Macrogenetic atlas of prokaryotes reveals selection-driven structures

Macrogenetics investigates patterns and predictors of intraspecific genetic variation across diverse taxa, offering a framework for understanding species diversity and addressing evolutionary hypotheses. Here, we present a macrogenetic atlas of prokaryotes (MAP), integrating genomic data (30 parameters in 12 categories) from 15,235 prokaryotic species and population genetic data (22 parameters in 7 categories) from 786 species with phylogenetic, phenotypic, and ecological information. MAP enables quantitative species characterization, straightforward cross-species comparisons, and easy generation, testing, and refinement of evolutionary hypotheses. For example, our analyses show that long- and short-range genetic linkage capture distinct evolutionary dynamics and independently shape genetic diversity, contradicting neutral theory. Instead, we propose that as within-species diversity increases, epistatic selection becomes an increasingly strong force structuring diversity, exemplified by convergent ecospecies structures in Streptococcus mitis and S. oralis . Overall, MAP represents a widely applicable resource ( www.genomap.cn ) and offers novel insights into the drivers of macroevolution and the life cycle of prokaryotic species.