The estimation of robust and accurate measures of branch support has proven challenging in the era of phylogenomics. In datasets of potentially millions of sites, bootstrap support for bifurcating relationships around very short internal branches can be inappropriately inflated. Such over-estimation of branch support may be particularly problematic in rapid radiations, where phylogenetic signal is low and incomplete lineage sorting severe. Here, we explore this issue by comparing various branch support estimates under both concatenated and coalescent frameworks, in the recent radiation Australo-Papuan murine rodents (Muridae: Hydromyini). Using nucleotide sequence data from 1245 independent loci and several phylogenomic inference methods, we unequivocally resolve the majority of genus-level relationships within Hydromyini. However, at four nodes we recover inconsistency in branch support estimates both within and among concatenated and coalescent approaches. In most cases, concatenated likelihood approaches using standard fast bootstrap algorithms did not detect any uncertainty at these four nodes, regardless of partitioning strategy. However, we found this could be overcome with two-stage resampling, i.e. across genes and sites within genes (using -bsam GENESITE in IQtree). In addition, low confidence at recalcitrant nodes was recovered using UFBoot2, a recent revision to the bootstrap protocol in IQtree, but this depended on partitioning strategy. Summary coalescent approaches also failed to detect uncertainty under some circumstances. For each of four recalcitrant nodes, an equivalent (or close to equivalent) number of genes were in strong support (> 75% bootstrap) of both the primary and at least one alternative topological hypothesis, suggesting notable phylogenetic conflict among loci not detected using some standard branch support metrics. Recent debate has focused on the appropriateness of concatenated versus multi-genealogical approaches to resolving species relationships, but less so on accurately estimating uncertainty in large datasets. Our results demonstrate the importance of employing multiple approaches when assessing confidence, and highlight the need for greater attention to the development of robust measures of uncertainty in the era of phylogenomics.

中文翻译：

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系统基因组学揭示了澳大利亚-巴布亚啮齿动物快速辐射的信心和冲突

在系统基因组学时代，对分支支持的稳健和准确测量的估计已被证明具有挑战性。在可能包含数百万个站点的数据集中，对围绕非常短的内部分支的分叉关系的引导支持可能会被不当夸大。这种对分支支持的高估可能在快速辐射中尤其成问题，其中系统发育信号低且谱系分类不完整。在这里，我们通过在最近的辐射 Australo-Papuan 鼠啮齿动物（Muridae：Hydromyini）中比较串联和合并框架下的各种分支支持估计来探讨这个问题。使用来自 1245 个独立基因座的核苷酸序列数据和几种系统发育推断方法，我们明确地解决了 Hydromyini 中的大多数属级关系。然而，在四个节点，我们恢复了连接和合并方法内部和之间的分支支持估计的不一致。在大多数情况下，无论分区策略如何，使用标准快速引导算法的级联似然方法都没有检测到这四个节点的任何不确定性。然而，我们发现这可以通过两阶段重采样来克服，即跨基因和基因内的位点（在 IQtree 中使用 -bsam GENESITE）。此外，使用 UFBoot2（IQtree 中引导协议的最新修订版）恢复了顽固节点的低置信度，但这取决于分区策略。在某些情况下，汇总合并方法也未能检测到不确定性。对于四个顽固节点中的每一个，等量（或接近等量）的基因都得到了强有力的支持 (> 75% bootstrap) 的主要和至少一个替代拓扑假设，表明使用一些标准分支支持度量未检测到的位点之间存在显着的系统发育冲突。最近的争论集中在解决物种关系的串联方法与多谱系方法的适当性上，但在准确估计大型数据集中的不确定性方面则较少。我们的结果证明了在评估置信度时采用多种方法的重要性，并强调需要更多地关注在系统基因组学时代开发可靠的不确定性措施。最近的争论集中在解决物种关系的串联方法与多谱系方法的适当性上，但在准确估计大型数据集中的不确定性方面则较少。我们的结果证明了在评估置信度时采用多种方法的重要性，并强调在系统基因组学时代，需要更多地关注开发可靠的不确定性度量。最近的争论集中在解决物种关系的串联方法与多谱系方法的适当性上，但在准确估计大型数据集中的不确定性方面则较少。我们的结果证明了在评估置信度时采用多种方法的重要性，并强调需要更多地关注在系统基因组学时代开发可靠的不确定性措施。