Out of chaos: Phylogenomics of Asian Sonerileae

Qiu-Jie Zhou; Jin-Hong Dai; Che-Wei Lin; Wei-Lun Ng; Truong Van Do; Jarearnsak Sae Wai; Fabián A Michelangeli; Marcelo Reginato; Ren-Chao Zhou; Ying Liu

doi:10.1016/j.ympev.2022.107581

Out of chaos: Phylogenomics of Asian Sonerileae

Mol Phylogenet Evol. 2022 Oct:175:107581. doi: 10.1016/j.ympev.2022.107581. Epub 2022 Jul 8.

Authors

Affiliations

¹ State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
² State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
³ Herbarium of Taiwan Forestry Research Institute, Taipei 100, Taiwan.
⁴ China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, Malaysia.
⁵ Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18th Hoang Quoc Viet Road, Cau Giay, Hanoi, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18th Hoang Quoc Viet Road, Cau Giay, Hanoi, Viet Nam.
⁶ Department of Biology, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand.
⁷ Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY 10458-5126, USA.
⁸ Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Campus do Vale Agronomia, RS, 91509900, Porto Alegre, Brazil.
⁹ State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China. Electronic address: zhrench@mail.sysu.edu.cn.
¹⁰ State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China. Electronic address: liuyng73@mail.sysu.edu.cn.

PMID: 35810973
DOI: 10.1016/j.ympev.2022.107581

Abstract

Sonerileae is a diverse Melastomataceae lineage comprising ca. 1000 species in 44 genera, with >70% of genera and species distributed in Asia. Asian Sonerileae are taxonomically intractable with obscure generic circumscriptions. The backbone phylogeny of this group remains poorly resolved, possibly due to complexity caused by rapid species radiation in early and middle Miocene, which hampers further systematic study. Here, we used genome resequencing data to reconstruct the phylogeny of Asian Sonerileae. Three parallel datasets, viz. single-copy ortholog (SCO), genomic SNPs, and whole plastome, were assembled from genome resequencing data of 205 species for this purpose. Based on these genome-scale data, we provided the first well resolved phylogeny of Asian Sonerileae, with 34 major clades identified and 74% of the interclade relationships consistently resolved by both SCO and genomic data. Meanwhile, widespread phylogenetic discordance was detected among SCO gene trees as well as species trees reconstructed using different tree estimation methods (concatenation/site-based coalescent method/summary method) or different datasets (SCO/genomic/plastome). We explored sources of discordance using multiple approaches and found that the observed discordance in Asian Sonerileae was mainly caused by a combination of biased distribution of missing data, random noise from uninformative genes, incomplete lineage sorting, and hybridization/introgression. Exploration of these sources can enable us to generate hypotheses for future testing, which is the first step towards understanding the evolution of Asian Sonerileae. We also detected high levels of homoplasy for some characters traditionally used in taxonomy, which explains current chaotic generic delimitations. The backbone phylogeny of Asian Sonerileae revealed in this study offers a solid basis for future taxonomic revision at the generic level.

Keywords: Discordance; Generic circumscription; Melastomataceae; Phylogeny; Sonerileae.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Genomics / methods
Hybridization, Genetic
Melastomataceae*
Phylogeny
Sequence Analysis, DNA