富含类群和基因组规模的 Opisthokonta 系统发育。

IF 9.8 1区 生物学 Q1 Agricultural and Biological Sciences
PLoS Biology Pub Date : 2024-09-16 eCollection Date: 2024-09-01 DOI:10.1371/journal.pbio.3002794
Hongyue Liu, Jacob L Steenwyk, Xiaofan Zhou, Darrin T Schultz, Kevin M Kocot, Xing-Xing Shen, Antonis Rokas, Yuanning Li
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引用次数: 0

摘要

Opisthokonta--一个包括动物界、真菌界及其单细胞近缘生物的主要类群--内部的古老分化仍然存在争议。为了评估建立基因组尺度 Opisthokonta 系统发生学的进展,我们使用不同的同源推断方法推断出的基因集进行了分类群最丰富的系统发生学分析,并建立了 Opisthokonta 多样化的地质年表。我们还进行了敏感性分析,根据以前证明可以改善系统发生推断的过滤标准,从完整数据矩阵中抽取基因或类群。我们发现,在不同的数据矩阵和所用的方法中,大约 85% 的内部分支是一致的。值得注意的是,使用不同的同源物推断方法是造成观察到的不一致的主要原因:使用同一套同源物进行的分析显示出高达 97% 至 98% 的一致性,而使用不同的同源物则导致较低的一致性(87% 至 91%)。对单细胞 Holozoa 关系的研究表明,在不同基因集中观察到的不稳定性可能源于微弱的系统发育信号。我们的研究结果提供了一个全面的Opisthokonta系统发生学框架,它将有助于揭示有关两大真核生物界起源和多样化的远古进化事件,并强调了研究系统发生学分析中同源推断的影响以解决远古分化问题的重要性。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
A taxon-rich and genome-scale phylogeny of Opisthokonta.

Ancient divergences within Opisthokonta-a major lineage that includes organisms in the kingdoms Animalia, Fungi, and their unicellular relatives-remain contentious. To assess progress toward a genome-scale Opisthokonta phylogeny, we conducted the most taxon rich phylogenomic analysis using sets of genes inferred with different orthology inference methods and established the geological timeline of Opisthokonta diversification. We also conducted sensitivity analysis by subsampling genes or taxa from the full data matrix based on filtering criteria previously shown to improve phylogenomic inference. We found that approximately 85% of internal branches were congruent across data matrices and the approaches used. Notably, the use of different orthology inference methods was a substantial contributor to the observed incongruence: analyses using the same set of orthologs showed high congruence of 97% to 98%, whereas different sets of orthologs resulted in somewhat lower congruence (87% to 91%). Examination of unicellular Holozoa relationships suggests that the instability observed across varying gene sets may stem from weak phylogenetic signals. Our results provide a comprehensive Opisthokonta phylogenomic framework that will be useful for illuminating ancient evolutionary episodes concerning the origin and diversification of the 2 major eukaryotic kingdoms and emphasize the importance of investigating effects of orthology inference on phylogenetic analyses to resolve ancient divergences.

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来源期刊
PLoS Biology
PLoS Biology BIOCHEMISTRY & MOLECULAR BIOLOGY-BIOLOGY
CiteScore
15.40
自引率
2.00%
发文量
359
审稿时长
3-8 weeks
期刊介绍: PLOS Biology is the flagship journal of the Public Library of Science (PLOS) and focuses on publishing groundbreaking and relevant research in all areas of biological science. The journal features works at various scales, ranging from molecules to ecosystems, and also encourages interdisciplinary studies. PLOS Biology publishes articles that demonstrate exceptional significance, originality, and relevance, with a high standard of scientific rigor in methodology, reporting, and conclusions. The journal aims to advance science and serve the research community by transforming research communication to align with the research process. It offers evolving article types and policies that empower authors to share the complete story behind their scientific findings with a diverse global audience of researchers, educators, policymakers, patient advocacy groups, and the general public. PLOS Biology, along with other PLOS journals, is widely indexed by major services such as Crossref, Dimensions, DOAJ, Google Scholar, PubMed, PubMed Central, Scopus, and Web of Science. Additionally, PLOS Biology is indexed by various other services including AGRICOLA, Biological Abstracts, BIOSYS Previews, CABI CAB Abstracts, CABI Global Health, CAPES, CAS, CNKI, Embase, Journal Guide, MEDLINE, and Zoological Record, ensuring that the research content is easily accessible and discoverable by a wide range of audiences.
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