Multiple paternally inherited chloroplast capture events associated with Taxus speciation in the Hengduan Mountains.
Multiple paternally inherited chloroplast capture events associated with Taxus speciation in the Hengduan Mountains.
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DOI：
10.1016/j.ympev.2023.107915
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发表时间：
2023-09
影响因子：
4.1
通讯作者：
Hantao Qin;Michael Mller;R. Milne;Yahuang Luo;Guang-Fu Zhu;De‐Zhu Li;Jie Liu;Lianming Gao
中科院分区：
文献类型：
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作者：
Hantao Qin;Michael Mller;R. Milne;Yahuang Luo;Guang-Fu Zhu;De‐Zhu Li;Jie Liu;Lianming Gao
山区为复杂的物种形成情景提供了多种生境和机会。杂交导致叶绿体捕获，这可以通过不一致的系统发育树揭示，是一种可能的结果。来自中国西南横断山区的四个allopatricTaxuslineages（三个种和一个未描述的谱系）表现出核和叶绿体同源性之间的系统发育关系冲突。在这里，我们使用多组学数据在人口水平上调查其历史speciationprocesses.Population基因组分析的基础上ddRAD-seq数据揭示了有限的当代种间基因流只涉及位于靠近另一个species.In一个历史的背景下，叶绿体和核数据（转录组）一致显示相互矛盾的系统发育关系forT。florinii和峨眉类型谱系。ILS和叶绿体重组被排除在可能的原因之外，转录组和ddRAD-seq数据揭示了缺乏嵌合体核基因组，这是杂种起源的特征。florinii似乎起源于T. florini捕获了T. chinensisplasttid类型，而相反方向的质体渐渗产生峨眉类型。根据群落调查和生态位分析，这四个种都具有不同的生态位，我们认为这两个种的起源是叶绿体捕获事件的罕见例子，尽管裸子植物的叶绿体DNA是父系遗传的。具体而言，allopartrically和/或生态分歧的亲本物种经历了罕见的二次接触，随后的杂交和互惠叶绿体捕获，产生两个新的谱系，其中每一个获得了独特的生态位。这些事件可能是由横断山脉的造山活动和中新世晚期亚洲季风的加强所触发的，并且可能代表了这些山脉中比目前已知的更常见的情景。
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 allopatricTaxuslineages (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 forT. floriniiand 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. floriniiappears to have originated when a lineage ofT. floriniicaptured theT. chinensisplastid 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.