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In this work we develop a microscopic physical model of early evolution,where phenotype,organism life expectancy, is directly related to genotype, thestability of its proteins in their native conformations which can be determinedexactly in the model. Simulating the model on a computer, we consistentlyobserve the Big Bang scenario whereby exponential population growth ensues assoon as favorable sequence-structure combinations (precursors of stableproteins) are discovered. Upon that, random diversity of the structural spaceabruptly collapses into a small set of preferred proteins. We observe thatprotein folds remain stable and abundant in the population at time scales muchgreater than mutation or organism lifetime, and the distribution of thelifetimes of dominant folds in a population approximately follows a power law.The separation of evolutionary time scales between discovery of new folds andgeneration of new sequences gives rise to emergence of protein families andsuperfamilies whose sizes are power-law distributed, closely matching the samedistributions for real proteins. On the population level we observe emergenceof species, subpopulations which carry similar genomes. Further we present asimple theory that relates stability of evolving proteins to the sizes ofemerging genomes. Together, these results provide a microscopic firstprinciples picture of how first gene families developed in the course of earlyevolution

A first-principles model of early evolution: Emergence of gene families, species and preferred protein folds