Experimental design in phylogenetics: testing predictions from expected information

Taxon and character sampling is central to phylogenetic experimental design yet we lack general rules. Goldman introduced a method to construct efficient sampling designs in phylogenetics, based on the calculation of expected Fisher information given a probabilistic model of sequence evolution. The considerable potential of this approach remains largely unexplored. In an earlier study, we applied Goldman’s method to a problem in the phylogenetics of caecilian amphibians and made an a priori evaluation and testable predictions of which taxon additions would increase information about a particular weakly supported branch of the caecilian phylogeny by the greatest amount. Using mitogenomic and rag1 sequences (some newly determined for this study) from additional caecilian species we studied how information (both expected and observed) and bootstrap support varies as each new taxon is individually added, providing the first empirical test of specific predictions made using Goldman’s method ...

分类单元与特征采样是系统发育实验设计的核心，但目前缺乏通用规则。Goldman提出了一种构建系统发育学高效采样设计的方法，该方法基于序列进化概率模型下期望费希尔信息（expected Fisher information）的计算。这种方法的巨大潜力在很大程度上仍未被发掘。在先前的一项研究中，我们将Goldman的方法应用于蚓螈两栖动物系统发育学的一个问题，对添加哪些分类单元能最大程度增加蚓螈系统发育树中某一弱支持分支的信息进行了先验评估和可检验预测。利用来自额外蚓螈物种的线粒体基因组序列和rag1序列（本研究中部分为新测定），我们研究了随着每个新分类单元的单独添加，信息（包括期望信息和观测信息）及bootstrap支持度（bootstrap support）如何变化，从而为使用Goldman方法做出的具体预测提供了首次实证检验……