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
作者： Xu, Ke-Wang 1 ; Yang, Yi 2 ; Chen, Hong 3 ; Lin, Chen-Xue 1 ; Jiang, Lei 1 ; Guo, Zhong-Long 1 ; Li, Meng 1 ; Hao, Ming-Zhuo 4 ; Meng, Kai-Kai 5 ;
作者机构： 1.Nanjing Forestry Univ, Coinnovat Ctr Sustainable Forestry Southern China, Key Lab State Forestry, Key Lab Natl Forestry & Grassland Adm Subtrop Fore, Nanjing 210037, Peoples R China
2.Jiangxi Agr Univ, Sch Agr Sci, Nanchang 330045, Peoples R China
3.Jiangsu Prov & Chinese Acad Sci, Inst Bot, Jiangsu Key Lab Res & Utilizat Plant Resources, Nanjing 210014, Peoples R China
4.Nanjing Forestry Univ, Coinnovat Ctr Sustainable Forestry Southern China, Nanjing 210037, Peoples R China
5.Minist Agr & Rural Affairs, Guangxi Subtrop Crops Res Inst, Guangxi Key Lab Qual & Safety Control Subtrop Frui, Key Lab Qual & Safety Control Subtrop Fruit & Vege, Nanning 530001, Peoples R China
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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