A multi-tissue de novo transcriptome assembly and relative gene expression of the vulnerable freshwater salmonid Thymallus ligericus.

Freshwater ecosystems are among the most endangered ecosystems worldwide. While numerous taxa are on the verge of extinction as a result of global changes and direct or indirect anthropogenic activity, genomic and transcriptomic resources represent a key tool for comprehending species' adaptability and serve as the foundation for conservation initiatives. The Loire grayling, Thymallus ligericus, is a freshwater European salmonid endemic to the upper Loire River basin. The species is comprised of fragmented populations that are dispersed over a small area and it has been identified as a vulnerable species. Here, we provide a multi-tissue de novo transcriptome assembly of T. ligericus. The completeness and integrity of the transcriptome were assessed before and after redundancy removal with lineage-specific libraries from Eukaryota, Metazoa, Vertebrata, and Actinopterygii. Relative gene expression was assessed for each of the analyzed tissues, using the de novo assembled transcriptome and a genome-based analysis using the available T. thymallus genome as a reference. The final assembly, with a contig N50 of 1221 and Benchmarking Universal Single-Copy Orthologs (BUSCO) scores above 94%, is made accessible along with structural and functional annotations and relative gene expression of the five tissues (NCBI SRA and FigShare databases). This is the first transcriptomic resource for this species, which provides a foundation for future research on this and other salmonid species that are increasingly exposed to environmental stressors.

Evaluating a species phylogeny using ddRAD SNPs: Cyto-nuclear discordance and introgression in the salmonid genus Thymallus (Salmonidae).

Hybridization and introgression are very common among freshwater fishes due to the dynamic nature of hydrological landscapes. Cyclic patterns of allopatry and secondary contact provide numerous opportunities for interspecific gene flow, which can lead to discordant paths of evolution for mitochondrial and nuclear genomes. Here, we used double digest restriction-site associated DNA sequencing (ddRADseq) to obtain a genome-wide single nucleotide polymorphism (SNP) dataset comprehensive for allThymallus (Salmonidae)species to infer phylogenetic relationships and evaluate potential recent and historical gene flow among species. The newly obtained nuclear phylogeny was largely concordant with a previously published mitogenome-based topology but revealed a few cyto-nuclear discordances. These incongruencies primarily involved the placement of internal nodes rather than the resolution of species, except for one European species where anthropogenic stock transfers are thought to be responsible for the observed pattern. The analysis of four contact zones where multiple species are found revealed a few cases of mitochondrial capture and limited signals of nuclear introgression. Interestingly, the mechanisms restricting interspecific gene flow might be distinct; while in zones of secondary contact, small-scale physical habitat separation appeared as a limiting factor, biologically based reinforcement mechanisms are presumed to be operative in areas where species presumably evolved in sympatry. Signals of historical introgression were largely congruent with the routes of species dispersal previously inferred from mitogenome data. Overall, the ddRADseq dataset provided a robust phylogenetic reconstruction of the genus Thymallus including new insights into historical hybridization and introgression, opening up new questions concerning their evolutionary history.

Morphological and molecular evidence of three species of pikes Esox spp. (Actinopterygii, Esocidae) in France, including the description of a new species.

This integrative taxonomy study of French pikes compares morphological characters and molecular sequence data (mitochondrial COI and nuclear Plagl2 genes). In addition to the expected E. lucius, DNA sequences and morphology both support a new species in France, E. aquitanicus sp. nov. from the Charente to the Adour drainages. It is characterized by a color pattern of sides with narrow 1-1.5-scale-wide oblique vertical bands, conferring it a marbled coat, a snout only 0.9 times larger than the postorbital length, an anal fin basis 1.1-1.2 times larger than the caudal peduncle length, 101 to 121 lateral scales, 53 to 57 vertebrae, as well as 24 diagnostic sites in the COI gene and 3 in the Plagl2 gene. Partial COI sequences (131 bp) from modern and historical specimens indicate also the presence of E. cisalpinus and E. lucius during the 19th century in Lake Geneva. Morphological and molecular data points to a possible hybridization between E. lucius with both other local pike species, representing a risk for them. Their endangerment status should be evaluated rapidly in order to take conservation measures.

Spatial and temporal trends in PCBs in sediment along the lower Rhône River, France.

Despite increasingly strict control of polychlorinated biphenyl (PCB) releases in France since the mid-1970s, PCB contamination of fish recently has emerged as a major concern in the lower Rhône River basin. We measured PCB concentrations in Rhône sediment to evaluate the effects of PCB releases from major urban and industrial areas, sediment redistribution by large floods, and regulatory controls on PCB trends from 1970 to present. Profiles of PCBs (the sum of seven indicator PCB congeners) were reconstructed from sediment cores collected from an off-river rural reference site and from three depositional areas along the Rhône upstream and downstream from the city of Lyon, France. Core chronology was determined from radionuclide profiles and flood deposits. PCB concentrations increased progressively in the downstream direction, and reached a maximum concentration in 1991 of 281 µg/kg at the most downstream site. At the rural reference site and at the upstream Rhône site, PCB concentrations peaked in the 1970s (maximum concentration of 13 and 78 µg/kg, respectively) and have decreased exponentially since then. PCB concentrations in the middle and downstream cores were elevated into the early 1990s, decreased very rapidly until 2000, and since then have remained relatively stable. Congener profiles for three time windows (1965-80, 1986-93, and 2000-08) were similar in the three sediment cores from the Rhône and different from those at the rural reference site. The results indicate that permitted discharges from a hazardous-waste treatment facility upstream from Lyon might have contributed to high concentrations into the 1980-90s, but that industrial discharges from the greater Lyon area and tributaries to the Rhône near Lyon have had a greater contribution since the 1990s. There is little indication that PCB concentration in sediments downstream from Lyon will decrease over at least the short term.

The Alps as barrier to dispersal in cold-adapted freshwater fishes? Phylogeographic history and taxonomic status of the bullhead in the Adriatic freshwater drainage.

The freshwater faunas of the Italian peninsula are isolated from the rest of Europe by the geographic barrier of the Alps and consequently have developed many endemic forms and contain few non-endemic species. However, some 'non-endemics' may either represent recent invaders of the Adriatic basin or cryptic endemic species. To test these two hypotheses against each other, we studied the origin and phylogenetic relationships of bullheads, cold adapted freshwater fishes of the genus Cottus, from both sides of the Alps and Dinaric Mountains. From the Adriatic basin, Cottus ferrugineus () was described as an endemic species, but the present analyses of sequences of the complete mitochondrial control region of 146 individuals from 43 localities showed no major differentiation between bullheads from both sides of the Alps. The very low diversification between representatives across the Alps suggests active transfers of haplotypes across this geographic barrier from the glacial cycles up to recent times. The transfers are most likely based on stream capture, since the cold-adapted bullhead is able to colonise the highest stretches of the water courses. No other freshwater fish in Europe is known to have experienced such an extensive gene flow across the highest European Mountains. In contrast, the Dinaric Mountains seem to have been a much more effective barrier between the Danube and the Adriatics. Our data reject the hypothesis of C. ferrugineus as an endemic species in the whole Adriatic drainage.