Figure 4

CTLDcp duplication dates. A. Average number of synonymous substitutions per synonymous site (Ks) for CTLDcp paralogue pairs based on full-sequence (triangle) and CTLD-only (diamond) alignments, measured with four different methods (see Methods). Error bars show one standard deviation in the CTLD-only measurements. All possible pairwise alignments between the MManR fragments and between the three CRTL1 paralogues were analyzed. Only homologous regions were used for MManR fragment alignments. B. A linearized phylogenetic tree built by the neighbor-joining method from Poisson-corrected distances between ClustalW-aligned sequences of CTLDs 3–5 from Fugu, mouse and human MManRs. Sequence of the human PLA2R region containing CTLDs 3–5 was used as an outgroup. T_hm – time of separation between human and mouse [96 Myr; 60], T_fish – time of separation between ray-finned and lobe-finned fishes [430 Myr; 32]. Time of duplication (T_dupl) was calculated using average between molecular clock calibrated with T_hm and with T_fish.