Data from: Adaptive divergence between lake and stream populations of an East African cichlid fish

Divergent natural selection acting in different habitats may build up barriers to gene flow and initiate speciation. This speciation continuum can range from weak or no divergence to strong genetic differentiation between populations. Here, we focus on the early phases of adaptive divergence in the East African cichlid fish Astatotilapia burtoni, which occurs both in Lake Tanganyika and inflowing rivers. We first assessed the population structure and morphological differences in A. burtoni from southern Lake Tanganyika. We then focused on four lake-stream systems and quantified body shape, ecologically relevant traits (gill raker and lower pharyngeal jaw) as well as stomach contents. Our study revealed the presence of several divergent lake-stream populations that rest at different stages of the speciation continuum, but show the same morphological and ecological trajectories along the lake-stream gradient. Lake fish have higher bodies, a more superior mouth position, longer gill rakers, and more slender pharyngeal jaws, and they show a plant/algae and zooplankton biased diet, whereas stream fish feed more on snails, insects and plant seeds. A test for reproductive isolation between closely related lake and stream populations did not detect population-assortative mating. Analyses of F1 offspring reared under common garden conditions indicate that the detected differences in body shape and gill raker length do not constitute pure plastic responses to different environmental conditions, but also have a genetic basis. Taken together, the A. burtoni lake-stream system constitutes a new model to study the factors that enhance and constrain progress toward speciation in cichlid fishes. Microsatellite genotypes of wild populationsMicrosatellite genotypes used for population genetic analysesA.burtoni_msats_Input.csvMtDNA sequence alignmentmtDNA sequence alignment used to construct haplotype networkAbur_D-loop_alignment.csvBody shape data of wild populationstps input file with landmark coordinates for body shape analyses of 20 populationsBS_morphometrics_wild_populations.tpsBody shape data of individuals from the pond experimenttps input file with landmark coordinates for body shape analyses of 20 populationsBS_morphometrics_pond_experiment.tpsGill raker data of wild populationsMetric measurements on specimens used to compare gill raker morphology in wild populationsgill_raker_wild_populations.csvGill raker data of F1 individualsMetric measurements on F1individuals used to compare gill raker morphologygill_raker_juveniles_pond_experiment.csvLower pharyngeal jaw morphology data of wild populationstps input file with landmark coordinates used for geometric morphometric on lower pharyngeal jawsLPJ_morphometrics.tpsData on stomach contentsStomach content components of wild populationsstomach.csvInput file for partial mantel tests and MRMInput file with pair-wise distances (lake-stream populations) to test for associations between genetic differentiation, morphometric traits and environmentinput file partial mantel test and MRM.csvInput file for simple mantel testsInput file with pair-wise distances (shoreline populations) to test for isolation-by-distanceinput file simple mantel test.csvSummary file for CERVUS analysesParentage assignment of the pond mating experimentsummaryFile_pond_experiment.csvMicrosatellite genotypes of F1 and parental fish (pond 1)Microsatellite genotypes used for parentage assignment in pond 1genotypeFILE_Pond_1.csvMicrosatellite genotypes of F1 and parental fish (pond 2)Microsatellite genotypes used for parentage assignment in pond 2genotypeFILE_Pond_2.csvMicrosatellite genotypes of F1 and parental fish (pond 3)Microsatellite genotypes used for parentage assignment in pond 3genotypeFILE_Pond_3.csvMicrosatellite genotypes of F1 and parental fish (pond 4)Microsatellite genotypes used for parentage assignment in pond 4genotypeFILE_Pond_4.csvMicrosatellite genotypes of F1 and parental fish (pond 5)Microsatellite genotypes used for parentage assignment in pond 5genotypeFILE_Pond_5.csv