Phylogenetic and molecular dating analyses of Chinese endemic genus Dipelta (Caprifoliaceae) based on nuclear RAD‐Seq and chloroplast genome data

IF 3.7 1区 生物学 Q1 Agricultural and Biological Sciences
Ya‐Nan Cao, Meng‐Hao Wang, Hang Ran, Bin Tian, Lu‐Xian Liu, Qing‐Nan Wu, Yan‐Yan Liu, Hong‐Wei Wang, Shan‐Shan Zhu
{"title":"Phylogenetic and molecular dating analyses of Chinese endemic genus Dipelta (Caprifoliaceae) based on nuclear RAD‐Seq and chloroplast genome data","authors":"Ya‐Nan Cao, Meng‐Hao Wang, Hang Ran, Bin Tian, Lu‐Xian Liu, Qing‐Nan Wu, Yan‐Yan Liu, Hong‐Wei Wang, Shan‐Shan Zhu","doi":"10.1111/jse.13076","DOIUrl":null,"url":null,"abstract":"<jats:italic>Dipelta</jats:italic> Maxim. (Caprifoliaceae) is a Tertiary relic genus endemic to China, which includes three extant species, <jats:italic>Dipelta floribunda, Dipelta yunnanensis</jats:italic>, and <jats:italic>Dipelta elegans</jats:italic>. Recent progress in the systematics and phylogeographics of <jats:italic>Dipelta</jats:italic> has greatly broadened our knowledge about its origin and evolution, however, conflicted phylogenetic relationships and divergence times have been reported and warrant further investigation. Here, we utilized chloroplast genomes and population‐level genomic data restriction site‐associated DNA‐single nucleotide polymorphisms (RAD‐SNPs) to evaluate the interspecific relationships, population genetic structure and demographic histories of this genus. Our results confirmed the sister relationship between <jats:italic>D. elegans</jats:italic> and the <jats:italic>D. yunnanensis</jats:italic>–<jats:italic>D. floribunda</jats:italic> group, but with cyto‐nuclear phylogenetic discordance observed in the latter. Coalescent simulations suggested that this discordance might be attributed to asymmetric “chloroplast capture” through introgressive hybridization between the two parapatric species. Our fossil‐calibrated plastid chronogram of Dipsacales and the coalescent modeling based on nuclear RAD‐SNPs simultaneously suggested that the three species of <jats:italic>Dipelta</jats:italic> diversified at the late Miocene, which may be related to the uplift of the eastern part of Qinghai–Tibet Plateau (QTP) and adjacent southwest China, and increasing Asian interior aridification since the late Miocene; while in the mid‐Pleistocene, the climatic transition and continuous uplift of the QTP, triggered allopatric speciation via geographical isolation for <jats:italic>D. floribunda</jats:italic> and <jats:italic>D. yunnanensis</jats:italic> regardless of bidirectional gene flow. Based on both plastid and nuclear genome‐scale data, our findings provide the most comprehensive and reliable phylogeny and evolutionary histories for <jats:italic>Dipelta</jats:italic> and enable further understanding of the origin and evolution of floristic endemisms of China.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.7000,"publicationDate":"2024-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Systematics and Evolution","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1111/jse.13076","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"Agricultural and Biological Sciences","Score":null,"Total":0}
引用次数: 0

Abstract

Dipelta Maxim. (Caprifoliaceae) is a Tertiary relic genus endemic to China, which includes three extant species, Dipelta floribunda, Dipelta yunnanensis, and Dipelta elegans. Recent progress in the systematics and phylogeographics of Dipelta has greatly broadened our knowledge about its origin and evolution, however, conflicted phylogenetic relationships and divergence times have been reported and warrant further investigation. Here, we utilized chloroplast genomes and population‐level genomic data restriction site‐associated DNA‐single nucleotide polymorphisms (RAD‐SNPs) to evaluate the interspecific relationships, population genetic structure and demographic histories of this genus. Our results confirmed the sister relationship between D. elegans and the D. yunnanensisD. floribunda group, but with cyto‐nuclear phylogenetic discordance observed in the latter. Coalescent simulations suggested that this discordance might be attributed to asymmetric “chloroplast capture” through introgressive hybridization between the two parapatric species. Our fossil‐calibrated plastid chronogram of Dipsacales and the coalescent modeling based on nuclear RAD‐SNPs simultaneously suggested that the three species of Dipelta diversified at the late Miocene, which may be related to the uplift of the eastern part of Qinghai–Tibet Plateau (QTP) and adjacent southwest China, and increasing Asian interior aridification since the late Miocene; while in the mid‐Pleistocene, the climatic transition and continuous uplift of the QTP, triggered allopatric speciation via geographical isolation for D. floribunda and D. yunnanensis regardless of bidirectional gene flow. Based on both plastid and nuclear genome‐scale data, our findings provide the most comprehensive and reliable phylogeny and evolutionary histories for Dipelta and enable further understanding of the origin and evolution of floristic endemisms of China.
基于核RAD-Seq和叶绿体基因组数据的中国特有蝶形花属的系统发育和分子年代学分析
Dipelta Maxim.(Dipelta Maxim(Caprifoliaceae)是中国特有的第三纪孑遗属,包括三个现生种:Dipelta floribunda、Dipelta yunnanensis 和 Dipelta elegans。最近在Dipelta系统学和系统地理学方面取得的进展极大地拓宽了我们对其起源和进化的认识,但也有报道称Dipelta的系统发生关系和分化时间存在冲突,需要进一步研究。在此,我们利用叶绿体基因组和种群水平的基因组数据限制性位点相关 DNA-单核苷酸多态性(RAD-SNPs)来评估该属的种间关系、种群遗传结构和人口历史。我们的结果证实了D. elegans与D. yunnanensis-D. floribunda组之间的姊妹关系,但在后者中观察到细胞核系统发育不一致。聚合模拟表明,这种不一致可能是由于这两个同域物种之间通过内向杂交进行了不对称的 "叶绿体捕获"。我们通过化石校准的Dipsacales质粒年代图和基于核RAD-SNPs的共生模型同时表明,Dipelta的三个物种在中新世晚期发生了分化,这可能与青藏高原东部和邻近的中国西南部的隆起以及中新世晚期以来亚洲内陆干旱化的加剧有关;而在早更新世中期,青藏高原的气候转变和持续隆起引发了D.云南滇金丝猴(D. yunnanensis)通过地理隔离实现了异源物种的形成,而不考虑基因的双向流动。基于质粒和核基因组尺度的数据,我们的研究结果为Dipelta提供了最全面、最可靠的系统发育和进化历史,有助于进一步了解中国特有植物的起源和进化。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
Journal of Systematics and Evolution
Journal of Systematics and Evolution Agricultural and Biological Sciences-Ecology, Evolution, Behavior and Systematics
CiteScore
7.40
自引率
8.10%
发文量
1368
审稿时长
6-12 weeks
期刊介绍: Journal of Systematics and Evolution (JSE, since 2008; formerly Acta Phytotaxonomica Sinica) is a plant-based international journal newly dedicated to the description and understanding of the biological diversity. It covers: description of new taxa, monographic revision, phylogenetics, molecular evolution and genome evolution, evolutionary developmental biology, evolutionary ecology, population biology, conservation biology, biogeography, paleobiology, evolutionary theories, and related subjects.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信