Department of Ichthyology, Sam Noble Oklahoma Museum of Natural History, 2401 Chautauqua Avenue, Norman, OK 73072, USA.
Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Richards Hall Norman, OK 73019, USA.
Syst Biol. 2021 Oct 13;70(6):1123-1144. doi: 10.1093/sysbio/syab018.
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.].
高通量测序技术被用于产生基因组规模的数据，这原本有望解决生命之树上长期存在的一些争议，尤其是在分支较短且处于深远时间尺度的区域。然而，这些数据集往往产生了许多得到很好支持但相互冲突的拓扑结构，以及高度可变的基因树分布。现在有许多超越非参数引导的分支支持度量标准，可用于评估一个系统发育假说的稳健性，以及量化基因树分歧的新方法。我们应用了多种分支支持度量标准，对一组古老的海洋鱼类（Teleostei: Pelagiaria）进行了研究，由于其历史早期快速积累的谱系，其种间关系一直难以解决。我们分析了数百个基因座，包括已发表的超保守元件和新生成的外显子数据，以及它们的侧翼区域，以代表该组 284 个有效物种中的 150 多个物种的所有 16 个现存科。无论使用哪种标记，种间关系的分支支持通常低于种内关系。一些用引导法高度支持的节点具有非常低的位点和基因树一致性，揭示了潜在的冲突。尽管存在这种冲突，但我们能够确定四个一致的种间支系，每个支系由两个或三个科组成。将外显子与其侧翼区域结合使用，也增加了 pelagiarian 树深支的分支长度。我们的结果表明，在评估古老进化辐射的置信度时，当前的分支支持和种系树估计度量标准存在局限性，并强调有必要采用替代方法来探索系统发育不确定性和基因数据集的分歧。
