Article Figures & Data
Figures
- Figure 1.—
Phylogeny of CD2. Branch lengths were estimated by maximum likelihood under the free-ratio model, which assumes an independent ω-value for each branch. ω-values are shown for each branch, with values >1 in boldface type. Branches with no ω-values shown had values equal to infinity.
- Figure 2.—
Multiple sequence alignment of CD2 sequences showing amino acid sites predicted to be under positive selection by model M8 (shown in red). Sites shown in blue are involved in CD58 and/or CD48 binding. Sites involved in CD58/CD48 binding and subject to positive selection are denoted by #. Note that all but two of the sites under positive selection are located in the extracellular domain of CD2.
- Figure 3.—
The three-dimensional structure of human CD2 extracellular domain [Protein Data Bank (PDB) http://www.rcsb.org/pdb/entry=1HNF]. Sites shown in red are those sites predicted to be under positive selection (model 8). The sites are labeled according to the numbering scheme used in the PDB file (ALA6 corresponds to site 14 in Table 1). Sites known to be involved in CD58 binding are shown in blue. A and B show two opposite faces of the CD2 molecule. The structure was displayed using RasMol V2.7.2.1.1 (http://www.openrasmol.org/software/rasmol/).
- Figure 4.—
Phylogeny of CD2 extracellular domain. Branch lengths were estimated by maximum likelihood under the free-ratio model, which assumes an independent ω-value for each branch. ω-values >1 are in boldface type.
Tables
- TABLE 1
Amino acid sites subject to positive selection in CD2
Model No. of parameters Parameters ℓ dN/dS Positively selected sites M0: one ratio 1 ω = 0.7853 −5712.56 = ω M1: neutral 1 p0 = 0.203, ω0 = 0 −5658.05 0.7974 p1 = 0.797, ω1 = 1 M2: selection 3 p0 = 0.187, ω0 = 0 −5633.99 1.1777 22, 89 p1 = 0.636, ω1 = 1 p2 = 0.177, ω2 = 3.053 M3: discrete 5 p0 = 0.515, ω0 = 0.2511 −5614.51 0.9678 11, 14, 20–23, 38, 48, 50, 58, 62–64, 66–69, 73, 76, 83, 85, 87, 89, 95, 104, 112, 116, 121, 123, 125, 127, 136, 137, 140, 148–150, 153–155, 157, 159, 166, 168, 174, 176, 179, 181–183, 185, 187, 195, 206, 210, 212, 239, 242, 282, 322 p1 = 0.459, ω1 = 1.5353 p2 = 0.027, ω2 = 5.022 M7: β 2 p = 0.368, q = 0.210 −5641.42 M8: β and ω 4 p0 = 0.591, p = 2.43, q = 5.040 −5616.05 14, 21, 22, 48, 50, 64, 67, 69, 89, 95, 123, 136, 149, 150, 153, 154, 159, 168, 174, 239 p1 = 0.409, ω = 1.805 - TABLE 2
LRTs to detect adaptive evolution
Models 2Δℓ χ2 value d.f. P-value M1 vs. M2 2(−5658.05–5633.99) 48.12 2 <0.001 M0 vs. M3 2(−5712.56–5614.51) 196.10 4 <0.001 M7 vs. M8 2(−5641.42–5616.05) 50.74 2 <0.001
