The use of high-throughput sequencing technologies to produce genome-scale data sets was expected to settle some long-standing controversies across the Tree of Life, particularly in areas where short branches occur at deep timescales. Instead, these data sets have often yielded many well-supported but conflicting topologies, and highly variable gene-tree distributions. A variety of branch-support metrics beyond the nonparametric bootstrap are now available to assess how robust a phylogenetic hypothesis may be, as well as new methods to quantify gene-tree discordance. We applied multiple branch-support metrics to a study of an ancient group of marine fishes (Teleostei: Pelagiaria) whose interfamilial relationships have proven difficult to resolve due to a rapid accumulation of lineages very early in its history. We analyzed hundreds of loci including published ultraconserved elements and newly generated exonic data along with their flanking regions to represent all 16 extant families for more than 150 out of 284 valid species in the group. Branch support was typically lower at inter- than intra-familial relationships regardless of the type of marker used. Several nodes that were highly supported with bootstrap had a very low site and gene-tree concordance, revealing underlying conflict. Despite this conflict, we were able to identify four consistent interfamilial clades, each comprised of two or three families. Combining exons with their flanking regions also produced increased branch lengths at the deep branches of the pelagiarian tree. Our results demonstrate the limitations of employing current metrics of branch support and species-tree estimation when assessing the confidence of ancient evolutionary radiations and emphasize the necessity to embrace alternative measurements to explore phylogenetic uncertainty and discordance in phylogenomic data sets.[Concatenation; exons; introns; phylogenomics; species-tree methods; target capture.]

中文翻译：

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测试分支支持替代指标的效用，以解决金枪鱼、Stromateoids 和盟友的古代进化辐射 (Teleostei: Pelagiaria)

使用高通量测序技术产生基因组规模的数据集有望解决生命之树中一些长期存在的争议，特别是在深度时间尺度上出现短分支的区域。相反，这些数据集通常会产生许多得到充分支持但相互冲突的拓扑结构，以及高度可变的基因树分布。现在可以使用非参数引导程序之外的各种分支支持指标来评估系统发育假设的稳健性，以及量化基因树不一致的新方法。我们将多个分支支持指标应用于对一组古老的海洋鱼类 (Teleostei: Pelagiaria) 的研究，这些鱼类的家族关系已被证明由于其历史早期谱系的快速积累而难以解决。我们分析了数百个基因座，包括已发表的超保守元素和新生成的外显子数据及其侧翼区域，以代表该组 284 个有效物种中超过 150 个的所有 16 个现存科。无论使用的标记类型如何，分支支持通常低于家庭内部关系。bootstrap 高度支持的几个节点的站点和基因树一致性非常低，揭示了潜在的冲突。尽管存在这种冲突，我们还是能够确定四个一致的家族间分支，每个分支由两三个家庭组成。将外显子与其侧翼区域相结合还可以在 pelagarian 树的深分支处产生增加的分支长度。我们的结果证明了在评估古代进化辐射的置信度时使用当前分支支持和物种树估计指标的局限性，并强调有必要采用替代测量来探索系统发育数据集中的系统发育不确定性和不一致。外显子；内含子；系统基因组学；物种树方法；目标捕获。]