Revisiting the determinants of molecular evolutionary rate variation

Abstract Rates of molecular evolution are key parameters for understanding the processes shaping biological diversity. These rates vary among lineages and loci, correlating with ecological, intrinsic biological, and genomic factors such as generation time, metabolic rate, climate, and DNA repair efficiency. Despite many correlational studies, the causal nature of these relationships remains unclear, limiting their interpretation at macroevolutionary scales. Estimating mutation rates is a difficult task that requires deep sequencing to detect germline mutations. Thus, fixed substitutions are often used as proxies for mutation rates, although they do not directly represent mutational processes due to natural selection and genetic drift. The interplay among mutation, selection, drift, and effective population size demands careful interpretation of rate variation among species. The main proposed hypotheses link life-history and environmental factors to genomic mutation, DNA repair efficiency, and fixation. However, interdependence and collinearity among these traits hinder causal inference, particularly in traditional correlational analyses. In this review, we revisit these hypotheses, highlighting their assumptions, predictions, and methodological limitations. We propose that advancing the understanding of molecular evolutionary rates requires a shift in focus: instead of seeking ultimate causes, we must identify the traits most proximately linked to the underlying mechanistic pathways, using causal models to disentangle direct and indirect effects in a standardized way across clades.