plosone-phylo
pone.0004004.g001.png
Orthology assignments for Capitella sp. I Hox genes.
Bayesian phylogenetic analysis was conducted using an alignment of the 60–amino acid homeodomain and the 12 amino acids immediately 3′ of the homeodomain for representative bilaterian Hox and Parahox genes. Capitella sp. I possesses orthologs for each Hox paralogy group (PG). Sequences from representative species include Tribolium castaneum (ecdysozoan); Nereis virens, Euprymna scolopes, and Capitella sp. I (lophotrochozoan); Flaccisagitta enflata and Spadella cephaloptera (chaetognath); Symsagitiffera roscoffensis and Nemertoderma westbladii (acoelomorphs); Branchiostoma floridae (deuterostome); and additional PG7 lophotrochozoan sequences (see Methods). Capitella sp. I sequences are delimited by arrows; Capitella sp. I Hox sequences are shown in bold. Numbers above branches indicate Bayesian posterior probabilities. Ovals delimit bootstrap support >50 at a node from either neighbor-joining (NJ) or maximum likelihood (ML) analyses, while squares show bootstrap support >50 from both NJ and ML analyses. Colors are unique to each Hox PG. Individual NJ and ML bootstrap consensus trees are shown in Figures S2 and S3, respectively.
pone.0004004.g001.png
Orthology assignments for Capitella sp. I Hox genes.
Bayesian phylogenetic analysis was conducted using an alignment of the 60–amino acid homeodomain and the 12 amino acids immediately 3′ of the homeodomain for representative bilaterian Hox and Parahox genes. Capitella sp. I possesses orthologs for each Hox paralogy group (PG). Sequences from representative species include Tribolium castaneum (ecdysozoan); Nereis virens, Euprymna scolopes, and Capitella sp. I (lophotrochozoan); Flaccisagitta enflata and Spadella cephaloptera (chaetognath); Symsagitiffera roscoffensis and Nemertoderma westbladii (acoelomorphs); Branchiostoma floridae (deuterostome); and additional PG7 lophotrochozoan sequences (see Methods). Capitella sp. I sequences are delimited by arrows; Capitella sp. I Hox sequences are shown in bold. Numbers above branches indicate Bayesian posterior probabilities. Ovals delimit bootstrap support >50 at a node from either neighbor-joining (NJ) or maximum likelihood (ML) analyses, while squares show bootstrap support >50 from both NJ and ML analyses. Colors are unique to each Hox PG. Individual NJ and ML bootstrap consensus trees are shown in Figures S2 and S3, respectively.