Putative molecular interactions of likely adaptive residues. (A) Yippee domain (orange) of MmMIS18β aligned to the Yippee-like domain of fission yeast MIS18 (PDB 5JH0; Subramanian et al., 2016). FREEDA automatically annotates residues with the highest probability of having evolved under positive selection (probability ≥ 0.9, magenta). Manual annotations show residues with lower probability (probability ≥ 0.7, blue) and conserved cysteins (green). (B) Enlarged CXXC motifs forming a tetrahedral module holding a zinc ion. (C) MmAURKC protein kinase domain (orange, with activation loop in gray) and AURK-binding domain of mouse INCENP (MmINCENP; yellow), both aligned to the human AURKC-INCENP complex with the BRD-7880 inhibitor bound to the ATP-binding site (black; PDB 6GR8; Abdul Azeez et al., 2019). Annotations show likely adaptive residues (magenta, probability ≥ 0.9; blue, probability ≥ 0.7) and conserved residue Y827 of MmINCENP (yellow). (D) Enlarged ATP-binding site. Dashed lines show the closest distance from side chains of residues that likely evolved under positive selection (S156 or N150) to the BRD-7880 inhibitor or to Y827 of MmINCENP. (E) MmCENP-O (blue) and MmCENP-P (yellow) aligned to human CENP-O and -P (HsCENP-O and -P) from the human CENP-OPQUR complex (PDB 7PB8; Yatskevich et al., 2022). Gray: C-terminal RWD domains; magenta: the most likely adaptive residues (probability ≥ 0.9). Magenta arcs highlight most likely adaptive residues within the C-terminal RWD domains facing opposite sides of the heterodimer, which likely interface with other centromeric proteins.