Generalization of the Central Models of Evolutionary Biology in the (post)Genomic Era
summary
Comparative analysis of hundreds of microbial genomes using the ATGC database and the COUNT maximum‑likelihood birth‑death‑innovation model reveals a robust tripartite gene‑frequency landscape (core, shell, cloud), extreme rate variation across lineages, and very rapid genome flux—often thousands of gene family gains/losses per nucleotide‑substitution timescale. Horizontal transfer dominates duplication (horizontal transfer >> duplication), inferred supergenome sizes are typically an order of magnitude larger than single genomes (supergenome ~10× genome), and a conserved relative‑rate “universal pacemaker” fits the data better than a strict molecular clock.
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