An updated tribal classification of Lamiaceae based on plastome phylogenomics

Abstract

Background A robust molecular phylogeny is fundamental for developing a stable classification and providing a solid framework to understand patterns of diversification, historical biogeography, and character evolution. As the sixth largest angiosperm family, Lamiaceae, or the mint family, consitutes a major source of aromatic oil, wood, ornamentals, and culinary and medicinal herbs, making it an exceptionally important group ecologically, ethnobotanically, and floristically. The lack of a reliable phylogenetic framework for this family has thus far hindered broad-scale biogeographic studies and our comprehension of diversification. Although significant progress has been made towards clarifying Lamiaceae relationships during the past three decades, the resolution of a phylogenetic backbone at the tribal level has remained one of the greatest challenges due to limited availability of genetic data. Results We performed phylogenetic analyses of Lamiaceae to infer relationships at the tribal level using 79 protein-coding plastid genes from 175 accessions representing 170 taxa, 79 genera, and all 12 subfamilies. Both maximum likelihood and Bayesian analyses yielded a more robust phylogenetic hypothesis relative to previous studies and supported the monophyly of all 12 subfamilies, and a classification for 22 tribes, three of which are newly recognized in this study. As a consequence, we propose an updated phylogenetically informed tribal classification for Lamiaceae that is supplemented with a detailed summary of taxonomic history, generic and species diversity, morphology, synapomorphies, and distribution for each subfamily and tribe. Conclusions Increased taxon sampling conjoined with phylogenetic analyses based on plastome sequences has provided robust support at both deep and shallow nodes and offers new insights into the phylogenetic relationships among tribes and subfamilies of Lamiaceae. This robust phylogenetic backbone of Lamiaceae will serve as a framework for future studies on mint classification, biogeography, character evolution, and diversification. Graphical abstract

Systematic Placement of the Enigmatic Southeast Asian Genus Paralamium and an Updated Phylogeny of Tribe Pogostemoneae (Lamiaceae Subfamily Lamioideae)

“…In our phylogenetic analyses based on 79 coding plastome sequences (CP79), Lamiaceae are supported as monophyletic (Figure 2; ML-BS = 100%/BI-PP = 1.00; all support values follow this order hereafter) and subfamilial relationships are identical to those recovered by Zhao et al (2021), and 11 tribes were recovered within Lamioideae (Figure 2). In all analyses, the focal species Paralamium griffithii was sister to Craniotome furcata (Link) Kuntze (100%, 1.00) within tribe Pogostemoneae of subfamily Lamioideae.…”

“…1 https://code.google.com/p/ea-utils/ The Initial annotations were implemented in the Plastid Genome Annotator (PGA) (Qu et al, 2019), and the published plastome of Phlomoides betonicoides (Diels) Kamelin & Makhm (MN617020; Zhao et al, 2020b) was set as a reference, then Geneious v.11.0.3 (Kearse et al, 2012), and tRNAscan-SE service (Lowe and Chan, 2016) were used adjusting of the putative starts, stops, intron positions, and tRNA boundaries as described by Zhao et al (2021) and Xiang et al (2020). Finally, the circular physical map of the plastome of Paralamium (Supplementary Figure 1) was drawn by the Organellar Genome DRAW tool (Lohse et al, 2013).…”

“…Lamiaceae, as currently defined, contains about 7000 species and is subdivided into 12 subfamilies (Li et al, 2016;Li and Olmstead, 2017;Zhao et al, 2021). Lamioideae, containing at least 1260 species and about 61 genera, is the second-largest subfamily (after Nepetoideae) within Lamiaceae in terms of both the number of species and genera (Harley et al, 2004).…”

“…During the past two decades, relationships and circumscription of constituent genera of Lamioideae have largely been clarified through both morphological Cantino, 1992, 1994;Cantino, 1992a,b;Cantino et al, 1992;Ryding, 1994aRyding, ,b,c, 1995Ryding, , 1998Ryding, , 2003Ryding, , 2008Salmaki et al, 2008;Xiang et al, 2013a;Seyedi and Salmaki, 2015) and molecular phylogenetic studies at various taxonomic levels (Wink and Kaufmann, 1996;Lindqvist and Albert, 2002;Albert, 2007, 2009;Scheen et al, 2008Scheen et al, , 2010Bendiksby et al, 2011Bendiksby et al, , 2014Salmaki et al, 2012Salmaki et al, , 2013Xiang et al, 2013b;Chen et al, 2014;Roy and Lindqvist, 2015;Li et al, 2016;Yao et al, 2016;Siadati et al, 2018). In particular, the molecular phylogenetics analyses of Scheen et al (2010), Bendiksby et al (2011), and Zhao et al (2021) have dramatically improved our understanding of both tribal classification and character evolution within Lamioideae. Systematic positions of several enigmatic genera which were previously unplaced within Lamioideae have been recently elucidated (Scheen et al, 2010;Bendiksby et al, 2011;Chen et al, 2014;Roy and Lindqvist, 2015;Olmstead, 2016;Zhao et al, 2021), while a few genera, namely the rare and monotypic Paralamium Dunn.…”

“…In particular, the molecular phylogenetics analyses of Scheen et al (2010), Bendiksby et al (2011), and Zhao et al (2021) have dramatically improved our understanding of both tribal classification and character evolution within Lamioideae. Systematic positions of several enigmatic genera which were previously unplaced within Lamioideae have been recently elucidated (Scheen et al, 2010;Bendiksby et al, 2011;Chen et al, 2014;Roy and Lindqvist, 2015;Olmstead, 2016;Zhao et al, 2021), while a few genera, namely the rare and monotypic Paralamium Dunn. and Metastachydium Airy Shaw ex C.Y.…”