神经翼目昆虫系统基因组学中多类型基因组数据的不一致表现及其解决方法

IF 4.9 1区 农林科学 Q1 ENTOMOLOGY
Ruyue Zhang, Liming Wang, Shuo Tian, Yang Liu, Yunlan Jiang, Xiaofan Zhou, Ding Yang, Xingyue Liu, Yuyu Wang
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引用次数: 0

摘要

生命之树的重建面临着基于基因组时代大数据的准确、稳健的系统发育推断的挑战。目前,通用单拷贝同源物(USCOs)、超保守元件(UCEs)和线粒体基因组(mitogenomics)被广泛用于重建系统发育。本研究基于42个新测序的低覆盖基因组(32.80X以上)的USCOs、UCEs和有丝分裂基因组,在各种类型的数据过滤、模型选择和树重建策略下,重构了草蛉及其亲缘目(Neuropterida)的所有目和所有科(Rhachiberothidae)。使用相对保守的标准,我们证明了在位点异质性模型(LG + PMSF (C20))下,基于氨基酸矩阵的多因子策略过滤的USCOs拓扑结构是最稳健的。平均自举支持度(ABS)是基因过滤的重要指标,在不同的重复数之间存在较大的差异。通过比较三种不同的校准方案(较深节点、较浅节点和两者的组合),在接近系统发育根的较深节点应用化石校准证明有助于更准确地估计进化时间尺度。这些结果突出了基因组数据的复杂性,并为克服系统基因组推断中的系统错误提供了一个综合解决方案。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Inconsistent performance of multi-type genomic data in phylogenomics of neuropteridan insects, with solutions toward conflicting results

Inconsistent performance of multi-type genomic data in phylogenomics of neuropteridan insects, with solutions toward conflicting results

Inconsistent performance of multi-type genomic data in phylogenomics of neuropteridan insects, with solutions toward conflicting results

Inconsistent performance of multi-type genomic data in phylogenomics of neuropteridan insects, with solutions toward conflicting results

Reconstructing the tree of life is facing challenges in inferring accurate and robust phylogeny based on large data in the genomic era. Currently, universal single-copy orthologs (USCOs), ultraconserved elements (UCEs) and mitochondrial genomes (mitogenomes) are widely used to reconstruct phylogeny. In this study, the higher-level phylogeny of lacewings and allied orders (Neuropterida) is reconstructed based on USCOs, UCEs and mitogenomes assembled from 42 newly sequenced low-coverage genomes (above 32.80X), representing all orders and all families except Rhachiberothidae, under various types of data filtering, model selection and strategies of tree reconstruction. Using relatively conservative criteria, we demonstrate that the topology based on amino acid matrices of the USCOs filtered by multifactorial strategies under the site heterogeneity model (LG + PMSF (C20)) is the most robust. The average bootstrap support (ABS) values, an important criterion in gene filtering, exhibit large variation among different repetitions. Applying fossil calibrations at deeper nodes close to the root of the phylogeny is demonstrated to facilitate more accurate estimation of evolutionary timescales by comparing three different calibration schemes (deeper nodes, shallower nodes and a combination of both). These results highlight the complexity of genomic data and offer an integrative solution to overcome systematic error in phylogenomic inference.

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来源期刊
Systematic Entomology
Systematic Entomology 生物-进化生物学
CiteScore
10.50
自引率
8.30%
发文量
49
审稿时长
>12 weeks
期刊介绍: Systematic Entomology publishes original papers on insect systematics, phylogenetics and integrative taxonomy, with a preference for general interest papers of broad biological, evolutionary or zoogeographical relevance.
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