Figure 1

RH2a opsin gene tree showing the African cichlid-specific duplication event that produced the RH2aα (thick, dotted, blue branches) and RH2aβ (thick, solid/dashed, red branches) opsins. Dashed red branches indicate RH2aβ lineages from Lake Tanganyikan cichlids. Numbers adjacent to nodes indicate clade posterior probability, and branch lengths indicate expected number of substitutions per nucleotide site. Branch model analyses (inset, upper left) revealed that ω was significantly elevated along the Lake Tanganyikan branches compared to the rest of the RH2aβ clade. Species code abbreviations indicate the first letter of the genus and first two letters of each species: Cfr, Crenicichla frenata; Lgo, Lucania goodei; Mau, Melanochromis auratus; Mze, Metriaclima zebra; Nbr, Neolamprologus brichardi; Ola, Oryzias latipes; Oni, Oreochromis niloticus; Ove, Ophthalmotilapia ventralis; Ppu, Pundamilia pundamilia; Pre, Poecilia reticulata; Tdu, Tropheus duboisi; Tin, Tramitichromis intermedius. Genbank accession numbers are included alongside the species codes.