plosone-phylo
pone.0011133.g002.png
Phylogenetic tree of all primate TAAR4 orthologs analyzed for ORF.
The tree is based on generally accepted primate phylogeny as described in [21]. Events causing pseudogenization (nucleotide insertions (ins) or -deletions (del) or stop mutations (stop)) are indicated in red on the affected branches. Positions stated correspond to codon position of the respective mouse ortholog. Pseudogenes (ψ) are highlighted in red. Emperor tamarin was found to be polymorphic. Detailed information about pseudogenization events is in Figure S4. A “free ratio” model implemented in PAML was used to calculate dN/dS-ratios (ω shown in bold below branches) and the number of non-synonymous and synonymous substitutions (shown in parentheses) for each branch. × indicates branches that were labeled to determine ωψ2 (see Table 1, Table S6) # indicates branches labeled in branch model/branch-site model to determine ωcerc.
pone.0011133.g002.png
Phylogenetic tree of all primate TAAR4 orthologs analyzed for ORF.
The tree is based on generally accepted primate phylogeny as described in [21]. Events causing pseudogenization (nucleotide insertions (ins) or -deletions (del) or stop mutations (stop)) are indicated in red on the affected branches. Positions stated correspond to codon position of the respective mouse ortholog. Pseudogenes (ψ) are highlighted in red. Emperor tamarin was found to be polymorphic. Detailed information about pseudogenization events is in Figure S4. A “free ratio” model implemented in PAML was used to calculate dN/dS-ratios (ω shown in bold below branches) and the number of non-synonymous and synonymous substitutions (shown in parentheses) for each branch. × indicates branches that were labeled to determine ωψ2 (see Table 1, Table S6) # indicates branches labeled in branch model/branch-site model to determine ωcerc.