Figure 1
From: SOXE neofunctionalization and elaboration of the neural crest during chordate evolution
Molecular Phylogenetic analysis of SOXE proteins by Maximum Likelihood method.
The evolutionary history was inferred by using the Maximum Likelihood method based on the Dayhoff matrix based model53. The tree with the highest log likelihood (−8351.5037) is shown. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 0.5064)). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 30 amino acid sequences. All positions with less than 95% site coverage were eliminated. That is, fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. There were a total of 273 positions in the final dataset. Evolutionary analyses were conducted in MEGA754,55. The trees are exported to Newick files, which is further modified by the figtree without changing the evolutionary distance. Homo sapiens (Hs), Mus musculus (Mm), Rattus norvegicus (Rn), Gallus gallus (Gg), Xenopus laevis (Xl), Danio rerio (Dr), Petromyzon marinus (Pm), Eptatretus burgeri(Eb), Branchiostoma lanceolatum(Amphi), Ciona intestinalis (Ci), Lytechinus variegatus (Lv), Drosophila melanogaster (Dm), Apis mellifera (Am), Nasonia vitripennis (Nv).
