Phylogenomic and macroevolutionary evidence for an explosive radiation of a plant genus in the Miocene
Creators: name: Kong, Hanghui
name: Condamine, Fabien L.
name: Yang, Lihua
name: Harris, AJ
name: Feng, Chao
name: Wen, Fang
name: Kang, Ming
Publisher: name: Zenodo
Year: 2021

description: Mountain systems harbor a substantial fraction of global biodiversity and, thus, provide excellent opportunities to study rapid diversification and to understand the historical processes underlying the assembly of biodiversity hotspots. The rich biodiversity in mountains is widely regarded as having arisen under the influence of geological and climatic processes as well as the complex interactions among them. However, the relative contribution of geology and climate in driving species radiation is seldom explored. Here, we studied the evolutionary radiation of <i>Oreocharis </i>(Gesneriaceae), which has diversified extensively throughout East Asia, especially within the Hengduan Mountains (HDM), using transcriptomic data and a time calibrated phylogeny for 88% (111/126) of all species of the genus. In particular, we applied phylogenetic reconstructions to evaluate the extent of incomplete lineage sorting accompanying the early and rapid radiation in the genus. We then fit macroevolutionary models to explore its spatial and diversification dynamics in <i>Oreocharis</i> and applied explicit birth-death models to investigate the effects of past environmental changes on its diversification. Evidence from 574 orthologous loci suggest that <i>Oreocharis</i> underwent an impressive early burst of speciation starting ca. 12 Ma in the Miocene, followed by a drastic decline in speciation toward the present. Although we found no evidence for a shift in diversification rate across the phylogeny of <i>Oreocharis</i>, we showed a difference in diversification dynamics between the HDM and non-HDM lineages, with higher diversification rates in the HDM. The diversification dynamic of <i>Oreocharis</i> is most likely positively associated with temperature-dependent speciation and dependency on the Asian monsoons. We suggest that the warm and humid climate of the mid-Miocene was probably the primary driver of the rapid diversification in <i>Oreocharis</i>, while mountain building of the HDM might have indirectly affected species diversification of the HDM lineage. This study highlights the importance of past climatic changes, combined with mountain building, in creating strong environmental heterogeneity and driving diversification of mountain plants, and suggests that the biodiversity in the HDM cannot directly be attributed to mountain uplift, contrary to many recent speculations.
description: <strong>DATA &amp; FILE OVERVIEW</strong> <strong>data:</strong><br> <strong>CenozoicTemperature from 65 Ma</strong><br> CenozoicTemperature.txt <strong>Asian Monsoons from 15 Ma</strong><br> AsianMonsoonsfrom_15 Ma.txt <strong>File List:</strong> <strong>Appendices S1-S17</strong> Funding provided by: Chinese Academy of Sciences Strategic Priority Research Program*<br>Crossref Funder Registry ID: <br>Award Number: XDB31000000Funding provided by: National Natural Science Foundation of China<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809<br>Award Number: 31970231Funding provided by: Chinese Academy of Sciences Strategic Priority Research Program<br>Crossref Funder Registry ID: <br>Award Number: XDB31000000