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Will the genomics revolution finally solve the Salmo systematics?

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Abstract

On one hand, studies on Salmo biological variations during the last centuries have led to the morphological description of several Salmo species (> 50). On the other hand, Salmo trutta is seen as a polymorphic species, i.e. including populations with different morphotypes and ecotypes, subdivided into nine genetically divergent evolutionary lineages. For 30 years, phylogeographic and phylogenetic investigations tried to solve the Salmo systematic problem using the mitochondrial control region, sometimes combined with other mitochondrial (e.g. protein-coding region or rRNA genes) or nuclear (e.g. allozymes or microsatellites) markers. With the advent of high-throughput next-generation sequencing, complete mitogenomes were made available for Salmo phylogenetic studies. Even better, complete genome or chromosomes with annotations as well as genes of interest can now be loaded from public database. However, in the genomic era, some challenges still need to be addressed such as an appropriate taxon sampling or the identification of orthologous genes before having an accurate phylogeny. In the present review, I examine how traditional molecular markers contributed to our knowledge of trout systematics, and what we can expect from the genomics revolution.

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Data availability

Mitogenome sequences that support the findings of this study are openly available in GenBank at https://www.ncbi.nlm.nih.gov/genbank/ under the accession numbers MW632104 to MW632113.

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Acknowledgements

The present review is a follow-up to a presentation done as invited speaker at the “Associazione Italiana Ittilogi Acque Dolci” thematic congress that took place in Cagliari (Sardinia, Italy) in September 2019. For this reason, I would like to thanks the organizers, Andrea Sabatini and Francesco Palmas (Università degli Studi di Cagliari, Sardinia, Italy) for their kind invitation and their warm welcome. I am also grateful to Bruno Guinand (Institut des Sciences de l’Evolution de Montpellier, France) who encouraged me to write this review. Thanks are also expressed to Andrea Splendiani and Vicenzo Caputo Barucchi (Università Politecnica delle Marche, Ancona, Italy), Aleš Snoj (University of Ljubljana, Slovenia) and Jose-Luis García-Marín (Universitat de Girona, Spain) who provided some trout tissue samples. I also warmly thank Andrea Splendiani and two anonymous reviewers for their helpful comments on the manuscript.

Funding

The French Government (CNRS) supported this study. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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    Christelle Tougard

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New DNA sequences were obtained from DNA stored at – 20 °C or fin clips stored in ethanol 96% and collected in the frame of previous studies. Therefore, no specific permissions were required for locations and activities involved in this study.

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Table S1

Detailed list of references taken into account for Figs. 1 and 2. (XLS 82 KB)

Table S2

Relationships between evolutionary lineages and morphospecies based on genetic studies. (XLS 29 KB)

Table S3

Details on models of sequence evolution and sampling (accession number, locality and reference) used for phylogenetic reconstruction with PhyML v3 (Guindon et al., 2010). (XLSX 47 KB)

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Tougard, C. Will the genomics revolution finally solve the Salmo systematics?. Hydrobiologia 849, 2209–2224 (2022). https://doi.org/10.1007/s10750-022-04872-2

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