Genetic and molecular evidence that brown trout Salmo trutta belonging to the Danubian lineage are a single biological species

Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics

The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic salmon (Salmo salar L.), was not without reason one of the first fish species for which a high-quality reference genome assembly was produced and published. Genomic advancements are becoming increasingly essential in both the genetic enhancement of farmed salmon and the conservation of wild salmon stocks. The salmon genome has also played a significant role in influencing our comprehension of the evolutionary and functional ramifications of the ancestral whole-genome duplication event shared by all Salmonidae species. Here we provide an overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species, focusing on those studies that aim to advance our understanding of salmonid ecology, physiology, and evolution, particularly for the purpose of improving aquaculture production. This review should make potential researchers pay attention to the current state of research on the salmonid genome, which should potentially attract interest in this important problem, and hence the application of new technologies (such as genome editing) in uncovering the genetic and evolutionary features of salmoniforms that underlie functional variation in traits of commercial and scientific importance.

Changing climate may mitigate the invasiveness risk of non-native salmonids in the Danube and Adriatic basins of the Balkan Peninsula (south-eastern Europe)

Salmonids are an extensively hatchery-reared group of fishes that have been introduced worldwide mainly for their high commercial and recreational value. The Balkan Peninsula (south-eastern Europe) is characterised by an outstanding salmonid diversity that has become threatened by the introduction of non-native salmonids whose potential risk of invasiveness in the region remains unknown and especially so under predicted climate change conditions. In this study, 13 extant and four horizon non-native salmonid species were screened for their risk of invasiveness in the Danube and Adriatic basins of four Balkan countries. Overall, six (35%) of the screened species were ranked as carrying a high risk of invasiveness under current climate conditions, whereas under predicted conditions of global warming, this number decreased to three (17%). Under current climate conditions, the very high risk (‘top invasive’) species were rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta (sensu stricto), whereas under predicted climate change, this was true only of O. mykiss. A high risk was also attributed to horizon vendace Coregonus albula and lake charr Salvelinus namaycush, and to extant Atlantic salmon Salmo salar and brook trout Salvelinus fontinalis, whose risk of invasiveness, except for S. fontinalis, decreased to medium. For the other eleven medium-risk species, the risk score decreased under predicted climate change, but still remained medium. The outcomes of this study reveal that global warming will influence salmonids and that only species with wider temperature tolerance, such as O. mykiss will likely prevail. It is anticipated that the present results may contribute to the implementation of appropriate management plans to prevent the introduction and translocation of non-native salmonids across the Balkan Peninsula. Additionally, adequate measures should be developed for aquaculture facilities to prevent escapees of non-native salmonids with a high risk of invasiveness, especially into recipient areas of high conservation value.

Mapping the Establishment and Invasiveness Potential of Rainbow Trout (Oncorhynchus mykiss) in Turkey: With Special Emphasis on the Conservation of Native Salmonids

Rainbow trout (Oncorhynchus mykiss) has become by far the most frequently farmed freshwater fish species in Turkey, whereas very little is known about its establishment and invasiveness potential. We explored this potential through a combination of Maxent habitat suitability model and the Aquatic Species Invasiveness Screening Kit (AS-ISK) on the river basin scale by generating an overall risk score (ORS). The outcome of this approach was also incorporated with the spatial analysis of native salmonid species by generating a relative vulnerability score (RVS) to prioritize susceptibility of native species (or populations) and to propose risk hotspots by identifying their potential geographic overlap and interaction with O. mykiss. Results suggest that the northern basins (Eastern Black Sea, Western Black Sea and Marmara basins) are the most suitable basins for O. mykiss. According to the Basic Risk Assessment (BRA) threshold scores, O. mykiss is classified as “high risk” for 3 (12.0%) of the 25 river basins screened (Western Black Sea, Eastern Black Sea and Maritza-Ergene), and as “medium risk” for the remaining basins. The climate change assessment (CCA) scores negatively contributed the overall invasiveness potential of O. mykiss in 22 (88.0%) of the river basins and resulted in zero contribution for the remaining three, namely Aras-Kura, Çoruh river and Eastern Black Sea. The ORS score of river basins was lowest for Orontes and highest for Western Black Sea, whereas it was lowest for Konya-closed basin and highest for Eastern Black Sea, when CCA was associated. The micro-basins occupied by Salmo rizeensis had the highest mean habitat suitability with O. mykiss. Among the all species, S. abanticus had the highest RVS, followed by S. munzuricus and S. euphrataeus. The overall outcome of the present study also suggests that the establishment and invasiveness potential of O. mykiss may decrease under future (climate warmer) in Turkey, except for the northeast region. This study can provide environmental managers and policy makers an insight into using multiple tools for decision-making. The proposed RVS can also be considered as a complementary tool to improve IUCN red list assessment protocols of species.

Population genetic structure of turbot (Scophthalmus maximus L., 1758) in the Black Sea

Turbot, Scophthalmus maximus, is a commercially important demersal flatfish species distributed throughout the Black Sea. Several studies performed locally with a limited number of specimens using both mitochondrial DNA (mtDNA) and microsatellite markers evidenced notable genetic variation among populations. However, comprehensive population genetic studies are required to help management of the species in the Black Sea. In the present study eight microsatellite loci were used to resolve the population structure of 414 turbot samples collected from 12 sites across the Black Sea. Moreover, two mtDNA genes, COI and Cyt-b, were used for taxonomic identification. Microsatellite markers of Smax-04 and B12-I GT14 were excluded from analysis due to scoring issues. Data analysis was performed with the remaining six loci. Loci were highly polymorphic (average of 17.8 alleles per locus), indicating high genetic variability. Locus 3/20CA17, with high null allele frequency (>30%), significantly deviated from HW equilibrium. Pairwise comparison of the F_ST index showed significant differences between most of the surveyed sampling sites (P < 0.01). Cluster analysis evidenced the presence of three genetic groups among sampling sites. Significant genetic differentiation between Northern (Sea of Azov and Crimea) and Southern (Turkish Black Sea Coast) Black Sea sampling sites were detected. The Mantel test supported an isolation by distance model of population structure. These findings are vital for long-term sustainable management of the species and development of conservation programs. Moreover, generated mtDNA sequences would be useful for the establishment of a database for S. maximus.

Comparative susceptibilities and immune-related gene expressions of brown trout strains and their hybrids infected with Lactococcus garvieae and Yersinia ruckeri

Brown trout are polymorphic salmonid species, and it is of importance to investigate whether hybridization affects disease resistance. In this study, susceptibility of brown trout (Salmo trutta Abant, Anatolian, Black Sea, and Caspius) strains and their hybrids to Lactococcus garvieae and Yersinia ruckeri as well as their immune-related gene expression profiles were studied. Results indicated that reciprocal hybridization did not affect disease resistance in brown trout strains. Purebred Black Sea strain of brown trout was the most resistant group against Y. ruckeri, followed by other Black Sea strain hybrids. On the other hand, purebred Anatolian strain was the most resistant group to L. garvieae, followed by other Anatolian strain hybrids. Expression pattern of target genes differed in families, but the overall gene expression was comparatively high in Y. ruckeri infected families. Upregulations were mainly significant at 7 and 28 d post infection while marginal regulations were observed 8 h after infection. Disease resistance status of strains was supported by high expression of immune-related genes such as major histocompatibility complex class I (MHC-I), immunoglobulin light chain (IgL), and antioxidant- and hemoglobin-related gene expression. Therefore, our findings suggest that Black Sea and Anatolian strains could be used to develop fish stock that are resistant for yersiniosis and lactocaccosis, respectively.