Assessing a Role of Genetic Drift for Deep-Time Evolutionary Events

Effective population size (N_e) determines the amount of genetic diversity and the fate of genetic variants in a species and thus is an essential parameter in evolutionary genetics. There are standard approaches to determine the N_e of evolving species. For example, the long-term N_e of an extant species is calculated based on its unbiased global mutation rate and the neutral genetic diversity of the species. However, approaches for inferring N_e of ancestral lineages are less known. Here, we introduce an evolutionary genetic statistic and an analytical procedure to assess the efficiency of natural selection for deep nodes by calculating rates of nonsynonymous nucleotide substitutions leading to radical (d_R) and conservative (d_C) amino acid replacements, respectively. Given that radical variants are more likely to be deleterious than conservative ones, an elevated d_R/d_C ratio in gene families across the genome means an accelerated genome-wide accumulation of the more deleterious type of mutations (i.e., radical variants), which indicates that natural selection is less efficient and genetic drift becomes more powerful. Earlier approaches that calculate d_R/d_C do not consider the impact of nucleotide composition (G+C content) on the d_R/d_C result, which is partially accounted for in more recent methods. Here, we use these methods to demonstrate that genetic drift may have driven the early evolution of Prochlorococcus, the most abundant carbon-fixing photosynthetic bacteria in the ocean.