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. 2016 Oct 17:6:34343.
doi: 10.1038/srep34343.

A large-scale chloroplast phylogeny of the Lamiaceae sheds new light on its subfamilial classification

Bo Li  1 , Philip D Cantino  2 , Richard G Olmstead  3 , Gemma L C Bramley  4 , Chun-Lei Xiang  5 , Zhong-Hui Ma  6 , Yun-Hong Tan  7 , Dian-Xiang Zhang  8
Affiliations

A large-scale chloroplast phylogeny of the Lamiaceae sheds new light on its subfamilial classification

Bo Li et al. Sci Rep. .

Abstract

Lamiaceae, the sixth largest angiosperm family, contains more than 7000 species distributed all over the world. However, although considerable progress has been made in the last two decades, its phylogenetic backbone has never been well resolved. In the present study, a large-scale phylogenetic reconstruction of Lamiaceae using chloroplast sequences was carried out with the most comprehensive sampling of the family to date (288 species in 191 genera, representing approximately 78% of the genera of Lamiaceae). Twelve strongly supported primary clades were inferred, which form the phylogenetic backbone of Lamiaceae. Six of the primary clades correspond to the current recognized subfamilies Ajugoideae, Lamioideae, Nepetoideae, Prostantheroideae, Scutellarioideae, and Symphorematoideae, and one corresponds to a portion of Viticoideae. The other five clades comprise: 1) Acrymia and Cymaria; 2) Hymenopyramis, Petraeovitex, Peronema, and Garrettia; 3) Premna, Gmelina, and Cornutia; 4) Callicarpa; and 5) Tectona. Based on these results, three new subfamilies-Cymarioideae, Peronematoideae, and Premnoideae-are described, and the compositions of other subfamilies are updated based on new findings from the last decade. Furthermore, our analyses revealed five strongly supported, more inclusive clades that contain subfamilies, and we give them phylogenetically defined, unranked names: Cymalamiina, Scutelamiina, Perolamiina, Viticisymphorina, and Calliprostantherina.

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Figures

Figure 1
Figure 1. Phylogenetic backbone of Lamiaceae based on simplification of trees generated from the analyses of the combined cpDNA (matK + ndhF + rbcL + rps16 + trnL-F) dataset D270.
Color-coded circles above branches indicate support values from BI, ML and MP analyses of the combined dataset D270, with or without gaps coded respectively, while those below branches indicate support values from BI, ML and MP analyses of the combined dataset D155, with or without gaps coded respectively. Subfamilies recognized by Olmstead (Ajugoideae, Lamioideae, Nepetoideae, Prostantheroideae, Scutellarioideae, Symphorematoideae, and Viticoideae s. str.) are shown in black bold font, while new subfamilies (Cymarioideae, Peronematoideae and Premnoideae) and two genera (Callicarpa and Tectona) that we do not assign to a subfamily are in red bold font. The arrows show the clade node of Lamiaceae and the nodes of five new clades (Cymalamiina, Scutelamiina, Perolamiina, Viticisymphorina, and Calliprostantherina).
Figure 2
Figure 2
Bayesian 50% majority-rule consensus tree (box on the top left corner shows the topology) based on the combined cpDNA (matK + ndhF + rbcL + rps16 + trnL-F) dataset D270, with gaps treated as simple indels, showing the taxa from Lamioideae, Cymarioideae, Scutellarioideae, Peronematoideae, Premnoideae, Ajugoideae, and Tectona. The topologies of the ML and MP trees are congruent with the BI tree. Bayesian posterior probability values ≥ 0.90 are marked with bold lines. Bootstrap values ≥ 50% in ML and MP analyses are plotted above the branches, successively, while “-” indicates support values of less than 50%. Multiple accessions of the same species are numbered according to Supplementary Table S1. A single generic name indicates that the combined sequences pooled from different species of the genus. Subfamilies and tribes recognized by Olmstead were covered by gray boxes with different grey level, while new subfamilies and clades proposed in this study were covered by pink boxes and marked in red bold font.
Figure 3
Figure 3
Bayesian 50% majority-rule consensus tree (box on the top left corner shows the topology) based on the combined cpDNA (matK + ndhF + rbcL + rps16 + trnL-F) dataset D270, with gaps treated as simple indels, showing the taxa from Nepetoideae, Viticoideae s. str., Symphoremoideae, Callicarpa, and Prostantheroideae. The topologies of the ML and MP trees are congruent with the BI tree. Bayesian posterior probability values ≥ 0.90 are marked with bold lines. Bootstrap values ≥ 50% in ML and MP analyses are plotted above the branches, successively, while “-” indicates support values of less than 50%. Multiple accessions of the same species are numbered according to Supplementary Table S1. A single generic name indicates that the combined sequences pooled from different species of the genus. Subfamilies and tribes recognized by Olmstead were covered by gray boxes with different grey level, while new subfamilies and clades proposed in this study were covered by pink boxes and marked in red bold font.
Figure 4
Figure 4. The Bayesian 50% majority-rule consensus phylogram based on combined cpDNA (matK + ndhF + rbcL + rps16 + trnL-F) dataset D155, with gaps treated as simple indels.
The topologies of the ML and MP trees are congruent with the BI tree. Support values displayed on the branches follow the order BI-PP/ML-BS/MP-BS (“−” Indicates support values of less than 0.90 in BI or 50% in ML and MP analyses, respectively). The bold lines indicate that the three support values get full scores simultaneously. Multiple accessions of the same species are numbered according to Supplementary Table S1. A single generic name represented that the combined sequences pooled from different species of the genus. Subfamilies recognized by Olmstead were covered by gray boxes with different grey level, while new subfamilies (Cymarioideae, Peronematoideae, and Premnoideae) and clades (Callicarpa and Tectona) proposed in this study were covered by pink boxes and marked in red bold font.
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References

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