title: Molecular phylogeny of four homeobox genes from the purple sea star Pisaster ochraceus.
abstract: Homeobox genes cloned from the purple sea star Pisaster ochraceus (Phylum Echinodermata/Class Asteroidea) were used along with related sequences available from members of other representative animal phyla to generate molecular phylogenies for Distal-less/Dlx, Hox5, Hox7, and Hox9/10 homeobox genes. Phylogenetic relationships were inferred based on the predicted 60 amino acid homeodomain, using amino acid (AA) and nucleotide (NT) models as well as the recently developed codon substitution models of sequence evolution. The resulting phylogenetic trees were mostly congruent with the consensus species-tree, grouping these newly identified genes with those isolated from other Asteroidea. This analysis also allowed a preliminary comparison of the performance of codon models with that of NT and AA evolutionary models in the inference of homeobox phylogeny. We found that, overall, the NT models displayed low reliability in recovering major clades at the Superphylum/Phylum level, and that codon models were slightly more dependable than AA models. Remarkably, in the majority of cases, codon substitution models seemed to outperform both AA and NT models at both the Class level and homeobox paralogy-group level of classification.
authors.affiliation: Department of Agricultural and Environmental Sciences, University of Udine, Via delle Scienze 208, 33100, Udine, Italy. giorgio.matassi@uniud.it.
authors.forename: Giorgio
authors.initials: G
authors.lastname: Matassi
authors.affiliation: Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA.
authors.forename: Janice Hitomi
authors.initials: JH
authors.lastname: Imai
authors.affiliation: Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA. adg13@nyu.edu.|Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, 345 E 24th Street, New York, NY, 10010, USA. adg13@nyu.edu.
authors.forename: Anna
authors.initials: A
authors.lastname: Di Gregorio
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D015698:Genomic Library; D018398:Homeodomain Proteins / Q000145:classification / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics*; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D013215:Starfish / Q000145:classification / Q000235:genetics*
chemical_list: D018398:Homeodomain Proteins
keywords: Asteroidea; Codon model; Distal-less; Dlx; Echinoderm; Gbx; Hemichordate; Homeobox; Hox; Phylogeny; Pisaster; Rx; Sea star; Transcription factor