Copyright (c) 2003 Society for Molecular Biology and Evolution

The extent to which viruses and their hosts codiverge remains an open question, given that numerous cases of both ‘cospeciation ’ and horizontal switching have been recently documented. DNA viruses that form persistent infections are thought to be the most likely candidates for phylogenetic congruence. Phylogenetic reconciliation analysis was used to compare established phylogenies for four RNA viruses and their hosts. The analysis employs a cophylogeny mapping technique, implemented in TREEMAP v2.0, to find the most parsimonious combinations of evolutionary events able to reconcile any incongruence. This technique is guaranteed to recover all potentially optimal solutions to the reconciled tree and specifically tests the null hypothesis that an associate phylogeny is no more congruent with a host phylogeny than would a random tree with the same taxon set. Phylogenies for Hantavirus, Spumavirus and avian sarkoma leukosis virus were found to be significantly similar to their host trees, whilst Lyssavirus and Arenavirus displayed no significant congruence. These results demonstrate that RNA viruses are able to form stable associations with their hosts over evolutionary timescales and that the details of such associations are consistent with persistent infection being a necessary but not sufficient precondition