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（trait data）的可获取性持续提升，此类数据涵盖形态特征、生态偏好以及生活史特征。这些表型数据（phenotypic data）为基因组区域与表型性状的关联分析提供了可行途径，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，在统一统计框架下同时分析序列与表型数据的推断方法仍较为匮乏。本研究提出TraitRateProp——一种可检验序列进化速率是否与二元表型性状相关的概率性方法。该方法还可检测进化速率在性状转变后受影响最为显著的特定序列位点，这提示功能/结构约束发生了改变。本研究首先通过模拟实验对TraitRateProp进行性能评估，随后将其应用于探究植物质体基因组向异养生活方式转变过程中的进化动态。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，且隶属于该大型开花植物类群中的不同属。分析结果显示，除4个基因座外，其余所有被分析的基因座在多次向异养生活方式转变后均呈现出更高的进化速率。