Myriad environmental and biological traits have been investigated for their roles in influencing the rate of molecular evolution across various taxonomic groups. However, most studies have focused on a single trait, while controlling for additional factors in an informal way, generally by excluding taxa. This study utilized a dataset of cytochrome c oxidase subunit I (COI) barcode sequences from over 7000 ray-finned fish species to test the effects of 27 traits on molecular evolutionary rates. Environmental traits such as temperature were considered, as were traits associated with effective population size including body size and age at maturity. It was hypothesized that these traits would demonstrate significant correlations with substitution rate in a multivariable analysis due to their associations with mutation and fixation rates, respectively. A bioinformatics pipeline was developed to assemble and analyze sequence data retrieved from the Barcode of Life Data System (BOLD) and trait data obtained from FishBase. For use in phylogenetic regression analyses, a maximum likelihood tree was constructed from the COI sequence data using a multi-gene backbone constraint tree covering 71% of the species. A variable selection method that included both single- and multivariable analyses was used to identify traits that contribute to rate heterogeneity estimated from different codon positions. Our analyses revealed that molecular rates associated most significantly with latitude, body size, and habitat type. Overall, this study presents a novel and systematic approach for integrative data assembly and variable selection methodology in a phylogenetic framework.

已经研究了无数环境和生物特征在影响不同分类群的分子进化速度方面的作用。然而，大多数研究都集中在一个单一的特征上，同时以非正式的方式控制其他因素，通常是通过排除分类群。本研究利用细胞色素c的数据集氧化酶亚基 I (COI) 条形码序列来自超过 7000 种射线鳍鱼类，以测试 27 种性状对分子进化速率的影响。考虑了温度等环境特征，以及与有效种群规模相关的特征，包括体型和成熟年龄。假设这些性状分别与突变和固定率相关，因此在多变量分析中与替代率显着相关。开发了一个生物信息学管道来组装和分析从生命条码数据系统 (BOLD) 检索到的序列数据和从 FishBase 获得的性状数据。用于系统发育回归分析，使用覆盖 71% 物种的多基因骨架约束树从 COI 序列数据构建最大似然树。包括单变量和多变量分析的变量选择方法用于鉴定有助于从不同密码子位置估计的比率异质性的性状。我们的分析表明，分子率与纬度、体型和栖息地类型最相关。总体而言，本研究为系统发育框架中的综合数据组装和变量选择方法提供了一种新颖且系统的方法。我们的分析表明，分子率与纬度、体型和栖息地类型最相关。总体而言，本研究为系统发育框架中的综合数据组装和变量选择方法提供了一种新颖且系统的方法。我们的分析表明，分子率与纬度、体型和栖息地类型最相关。总体而言，本研究为系统发育框架中的综合数据组装和变量选择方法提供了一种新颖且系统的方法。