Data from: A new method to localize and test the significance of incongruence: detecting domain shuffling in the nuclear receptor superfamily

When a data set is partitioned, the resulting subsets may contain phylogenetically conflicting signals if they have different evolutionary histories. In a data set with many taxa, a single taxon that contains multiple phylogenetic histories may result in significant global incongruence, but no methods are available in a parsimony framework to localize incongruence to specific clades in a phylogeny and test the significance of incongruence on a local scale. Here we present a new method to quantify the conflict between data partitions for any clade in a phylogeny and to test the statistical significance of that conflict using a metric called the local incongruence length difference. We apply this method to the evolutionary history of the nuclear receptor superfamily, a large group of transcriptional regulators that play essential roles in metazoan development and physiology. All nuclear receptors are composed of several discrete domains, including one that binds to DNA response elements on specific target genes and another that binds to the appropriate ligand. We have performed combined and separate phylogenetic analyses of these two domains and have tested the hypothesis that nuclear receptors have evolved by a simple process of lineage splitting and divergence, without domain shuffling or other forms of sequence transfer between proteins. Our analysis indicates that significant conflict exists between the partitioned domains at a limited number of nodes on the tree, suggesting that several groups of receptors are "hybrid proteins" formed by domain shuffling or other forms of sequence transfer between more ancient nuclear receptors.

当数据集被划分后，若所得子集具有不同的进化历史，则可能包含系统发育冲突信号（phylogenetically conflicting signals）。在包含众多分类群（taxa）的数据集里，单个包含多种进化历史的分类群（taxon）可能会导致显著的全局系统发育不一致性，但目前简约法框架（parsimony framework）下尚无方法能够将不一致性定位到系统发育中的特定进化支（clade），并在局部尺度上检验不一致性的显著性。本文提出一种新方法，可量化系统发育中任意进化支对应的数据集划分之间的冲突，并通过名为局部不一致性长度差（local incongruence length difference）的指标检验该冲突的统计学显著性。我们将该方法应用于核受体超家族（nuclear receptor superfamily）的进化历史研究——核受体超家族是一类庞大的转录调控因子家族，在后生动物（metazoan）的发育与生理过程中发挥核心作用。所有核受体均由多个离散结构域（domain）组成，其中一个结构域可结合特定靶基因上的DNA应答元件，另一个结构域则可结合相应的配体（ligand）。我们对这两个结构域分别开展了联合与独立的系统发育分析，并检验了如下假说：核受体仅通过谱系分裂与分化的简单过程进化，未发生结构域洗牌（domain shuffling）或蛋白质间序列转移等其他形式的演化事件。分析结果显示，在系统发育树的少数节点处，划分得到的结构域之间存在显著冲突，这表明部分受体类群属于"杂交蛋白"，由古老核受体之间的结构域洗牌或其他形式的蛋白质间序列转移形成。