Figure 2.

Phylogeny and domain organization of CED-4/Apaf-1 homologs. This phylogeny was calculated using a Bayesian approach (MrBayes) based on a MAFFT alignment of the NB-ARC domains. Posterior probability values are shown for each branch (top numbers). Bootstrap support values for branches that are supported by a minimal evolution method (FastME) based on a PROBCONS alignment are also shown (bottom numbers; for detailed information, see Materials and methods). Furthermore, phylogenies based on full-length alignments of the subset of all Apaf-1 homologs exhibiting a CARD-NB-ARC-WD40 domain composition (all vertebrate sequences, 1_BRAFL, 18_NEMVE, and Dark_DROME) as well as 28_DROPS, CED4_CAAEL, and 31_CAEBR showed precisely the same picture: a clade of vertebrate, amphioxus, and Nematostella sequences under exclusion of insect and nematode sequences. For a detailed list of protein sequences see Additional data file 2. For clarity, sequences from S. purpuratus (2), and B. floridae (6), which appear to be redundant and/or results of erroneous assemblies, are not included in this figure; however, their inclusion/exclusion does not change the quality/interpretation of this phylogeny. All sequences are from complete genomes, except the individual sequences from Aedes aegypti, Caenorhabditis briggsae, Drosophila pseudoobscura, and Tribolium castaneum.