Inferring phylogenetic structure, hybridization and divergence times within Salmoninae (Teleostei: Salmonidae) using RAD-sequencing

Molecular Phylogenetics and Evolution
Laurène A LecaudeySteven J Weiss

Abstract

Phylogenetic studies focusing on Salmonidae have revealed significant obstacles in trying to clarify some interspecific relationships within the Salmoninae subfamily, due to a limited number of markers typed, conflicting phylogenetic signals and ancient hybridization events. To infer reliable phylogenetic relationships, evaluate several putative scenarios of ancient hybridization, and estimate divergence times within Salmoninae, we applied restriction-site associated DNA sequencing (RAD-seq) to 43 samples, including 26 genetic lineages across 21 species, largely representing the subfamily, with an emphasis on the genus Salvelinus. We identified 28,402 loci and 28,363 putatively unlinked SNPs, which were used in downstream analyses. Using an iterative k-means partitioned dataset and a Maximum Likelihood approach; we generated a well-supported phylogeny, providing clear answers to several previous phylogenetic uncertainties. We detected several significant introgression signals, presumably ancient, in the genus Salvelinus. The most recent common ancestor of Salmonidae dates back to approximately 58.9MY ago (50.8-64 MY) and the crown age of Salmoninae was estimated to be 37.7 MY (35.2-40.8 MY) using a Bayesian molecular dating ana...Continue Reading

Citations

Aug 29, 2019·Anais Da Academia Brasileira De Ciências·Camilla S LimaFabrício R Santos
Jan 24, 2021·Journal of Fish Biology·Bruno GuinandChristelle Tougard
Jun 3, 2021·Animals : an Open Access Journal From MDPI·Yuri Phedorovich Kartavtsev
May 21, 2021·Molecular Phylogenetics and Evolution·Iraj Hashemzadeh SegherlooLouis Bernatchez
Jul 17, 2021·Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology·Heather IkertPaul M Craig
Oct 27, 2021·Cladistics : the International Journal of the Willi Hennig Society·David OrtizMalahat Dianat

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