Ultraconserved genomic elements (UCEs) are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes does not require prior knowledge of genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here we characterized UCEs from 11 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated 4 different sets of UCE markers by genomic category from 5 different studies including: birds, mammals, fish, Hymenoptera (ants, wasps, and bees) and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by 2 or more UCEs, corresponding to non-overlapping segments of a single gene. We considered these UCEs to be non-independent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging co-genic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees was significantly improved across all datasets apparently driven by the increase in loci length. Additionally, we conducted simulations and found that gene trees generated from merged UCEs were more accurate than those generated by unmerged UCEs. As loci length improves gene tree accuracy, this modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses.

中文翻译：

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UCE 的基因组表征和管理改善了物种树的重建

在系统发育分析中，超保守基因组元件 (UCE) 通常被视为独立的基因座。UCE 探针的鉴定流程不需要遗传同一性的先验知识，只需选择高度保守、单拷贝、无重复且具有特定长度的基因座。在这里，我们表征了从鸟类到海洋无脊椎动物的动物生命树的 11 项系统发育研究中的 UCE。我们发现在脊椎动物谱系中，UCE 主要是内含子和基因间的，而在无脊椎动物中，大多数是外显子。然后，我们根据来自 5 项不同研究的基因组类别整理了 4 组不同的 UCE 标记，这些研究包括：鸟类、哺乳动物、鱼类、膜翅目（蚂蚁、黄蜂和蜜蜂）和鞘翅目（甲虫）。在 UCE 捕获的基因中，我们发现许多基因由 2 个或更多 UCE 表示，对应于单个基因的非重叠片段。我们认为这些UCEs是非独立的，将属于特定基因的所有UCEs合并，构建基因树和种树，然后评估合并同基因UCEs对基因和种树重建的后续影响。在所有数据集中，对合并 UCE 基因树的平均引导支持得到显着改善，这显然是由基因座长度的增加驱动的。此外，我们进行了模拟，发现合并 UCE 生成的基因树比未合并 UCE 生成的基因树更准确。由于基因座长度提高了基因树的准确性，这种适度的 UCE 表征和管理影响了下游分析，并证明了将基本基因组表征纳入系统发育分析的优势。