A Comparative Analysis of Long-Term Effective Population Sizes Across Eukaryotes

The effective population size (N_e) is a fundamental parameter in population genetics. Despite its central importance, there are relatively few estimates of N_e available and there have been limited attempts to compare values across eukaryotes. Here, we estimate long-term effective population sizes for 120 species, broadly distributed across the eukaryotic tree of life, using nucleotide diversity and direct mutation rate estimates. We find that N_e varies by nearly 4 orders of magnitude and that it shows strong phylogenetic structure across broad taxonomic scales but not within individual lineages. Phylogenetically controlled regressions reveal that Nₑ correlates with key life history traits, including generation time and propagule size, and that nucleotide diversity serves as a useful proxy for Nₑ. Finally, we show that small Nₑ is generally associated with a reduction in the efficacy of natural selection, as indicated by an elevated ratio of non-synonymous to synonymous diversity (π_N/π_S), but not with an increase in genome size after accounting for phylogenetic non-independence. These results provide a broad comparative perspective on the factors driving variation in Nₑ and its evolutionary consequences across eukaryotes.