Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes

Abstract

Next-generation sequencing technologies have facilitated new phylogenomic approaches to help clarify previously intractable relationships while simultaneously highlighting the pervasive nature of incongruence within and among genomes that can complicate definitive taxonomic conclusions. Salvia L., with ∼1,000 species, makes up nearly 15% of the species diversity in the mint family and has attracted great interest from biologists across subdisciplines. Despite the great progress that has been achieved in discerning the placement of Salvia within Lamiaceae and in clarifying its infrageneric relationships through plastid, nuclear ribosomal, and nuclear single-copy genes, the incomplete resolution has left open major questions regarding the phylogenetic relationships among and within the subgenera, as well as to what extent the infrageneric relationships differ across genomes. We expanded a previously published anchored hybrid enrichment dataset of 35 exemplars of Salvia to 179 terminals. We also reconstructed nearly complete plastomes for these samples from off-target reads. We used these data to examine the concordance and discordance among the nuclear loci and between the nuclear and plastid genomes in detail, elucidating both broad-scale and species-level relationships within Salvia. We found that despite the widespread gene tree discordance, nuclear phylogenies reconstructed using concatenated, coalescent, and network-based approaches recover a common backbone topology. Moreover, all subgenera, except for Audibertia, are strongly supported as monophyletic in all analyses. The plastome genealogy is largely resolved and is congruent with the nuclear backbone. However, multiple analyses suggest that incomplete lineage sorting does not fully explain the gene tree discordance. Instead, horizontal gene flow has been important in both the deep and more recent history of Salvia. Our results provide a robust species tree of Salvia across phylogenetic scales and genomes. Future comparative analyses in the genus will need to account for the impacts of hybridization/introgression and incomplete lineage sorting in topology and divergence time estimation.

Hiding in plain sight: Integrative analyses uncover a cryptic Salvia species in Europe

“…sect. Plethiosphace , and their close phylogenetic proximity is supported by molecular evidence (Will & Claßen‐Bockhoff, 2017; Kriebel & al., 2019; Rose & al., 2021). From each population, one or two individuals were sampled in the field by collecting leaf material into silica‐gel.…”

“…During the last two decades, several studies demonstrated the paraphyly of this large genus (Walker & al., 2004; Walker & Sytsma, 2007; Will & Claßen‐Bockhoff, 2014, 2017; Kriebel & al., 2020, 2021; Rose & al., 2021), and that the staminal lever evolved independently three (Walker & Sytsma, 2007; Drew & Sytsma, 2012) or five times (Will & Claßen‐Bockhoff, 2017), each time resulting in convergent morphology and function. As a direct consequence of these studies, there is an ongoing debate regarding the exact circumscription of the genus with two major taxonomic treatments proposed, both based on previous studies with extensive molecular and morphological analyses and sampling a large number of taxa: maintaining Salvia with the inclusion of additional 15 species belonging to Dorystaechas Boiss.…”

“…Salvia phylogenetics mostly relied on classical phylogenetic methods (i.e., Sanger‐sequencing of candidate‐genes from the plastid and nuclear genomes) that provided substantial phylogenetic resolution between main lineages within the genus, but often failed to effectively separate closely related species (Walker & Sytsma, 2007; Takano & Okada, 2011; Jenks & al., 2013; Li & al., 2013; Walker & al., 2015; Will & Claßen‐Bockhoff, 2017; Hu & al., 2018). Genomic approaches usually provide better resolution in the latter case (Rannala & Yang, 2008; Lemmon & Lemmon, 2013; McCormack & al., 2013), as was demonstrated in the genus Salvia as well (Kriebel & al., 2019; Rose & al., 2021). Using different genomic approaches, Rose & al.…”

“…Using different genomic approaches, Rose & al. (2021) generated congruent topologies from nuclear and plastome datasets, but they concluded that there is widespread discordance among individual gene trees possibly arising from incomplete lineage sorting and horizontal gene flow. Reduced representation genomic library (RRL) methods are cost and labor efficient approaches in generating high‐resolution genomic data of non‐model organisms (Davey & al., 2011), which typically provide thousands of single nucleotide polymorphisms (SNPs) for phylogenomic inference (Leaché & Oaks, 2017).…”

“…Genomic approaches usually provide better resolution in the latter case (Rannala & Yang, 2008;Lemmon & Lemmon, 2013;McCormack & al., 2013), as was demonstrated in the genus Salvia as well (Kriebel & al., 2019;Rose & al., 2021). Using different genomic approaches, Rose & al. (2021) generated congruent topologies from nuclear and plastome datasets, but they concluded that there is widespread discordance among individual gene trees possibly arising from incomplete lineage sorting and horizontal gene flow.…”