Structure and evolution of Cernunnos-XLF proteins inmammals. The scale of all plots corresponds to the protein alignment of 299 amino acids, and positions in the coding sequence (CDS) were scaled accordingly. A. Structure of human Cernunnos-XLF CDS and protein. The first scheme shows the positions of the major predicted domains in the Cernunnos-XLF protein [after ref. 5]. The N-terminal globular head domain is marked in yellow, the remaining coiled-coil structure in blue, the putative nuclear localization signal is in red. The second scheme shows the positions of the coding exons (2–8) in the CDS (the odd exons are black and the even ones are white). B. CDS substitutions during evolution. The expected ancestral coding sequence was estimated using maximum likelihood codon reconstruction implemented in PAML. Nonsynonymous/synonymous (ω = Ka/Ks) ratios were free to vary in all branches. Positions marked in green correspond to synonymous changes in a given lineage. Bars representing nonsynonymous changes are black if conservative, red if nonconservative (see methods). "MCH-CH" corresponds to the ancestral lineage between the common ancestor of macaque, chimpanzee, and human (MCH) to the common ancestor of human and chimpanzee (CH), "anc-MCH" represents the lineage from the common ancestor of all taxons to MCH (see Fig. 2). C. Conservation at the nucleotide level in primates, and protein level in primates and mammals. The Y axis corresponds to the proportion of conserved (identical) positions in the CDS (a 60-bp overlapping window and 6-bp steps) and the protein alignment (window 20-aa, step 2-aa). D. Predicted structure of the Cernunnos-XLF protein. The structure for the first 185 aa was predicted by structural alignment to XRCC4 (see methods). The red parts highlight positions that are different between human and chimpanzee, aa 124 changed in the human lineage, aa 127 in the chimpanzee branch. Three other positions were changed in humans – aa 216, 223, 235 (see Fig. 2B).