Abstract
The evolutionary relationships of Salvia have been difficult to estimate. In this study, we used the Next Generation Sequencing method Hyb-Seq to evaluate relationships among 90 Lamiaceae samples, including representatives of Mentheae, Ocimeae, Salvia subgenera Audibertia, Leonia, Salvia, and 69 species of subgenus Calosphace, representing 32 of Epling's sections. A bait set was designed in MarkerMiner using available transcriptome data to enrich 119 variable nuclear loci. Nuclear and chloroplast loci were assembled with hybphylomaker (HPM), followed by coalescent approach analyses for nuclear data (ASTRAL, BEAST) and a concatenated Maximum Likelihood analysis of chloroplast loci. The HPM assembly had an average of 1,314,368 mapped reads for the sample and 527 putative exons. Phylogenetic inferences resolved strongly supported relationships for the deep-level nodes, agreeing with previous hypotheses which assumed that subgenus Audibertia is sister to subgenus Calosphace. Within subgenus Calosphace, we recovered eight monophyletic sections sensu Epling, Cardinalis, Hastatae, Incarnatae, and Uricae in all the analyses (nDNA and cpDNA), Biflorae, Lavanduloideae, and Sigmoideae in nuclear analyses (ASTRAL, BEAST) and Curtiflorae in ASTRAL trees. Network analysis supports deep node relationships, some of the main clades, and recovers reticulation within the core Calosphace. The chloroplast phylogeny resolved deep nodes and four monophyletic Calosphace sections. Placement of S. axillaris is distinct in nuclear evidence and chloroplast, as sister to the rest of the S. subg. Calosphace in chloroplast and a clade with “Hastatae clade” sister to the rest of the subgenus in nuclear evidence. We also tested the monophyly of S. hispanica, S. polystachia, S. purpurea, and S. tiliifolia, including two samples of each, and found that S. hispanica and S. purpurea are monophyletic. Our baits can be used in future studies of Lamiaceae phylogeny to estimate relationships between genera and among species. In this study, we presented a Hyb-Seq phylogeny for complex, recently diverged Salvia, which could be implemented in other Lamiaceae.
Highlights
IntroductionPhylogenetic relationships for many plant groups have been studied through the last 30–40 years at deep (APG, 1998; Zeng et al, 2017; Breinholt et al, 2021) and shallow phylogenetic levels (Wells et al, 2020), mostly through Sanger sequencing (Sanger et al, 1977) and recently through Generation Sequencing (Wanke et al, 2017; Carlsen et al, 2018; HerrandoMoraira and The Cardueae Radiations Group, 2018; Villaverde et al, 2018; Carter et al, 2019; Johnson et al, 2019)
10 species were sampled from tribe Mentheae [Agastache pallidiflora subsp. neomexicana (Briq.) Lint and Epling, Dracocephalum parviflorum Nutt., Hedeoma drummondii Benth., Lepechinia hastata
Fewer base pairs were recovered for the outgroup than the ingroup and the highest recovery was in S. officinalis, one of the transcriptomes used to design the Salvia baits
Summary
Phylogenetic relationships for many plant groups have been studied through the last 30–40 years at deep (APG, 1998; Zeng et al, 2017; Breinholt et al, 2021) and shallow phylogenetic levels (Wells et al, 2020), mostly through Sanger sequencing (Sanger et al, 1977) and recently through Generation Sequencing (Wanke et al, 2017; Carlsen et al, 2018; HerrandoMoraira and The Cardueae Radiations Group, 2018; Villaverde et al, 2018; Carter et al, 2019; Johnson et al, 2019). 1,000 species (Harley et al, 2004; Drew et al, 2017), are among the largest angiosperm genera (Frodin, 2004). They are widely distributed with many economically important species (Wu et al, 2012; Lopresti, 2017). Previous Salvia phylogenies that employed few, e.g.,
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