Toward a comprehensive phylogeny for mammalian and avian herpesviruses

With the aim of deriving a definitive phylogenetic tree for as many mammali an and avian herpesvirus species as possible, alignments were made of amino acid sequences from eight conserved and ubiquitously present genes of herp esviruses, with 48 virus species each represented by at least one gene. Phy logenetic trees for both single-gene and concatenated alignments were evalu ated thoroughly by maximum-likelihood methods, with each of the three herpe svirus subfamilies (the Alpha-, Beta-, and Gammaherpesvirinae) examined ind ependently. Composite trees were constructed starting with the top-scoring tree based on the broadest set of genes and supplemented by addition of vir us species from trees based on narrower gene sets, to give finally a 46-spe cies tree; branching order for three regions within the tree remained unres olved. Sublineages of the Alpha- and Betaherpesvirinae showed extensive cos peciation with host lineages by criteria of congruence in branching pattern s and consistency in extent of divergence. The Gammaherpesvirinae presented a more complex picture, with both higher and lower substitution rates in d ifferent sublineages. The final tree obtained represents the most detailed view to date of phylogenetic relationships in any family of large-genome vi ruses.