Two new species of atlantic trout (Actinopterygii, Salmonidae) from Morocco

Genetic structure of Ponto-Caspian trout populations shows gene flow among river drainages and supports resident Salmo rizeensis as a genetically distinct taxon

To assess the genetic structure of Ponto-Caspian brown trout (Salmo trutta complex) populations, we analyzed both mitochondrial DNA sequences and genotypes at 10 microsatellite loci of fish caught in the Black Sea and from nine river catchments in Georgia, flowing into either the Black or Caspian seas. The results show that: (1) there is substantial genetic differentiation among Ponto-Caspian trout populations, both among the populations of different nominal species and within those of the same species; (2) the genetic distance between conspecific populations from the Black and Caspian Sea basins exceeds that among the populations within the same basin. Moreover, within drainages, genetic distance correlates with the geographic distance; (3) the Black Sea itself is not a barrier to gene flow among the watersheds draining into the Black Sea; (4) some populations in the headwaters of the rivers draining into the Black Sea Basin fall out of this pattern and likely form a separate, non-anadromous (resident) taxon, previously described from northeastern Turkey as Salmo rizeensis. This hypothesis is supported by mitochondrial DNA phylogeny. The presence of both anadromous and resident populations in a single river basin calls for a substantial re-thinking of speciation patterns and taxonomy of Eurasian brown trout.

A genomic perspective on an old question: Salmo trouts or Salmo trutta (Teleostei: Salmonidae)?

There are particular challenges in defining the taxonomic status of recently radiated groups due to the low level of phylogenetic signal. Members of the Salmo trutta species-complex, which mostly evolved during and following the Pleistocene, show high morphological and ecological diversity that, along with their very wide geographic distribution, have led to morphological description of 47 extant nominal species. However, many of these species have not been supported by previous phylogenetic studies, which could be partly due to lack of significant genetic differences among them, the limited resolution offered by molecular methods previously used, as well as the often local scale of these studies. The development of next-generation sequencing (NGS) and related analytical tools have enhanced our ability to address such challenging questions. In this study, Genotyping-by-Sequencing (GBS) of 15,169 filtered SNPs and mitochondrial DNA (mtDNA) D-loop sequences were combined to assess the phylogenetic relationships among 166 brown trouts representing 21 described species and three undescribed groups collected from 84 localities throughout their natural distribution in Europe, west Asia, and North Africa. The data were analysed using different clustering algorithms (admixture analysis and discriminant analysis of principal components-DAPC), a Bayes Factor Delimitation (BFD) test, species tree reconstruction, gene flow tests (three- and four-population tests), and Rogue taxa identification tests. Genomic contributions of the Atlantic lineage brown trout were found in all major sea basins excluding the North African and Aral Sea basins, suggesting introgressive hybridization of native brown trouts driven by stocking using strains of the Atlantic lineage. After removing the phylogenetic noise caused by the Atlantic brown trout, admixture clusters and DAPC clustering based on GBS data, respectively, resolved 11 and 13 clusters among the previously described brown trout species, which were also supported by BFD test results. Our results suggest that natural hybridization between different brown trout lineages has probably played an important role in the origin of several of the putative species, including S. marmoratus, S. carpio, S. farioides, S. pellegrini, S. caspius (in the Kura River drainage) and Salmo sp. in the Danube River basin. Overall, our results support a multi-species taxonomy for brown trouts. They also resolve some species in the Adriatic-Mediterranean and Black Sea drainages as members of very closely related genomic clusters that may need taxonomic revision. However, any final conclusions pertaining to the taxonomy of the brown trout complex should be based on an integrative approach combining genomic, morphological, and ecological data. To avoid challenges in taxonomy and conservation of species complexes like brown trouts, it is suggested to describe species based on genomic clusters of populations instead of describing species based only on morphologically differentiated single type populations.

Present and Future Salmonid Cytogenetics

Salmonids are extremely important economically and scientifically; therefore, dynamic developments in their research have occurred and will continue occurring in the future. At the same time, their complex phylogeny and taxonomy are challenging for traditional approaches in research. Here, we first provide discoveries regarding the hitherto completely unknown cytogenetic characteristics of the Anatolian endemic flathead trout, Salmo platycephalus, and summarize the presently known, albeit highly complicated, situation in the genus Salmo. Secondly, by outlining future directions of salmonid cytogenomics, we have produced a prototypical virtual karyotype of Salmo trutta, the closest relative of S. platycephalus. This production is now possible thanks to the high-quality genome assembled to the chromosome level in S. trutta via soft-masking, including a direct labelling of repetitive sequences along the chromosome sequence. Repetitive sequences were crucial for traditional fish cytogenetics and hence should also be utilized in fish cytogenomics. As such virtual karyotypes become increasingly available in the very near future, it is necessary to integrate both present and future approaches to maximize their respective benefits. Finally, we show how the presumably repetitive sequences in salmonids can change the understanding of the overall relationship between genome size and G+C content, creating another outstanding question in salmonid cytogenomics waiting to be resolved.

Salmo macrostigma (Teleostei, Salmonidae): Nothing more than a brown trout (S. trutta) lineage?

We examined specimens of the macrostigma trout Salmo macrostigma, which refers to big black spots on the flanks, to assess whether it is an example of taxonomic inflation within the brown trout Salmo trutta complex. Using new specimens, publicly available data and a mitogenomic protocol to amplify the control and cytochrome b regions of the mitochondrial genome from degraded museum samples, including one syntype specimen, the present study shows that the macrostigma trout is not a valid species. Our results suggest the occurrence of a distinct evolutionary lineage of S. trutta in North Africa and Sicily. The name of the North African lineage is proposed for this lineage, which was found to be sister to the Atlantic lineage of brown trout, S. trutta.

Nowhere to swim to: climate change and conservation of the relict Dades trout Salmo multipunctata in the High Atlas Mountains, Morocco

Montane biota is vulnerable to climate change, especially in the case of relict species in environmentally extreme areas. The Dades trout Salmo multipunctata is a relict species from the Draa basin, on the southern slopes of the High Atlas Mountains, Morocco. Apart from its genetic and morphological singularity almost nothing is known about this species. We surveyed the whole potential distribution range of the Dades trout and found that only two isolated populations exist (in the Dades and M'Goun catchments), occupying an extremely small range, < 22 km of stream reaches in a narrow altitudinal range (c. 2,150–2,375 m). The species was found more frequently and more abundantly at intermediate elevations within its range, and somatic condition increased with altitude. Climatically suitable areas for the Dades trout will be confined to mountain summits without permanent water bodies by 2070. The Dades trout is a Critically Endangered species in need of active management for its persistence. We propose actions for the long-term conservation of the species, including catchment-scale erosion control, riverbed restoration, local-scale measures to mitigate global warming, and an ex situ breeding programme.