J Syst Evol ›› 2021, Vol. 59 ›› Issue (5): 897-914.DOI: 10.1111/jse.12745

• Research Articles • Previous Articles     Next Articles

A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily

Hong-Xin Wang1†, Diego F. Morales-Briones2†, Michael J. Moore3, Jun Wen4, and Hua-Feng Wang1*   

  1. 1 Key Laboratory of Tropical Biological Resources of Ministry of Education, College of Tropical Crops, Hainan University, Haikou 570228, China
    2 Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, 140 Gortner Laboratory, Saint Paul, MN 55108, USA
    3 Department of Biology, Oberlin College, Oberlin, OH 44074, USA
    4 Department of Botany, National Museum of Natural History, MRC‐166, Smithsonian Institution, Washington, DC 20013‐7012, USA
  • Received:2021-11-02 Accepted:2021-03-16 Online:2021-04-05 Published:2021-09-01

Abstract: The use of diverse data sets in phylogenetic studies aiming for understanding evolutionary histories of species can yield conflicting inference. Phylogenetic conflicts observed in animal and plant systems have often been explained by hybridization, incomplete lineage sorting (ILS), or horizontal gene transfer. Here, we used target enrichment data, species tree, and species network approaches to infer the backbone phylogeny of the family Caprifoliaceae, while distinguishing among sources of incongruence. We used 713 nuclear loci and 46 complete plastome sequence data from 43 samples representing 38 species from all major clades to reconstruct the phylogeny of the family using concatenation and coalescence approaches. We found significant nuclear gene tree conflict as well as cytonuclear discordance. Additionally, coalescent simulations and phylogenetic species network analyses suggested putative ancient hybridization among subfamilies of Caprifoliaceae, which seems to be the main source of phylogenetic discordance. Ancestral state reconstruction of six morphological characters revealed some homoplasy for each character examined. By dating the branching events, we inferred the origin of Caprifoliaceae at approximately 66.65 Ma in the late Cretaceous. By integrating evidence from molecular phylogeny, divergence times, and morphology, we here recognize Zabelioideae as a new subfamily in Caprifoliaceae. This work shows the necessity of using a combination of multiple approaches to identify the sources of gene tree discordance. Our study also highlights the importance of using data from both nuclear and plastid genomes to reconstruct deep and shallow phylogenies of plants.

Key words: Caprifoliaceae, hybridization, introgression, phylogenetic networks, Zabelia, Zabelioideae