Analyses of Plastome Sequences Improve Phylogenetic Resolution and Provide New Insight Into the Evolutionary History of Asian Sonerileae/Dissochaeteae.

Qiujie Zhou,Jinhong Dai,Wei Lun Ng,Tetsuo Denda,Ying Liu,Renchao Zhou,Che-Wei Lin

doi:10.3389/fpls.2019.01477

Abstract

Sonerileae/Dissochaeteae (Melastomataceae) comprises ca. 50 genera, two thirds of which occur in Southeast Asia. Phylogenetic relationships within this clade remain largely unclear, which hampers our understanding of its origin, evolution, and biogeography. Here, we explored the use of chloroplast genomes in phylogenetic reconstruction of Sonerileae/Dissochaeteae, by sampling 138 species and 23 genera in this clade. A total of 151 complete plastid genomes were assembled for this study. Plastid genomic data provided better support for the backbone of the Sonerileae/Dissochaeteae phylogeny, and also for relationships among most closely related species, but failed to resolve the short internodes likely resulted from rapid radiation. Trees inferred from plastid genome and nrITS sequences were largely congruent regarding the major lineages of Sonerileae/Dissochaeteae. The present analyses recovered 15 major lineages well recognized in both nrITS and plastid phylogeny. Molecular dating and biogeographical analyses indicated a South American origin for Sonerileae/Dissochaeteae during late Eocene (stem age: 34.78 Mya). Two dispersal events from South America to the Old World were detected in late Eocene (33.96 Mya) and Mid Oligocene (28.33 Mya) respectively. The core Asian clade began to diversify around early Miocene in Indo-Burma and dispersed subsequently to Malesia and Sino-Japanese regions, possibly promoted by global temperature changes and East Asian monsoon activity. Our analyses supported previous hypothesis that Medinilla reached Madagascar by transoceanic dispersal in Miocene. In addition, generic limits of some genera concerned were discussed.

Highlights

The Southeast Asia (SEA) is known for its complex geological history (Turner et al, 2001) and unique and rich biota (Mittermeier et al, 1999; Sodhi et al, 2004)
All newly obtained genomes are evolutionally conservative and similar to the ones previously published in Melastomataceae (Reginato et al, 2016; Ng et al, 2017; Zhou et al, 2017, Tan et al, 2019)
A gene map for the chloroplast genome of Phyllagathis rotundifolia (Jack) Blume is shown in Figure S1 as a representative

Summary

Introduction

The Southeast Asia (SEA) is known for its complex geological history (Turner et al, 2001) and unique and rich biota (Mittermeier et al, 1999; Sodhi et al, 2004). This region, covering only 4% of the earth’s land area, harbors approximately 20%–25% of the higher plant species on the planet (Woodruff, 2010; Corlett, 2014). According to Myers et al (2000), SEA includes three out of the world’s eight hottest biodiversity hotspots for conservation priorities How these diverse plants originate, disperse, and evolve remains largely unanswered. Sonerileae/Dissochaeteae comprises over 1000 species in ca. 50 genera, two thirds of which occur in SEA

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Conclusion