plosone-phylo
Figure 2
Functional divergence analysis of TSPOs before and after gene duplication.A. NJ-tree of TSPOs from human to worm. The evolutionary history was inferred using the Neighbor-Joining method [97]. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to the branches. The tree is drawn to scale with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Dayhoff matrix-based method and are given in the units of the number of amino acid substitutions per site. All positions containing alignment gaps and missing data were eliminated only in pairwise sequence comparisons (pairwise deletion option). A total of 187 positions were analyzed in the final dataset. Phylogenetic analyses were conducted in MEGA4 [27]. The following sequences with accession numbers were used for the analysis: TSPO-Danio (NP_001006032), TSPO-Oncorhychus (AAK31586), TSPO-Tetradon (CAG06923), TSPO-Xeopus (AAH41505), TSPO-Drosophola (NP_608531), TSPO-elegans (NP_001129759), TSPO1-Pig (NP_998918), TSPO1-Mouse (P50637), TSPO1-Rat (NP_036647 NP_036647), TSPO1-CRA-b-Humans (NM_000714), TSPO1-Gallus (XP_416451), TSPO2-Gallus (XP_418037), TSPO2-Rat (XP_001063305), TSPO2-Mouse (NP_081568), TSPO2-Humans (NP_001010873), TSPO2-Pig (N166970). B. Site-specific profile for predicting critical amino acid residues responsible for type-I functional divergence between clusters TSPO (from invertebrates) and TSPO1 or TSPO2 as measured by posterior probability (Q1). Only one site, H159 (hTSPO1), is over 0.6 of Q1 value between TSPO/TSPO1, whereas there are 11 sites over 0.6 of Q1 value between TSPO/TSPO2.
Figure 2
Functional divergence analysis of TSPOs before and after gene duplication.A. NJ-tree of TSPOs from human to worm. The evolutionary history was inferred using the Neighbor-Joining method [97]. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to the branches. The tree is drawn to scale with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Dayhoff matrix-based method and are given in the units of the number of amino acid substitutions per site. All positions containing alignment gaps and missing data were eliminated only in pairwise sequence comparisons (pairwise deletion option). A total of 187 positions were analyzed in the final dataset. Phylogenetic analyses were conducted in MEGA4 [27]. The following sequences with accession numbers were used for the analysis: TSPO-Danio (NP_001006032), TSPO-Oncorhychus (AAK31586), TSPO-Tetradon (CAG06923), TSPO-Xeopus (AAH41505), TSPO-Drosophola (NP_608531), TSPO-elegans (NP_001129759), TSPO1-Pig (NP_998918), TSPO1-Mouse (P50637), TSPO1-Rat (NP_036647 NP_036647), TSPO1-CRA-b-Humans (NM_000714), TSPO1-Gallus (XP_416451), TSPO2-Gallus (XP_418037), TSPO2-Rat (XP_001063305), TSPO2-Mouse (NP_081568), TSPO2-Humans (NP_001010873), TSPO2-Pig (N166970). B. Site-specific profile for predicting critical amino acid residues responsible for type-I functional divergence between clusters TSPO (from invertebrates) and TSPO1 or TSPO2 as measured by posterior probability (Q1). Only one site, H159 (hTSPO1), is over 0.6 of Q1 value between TSPO/TSPO1, whereas there are 11 sites over 0.6 of Q1 value between TSPO/TSPO2.