Neighbor-joining tree of selected NR core DBD sequences (as defined inRastinejad 1997) generated by the GCG Growtree program. One thousand neighbor-joining bootstrap replicates were performed on the same data set using the Paupsearch function of GCG 9.1. Bootstrap values for supported branches are indicated by hatch marks: (/) 50%-79%; (//) 80-94%; (///) 95-100%. Paupsearch was also used to perform maximum parsimony analysis; branchpoints preserved in the resulting consensus tree are denoted by dots. C. elegans sequences are included for all NR genes characterized in this or other studies (* and see Tables 1 T2 T3), all genes for which C. briggsae orthologs were identified, and selected representatives of other major groupings defined in a larger tree containing all 224 nontruncated nematode DBD sequences. Sequences not yet assigned nhr designations are indicated by genome project ORF numbers. Also included are all knownC. briggsae NR sequences (designated by clone name) and both vertebrate and insect sequences representing the major classes defined by Laudet (1997). Curly brackets indicate phylogenetically conserved NR classes that contain nematode members. Sequence name prefixes denote species of origin: (Aam) the tick Amblyomma americanum, (Cb)C. briggsae, (Ce) C. elegans, (Dm) Drosophila melanogaster, (Hs) Homo sapiens, (Xl) Xenopus laevis. Nematode sequences are available through the Genome Sequencing Project servers and, for C. elegans, in GenBank, and can be retrieved by text searches for the cosmid designation. GenBank accession numbers for previously published nematode sequences and non-nematode sequences included are (AF020187), AamEcR; (U37424), CeNHR-2; (U13075), CeNHR-23; (X51548), DmE75; (U01087), DmE78; (M74078), DmEcR; (M63711), DmFTZ-F1; (pir:S36218), DmHNF-4; (M90806), DmHR3; (X89246), DmHR38; (U31517), DmHR78; (U36792), DmHR96; (X14153,) DmKNRL; (M28863), DmSVP; (M34639), DmTLL; (X53417), DmUSP; X16155), HsCOUP-TFI; (L29496), HsAR; (X03635), HsER; (X51416), HsERR1; (U64876), HsGCNF; (U22662), HsLXRa; (M16801), HsMR; (X75918), HsNOT; (L02932), HsPPARα; (Z30972), HsPPARγ; (X06538), HsRARα; (M24857), HsRARγ; (X55066), HsReverba; (U04898), HsRORα; (U76388), HsSF-1; (Y13276), HsTL; (L27586), HsTR4; (X55005), HsTRα; (M26747), HsTRβ; (Z37526), XlHNF-4; (L11443), XlRXRγ; (X75163), XlVDLOR; (U91846), XlVDR.
