Data from: An integrated model of phenotypic trait changes and site-specific sequence evolution

Recent years have seen a constant rise in the availability of trait data, including morphological features, ecological preferences, and life history characteristics. These phenotypic data provide means to associate genomic regions with phenotypic attributes, thus allowing the identification of phenotypic traits associated with the rate of genome and sequence evolution. However, inference methodologies that analyze sequence and phenotypic data in a unified statistical framework are still scarce. Here, we present TraitRateProp, a probabilistic method that allows testing whether the rate of sequence evolution is associated with a binary phenotypic character trait. The method further allows the detection of specific sequence sites whose evolutionary rate is most noticeably affected following the character transition, suggesting a shift in functional/structural constraints. TraitRateProp is first evaluated in simulations and then applied to study the evolutionary process of plastid plant genomes upon a transition to a heterotrophic lifestyle. To this end, we analyze 25 plastid genes across 85 orchid species, spanning different lifestyles and representing different genera in this large family of flowering plants. Our results indicate higher evolutionary rates following repeated transitions to a heterotrophic lifestyle in all but four of the loci analyzed.近年来，性状数据的可获取性持续提升，涵盖形态特征、生态偏好以及生活史特征。这些表型数据为关联基因组区域与表型性状提供了途径，进而可识别与基因组及序列进化速率相关的表型性状。然而，在统一统计框架内分析序列与表型数据的推断方法仍较为稀缺。本文提出TraitRateProp——一种可检验序列进化速率是否与二元表型性状相关联的概率方法。该方法还可检测在性状转变后进化速率受到最显著影响的特定序列位点，这暗示了功能/结构约束的改变。本研究首先通过模拟实验对TraitRateProp进行评估，随后将其应用于探究植物质体基因组在转变为异养生活方式后的进化过程。为此，我们分析了85种兰科植物的25个质体基因，这些物种涵盖不同生活方式，隶属于开花植物大科兰科下的多个属。我们的结果显示，在所分析的基因座中，除4个基因座外，其余所有基因座在多次转变为异养生活方式后均呈现出更高的进化速率。