ABSTRACT
Seventy-two
full genomes corresponding to nine mammalian (67 strains) and two avian
(5 strains) polyomavirus species were analyzed using maximum likelihood
and Bayesian methods of phylogenetic inference. Our fully resolved and
well-supported (bootstrap proportions > 90%; posterior
probabilities = 1.0) trees separate the bird polyomaviruses
(avian polyomavirus and goose hemorrhagic polyomavirus) from the
mammalian polyomaviruses, which supports the idea of spitting the genus
into two subgenera. Such a split is also consistent with the different
viral life strategies of each group. Simian (simian virus 40, simian
agent 12 [Sa12], and lymphotropic polyomavirus) and rodent (hamster
polyomavirus, mouse polyomavirus, and murine pneumotropic polyomavirus
[MPtV]) polyomaviruses did not form monophyletic groups. Using our best
hypothesis of polyomavirus evolutionary relationships and established
host phylogenies, we performed a cophylogenetic reconciliation analysis
of codivergence. Our analyses generated six optimal cophylogenetic
scenarios of coevolution, including 12 codivergence events (P< 0.01), suggesting that Polyomaviridae coevolved with
their avian and mammal hosts. As individual lineages, our analyses
showed evidence of host switching in four terminal branches leading to
MPtV, bovine polyomavirus, Sa12, and BK virus, suggesting a combination
of vertical and horizontal transfer in the evolutionary history of the
polyomaviruses.