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The recA/RAD51 gene family encodes a diverse set of recombinase proteins thateffect homologous recombination, DNA-repair, and genome stability. The recAgene family is expressed in almost all species of Eubacteria, Archaea, andEukaryotes, and even in some viruses. To date, efforts to resolve the deepevolutionary origins of this ancient protein family have been hindered, inpart, by the high sequence divergence between families (i.e. ~30% identitybetween paralogous groups). Through (i) large taxon sampling, (ii) the use of aphylogenetic algorithm designed for measuring highly divergent paralogs, and(iii) novel Evolutionary Spatial Dynamics simulation and analytical tools, weobtained a robust, parsimonious and more refined phylogenetic history of therecA/RAD51 superfamily. Taken together, our model for the evolution ofrecA/RAD51 family provides a better understanding of ancient origin of recAproteins and multiple events leading to the diversification of recA homologs ineukaryotes, including the discovery of additional RAD51 sub-families.

Extraction of Deep Phylogenetic Signal and Improved Resolution of Evolutionary Events within the recA/RAD51 Phylogeny