Fig. 1

Evolution of core histone genes from Marseilleviridae (MV). Phylogenetic analysis of all known histone-containing proteins predicted to be encoded in Marseilleviridae genomes, including Lausannevirus, Insectomime virus, Cannes 8 virus, Marseillevirus, and Melbourne virus, shows that these are slow evolving. This analysis also shows that Marseillevirus, Lausannevirus, and the Insectomime viral repertoires are representative of the full divergence within the MV family and are used exclusively in the remaining figures. a Shown is a phylogenetic analysis of the concatenated histone repertoires of each available MV genome conducted by the maximum likelihood (ML) method with the Le and Gascuel [8] amino acid substitution model [55]. The optimal tree with the highest log likelihood is shown along with the percentage of trees in which the associated taxa clustered together in the bootstrap test of 500 replicates. A discrete Gamma distribution was used to model evolutionary rate differences among sites (five categories). Branch lengths are measured in the number of substitutions per site. All positions with less than 70% site coverage were eliminated leaving a total of 635 positions in the final dataset. b A phylogenetic analysis of the concatenated histone repertoires of each available MV genome using the neighbor-joining method [56] gives the same result as in a. The percentages from 500 bootstrap replicate trees in which the associated taxa clustered together are shown next to the branches. Evolutionary distances were computed using the JTT matrix-based method [57] and are in the units of the number of amino acid substitutions per site. The rate variation among sites was modeled with a gamma distribution (shape parameter = 1). All positions containing gaps or missing data were eliminated leaving a total of 580 positions in the final dataset. Both the ML and NJ trees were computed using a ClustalW-based alignment of the concatenated peptide sequences from the H2B-H2A, H4-H3, and H2A-domain-containing (H2ADC) genes found in all MV genomes, and the MEGA6 software package [53]