Species that show replicate adaptation of divergent populations along the same environmental gradient are important model systems to examine how new species form in natural populations. Astatotilapia burtoni is an East African cichlid fish occurring in Lake Tanganyika (LT) and affluent rivers. In southern LT, A. burtoni lake-stream population pairs display different degrees of genetic and morphological differentiation, suggesting that they rest at different stages of the ‘speciation continuum’.To investigate the molecular basis of adaptation along the lake-stream environmental gradient, we performed whole genome resequencing of 12 individuals per population in three A. burtoni lake-stream population pairs, as well as one lake-stream population pair of another cichlid species, Haplochromis stappersii (sympatric with A. burtoni in northern LT). We first assessed population structure and morphological differences in both species from northern LT and compared them to the A. burtoni populations from the southern part of the lake.
Body shape analyses of A. burtoni and H. stappersi from the North revealed morphological differences along the lake-stream gradient, but they did not follow the same trajectories as in the southern populations. Using more than 7 millions SNPs, we detected contrasting patterns of genetic differentiation between lake and stream populations from the North and South of LT. Finally, FST outlier analyses among lake-stream population pairs revealed candidate genes of local adaptation involved in sensory systems, in communication (e.g. coloration) as well as in immunity. Overall, these results provide insights into cichlid speciation genomics and bring further understanding of how selection acts on natural populations.