Resolving deep nodes in an ancient radiation of neotropical fishes in the presence of conflicting signals from incomplete lineage sorting

Resolving patterns of ancient and rapid diversifications is one of the most challenging tasks in evolutionary biology. These difficulties arise from confusing phylogenetic signals that are associated with the interplay of incomplete lineage sorting and homoplasy. Phylogenomic analyses of hundreds, or even thousands, of loci offer the potential to resolve such contentious relationships. Yet, how much useful phylogenetic information these large data sets contain remains uncertain and often goes untested. Here, we assess the utility of different data filtering approaches to maximize phylogenetic information and minimize noise when reconstructing an ancient radiation of Neotropical electric knifefishes (Order Gymnotiformes) using ultraconserved elements. We found two contrasting hypotheses of gymnotiform evolutionary relationships depending on whether phylogenetic inferences were based on concatenation or coalescent methods. In the first case, all analyses inferred a previously—and commonly..., Online Appendix 1Extended Methods section including: DNA Extraction and Library Preparation, and Target Enrichment and Sequencing of UCEs.Aldaetal_SystBio_Appendix1.pdfOnline Appendix 2Extended Methods section including: Assembly and Alignment of Sequence Capture Data.Aldaetal_SystBio_Appendix2.pdfgymno_full_dataset_min75_completeIndividual UCE loci alignments that are common to at least 75% of taxa in the full dataset of Gymnotiformes (966 loci, 47 taxa). Codes for individual names in README.gymno_reduced_dataset_min75_completeIndividual UCE loci alignments that are common to at least 75% of taxa in the reduced dataset of Gymnotiformes (1472 loci, 11 taxa). Name codes in README.txt.gymno_reduced_dataset_100_completeIndividual UCE loci alignments that are common to 100% of taxa in the reduced dataset of Gymnotiformes (368 loci, 11 taxa). Codes for individual names in README.gymno_full_dataset_min75_concatenated.nexConcatenated matrix of UCE loci in common to at least 75% of taxa in the ...

解析古老快速辐射演化的模式是演化生物学领域最具挑战性的研究课题之一。此类难题源于与不完全谱系分选（incomplete lineage sorting）和趋同演化（homoplasy）相互作用相关的混淆性系统发育信号。对数百乃至数千个基因座开展系统发育组学分析，具备解决这类争议性亲缘关系的潜力。然而，此类大型数据集究竟蕴含多少可用的系统发育信息，目前仍无定论，且相关检验常被忽略。

本研究针对新热带区电鳗类（裸背电鳗目Gymnotiformes）的古老辐射演化事件，采用超保守元件（ultraconserved elements, UCEs）开展系统发育重建，评估不同数据过滤策略在最大化系统发育信息含量、最小化噪声干扰方面的效用。研究发现，依据串联法（concatenation）或溯祖分析法（coalescent methods）开展系统发育推断时，会得到两种截然不同的裸背电鳗目演化关系假说：在第一种假说框架下，所有分析均支持此前已提出且被广泛认可的……

在线附录1：包含DNA提取、文库构建以及超保守元件靶向富集与测序的扩展方法章节，文件名为Aldaetal_SystBio_Appendix1.pdf。
在线附录2：包含序列捕获数据组装与比对的扩展方法章节，文件名为Aldaetal_SystBio_Appendix2.pdf。

gymno_full_dataset_min75_complete：针对完整裸背电鳗目数据集（966个基因座，47个分类单元），包含至少75%分类单元所共有的单个超保守元件基因座比对文件，分类单元名称代码详见README文件。
gymno_reduced_dataset_min75_complete：针对精简裸背电鳗目数据集（1472个基因座，11个分类单元），包含至少75%分类单元所共有的单个超保守元件基因座比对文件，分类单元名称代码详见README.txt文件。
gymno_reduced_dataset_100_complete：针对精简裸背电鳗目数据集（368个基因座，11个分类单元），包含所有100%分类单元所共有的单个超保守元件基因座比对文件，分类单元名称代码详见README文件。
gymno_full_dataset_min75_concatenated.nex：包含至少75%分类单元所共有的超保守元件基因座的串联矩阵文件……