Phylotranscriptomic discordance is best explained by incomplete lineage sorting within Allium subgenus Cyathophora and thus hemiplasy accounts for interspecific trait transition.

IF 8.7 1区 医学 Q1 OBSTETRICS & GYNECOLOGY
American journal of obstetrics and gynecology Pub Date : 2023-07-17 eCollection Date: 2024-01-01 DOI:10.1016/j.pld.2023.07.004
Zengzhu Zhang, Gang Liu, Minjie Li
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引用次数: 0

Abstract

The transition of traits between genetically related lineages is a fascinating topic that provides clues to understanding the drivers of speciation and diversification. Much can be learned about this process from phylogeny-based trait evolution. However, such inference is often plagued by genome-wide gene-tree discordance (GTD), mostly due to incomplete lineage sorting (ILS) and/or introgressive hybridization, especially when the genes underlying the traits appear discordant. Here, by collecting transcriptomes, whole chloroplast genomes (cpDNA), and population genetic datasets, we used the coalescent model to turn GTD into a source of information for ILS and employed hemiplasy to explain specific cases of apparent "phylogenetic discordance" between different morphological traits and probable species phylogeny in the Allium subg. Cyathophora. Both concatenation and coalescence methods consistently showed the same phylogenetic topology for species tree inference based on single-copy genes (SCGs), as supported by the KS distribution. However, GTD was high across the genomes of subg. Cyathophora: ∼27%-38.9% of the SCG trees were in conflict with the species tree. Plasmid and nuclear incongruence was also present. Our coalescent simulations indicated that such GTD was mainly a product of ILS. Our hemiplasy risk factor calculations supported that random fixation of ancient polymorphisms in different populations during successive speciation events along the subg. Cyathophora phylogeny may have caused the character transition, as well as the anomalous cpDNA tree. Our study exemplifies how phylogenetic noise can be transformed into evolutionary information for understanding character state transitions along species phylogenies.

系统转录组不一致的最佳解释是薤白亚属 Cyathophora 内不完全的世系分类,因此半混杂现象是种间性状转变的原因。
基因相关种系之间性状的转变是一个引人入胜的话题,它为了解物种分化和多样化的驱动因素提供了线索。从基于系统发育的性状进化过程中可以了解到很多有关这一过程的信息。然而,这种推断往往受到全基因组基因树不一致性(GTD)的困扰,这主要是由于不完全品系分类(ILS)和/或内向杂交造成的,尤其是当性状的基础基因出现不一致时。在这里,通过收集转录组、全叶绿体基因组(cpDNA)和种群遗传数据集,我们利用聚合模型将GTD转化为ILS的信息源,并利用半聚合(hemiplasy)来解释薤白亚种中不同形态性状与可能的物种系统发育之间明显的 "系统发育不一致 "的具体情况。在基于单拷贝基因(SCGs)的物种树推断中,连接法和聚合法始终显示出相同的系统发生拓扑结构,这一点得到了 KS 分布的支持。然而,在 Cyathophora 亚种的基因组中,GTD 很高:27%-38.9% 的 SCG 树与物种树相冲突。质粒和核不一致的情况也同样存在。我们的聚合模拟表明,这种 GTD 主要是 ILS 的产物。我们的半混杂风险因子计算表明,在 Cyathophora 亚种的系统发育过程中,不同种群中古多态性的随机固定可能是导致特征转变以及 cpDNA 树异常的原因。我们的研究举例说明了如何将系统发育噪音转化为进化信息,以了解物种系统发育过程中的特征状态转变。
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来源期刊
CiteScore
15.90
自引率
7.10%
发文量
2237
审稿时长
47 days
期刊介绍: The American Journal of Obstetrics and Gynecology, known as "The Gray Journal," covers the entire spectrum of Obstetrics and Gynecology. It aims to publish original research (clinical and translational), reviews, opinions, video clips, podcasts, and interviews that contribute to understanding health and disease and have the potential to impact the practice of women's healthcare. Focus Areas: Diagnosis, Treatment, Prediction, and Prevention: The journal focuses on research related to the diagnosis, treatment, prediction, and prevention of obstetrical and gynecological disorders. Biology of Reproduction: AJOG publishes work on the biology of reproduction, including studies on reproductive physiology and mechanisms of obstetrical and gynecological diseases. Content Types: Original Research: Clinical and translational research articles. Reviews: Comprehensive reviews providing insights into various aspects of obstetrics and gynecology. Opinions: Perspectives and opinions on important topics in the field. Multimedia Content: Video clips, podcasts, and interviews. Peer Review Process: All submissions undergo a rigorous peer review process to ensure quality and relevance to the field of obstetrics and gynecology.
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