Journal Article

Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)

Ji, Yunheng, Yang, Lifang, Yang, Jin, Yang, Zhenyan, Chase, Mark W., Liu, Changkun, Yang, Jun-Bo, Yi, Ting-Shuang

2019

Overview

Background Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to reconstruct a robust phylogenetic tree and explore historical biogeography and clade diversification in the genus. Results All 29 species currently recognized in Paris were sampled. Whole plastomes and nrDNA sequences were generated by the genome skimming approach. Phylogenetic relationships were reconstructed using the maximum likelihood and Bayesian inference methods. Based on the phylogenetic framework and molecular dating, biogeographic scenarios and historical diversification of Paris were explored. Significant conflicts between plastid and nuclear datasets were identified, and the plastome tree is highly congruent with past interpretations of the morphology. Ancestral area reconstruction indicated that Paris may have originated in northeastern Asia and northern China, and has experienced multiple dispersal and vicariance events during its diversification. The rate of clade diversification has sharply accelerated since the Miocene/Pliocene boundary. Conclusions Our results provide important insights for clarifying some of the long-standing taxonomic debates in Paris . Cytonuclear discordance may have been caused by ancient and recent hybridizations in the genus. The climatic and geological changes since the late Miocene, such as the intensification of Asian monsoon and the rapid uplift of Qinghai-Tibet Plateau, as well as the climatic fluctuations during the Pleistocene, played essential roles in driving range expansion and radiative diversification in Paris . Our findings challenge the theoretical prediction that large genome sizes may limit speciation.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Agriculture / Angiosperms / Bayesian analysis / Bayesian theory / Biogeography / Biological Evolution / Biomedical and Life Sciences / Biotechnology industries / China / Cytonuclear discordance / data collection / Deoxyribonucleic acid / Discordance / Dispersal / DNA / Economic importance / Gene sequencing / Genes / Genetic research / genome / Genome, Plastid / Genomes / Genomics / Genomics and evolution / genus / geographical distribution / Large genome size / Life Sciences / Melanthiaceae / Melanthiaceae - genetics / Miocene / Miocene epoch / monsoon season / Monsoons / Morphology / Nucleotide sequence / Parideae / Phylogenetics / Phylogeny / Plant Dispersal - genetics / Plant Sciences / Plastid phylogenomics / Plastomes / Pleistocene / Pleistocene epoch / Pliocene / Pliocene epoch / prediction / Radiative diversification / Range extension / Research Article / Ribosomal DNA / Speciation / species / Statistical inference / Taxonomy / Tree Biology / trees / Uplift