Figure 1: Molecular Phylogenetic Analysis of Nuclear Receptors. We generated a phylogenetic tree using the Maximum Likelihood method based on the Dayhoff matrix based model [266] from amino acid sequences of selected conserved NRs. Sequences were obtained from the NCBI database, aligned using Clustal W, and trimmed to include only the extended DBD for each sequence record (this is helpful when including C. elegans NRs, which have highly-diverged LBDs [11,185]). The tree with the highest log likelihood (-10026.43) is shown. The small number placed at each branch indicates the percentage of trees in which the associated taxa clustered together in 100 bootstrap replicates. Initial tree for the heuristic search was obtained by applying Neighbor-Joining and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The tree was rooted to the atypical (NR0) nuclear receptor knirps as an outgroup. Analysis was conducted using MEGA7 [267]. For each class, a C. elegans (or Brugiamalayi), Drosophila, Mus musculus, and Danio rerio ortholog was included (when present), organizing the analysis around two ecydysozoans and two vertebrates. Additional NRs were added from the complete genome of the echinoderm S. purpuratus, and two lophotrochozoan species. The lophotrochozoan species included varied due to the differences in completeness and annotation of these genomes, as well as a few possible cases of gene loss. Whenever possible, a representative annelid and mollusk was included. Species abbreviations: Dm Drosophila melanogaster, Ce Caenorhabditis elegans, Dr Danio rerio, Mm Mus musculus, Bm Brugia malayi, Sp Strongylocentrotus purparatis, Ac Aplysia californica, Cg Crassostrea gigas, Ct Capitella teleta, Hr Helobdella robusta, and Lg Lottia gigantea. This phylogenetic analysis establishes relationships among the major conserved nuclear receptor that is largely consistent with previously-published studies (e.g., [6]), but includes new data from the more recently-completed invertebrate genomes.