Plastid phylogenomics and biogeographic analysis support a trans-Tethyan origin and rapid early radiation of Cornales in the Mid-Cretaceous

• Published in: Molecular phylogenetics and evolution 2019-11, Vol.140, p.106601-106601, Article 106601
• Main Authors: Fu, Chao-Nan, Mo, Zhi-Qiong, Yang, Jun-Bo, Ge, Xue-Jun, Li, De-Zhu, Xiang, Qiu-Yun (Jenny), Gao, Lian-Ming
• Format: Article
• Language: English
• Subjects: Base Composition - genetics; Biogeography; Calibration; Character coding; Codon - genetics; Cornales; Fossils; Genetic Variation; Genome, Plastid; Magnoliopsida - genetics; Phylogenomics; Phylogeny; Phylogeography; Plastid genome; Plastids - genetics; Time Factors
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2019.106601

(A) Dated phylogenetic tree based on the treePL method using PCS12 dataset. The individuals within each family were merged to triangle with the size corresponding the individual number sampled. (B) Inferred major biogeographic events of families in Cornales. [Display omitted] •Interfamilial relationships of Cornales were completely resolved with high support by the plastid genome data.•Data including synonymous substitution sites biased phylogenetic inference of Hydrostachyaceae, a long branched lineage.•Total evidence supports a trans-Tethyan origin and rapid early radiation of Cornales in the Mid-Cretaceous. The Cornales is a relatively small but morphologically diverse order in the basal position of the Asterids clade. Previous study hypothesized that the order might have undergone ancient rapid radiation during the Cretaceous when major angiosperm lineages were established. We conducted the phylogenomic analysis of Cornales using 81 plastid genome sequences with 67 newly generated in this study to test the hypothesis. This sampling represents all the families and 31 out of 48 genera in the order. Phylogenetic analyses were conducted using different datasets to examine the effects of different coding positions and character coding methods. We further conducted divergence time, diversification rate, and biogeographic analyses to understand the early evolutionary history of Cornales in space and time. Our phylogenetic analyses of four datasets (the amino acid characters, the 1st and 2nd codon positions of protein coding genes, nucleotide characters with degenerated coding method, and noncoding regions) resulted in a robust phylogeny congruent with results of previous studies, showing (((Cornaceae-Alangiaceae)-(Curtisiaceae-Grubbiaceae))-(((Nyssaceae-Davidiaceae)-Mastixiaceae)-((Hydrostachyaceae-(Hydrangeaceae-Loasaceae))). Phylogenetic relationships within families were also well resolved. Conflicts in the placement of Hydrostachyaceae were found from analyses of two datasets, the nucleotide characters of all codon position and the 3rd codon positions, where the family was united with Loasaceae, but not strongly supported. Results from divergence time analyses suggested a mid-Cretaceous origin of Cornales followed by rapid early diversification into major clades/families within 10 million years. The early diversification of Cornales may have been facilitated by divergence in habitat and morphology following geographic dispersals. The ancestral distributio