Frontiers in Marine Science (Oct 2015)
Inferring phylogenetic structure and ancient hybridization within Salmonidae using next-generation sequencing
Abstract
Phylogenetic studies focusing on Salmonidae have thus far revealed significant drawbacks to elucidate some of the interspecific relationships within the family, due to limited number of markers, conflicting phylogenetic signals and hybridization events. In an attempt to resolve these issues, we applied restriction-site associated DNA sequencing (RAD-seq) to 44 samples, including 23 different species across the family Salmonidae, with an emphasis on the genus Salvelinus. The aim of our study is to infer reliable interspecific phylogenetic relationships, evaluate several putative scenarios of ancient hybridization and detect possible reticulate patterns of evolution among salmonid fishes. RAD-seq can be particularly useful for systematic studies of closely related taxa, as it provides genome-wide informative characters and allows the detection of introgression. To our knowledge, this is the first next generation sequencing effort applied to salmonid phylogeny and related questions of their evolutionary history. Using the software pipeline pyRAD, we identified 28,402 orthologous loci, which were subsequently used in our downstream analyses. Phylogenetic inferences drawn from a maximum likelihood analysis reveal some interesting results. Salvelinus and Oncorhynchus appear as sister lineages, which contradicts some of the previous phylogenetic analyses. Additionally, despite constituting a separate genus, Salvethymus clusters within the genus Salvelinus, which is consistent with the findings of previous studies and therefore questions its taxonomic status. A monophylum of Salvelinus leucomaenis and Salvelinus levanidovi is the sister group to the remainder of the genus Salvelinus. The genus Parahucho appears as the sister clade to Salmo, which also contradicts some previously published inferences. Finally, we present a practical application of a relatively novel approach to test for putative ancient hybridization events. Since this is the first Salmonidae phylogeny based on RAD-seq data, our findings represent a valuable contribution to the systematics of this important family of freshwater fishes. Our results provide a better understanding of the mechanisms of speciation and ecological adaptation of Salmonidae, as well as the effect of hybridization on speciation, within an evolutionary framework.
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