The phylogenetic tree of selected plant myosins reveals distinct subtypes. Maximum-likelihood topology generated under the JTT + Γ model in RAxML showing branch lengths for the motor domains of 221 ingroup class VIII and XI myosins and five class V outgroup myosins. CD-Hit (90% idenity) was used to obtain a representative dataset for subtype classification and visualization. Support for the major branchings indicating the grouping of the plant myosins into different class VIII and class XI subtypes is given as posterior probability (MrBayes), likelihood bootstrap (RAxML) and neighbour-joining bootstrap (ClustalW), all in percentages (the trees including all branch support values are available as Additional file 3). Despite the general strong support for major branches by all methods (like the separation of spermatophytes from mosses and ferns), some of the subtype groupings are not similarly supported. For instance, the separation of subtype 11C from subtype 11D myosins, which is well supported by MrBayes (posterior probability support of 98%), is only poorly supported in the neighbour-joining tree (18%). Class V myosins of Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus and Saccharomyces cerevisiae were used as outgroup. The scale bar corresponds to estimated amino acid substitutions per site. All species abbreviations used in the tree are listed in Figure 2 and Additional file 13.
Mühlhausen and Kollmar BMC Evolutionary Biology 2013 13:202 doi:10.1186/1471-2148-13-202