Nuclear and plastid phylogenomic analyses provide insights into the reticulate evolution, species delimitation, and biogeography of the Sino‐Japanese disjunctive Diabelia (Caprifoliaceae)

Abstract

Understanding biological diversity and the mechanisms of the Sino-Japanese disjunctions are major challenges in eastern Asia biogeography. The Sino-Japanese flora has been broadly studied as an ideal model for plant phylogeography. Diabelia Landrein (Caprifoliaceae) is an East Asian genus, with a disjunctive distribution across the Sino-Japanese region. However, relationships within Diabelia remain elusive. In this study, we reconstructed the phylogeny of Diabelia and inferred historical biogeography and evolutionary patterns based on nuclear and plastid sequences from target enrichment and genome skimming approaches, respectively. We found that the main clades within Diabelia were discordant between nuclear and plastid trees. Both nuclear and plastid phylogenetic analyses supported five main clades: Diabelia serrata (Siebold & Zucc.) Landrein, Diabelia tetrasepala (Koidz.) Landrein, Diabelia sanguinea (Makino) Landrein, Diabelia stenophylla (Honda) Landrein, and Diabelia spathulata (Siebold & Zucc.) Landrein. Species network analyses revealed that Diabelia tetrasepala is likely the result of a hybridization event. Divergence time estimation and ancestral area reconstructions showed that Diabelia originated in Japan during the early Miocene, with subsequent vicariance and dispersal events between Japan and Korea, and between Japan and China. Overall, our results support the division of Diabelia into five main clades and the recognition of five species in the genus. This research provides new insights into the species delimitation and speciation processes of taxonomically complex lineages such as Diabelia.

New insights into infrageneric relationships of Lonicera (Caprifoliaceae) as revealed by nuclear ribosomal DNA cistron data and plastid phylogenomics

“…All other parameters were left at default settings. In the plastome data, because the sampling included Diabelia serrata and Dipelta floribunda, we used the seed fossil of Dipelta to constrain the stem age (offset 34.9 Ma, log-normal prior distribution 34.1-36.1 Ma) (Wang et al, 2015(Wang et al, , 2020(Wang et al, , 2021Ke et al, 2022;Sun et al, 2022). In addition to the fossil calibration, the root age was set to 76.9 Ma (mean 76.9 Ma, normal prior distribution 68.1-85.7 Ma; Fig.…”

Rapid structural evolution of Dendrobium mitogenomes and mito‐nuclear phylogeny discordances in Dendrobium (Orchidaceae)

“…The clade supports were inferred by local posterior probabilities (Sayyari & Mirarab, 2016). The InferNetwork_MPL command was applied to infer species networks using the individual gene trees (Ke et al, 2021). Five network searches with one to five reticulation events were performed with 10 runs for individual search, estimating the optimal species network using maximum pseudo-likelihood.…”

“…The CalGTProb command was also applied to estimate the likelihoods of nuclear, mitochondrial, and ASTRAL trees. The model selection was performed using the Akaike information criterion (AIC) and the Bayesian information criterion (BIC) (Ke et al, 2021).…”