Fig 1.
Parental species and measures of variation in barring pattern and pigment level.
Representative parental for (a) Aulonocara koningsi and (b) Metriaclima mbenjii, including quantification of the region in the orange rectangle into grayscale values. The horizontal bar in graphs in (a) and (b) are the average grayscale intensity value, which was calculated for each individual and used to characterize bar and interbars, indicated by black and gray marks, respectively, in (a) and (b). From grayscale plots for each individual, measures of (c) eumelanin pigment level and (d) bar patterning were calculated as visualized, using the individual shown in Fig 1A as an example. Colors in (c) and (d) match colors used in Fig 3.
Fig 2.
Variation in barring levels and patterns among Aulonocara koningsi, Metriaclima mbenjii, and their F2 hybrids.
One set of measures relates to pigment levels produced by melanophores and are (a) darkest intensity, (b) lightest intensity, (c) range of intensity, (d) covariance, (e) average intensity of bars, (f) average intensity of interbars, and (g) differential intensity bars versus interbars. A second set of measures relates to the pattern of the bars and are (h) the number of bars, (i) percent barring, calculated as sum of total width of bars divided by total width of the isolated region, (j) average width of bars, and (k) average width of interbars. Significance in violin plots is based on ANOVA analysis followed by Tukeys HSD (data in S3 Table; p-values indicated by * <0.05, ** <0.01, *** <0.005).
Fig 3.
Quantitative trait loci (QTL) mapping identifies 48 intervals associated with variation in barring between Metriaclima mbenjii and Aulonocara koningsi.
Each linkage group (LG, i.e., chromosome) has markers indicated by hash marks. Bar widths indicate 95% confidence interval for each QTL and bar color indicates the pigment trait analyzed. Candidate genes previously associated with variation in eumelanin production and development of stripes or bars (see main text for references) are in pink text, with their genomic locations indicated on linkage groups. Additional candidate genes pax3a and pmela are located in unplaced scaffolds in the M. zebra UMD2a reference genome and not included here. Illustrations of each trait are in Fig 1. QTL scans at the genome and linkage group level are in S3 and S4 Figs, respectively. Details of the QTL scan, including statistical model and physical locations defining each QTL are in S2 Table.
Fig 4.
Quantitative trait loci (QTL) that underlie variation in pigment levels and pigment patterning are largely distinct.
Included are all linkage groups—(a) LG4, (b) LG13, (c) LG14, and (d) LG20—in which QTL for pigment level and patterning have overlapping 95% confidence intervals as visualized in Fig 3. Colors represent trait, as indicated by the legend and as illustrated in Fig 1. Peak markers for each QTL are indicated by an asterisk in a color matching the trait. The solid horizontal line in each panel represents 5% significance, measured as the average value from each of the featured scans on that specific linkage group; averaging this significance did not cause any of these QTL to change from significant to non-significant or vice versa. Further details of the QTL are in S4 Fig and S2 Table.