Taxonomy and biogeography ofDiapensia(Diapensiaceae) based on chloroplast genome data

Abstract

Diapensia L. is the second largest genus of Diapensiaceae. The taxonomic treatment within Diapensia and relationships within Diapensiaceae have been disputed. Chloroplast genome sequence data have proved to be useful for plant phylogenetic analyses and species delimitation. In this study, we de novo sequenced and assembled 22 chloroplast genomes of 15 species of Diapensiaceae, including all recognized species of Diapensia with multiple samples. A super‐matrix containing a total of 107 genes and 18 taxa was constructed for phylogenetic analyses to resolve phylogenetic relationships among genera of the family and within Diapensia. The resulting phylogenetic tree showed the following strongly supported relationships: (Galax, (Pyxidanthera, (Berneuxia, ((Schizocodon, Diapensia), and Shortia s.s.)))). The dated phylogeny and reconstructed lineage‐through‐time plot for the family indicated rapid diversification in the Neogene and an acceleration of diversification rate after c. 8 Ma. Biogeographic analysis suggested that Diapensia originated in the Northeast Asian mountains approximately 6.06 Ma, followed by northward dispersal to the Arctic and southwestward dispersal to the Himalaya–Hengduan Mountains. Phylogenetic relationships within Diapensia were well resolved. Based on the phylogenetic results, we proposed to reinstate the species status of Diapensia bulleyana Forrest ex Diels, and raised D. purpurea f. albida to the species rank (D. albida [W. E. Evans] J. F. Ye comb. & stat. nov.). The distribution ranges of all species delineated based on the phylogenetic results were revised accordingly based on specimen occurrences. Our study adds new examples for the power of plastid genome data for resolving phylogenetic relationships and clarifying taxonomic disputes among closely related species.

Biogeography and ecological niche evolution in Diapensiaceae inferred from phylogenetic analysis

“…Similar to Higashi et al (2015), we found that Schizocodon and Shortia are both monophyletic. The general topology we recovered on the basis of combined nuclear and plastid data set agrees with plastome‐based inferences for the family (Ye et al, 2020).…”

Phylogenomic and comparative analyses of Rheum (Polygonaceae, Polygonoideae)

“…The chloroplast genome is usually maternally inherited in most angiosperms and consists of two copies of inverted repeat (IR) regions divided by one small single‐copy region (SSC) and one large single copy region (LSC) (Bendich, 2004). With advancements in second generation sequencing technology, chloroplast genomes have been frequently used to address phylogenetic relationships among closely related species (Ma et al, 2020; Mu et al, 2020; Ye et al, 2020). The chloroplast genome contains sequence variation that can offer sufficient phylogenetic information to resolve closely related species, including species that have experienced complex evolution histories.…”

In memory of Professor Tang Yan‐Cheng: New perspectives in systematic and evolutionary biology

“…Such studies enable simultaneous study of morphologically distinguishing characteristics for resolved clades in the phylogeny (Willis et al, 2017). All three studies (Hu et al, 2020;Su et al, 2020;Ye et al, 2020) clarified previous taxonomic debates in these taxa and enabled the authors to propose revised taxonomic treatments based on a large amount of molecular phylogenetic data. Furthermore, the phylogeny of Magnolia, in particular, provides a comprehensive framework that may prove useful in breeding programs in this horticulturally important genus.…”