Phylogeny, genetic variability and colour polymorphism of an emerging animal model: The short-lived annual Nothobranchius fishes from southern Mozambique

► Analyses recovered three major clades with overlapping distribution. ► Each major clade was strongly geographically structured. ► Colour morphs (sympatric) had no phylogenetic signal in Nothobranchius furzeri. ► Colour morphs (parapatric) reciprocally monophyletic in Nothobranchius rachovii group. ► Polymorphism in Melanocortin1 receptor gene not related to colour phenotypes.