Species-tree topology impacts the inference of ancient whole-genome duplications across the angiosperm phylogeny

IF 2.4 2区 生物学 Q2 PLANT SCIENCES
Michael T. W. McKibben, Geoffrey Finch, Michael S. Barker
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引用次数: 0

Abstract

Premise

The history of angiosperms is marked by repeated rounds of ancient whole-genome duplications (WGDs). Here we used state-of-the-art methods to provide an up-to-date view of the distribution of WGDs in the history of angiosperms that considers both uncertainty introduced by different WGD inference methods and different underlying species-tree hypotheses.

Methods

We used the distribution synonymous divergences (Ks) of paralogs and orthologs from transcriptomic and genomic data to infer and place WGDs across two hypothesized angiosperm phylogenies. We further tested these WGD hypotheses with syntenic inferences and Bayesian models of duplicate gene gain and loss.

Results

The predicted number of WGDs in the history of angiosperms (~170) based on the current taxon sampling is largely similar across different inference methods, but varies in the precise placement of WGDs on the phylogeny. Ks-based methods often yield alternative hypothesized WGD placements due to variation in substitution rates among lineages. Phylogenetic models of duplicate gene gain and loss are more robust to topological variation. However, errors in species-tree inference can still produce spurious WGD hypotheses, regardless of method used.

Conclusions

Here we showed that different WGD inference methods largely agree on an average of 3.5 WGD in the history of individual angiosperm species. However, the precise placement of WGDs on the phylogeny is subject to the WGD inference method and tree topology. As researchers continue to test hypotheses regarding the impacts ancient WGDs have on angiosperm evolution, it is important to consider the uncertainty of the phylogeny as well as WGD inference methods.

物种树拓扑结构影响整个被子植物系统发育过程中古老的全基因组复制的推断。
前言:被子植物的历史以反复发生古老的全基因组重复(WGD)为标志。在此,我们使用最先进的方法提供了被子植物历史上 WGDs 分布的最新观点,该观点考虑了不同 WGD 推断方法和不同基本物种树假说所带来的不确定性:方法:我们利用转录组和基因组数据中旁系和直系同义差异(Ks)的分布来推断WGD,并将其置于两个假定的被子植物系统发生中。我们还利用同源推断和贝叶斯重复基因增减模型进一步检验了这些WGD假说:结果:根据目前的分类群取样,被子植物历史上 WGD 的预测数量(约 170 个)在不同的推断方法中基本相似,但在 WGD 在系统发育上的精确位置上存在差异。基于 Ks 的方法往往会由于世系间替代率的差异而产生不同的 WGD 假设位置。重复基因增减的系统发生学模型对拓扑结构的变化更为稳健。然而,无论使用哪种方法,物种树推断中的错误仍会产生虚假的 WGD 假设:在这里,我们发现不同的WGD推断方法在被子植物个体历史中平均3.5个WGD上基本一致。然而,WGD 在系统发育中的精确位置取决于 WGD 推断方法和树的拓扑结构。在研究人员继续检验古代WGD对被子植物进化影响的假设时,必须考虑到系统发育的不确定性以及WGD推断方法。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
American Journal of Botany
American Journal of Botany 生物-植物科学
CiteScore
4.90
自引率
6.70%
发文量
171
审稿时长
3 months
期刊介绍: The American Journal of Botany (AJB), the flagship journal of the Botanical Society of America (BSA), publishes peer-reviewed, innovative, significant research of interest to a wide audience of plant scientists in all areas of plant biology (structure, function, development, diversity, genetics, evolution, systematics), all levels of organization (molecular to ecosystem), and all plant groups and allied organisms (cyanobacteria, algae, fungi, and lichens). AJB requires authors to frame their research questions and discuss their results in terms of major questions of plant biology. In general, papers that are too narrowly focused, purely descriptive, natural history, broad surveys, or that contain only preliminary data will not be considered.
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