Phylogenomic analyses re-evaluate the backbone of Corylus and unravel extensive signals of reticulate evolution

Abstract

Phylogenomic analyses have shown that reticulate evolution greatly affects the accuracy of phylogenetic inferences, and thus may challenge the authority of bifurcating phylogenetic trees. In this study, we re-evaluated the phylogenetic backbone of the genus Corylus based on complete taxon sampling and genomic data. We assembled 581 single-copy nuclear genes and whole plastomes from 64 genome resequencing datasets to elucidate the reticulate relationships within Corylus. Nuclear coalescent and concatenation phylogenies revealed identical and fully supported backbone, clarifying the sisterhood between sect. Acanthochlamys and sect. Siphonochlamys as well as the phylogenetic position of C. fargesii and C. wangii, which have yet been addressed in previous phylogenetic studies. However, the monophyly of C. jacquemontii and C. kwechowensis and the distinction between C. ferox and C. ferox var. thibetica were not supported. Gene trees-species tree conflicts and cytonuclear discordance were identified, with multiple evidences supporting that hybridization/introgression, coupled with incomplete lineage sorting, have led to substantial phylogenetic incongruence in Corylus. Moreover, typical geographical clustering rather than strict monophyletic pattern in plastome phylogeny implies chloroplast capture within Corylus and offers evidence of cytoplasmic introgression. Overall, this study provides a robust phylogenomic backbone for Corylus and unravels that reticulate evolution can greatly shape taxonomic revision.