Whole genome data confirm pervasive gene discordance in the evolutionary history of Coenonympha (Nymphalidae) butterflies

IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Molecular Phylogenetics and Evolution Pub Date : 2024-10-28 DOI:10.1016/j.ympev.2024.108222
Matthew P. Greenwood , Thibaut Capblancq , Niklas Wahlberg , Laurence Després
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Abstract

Phylogenetic inference is challenged by genealogical heterogeneity amongst molecular markers. Such discordance is driven predominantly by incomplete lineage sorting (ILS) and interspecific gene flow, and bears attendant consequences for the accurate resolution of species relationships. Understanding the distribution of gene conflict in organismal genomes is, therefore, a key aspect of phylogenetic analysis. In this study, three large phylogenomic datasets (i.e., whole mitogenomes, conserved nuclear protein-coding loci, and genomic windows) are used to probe the extent to which discordance pervades the unresolved phylogeny of Coenonympha (Nymphalidae) butterflies. Gene tree discordance is found to be elevated at multiple historically recalcitrant phylogenetic positions. In particular, species relationships near the crown of Coenonympha and within a rapidly diversifying subclade (the hero group) remain difficult to resolve, suggesting that ILS and gene flow have obscured the evolution of this genus. These findings have implications for the taxonomy of this butterfly group and the study of its diversification history. In addition, this work lends support to a growing body of evidence that gene conflict driven by biological processes stands to confound phylogeny, even when extensive data are used.

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全基因组数据证实了蛱蝶科(Coenonympha)蝴蝶进化史中普遍存在的基因不一致现象。
系统发育推断受到分子标记间系谱异质性的挑战。这种不一致性主要是由不完全世系分选(ILS)和种间基因流动造成的,并对物种关系的准确解析产生相应的影响。因此,了解生物基因组中基因冲突的分布是系统发育分析的一个关键方面。本研究利用三个大型系统发生组数据集(即全有丝分裂基因组、保守的核蛋白编码位点和基因组窗口)来探究蛱蝶科(Coenonympha)蝴蝶未解决的系统发生中的不一致程度。研究发现,在多个历史上难以解决的系统发育位置上,基因树的不一致性较高。特别是,蝶冠附近的物种关系和一个快速多样化的亚支系(英雄群)内的物种关系仍然难以解决,这表明ILS和基因流掩盖了该属的进化。这些发现对该蝶类的分类学及其多样化历史的研究具有重要意义。此外,这项工作还为越来越多的证据提供了支持,这些证据表明,即使使用了大量数据,由生物过程驱动的基因冲突也会混淆系统发生学。
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来源期刊
Molecular Phylogenetics and Evolution
Molecular Phylogenetics and Evolution 生物-进化生物学
CiteScore
7.50
自引率
7.30%
发文量
249
审稿时长
7.5 months
期刊介绍: Molecular Phylogenetics and Evolution is dedicated to bringing Darwin''s dream within grasp - to "have fairly true genealogical trees of each great kingdom of Nature." The journal provides a forum for molecular studies that advance our understanding of phylogeny and evolution, further the development of phylogenetically more accurate taxonomic classifications, and ultimately bring a unified classification for all the ramifying lines of life. Phylogeographic studies will be considered for publication if they offer EXCEPTIONAL theoretical or empirical advances.
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