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Fig. 3 | BMC Evolutionary Biology

Fig. 3

From: Expansion of sweet taste receptor genes in grass carp (Ctenopharyngodon idellus) coincided with vegetarian adaptation

Fig. 3

Molecular phylogenetic analysis by maximum likelihood method of T1R2. The evolutionary history was inferred by using the Maximum Likelihood method based on the JTT matrix-based model. The tree with the highest log likelihood (− 39,600.8248) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. 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 = 2.8034)). The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 1.3917% sites). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 73 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 503 positions in the final dataset. Evolutionary analysis was conducted in MEGA7. The T1R2s amino acid sequences of fishes and mammals used are given in the electronic Additional file 3: Table S2

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