Taxon Influence Index: assessing taxon-induced incongruities in phylogenetic inference

Understanding the evolutionary history of species is at the core of molecular evolution and is done using several inference methods. The critical issue is to quantify the uncertainty of the inference. The posterior probabilities in Bayesian phylogenetic inference and the bootstrap values in frequentist approaches measure the variability of the estimates due to the sampling of sites from genes and the sampling of genes from genomes. However, they do not measure the uncertainty due to taxon sampling. Taxa that experienced molecular homoplasy, recent selection, a spur of evolution and so forth may disrupt the inference and cause incongruences in the estimated phylogeny. We define a Taxon Influence Index to assess the influence of each taxon on the phylogeny. We found that although most taxa have a weak influence on the phylogeny, a small fraction of influential taxa strongly alter it, even in clades only loosely related to them. We conclude that highly influential taxa should be given special attention and sampling them more thoroughly can lead to more dependable phylogenies.

阐明物种的演化历程是分子进化研究的核心议题，当前学界通常借助多种推断方法开展相关研究。其中的关键科学问题在于量化推断结果的不确定性。贝叶斯系统发育推断（Bayesian phylogenetic inference）中的后验概率，与频率学派框架下的自举值（bootstrap values），可用于衡量由基因位点采样与基因组内基因采样所导致的估计值变异，但此类指标无法反映类群采样带来的不确定性。经历分子同塑性、近期选择、演化爆发等演化事件的类群，可能干扰系统发育推断过程，致使估计得到的系统发育树出现拓扑冲突。为此我们定义了类群影响指数（Taxon Influence Index），用以评估每个类群对系统发育树的影响程度。研究结果表明，尽管绝大多数类群对系统发育树的影响微弱，但仅占少数的高影响力类群会显著改变系统发育拓扑结构，即便在与其亲缘关系较远的支系（clade）中亦是如此。综上，我们认为应当对高影响力类群予以特别关注，通过对这类类群开展更充分的采样，可获得更为可靠的系统发育推断结果。