused by the Torres Strait barrier. However, this geographical barrier did not seem to affect Sm. fehlmanni. Historical and demographic hypotheses are raised to explain the different patterns of population structure and distribution between these species. Strategies aiming to conserve amphidromous fish should consider the presence of cryptic evolutionary lineages to prevent stock depletion.

Involvement of thyroid hormones in the control of larval metamorphosis in Sicyopterus lagocephalus (Teleostei: Gobioidei) at the time of river recruitment

After oceanic migration, post-larvae of the amphidromous Sicyopterus lagocephalus recruit to rivers in Reunion Island. As they enter the river mouth, post-larvae undergo many morphological, physiological and behavioural changes. These drastic changes, which allow them to change feeding regime and to colonise the juvenile and adult freshwater habitat, are defined as metamorphosis. The endocrine control of these changes has never been investigated in Gobioid fish. Here, we investigated whether thyroid hormones (TH) influence metamorphosis in recruiting S.lagocephalus. An analytical study was first performed on a cohort of 2400 fish caught at post-larval stage 1 and maintained for 37 days after capture in a flume tank (fluvarium), which replicates as closely as possible the natural conditions. Biometrical parameters (total and standard lengths, corner of mouth angle, body mass and condition factor) and whole-body thyroxine (T(4)) and triiodothyronine (T(3)) contents were measured on fish, sampled at regular intervals during these 37 days (192 fish). TH levels, measured by radioimmunoassays, were highest when morphological changes, such as the change in the position of the mouth, were most important. An experimental approach was then used to test the effect of the hormonal treatment (T(4) or thiourea, TU, a TH inhibitor) on biometrical parameters of 576 post-larvae. The change in the position of the mouth was significantly accelerated in the T(4)-treated post-larvae, while it was significantly delayed in the TU-treated post-larvae, compared to controls. Our study suggests that S.lagocephalus post-larva undergoes a true metamorphic event under the control of thyroid hormones at the time of its recruitment into the river.

[Treatment of bacterial meningitis in children]

The initial treatment of infantile and childhood bacterial meningitis is now well standardized, but three current aspects are discussed in this paper. Although classically, ampicillin can still be given as the initial treatment of bacterial meningitis in children, current epidemiologic data demonstrate the emergence of resistant strains of Haemophilus and Pneumococcus, and consequently use of a third-generation cephalosporin should be preferred. Concerning duration of treatment, 4 to 5 days seem adequate for meningococci and 7 days for Haemophilus influenzae and pneumococci. Lastly, the usefulness of adjunctive antiinflammatory treatment is considered. The purpose of this treatment is to lower the risk of cerebral complications and neurosensory impairment. Current data suggest that use of corticosteroids as early as possible may be helpful. Improved understanding of the pathophysiology of pediatric bacterial meningitis has led to other forms of treatment being proposed, but their value remains to be proven.

Treatment of infantile spasms with intravenous gamma-globulins

In a prospective study, 23 children with infantile spasms received intravenous gammaglobulins in high doses. 19 patients present a West syndrome. 4 older patients were included in the study because infantile spasms had preceded their Lennox-Gastaut syndrome. None of the patients had recently undergone corticosteroid therapy. No effect was observed in 15 patients, while transitory clinical and/or electroencephalographic improvement was noted in 3. Complete normalization was obtained in the remaining 5 patients, of whom 4 had severe brain lesions. No correlation existed between the therapeutic results and immunological abnormalities, a deficiency in IgG subclasses in particular. On the whole, the therapeutic results were disappointing. But the existence of some cases in which spectacular electroencephalographic and/or clinical improvement was obtained leads us to suggest that IV gamma-globulins be used as auxiliary treatment in infantile spasms.

[Reduction of antibiotic treatment of bacterial meningitis in children. Value of C-reactive protein monitoring]

The duration of antibiotic treatment of bacterial meningitis is always a topical issue. In our study (58 children), 21 of 24 meningococcal meningitis were treated for 4 or 5 days, 16 of 22 Haemophilus influenzae and 4 of 6 pneumococcal meningitis were treated for 7 days without increase in neurologic sequelae. A return of blood CRP levels to normal values was observed in all these patients simultaneously. Thus, CRP seems to be a good biological parameter for discussing treatment discontinuation. Furthermore, in some complications such as subdural effusion, a new increase of CRP levels was observed after the 5th day. A sequential follow-up of CRP levels at days J0, 5, 7, 10, seems a very useful tool for management of bacterial meningitis.