亲爱的研友该休息了!由于当前在线用户较少,发布求助请尽量完整的填写文献信息,科研通机器人24小时在线,伴您度过漫漫科研夜!身体可是革命的本钱,早点休息,好梦!

Incomplete lineage sorting and gene flow within Allium (Amayllidaceae)

生物 溯祖理论 系统发育树 系统发育学 进化生物学 系统发育网络 网状进化 最大节俭 单系 分子系统发育学 遗传学 基因 克莱德
作者
Z Zhang,Gang Liu,Minjie Li
出处
期刊:Molecular Phylogenetics and Evolution [Elsevier]
卷期号:: 108054-108054
标识
DOI:10.1016/j.ympev.2024.108054
摘要

The phylogeny and systematics of the genus Allium have been studied with a variety of diverse data types, including an increasing amount of molecular data. However, strong phylogenetic discordance and high levels of uncertainty have prevented the identification of a consistent phylogeny. The difficulty in establishing phylogenetic consensus and evidence for genealogical discordance make Allium a compelling test case to assess the relative contribution of incomplete lineage sorting (ILS), gene flow and gene tree estimation error on phylogenetic reconstruction. In this study, we obtained 75 transcriptomes of 38 Allium species across 10 subgenera. Whole plastid genome, single copy genes and consensus CDS were generated to estimate phylogenetic trees both using coalescence and concatenation methods. Multiple approaches including coalescence simulation, quartet sampling, reticulate network inference, sequence simulation, theta of ILS and reticulation index were carried out across the CDS gene trees to investigate the degrees of ILS, gene flow and gene tree estimation error. Afterward, a regression analysis was used to test the relative contributions of each of these forms of uncertainty to the final phylogeny. Despite extensive topological discordance among gene trees, we found a fully supported species tree that agrees with the most of well-accepted relationships and establishes monophyly of the genus Allium. We presented clear evidence for substantial ILS across the phylogeny of Allium. Further, we identified two ancient hybridization events for the formation of the second evolutionary line and subg. Butomissa as well as several introgression events between recently diverged species. Our regression analysis revealed that gene tree inference error and gene flow were the two most dominant factors explaining for the overall gene tree variation, with the difficulty in disentangling the effects of ILS and gene tree estimation error due to a positive correlation between them. Based on our efforts to mitigate the methodological errors in reconstructing trees, we believed ILS and gene flow are two principal reasons for the oft-reported phylogenetic heterogeneity of Allium. This study presents a strongly-supported and well-resolved phylogenetic backbone for the sampled Allium species, and exemplifies how to untangle heterogeneity in phylogenetic signal and reconstruct the true evolutionary history of the target taxa.

科研通智能强力驱动
Strongly Powered by AbleSci AI
更新
大幅提高文件上传限制,最高150M (2024-4-1)

科研通是完全免费的文献互助平台,具备全网最快的应助速度,最高的求助完成率。 对每一个文献求助,科研通都将尽心尽力,给求助人一个满意的交代。
实时播报
额狐狸发布了新的文献求助10
1秒前
李鱼丸完成签到,获得积分10
4秒前
matilda完成签到 ,获得积分10
11秒前
Ava应助_ban采纳,获得10
20秒前
希望天下0贩的0应助LYL采纳,获得10
28秒前
35秒前
36秒前
XiongLuck给XiongLuck的求助进行了留言
40秒前
40秒前
40秒前
方远锋完成签到,获得积分10
41秒前
星辰大海应助林lin采纳,获得10
44秒前
无花果应助科研通管家采纳,获得10
48秒前
上官若男应助科研通管家采纳,获得10
48秒前
爱静静应助科研通管家采纳,获得30
48秒前
48秒前
爱静静应助科研通管家采纳,获得10
48秒前
WerWu完成签到,获得积分10
51秒前
chen完成签到,获得积分10
58秒前
1分钟前
bkagyin应助CSS采纳,获得10
1分钟前
XiongLuck发布了新的文献求助10
1分钟前
1分钟前
1分钟前
liu完成签到,获得积分10
1分钟前
liu发布了新的文献求助10
1分钟前
徐叽钰应助liu采纳,获得20
1分钟前
1分钟前
魔幻问薇完成签到 ,获得积分10
1分钟前
顾矜应助huanglu采纳,获得10
1分钟前
不开心就吃糖完成签到 ,获得积分10
1分钟前
小蘑菇应助XiongLuck采纳,获得10
1分钟前
梅赛德斯奔驰完成签到,获得积分10
1分钟前
任ren完成签到 ,获得积分10
1分钟前
Akim应助cyk采纳,获得10
2分钟前
潼潼完成签到 ,获得积分10
2分钟前
kaustal完成签到,获得积分10
2分钟前
2分钟前
2分钟前
清新的芷发布了新的文献求助10
2分钟前
高分求助中
The Young builders of New china : the visit of the delegation of the WFDY to the Chinese People's Republic 1000
юрские динозавры восточного забайкалья 800
English Wealden Fossils 700
Chen Hansheng: China’s Last Romantic Revolutionary 500
宽禁带半导体紫外光电探测器 388
Case Research: The Case Writing Process 300
Global Geological Record of Lake Basins 300
热门求助领域 (近24小时)
化学 医学 生物 材料科学 工程类 有机化学 生物化学 物理 内科学 纳米技术 计算机科学 化学工程 复合材料 基因 遗传学 催化作用 物理化学 免疫学 量子力学 细胞生物学
热门帖子
关注 科研通微信公众号,转发送积分 3142628
求助须知:如何正确求助?哪些是违规求助? 2793540
关于积分的说明 7806835
捐赠科研通 2449789
什么是DOI,文献DOI怎么找? 1303444
科研通“疑难数据库(出版商)”最低求助积分说明 626917
版权声明 601314