Time to update the sectional classification of Ilex (Aquifoliaceae): New insights from Ilex phylogeny, morphology, and distribution

Abstract

Resolving the infrageneric classification of species‐rich genera has been challenging in plant taxonomy. Ilex L. is a subcosmopolitan genus with over 600 species of dioecious trees and shrubs. Many classification systems based on morphological data have been proposed during the past 250 years. However, these systems (such as Loesener's and Galle's systems) may not truly reflect Ilex's evolutionary trajectories because most of those system's infrageneric hierarchies are not monophyletic. In this study, we reconstructed a phylogeny of Ilex L. comprising 15 moderately to highly supported clades using rigorously identified samples (202 species) and closely authenticated gene sequences of three nuclear genes [internal transcribed spacer (ITS), external transcribed spacer (ETS), and nepGS]. The newly generated phylogenetic tree resembles essentially that of the nuclear tree of Manen et al., but shows conspicuous topological differences with the phylogeny of Yao et al. Closely scrutinizing morphological variation and distributional patterns of 202 species, this study found that most lineages of Ilex identified herein are well defined by a particular trait or a combination of morphological and distributional traits, displaying phylogeny–morphology–distribution conformity that has seldom been uncovered in previous studies. Given the general phylogeny–morphology–distribution conformity revealed in this genus, we put forward an updated sectional classification system for Ilex that temporarily contains 14 sections. The new classification will provide a robust framework for studying the evolution and diversification of this ecologically and economically important genus.

HollyGTD: an integrated database for holly (Aquifoliaceae) genome and taxonomy

“…Photos of leaves, flowers, pollens, whole plants, and so on were collected from our group. The phylogenetic tree was obtained from Yang’s research ( Yang et al., 2023 ).…”

“…Tissue Expression tool interactively displays transcriptomic datasets among distinct developmental stages of fruits and leaves. Phylogenetic Tree enables users to search against the most recent taxonomic relationship of Aquifoliaceae according to Yang’s study ( Yang et al., 2023 ). Literature is used to fast retrieval and access published researches on holly.…”

“…However, there is still no integrative database for comparative genomics and transcriptomics of hollies to study gene function and genome evolution. The research community for holly has gathered a significant amount of taxonomic information over the last few decades, including type locality, type specimens, and herbarium code ( Manen et al., 2010 ; Xu et al., 2022b ; Yang et al., 2023 ). But the lack of a standardized platform for data processing and visualization limits the accessibility of such data.…”

The Genetic Diversity of Natural Ilex chinensis Sims (Aquifoliaceae) Populations as Revealed by SSR Markers

“…In terms of phylogeny, DNA molecular evidence has been widely used to reveal evolutionary relationships between species. A series of regional and global studies have been reported [1,[4][5][6][7]23,24]. As for genome studies, currently, only a small number of reports focus on the whole genome [25,26] and mitochondria genome [27].…”

Hybrid origin and status of the endangered Ilex sanqingshanensis revealed by molecular and morphological evidence

“…Morphological intermediacy further divulges clues of hybridizations for its common application in the identi cation of natural hybrids (Marczewski et al 2016). As the development of molecular approaches, there are more available tools to help to unmask hybrids, including but not limited to incomplete ITS (internal transcribed spacer region) concerted evolution (Grimm & Denk 2008 Ilex, the sole genus of Aquifoliaceae, consists of at least 14 sections (Yang et al 2022) and holds more than 600 species as well as a lot of interspeci c hybrids both naturally occurring and cultivated (Galle 1997;Powell et al 2000;Loizeau et al 2005;Chen et al 2008). To date, the con rmed inarti cial Ilex crosses have only been found to be intra-sectional; however, most natural hybrids are concentrated in the largest section, I. sect.…”