Department of Biology, Colorado State University, Fort Collins, CO 80523, USA.
Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA.
Mol Phylogenet Evol. 2021 May;158:107092. doi: 10.1016/j.ympev.2021.107092. Epub 2021 Feb 2.
In two-step coalescent analyses of phylogenomic data, gene-tree topologies are treated as fixed prior to species-tree inference. Although all gene-tree conflict is assumed to be caused by lineage sorting when applying these methods, in empirical datasets much of the conflict can be caused by estimation error. Weakly supported and even arbitrarily resolved clades are important sources of this estimation error for gene trees inferred from few informative characters relative to the number of sampled terminals, and the resulting extraneous conflict among gene trees can negatively impact species-tree inference. In this study, we quantified the relative severity of alternative methods for collapsing gene-tree branches for seven empirical datasets and quantified their effects on species-tree inference. The branch-collapsing methods that we employed were based on the strict consensus of optimal topologies, various bootstrap thresholds, and 0% approximate likelihood ratio test (SH-like aLRT) support. Up to 86% of internal gene-tree branches are dubiously or arbitrarily resolved in reanalyses of these published phylogenomic datasets, and collapsing these branches increased inferred species-tree coalescent branch lengths by up to 455%. For two datasets, the longer inferred branch lengths sometimes impacted inference of anomaly-zone conditions. Although branch-collapsing methods did not consistently affect the species-tree topology, they often increased branch support. The more severe and clearly justified gene-tree branch-collapsing methods, which we recommend be broadly applied for two-step coalescent analyses, are use of the strict consensus in parsimony analyses and the collapse clades with 0% SH-like aLRT support in likelihood analyses. Collapsing dubiously or arbitrarily resolved branches in gene trees sometimes improved congruence between coalescent-based results and concatenation trees. In such cases, we contend that the resolution provided by concatenation should be preferred and that incomplete lineage sorting is a poor explanation for the initial conflict between phylogenetic approaches.
在两步合并分析中，在进行物种树推断之前，基因树拓扑结构被视为固定的。虽然在应用这些方法时，所有的基因树冲突都被认为是由谱系分选引起的，但在经验数据集中，大部分冲突是由估计误差引起的。对于从相对较少的信息量特征推断出的基因树来说，支持较弱甚至任意解决的分支是这种估计误差的重要来源，并且基因树之间的这种多余冲突会对物种树推断产生负面影响。在这项研究中，我们量化了七种经验数据集的基因树分支合并方法的相对严重程度，并量化了它们对物种树推断的影响。我们使用的分支合并方法基于最优拓扑的严格共识、各种引导阈值和 0%近似似然比检验（SH-like aLRT）支持。在对这些已发表的基因组数据集的重新分析中，高达 86%的内部基因树分支是可疑的或任意解决的，合并这些分支增加了推断的物种树合并分支长度最多达 455%。对于两个数据集，推断的较长分支长度有时会影响异常区条件的推断。尽管分支合并方法并不一致地影响物种树拓扑结构，但它们经常增加分支支持。更严重和明确合理的基因树分支合并方法，我们建议广泛应用于两步合并分析，是使用简约分析中的严格共识和在似然分析中合并具有 0% SH-like aLRT 支持的分支。在基因树中合并可疑或任意解决的分支有时可以提高基于合并的结果与串联树之间的一致性。在这种情况下，我们认为串联提供的分辨率应该是首选的，并且不完全谱系分选是最初两种方法之间冲突的一个较差解释。
