Resolving relationships despite past hybridization in Aliciella subsection Subnuda (Polemoniaceae)

IF 3.7 1区 生物学 Q1 Agricultural and Biological Sciences Journal of Systematics and Evolution Pub Date : 2023-07-28 DOI:10.1111/jse.13010
Theresa C. Saunders, J. Mark Porter, Leigh A. Johnson
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Abstract

Phylogenetics is crucial in the study of evolutionary processes and events transpiring in the course of species diversification. Phylogenetic studies within kingdom Plantae often reveal hybridization and introgression. Here, we study a subsection rife with historic hybridization and discuss the impacts of such processes on evolutionary trajectories. Aliciella subsection Subnuda comprises seven species of herbaceous plants occurring in Utah, the Navajo Nation, and the Four Corners region of North America. Previous molecular and morphological work left relationships in the subsection unresolved. Here, we use comparative DNA sequencing of nuclear ITS and chloroplast DNA regions and genome-wide RAD-seq data to clarify phylogenetic relationships and examine the role of hybridization in the subsection. We construct haplotype and nucleotype networks from chloroplast and nuclear ITS sequence matrices and compare nuclear and chloroplast phylogenies to identify multiple putative chloroplast capture events. The RAD-seq maximum likelihood phylogeny and multispecies coalescent species tree robustly resolve relationships between six species-level clades. We use STRUCTURE and HyDe on the RAD-seq data to evaluate the influence of hybridization within the subsection. The HyDe results suggest that hybridization has occurred among all species in the subsection at some point in their history. Cytonuclear discordance reveals historic chloroplast capture, and we discuss potential causes of the observed discordance. Our study robustly resolves relationships in Aliciella subsection Subnuda and provides a framework for discussing its speciation despite a history of hybridization and introgression.

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尽管 Aliciella subsection Subnuda(Polemoniaceae)过去发生过杂交,但仍能确定其关系
系统发生学对于研究物种多样化过程中的进化过程和事件至关重要。植物界的系统发育研究经常揭示杂交和引入。在这里,我们研究了一个充斥着历史性杂交的亚门,并讨论了这种过程对进化轨迹的影响。Aliciella亚科Subnuda由分布在犹他州、纳瓦霍部落和北美四角地区的7种草本植物组成。以前的分子和形态学研究没有解决该亚科的关系问题。在这里,我们利用核 ITS 和叶绿体 DNA 区域的比较 DNA 测序以及全基因组 RAD-seq 数据来阐明该亚种的系统发育关系,并研究杂交在该亚种中的作用。我们从叶绿体和核 ITS 序列矩阵中构建了单倍型和核型网络,并比较了核和叶绿体的系统发育,以确定多个推定的叶绿体捕获事件。RAD-seq 最大似然系统发生和多物种聚合物种树稳健地解析了六个物种级支系之间的关系。我们使用 STRUCTURE 和 HyDe 对 RAD-seq 数据进行分析,以评估分枝内杂交的影响。HyDe 结果表明,该亚区的所有物种在其历史的某个时期都发生过杂交。细胞核不一致性揭示了叶绿体捕获的历史,我们讨论了观察到的不一致性的潜在原因。我们的研究有力地解决了亚种苏木属(Aliciella subsection Subnuda)的关系问题,并提供了一个框架来讨论其物种分化问题,尽管其历史上曾发生过杂交和引入。
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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.
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