Extensive cytonuclear discordance revealed by phylogenomic analyses suggests complex evolutionary history in the holly genus Ilex (Aquifoliaceae)

文献类型： 外文期刊

第一作者： Xu, Ke-Wang

作者： Xu, Ke-Wang;Lin, Chen-Xue;Jiang, Lei;Guo, Zhong-Long;Li, Meng;Yang, Yi;Chen, Hong;Hao, Ming-Zhuo;Meng, Kai-Kai

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关键词： Aquifoliales; Ilex; Incomplete lineage sorting; Hybridization; Phylogenomic discordance

期刊名称：MOLECULAR PHYLOGENETICS AND EVOLUTION （ 影响因子：3.6； 五年影响因子：4.0 ）

ISSN： 1055-7903

年卷期： 2025 年 204 卷

页码：

收录情况： SCI

摘要： 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).

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