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.

当对数据集进行分区操作时，若各子集拥有不同的进化历史，生成的子集可能携带系统发育冲突信号（phylogenetically conflicting signals）。对于包含大量分类群（taxa）的数据集，单个携有多套进化历史的分类群可能引发显著的全局系统发育冲突，但目前简约法框架（parsimony framework）下尚无方法可将冲突定位至系统发育的特定支系（clades），并在局部尺度上检验冲突的显著性。本文提出一种新方法，可量化系统发育中任意支系的数据集分区之间的冲突，并通过一种名为局部冲突长度差异（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（transcriptional regulators）家族，在后生动物（metazoan）的发育与生理过程中发挥关键作用。所有核受体均由多个离散结构域组成，其中一个结构域可结合特定靶基因上的DNA应答元件（DNA response elements），另一个则可结合相应的配体（ligand）。我们对这两个结构域分别开展了系统发育分析（phylogenetic analyses），并联合进行了整合分析，同时检验了“核受体仅通过简单的谱系分裂与分化（lineage splitting and divergence）进化，未发生结构域改组（domain shuffling）或蛋白质间序列转移（sequence transfer）”这一假说。我们的分析结果表明，在系统发育树的少数节点处，分区后的两个结构域之间存在显著冲突，这暗示有若干受体组属于由古老核受体间结构域改组或其他形式序列转移形成的杂合蛋白（hybrid proteins）。