Macrogenetic atlas of prokaryotes

Macrogenetics investigates the patterns and predictors of intraspecific genetic variation across diverse taxa, offering a framework to address longstanding evolutionary hypotheses. Here, we present a comprehensive macrogenetic atlas of prokaryotes (MAP), integrating genomic data (summarized by 30 parameters in 12 categories) from 15,235 prokaryotic species and population genetic data (35 parameters in 7 categories) from 786 species with phylogenetic, phenotypic, and ecological data. We illustrate the power and potential of the MAP by addressing a series of fundamental questions. For example, we provide evidence that genome size in prokaryotes depends on a balance between deletion bias and the beneficial effects of additional genes. Moreover, we show that long-range and short-range linkage disequilibrium represent quite different features of evolutionary dynamics and contribute independently to genetic diversity. Notably, we show that as within-species diversity increases, selection becomes an increasingly strong force structuring diversity, for example creating convergent ecospecies structures in Streptococcus mitis and S. oralis . Overall, our atlas represents a widely applicable resource and offers novel insights into the drivers of macroevolution and the life-cycle of prokaryotic species.