Revisiting the mitogenomic phylogeny of Salmoninae: new insights thanks to recent sequencing advances.

Jose L Horreo

doi:10.7717/peerj.3828

Abstract

The phylogeny of the Salmonidae family, the only living one of the Order Salmoniformes, remains still unclear because of several reasons. Such reasons include insufficient taxon sampling and/or DNA information. The use of complete mitochondrial genomes (mitogenomics) could provide some light on it, but despite the high number of mitogenomes of species belonging to this family published during last years, an integrative work containing all this information has not been done. In this work, the phylogeny of 46 Salmonidae species was inferred from their mitogenomic sequences. Results include a Bayesian molecular-dated phylogenetic tree with very high statistical support showing Coregoninae and Salmoninae as sister subfamilies, as well as several new phylogenetic relationships among species and genus of the family. All these findings contribute to improve our understanding of the Salmonidae systematics and could have consequences on related evolutionary studies, as well as highlight the importance of revisiting phylogenies with integrative studies.

Highlights

The Salmonidae family is the only living one of the Order Salmoniformes, and it comprises three different subfamilies: Salmoninae, Coregoninae and Thymallinae
The here presented topology resolved with mitogenomic sequences Coregoninae and Salmoninae as sister subfamilies with a common ancestor 47.1 million years (Mya) ago, as some authors have previously proposed with nuclear genes (Near et al, 2012), as well as combining DNA and morphological data (Alexandrou et al, 2013)
This study, the only done with the mitogenome of 46 different salmonid species, supports Coregoninae and Salmoninae as the sister groups within the Salmonidae family, and provides new insights into the phylogenetic relationships among genus and species of this family, including node molecular molecular node dating (Table 2)

Summary

Introduction

The Salmonidae family is the only living one of the Order Salmoniformes, and it comprises three different subfamilies: Salmoninae, Coregoninae and Thymallinae. It is known that the use of only one or few representative genes can be useful for inferring true phylogenies (Horreo, 2012), but in this family it has not been enough probably due to processes such as genome duplication (e.g., Alexandrou et al, 2013; Macqueen & Johnston, 2014) In this sense mitogenomics, or the study of complete mitochondrial genomes, has been proposed some years ago as an useful tool for phylogenetic inferences in almost all kind of organisms, including mammals (Arnason et al, 2002), birds (Pacheco et al, 2011), insects (Wei et al, 2010), cnidarians (Kayal et al, 2013), and others. The Salmonidae family do not have, to date, an integrative analysis including all the new mitogenomes published last years in order to clarify the phylogenetic relationships among all their species as well as among their genus; this was precisely the aim of this work

Methods

Results

Conclusion