Bioinformatic evaluation of Hyb-Seq data for three species of Salvia subgenus Calosphace (Lamiaceae)

Abstract

Salvia subgenus Calosphace is the most diverse of the five subgenera. Of wide distribution in America, being Mexico and Central America the most diverse areas. Phylogenetic studies utilizing Sanger sequencing for both nuclear and chloroplast markers, have solved the deep relationships but shallow relationships generally remain unsolved with politomies. Recent technological and bioinformatic advances resulted in Next Generation Sequencing (NGS) which when applied to phylogenetic inferences result in robust hypotheses at shallow levels. Here we evaluate 30 species in Calosphace through next gen Hyb-Seq to assess monophyly of three species' with two samples each from distinct provenances and define their phylogenetic position. 98 nuclear genes were amplified, mapping, alignment and gene filtering were performed in HybPhyloMaker pipeline. Gene trees and species trees were built in FastTree y ASTRAL respectively. Five main clades are resolved, two of which agree to sections sensu Epling. Salvia hispanica y S. purpurea are both monophyletic species with high local posterior probability, however S. polystachia is not. Additionally, two MAUVE analyses were performed, few rearrangements are shown between S. hispanica and S. purpurea paired samples, non the less important rearrangements are shown for S. polystachia. Hyb-seq data aid in solving phylogenetic relationships at shallow level in Salvia phylogeny, and allows us to identify species which need to be subjected to additional and more thorough analyses to better clarify species relationships.