Fig. S1 (a) Partitioning of the fish body into skin and fin compartments for pigment extraction (black polygons) and positions photographed in Fig 1b-1g (numbered 1 – 4), drawn onto a photograph of a male Tropheus from Moliro (red morph). (b-g) Photomicrographs of the skin of a bluish male from Chaitika (b, dorsal; c, lateral), a yellow-blotch male from Mbita (d, dorsal; e, in the lateral yellow blotch) and a red male from Moliro (f, dorsal; g, in the red area at the caudal peduncle). The magnification used for 1c and 1g was twice as high as for the other photomicrographs. Photomicrographs were taken with an Olympus digital camera (Olympus E-1 – Zuiko Digital 14-54mm f 2.8-3.5) mounted on an Olympus SZX-ILLB2-200 dissecting microscope using the software Olympus Viewer and Studio (Copyright 2003 Olympus Corporation).

Fig. S2 Outlier locus allele frequencies of the dominant allele (p-values on the y-axis; exact values are given in the table below the graphs) in the studied populations. Colors on the x-axis indicate the different morphs.

Table S1 Outlier loci in comparisons between populations of the same morph. Within each population comparison, detected outlier loci are listed according to decreasing log10(BF) values. Underlined markers were detected in more than one comparison within the same color morph; markers written in italic letters were detected in different morphs; markers in bold print are those which had been detected in the between-morph comparisons.

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