Framework Phylogeny, Evolution and Complex Diversification of Chinese Oaks

Abstract

Oaks (Quercus L.) are ideal models to assess patterns of plant diversity. We integrated the sequence data of five chloroplast and two nuclear loci from 50 Chinese oaks to explore the phylogenetic framework, evolution and diversification patterns of the Chinese oak’s lineage. The framework phylogeny strongly supports two subgenera Quercus and Cerris comprising four infrageneric sections Quercus, Cerris, Ilex and Cyclobalanopsis for the Chinese oaks. An evolutionary analysis suggests that the two subgenera probably split during the mid-Eocene, followed by intergroup divergence within the subgenus Cerris around the late Eocene. The initial diversification of sections in the subgenus Cerris was dated between the mid-Oligocene and the Oligocene–Miocene boundary, while a rapid species radiation in section Quercus started in the late Miocene. Diversification simulations indicate a potential evolutionary shift on section Quercus, while several phenotypic shifts likely occur among all sections. We found significant negative correlations between rates of the lineage diversification and phenotypic turnover, suggesting a complex interaction between the species evolution and morphological divergence in Chinese oaks. Our infrageneric phylogeny of Chinese oaks accords with the recently proposed classification of the genus Quercus. The results point to tectonic activity and climatic change during the Tertiary as possible drivers of evolution and diversification in the Chinese oak’s lineage.

The complete chloroplast genome sequence of Quercus ningangensis and its phylogenetic implication

“…Within the section Cyclobalanopsis, Q. gilva and Q. sichourensis did not form a CTB lineage sister to the STB lineage, as demonstrated in previous studies (Deng et al 2018;Hipp et al 2020;Yang et al 2020). Our results showed that the phylogenetic position of Q. ningangensis was located between Q. sichourensis and Q. acuta.…”

“…It has four trichome types, including fasciculate, simple stellate, appressed lateral attached, and uniseriate, which is one of the most diversified in this section (Deng et al 2014). However, recent phylogenetic and phylogenomic studies have not included samples of this species (Deng et al 2018;Hipp et al 2020;Yang et al 2020).…”

Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China

“…Several studies have examined the phylogenetic relationships of species in this group based on a few markers (e.g. Yang et al, 2017Yang et al, , 2020 or reduced-representation genomic data (RAD-seq) (Jiang et al, 2019;Hipp et al, 2020), and many topological conflicts were found among them, even when using the same type of dataset. Extensive introgression among these species and ILS may be the reasons for their unresolved relationships.…”