Genomic revolution and its impact on salmo taxonomy and conservation

Christelle Tougard1 and Bruno Guinand1

1 - ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier France

Christelle Tougard

Resolving the taxonomy of the genus Salmo is one old issue in fish molecular phylogenetics. Indeed, the predominant use of morphological characters in a group in which species themselves are often fragmented populations characterized by complex life history, ecotypic and phenotypic patterns initiated a confusing and puzzling taxonomy that still hampered (i) the understanding of the Salmo evolutionary history and (ii) the development of appropriate strategies to protect natural trout diversity. Apart of few species such the Atlantic salmon (S. salar), numerous taxonomic uncertainties remain within the S. trutta species complex that might be putatively considered – depending on authors – as a single polytypic species with a huge intraspecific diversity or as distinct and sometimes endemic Salmo species (N ≥ 50). Despite the emergence of next generation sequencing technologies that could make available several thousand of nuclear loci and the access to sequenced genomes that revolutionized population genetics, phylogeographic and phylogenetic studies, our knowledge on the taxonomy of genus Salmo has not progressed that much. We hereby review the current limits about the phylogeny and the taxonomy of this genus. It effectively remains challenged by intrinsic sequencing issues (e.g. signature of whole-genome duplication) that may obscure the phylogenetic signal, and also genomic and/or associated bioinformatic costs that are still high for some researchers. However, area-restricted and/or low taxon sampling of both museum-preserved and extant taxa in published studies also do not favour the emergence of clear phylogeographic/phylogenetic patterns and strongly limit the investigation of its evolutionary history and taxonomic revision.

Keywords: genetic diversity, next generation sequencing technologies, Salmo trutta species complex, strengths and limits