Multiple paternally inherited chloroplast capture events associated with Taxus speciation in the Hengduan Mountains

doi:10.1016/j.ympev.2023.107915

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	Multiple paternally inherited chloroplast capture events associated with Taxus speciation in the Hengduan Mountains
	Qin,Han-Tao; Moller,Michael; Milne,Richard; Luo,Ya-Huang; Zhu,Guang-Fu; Li,De-Zhu; Liu,Jie; Gao,Lian-Ming
	2023
发表期刊	MOLECULAR PHYLOGENETICS AND EVOLUTION
ISSN	1095-9513
卷号	189 页码:107915
摘要	Mountainous regions provide a multitude of habitats and opportunities for complex speciation scenarios. Hybridization leading to chloroplast capture, which can be revealed by incongruent phylogenetic trees, is one possible outcome.Four allopatric Taxus lineages (three species and an undescribed lineage) from the Hengduan Mountains, southwest China, exhibit conflicting phylogenetic relationships between nuclear and chloroplast phylogenies. Here, we use multi-omic data at the population level to investigate their historical speciation processes.Population genomic analysis based on ddRAD-seq data revealed limited contemporary inter-specific gene flow involving only populations located close to another species.In a historical context, chloroplast and nuclear data (transcriptome) consistently showed conflicting phylogenetic relationships for T. florinii and the Emei type lineage. ILS and chloroplast recombination were excluded as possible causes, and transcriptome and ddRAD-seq data revealed an absence of the mosaic nuclear genomes that characterize hybrid origin scenarios.Therefore, T. florinii appears to have originated when a lineage of T. florinii captured the T. chinensis plastid type, whereas plastid introgression in the opposite direction generated the Emei Type. All four species have distinct ecological niche based on community investigations and ecological niche analyses.We propose that the origins of both species represent very rare examples of chloroplast capture events despite the paternal cpDNA inheritance of gymnosperms. Specifically, allopatrically and/or ecologically diverged parental species experienced a rare secondary contact, subsequent hybridization and reciprocal chloroplast capture, generating two new lineages, each of which acquired a unique ecological niche. These events might have been triggered by orogenic activities of the Hengduan Mountains and an intensification of the Asian monsoon in the late Miocene, and may represent a scenario more common in these mountains than presently known.
关键词	Chloroplast capture Genomic data Hybridization Hengduan Mountains Phylogeny tree discordance Taxus POPULATION-SIZE CHANGES TIBETAN PLATEAU MARGIN CYTOPLASMIC INHERITANCE HYBRID SPECIATION GENETIC DIVERSITY PINUS-DENSATA R PACKAGE TOOL SET HYBRIDIZATION BIODIVERSITY
DOI	10.1016/j.ympev.2023.107915
收录类别	SCI
WOS记录号	WOS:001078416700001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/75494
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	Qin,Han-Tao,Moller,Michael,Milne,Richard,et al. Multiple paternally inherited chloroplast capture events associated with Taxus speciation in the Hengduan Mountains[J]. MOLECULAR PHYLOGENETICS AND EVOLUTION,2023,189:107915.
APA	Qin,Han-Tao.,Moller,Michael.,Milne,Richard.,Luo,Ya-Huang.,Zhu,Guang-Fu.,...&Gao,Lian-Ming.(2023).Multiple paternally inherited chloroplast capture events associated with Taxus speciation in the Hengduan Mountains.MOLECULAR PHYLOGENETICS AND EVOLUTION,189,107915.
MLA	Qin,Han-Tao,et al."Multiple paternally inherited chloroplast capture events associated with Taxus speciation in the Hengduan Mountains".MOLECULAR PHYLOGENETICS AND EVOLUTION 189(2023):107915.

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