Evolution of the ATF3:sws1:miR-99a three-node motif in the five cichlids and Lake Malawi species. (A) On the top left, ATF3 motif prediction in M. zebra, P. nyererei, and A. burtoni sws1 gene promoter (red box) and substitution demarcated in O. niloticus sws1 gene promoter (orange arrow). On the bottom left, miR-99a-binding site prediction in M. zebra sws1 3′-UTR (green box) and substitution demarcated in P. nyererei, A. burtoni, N. brichardi, and O. niloticus sws1 3′-UTR (orange arrow). According to these predicted sites, evolution of the ATF3:sws1:miR-99a three-node motif in the five cichlid phylogeny is depicted based on presence (green circle) and absence (red circle). (B) Simplified presence (green circle) and absence (red circle) of the ATF3:sws1:miR-99a three-node motif in Lake Malawi species based on SNP genotypes overlapping ATF3 TFBS and miR-99a-binding sites in M. zebra sws1 gene promoter and 3′-UTR (orange arrows, A). Lake Malawi phylogeny reproduced from published ASTRAL phylogeny (Malinsky et al. 2018). Phylogenetic branches labelled with genus, species, or clade identifiers. Within the shallow benthics, species within some clades are summarized by numbers: 1 = Hemitaeniochromis, Protomelas; 2 = Hemitilapia, Otopharnyx, Mylochromis; 3 = Champsochromis, Tyrannochromis, Trematocranus, Otopharnyx, Mylochromis, Stigmatochromis, Taeniochromis, Buccochromis, Ctenopharynx; 4 = Mylochromis; 5 = Taeniolethrinops. Expanded genotype, phenotype, and ecotype phylogeny in supplementary figures S16 and S17, Supplementary Material online.