Phylogeny and population structure analysis of Rhamphochromis species. (A) Maximum likelihood phylogenetic tree reconstructed using whole-genome single-nucleotide polymorphism (SNP) data from all 66 Rhamphochromis individuals and two outgroup taxa. Bootstrap values are available in Supplemental Figure S1, and all nodes separating each species have a bootstrap of 100%. (B) Population structure of Rhamphochromis estimated using the ADMIXTURE program with admixture proportions of individuals from K = 2 to K = 10. Each color represents one population. Each individual is represented by a vertical bar, with the length of each colored segment indicating the proportion of genetic contribution from the respective ancestral population. (C,D) PCA plots of the first four components of Rhamphochromis individuals based on whole-genome SNP data.