Figure 3

A maximum likelihood phylogeny of the core eIF4E domain using the Le and Gascuel (LG) amino acid substitution matrix with gamma site to site rates and including representatives of the three major alveolate lineages (ciliates, apicomplexans, and dinoflagellates) and the outgroup heterokonts. Bootstrap values (1000 replicates) above 55% are shown. The three major clades are highlighted with the right-most brackets. The major clades were defined by the presence of core dinoflagellates and the outgroup heterokonts. The different heterokont, ciliate and apicomplexan clades are labeled, while the nine core dinoflagellate sub-clades are denoted with brackets and the clade names used in the text. The individual species labels have been removed for clarity with three examples of core dinoflagellates represented by colored dots as shown in the key. The distribution of two syndinean dinoflagellates and Perkinsus marinus are also shown. The Class II eIF4E found only in heterokonts is shown in a grey background. Long branches for the ciliates in eIF4E-1 and Chromera velia were broken and joined with dotted lines to fit onto the page. The inset category plot shows the number of eIF4E family members in each of the nine eIF4E sub-clades across all eleven core dinoflagellates with the same color coding for the three example core dinoflagellate species as on the phylogeny. The tree including genus and species names is available in Additional file 3 in nexus format.