综合框架揭示了橡树和栎科(Fagaceae)近缘植物早期辐射过程中广泛的基因流动。

IF 9.3 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Shui-Yin Liu, Ying-Ying Yang, Qin Tian, Zhi-Yun Yang, Shu-Feng Li, Paul J Valdes, Alex Farnsworth, Heather R Kates, Carolina M Siniscalchi, Robert P Guralnick, Douglas E Soltis, Pamela S Soltis, Gregory W Stull, Ryan A Folk, Ting-Shuang Yi
{"title":"综合框架揭示了橡树和栎科(Fagaceae)近缘植物早期辐射过程中广泛的基因流动。","authors":"Shui-Yin Liu, Ying-Ying Yang, Qin Tian, Zhi-Yun Yang, Shu-Feng Li, Paul J Valdes, Alex Farnsworth, Heather R Kates, Carolina M Siniscalchi, Robert P Guralnick, Douglas E Soltis, Pamela S Soltis, Gregory W Stull, Ryan A Folk, Ting-Shuang Yi","doi":"10.1111/jipb.13773","DOIUrl":null,"url":null,"abstract":"<p><p>Although the frequency of ancient hybridization across the Tree of Life is greater than previously thought, little work has been devoted to uncovering the extent, timeline, and geographic and ecological context of ancient hybridization. Using an expansive new dataset of nuclear and chloroplast DNA sequences, we conducted a multifaceted phylogenomic investigation to identify ancient reticulation in the early evolution of oaks (Quercus). We document extensive nuclear gene tree and cytonuclear discordance among major lineages of Quercus and relatives in Quercoideae. Our analyses recovered clear signatures of gene flow against a backdrop of rampant incomplete lineage sorting, with gene flow most prevalent among major lineages of Quercus and relatives in Quercoideae during their initial radiation, dated to the Early-Middle Eocene. Ancestral reconstructions including fossils suggest ancestors of Castanea + Castanopsis, Lithocarpus, and the Old World oak clade probably co-occurred in North America and Eurasia, while the ancestors of Chrysolepis, Notholithocarpus, and the New World oak clade co-occurred in North America, offering ample opportunity for hybridization in each region. Our study shows that hybridization-perhaps in the form of ancient syngameons like those seen today-has been a common and important process throughout the evolutionary history of oaks and their relatives. Concomitantly, this study provides a methodological framework for detecting ancient hybridization in other groups.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3000,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"An integrative framework reveals widespread gene flow during the early radiation of oaks and relatives in Quercoideae (Fagaceae).\",\"authors\":\"Shui-Yin Liu, Ying-Ying Yang, Qin Tian, Zhi-Yun Yang, Shu-Feng Li, Paul J Valdes, Alex Farnsworth, Heather R Kates, Carolina M Siniscalchi, Robert P Guralnick, Douglas E Soltis, Pamela S Soltis, Gregory W Stull, Ryan A Folk, Ting-Shuang Yi\",\"doi\":\"10.1111/jipb.13773\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Although the frequency of ancient hybridization across the Tree of Life is greater than previously thought, little work has been devoted to uncovering the extent, timeline, and geographic and ecological context of ancient hybridization. Using an expansive new dataset of nuclear and chloroplast DNA sequences, we conducted a multifaceted phylogenomic investigation to identify ancient reticulation in the early evolution of oaks (Quercus). We document extensive nuclear gene tree and cytonuclear discordance among major lineages of Quercus and relatives in Quercoideae. Our analyses recovered clear signatures of gene flow against a backdrop of rampant incomplete lineage sorting, with gene flow most prevalent among major lineages of Quercus and relatives in Quercoideae during their initial radiation, dated to the Early-Middle Eocene. Ancestral reconstructions including fossils suggest ancestors of Castanea + Castanopsis, Lithocarpus, and the Old World oak clade probably co-occurred in North America and Eurasia, while the ancestors of Chrysolepis, Notholithocarpus, and the New World oak clade co-occurred in North America, offering ample opportunity for hybridization in each region. Our study shows that hybridization-perhaps in the form of ancient syngameons like those seen today-has been a common and important process throughout the evolutionary history of oaks and their relatives. Concomitantly, this study provides a methodological framework for detecting ancient hybridization in other groups.</p>\",\"PeriodicalId\":195,\"journal\":{\"name\":\"Journal of Integrative Plant Biology\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":9.3000,\"publicationDate\":\"2024-09-19\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Integrative Plant Biology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1111/jipb.13773\",\"RegionNum\":1,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Integrative Plant Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1111/jipb.13773","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0

摘要

尽管生命之树上古代杂交的频率比以前想象的要高,但很少有人致力于揭示古代杂交的程度、时间轴以及地理和生态背景。利用核DNA和叶绿体DNA序列的新数据集,我们进行了多方面的系统发生组调查,以确定橡树(Quercus)早期进化中的古老网状结构。我们记录了栎科植物主要世系和栎属近缘植物之间广泛的核基因树和细胞核不一致性。我们的分析发现,在猖獗的不完全品系分选背景下,基因流动的特征非常明显,在栎科植物的主要品系和近缘植物的最初辐射期间,基因流动最为普遍,可追溯到始新世早中期。包括化石在内的祖先重建表明,Castanea + Castanopsis、Lithocarpus 和旧大陆橡树支系的祖先可能在北美和欧亚大陆共生,而 Chrysolepis、Notholithocarpus 和新大陆橡树支系的祖先则在北美共生,这为每个地区的杂交提供了充分的机会。我们的研究表明,在橡树及其近缘植物的整个进化史中,杂交--也许是以今天所见的古代合子的形式--是一个常见而重要的过程。同时,这项研究也为检测其他类群的古老杂交提供了一个方法框架。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
An integrative framework reveals widespread gene flow during the early radiation of oaks and relatives in Quercoideae (Fagaceae).

Although the frequency of ancient hybridization across the Tree of Life is greater than previously thought, little work has been devoted to uncovering the extent, timeline, and geographic and ecological context of ancient hybridization. Using an expansive new dataset of nuclear and chloroplast DNA sequences, we conducted a multifaceted phylogenomic investigation to identify ancient reticulation in the early evolution of oaks (Quercus). We document extensive nuclear gene tree and cytonuclear discordance among major lineages of Quercus and relatives in Quercoideae. Our analyses recovered clear signatures of gene flow against a backdrop of rampant incomplete lineage sorting, with gene flow most prevalent among major lineages of Quercus and relatives in Quercoideae during their initial radiation, dated to the Early-Middle Eocene. Ancestral reconstructions including fossils suggest ancestors of Castanea + Castanopsis, Lithocarpus, and the Old World oak clade probably co-occurred in North America and Eurasia, while the ancestors of Chrysolepis, Notholithocarpus, and the New World oak clade co-occurred in North America, offering ample opportunity for hybridization in each region. Our study shows that hybridization-perhaps in the form of ancient syngameons like those seen today-has been a common and important process throughout the evolutionary history of oaks and their relatives. Concomitantly, this study provides a methodological framework for detecting ancient hybridization in other groups.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Journal of Integrative Plant Biology
Journal of Integrative Plant Biology 生物-生化与分子生物学
CiteScore
18.00
自引率
5.30%
发文量
220
审稿时长
3 months
期刊介绍: Journal of Integrative Plant Biology is a leading academic journal reporting on the latest discoveries in plant biology.Enjoy the latest news and developments in the field, understand new and improved methods and research tools, and explore basic biological questions through reproducible experimental design, using genetic, biochemical, cell and molecular biological methods, and statistical analyses.
×
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