Phylogenetic analysis of NR2E NRs. Maximum Likelihood trees of ClustalW-aligned amino acid sequences were calculated using MEGA 5.0 [35,36]. Highly-divergent regions N-terminal to the DBD and C-terminal to the LBD were not included. A consensus tree generated from 500 bootstrap replicates and rooted to the Homo sapiens retinoic acid receptor gamma outgroup sequence is shown. Further details are provided in Methods. Species abbreviations (used throughout): Ce (or no annotation):Caenorhabditis elegans, Cb: Caenorhabditis briggsae, Bm: Brugia malayi, Pp: Pristionchus pacificus, Dm: Drosophila melanogaster, Ag: Anopheles gambiae, Tc: Tribolium castaneum, Sk: Saccoglossus kowalevskii, Sp: Strongylocentrotus purpuratus, Dr: Danio rerio, Xl: Xenopus laevis, Mm: Mus musculus, Gg: Gallus gallus, Hs: Homo sapiens, Nv: Nematostella vectensis, Aa: Aedes aegypti. Tree is proportionally scaled, with the scale bar indicating sequence distance in units of substitutions. Single diamonds identify branchpoints that were supported by >50 % of bootstrap replicates; double diamonds identify branchpoints that were supported by >95 % of bootstrap replicates. Numbers in red above selected branches show Ka/Ks ratios for the LBD portion only of NRs.
Weber et al. BMC Evolutionary Biology 2012 12:81 doi:10.1186/1471-2148-12-81