Xu Ke-Wang, Yang Yi, Chen Hong, Lin Chen-Xue, Jiang Lei, Guo Zhong-Long, Li Meng, Hao Ming-Zhuo, Meng Kai-Kai
Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Science, Nanjing Forestry University, Nanjing 210037, China.
School of Agricultural Sciences, Jiangxi Agricultural University, Nanchang 330045, China.
Mol Phylogenet Evol. 2025 Mar;204:108255. doi: 10.1016/j.ympev.2024.108255. Epub 2024 Nov 30.
Ilex L., the exclusive genus of Aquifoliaceae, encompasses over 600 dioecious wood species with a highly irregular distribution, predominantly found in South America and Asia. The phylogeny and classification of this genus remain enigmatic due to significant early extinctions, constrained morphological diversity, recent hybridization/introgression, and conflicting signals from previously utilized markers. This study presents phylogenetic reconstructions based on complete chloroplast genome sequences and single nucleotide polymorphisms (SNPs) derived from genome resequencing data. A total of 116 accessions of Ilex, representing approximately 108 taxa, were included as the ingroup, with five accessions of two species serving as outgroups. Analysis of the chloroplast genome and nuclear SNP data individually resulted in two robust phylogenetic trees, revealing substantial discrepancies between the chloroplast genome and nuclear SNP phylogenies at both the species and clade levels. The chloroplast genome sequences successfully resolved relationships within this genus into eight strongly supported major clades, while the nuclear SNPs resolved relationships into seven highly supported major clades. Our nuclear SNP phylogenetic tree, in comparison to the chloroplast genome tree, aligns more closely with the recently updated classification of Ilex in multiple instances. The extensive cytonuclear discordance identified may be attributed to recent hybridization events and incomplete lineage sorting (ILS).
冬青属（Ilex L.）是冬青科唯一的属，包含600多种雌雄异株的木本植物，分布极不均匀，主要分布在南美洲和亚洲。由于早期大量灭绝、形态多样性受限、近期杂交/基因渗入以及先前使用的标记产生的矛盾信号，该属的系统发育和分类仍然扑朔迷离。本研究基于完整的叶绿体基因组序列和来自基因组重测序数据的单核苷酸多态性（SNP）进行系统发育重建。总共纳入了116份冬青属材料，代表约108个分类群，作为内类群，另外选取两个物种的5份材料作为外类群。分别对叶绿体基因组和核SNP数据进行分析，得到了两棵可靠的系统发育树，揭示了叶绿体基因组和核SNP系统发育在物种和分支水平上都存在显著差异。叶绿体基因组序列成功地将该属内的关系解析为八个得到强烈支持的主要分支，而核SNP则将关系解析为七个得到高度支持的主要分支。与叶绿体基因组树相比，我们的核SNP系统发育树在多个实例中与最近更新的冬青属分类更为接近。所发现的广泛的细胞核-细胞质不一致可能归因于近期的杂交事件和不完全谱系分选（ILS）。
