Code for paper "Evolution and maintenance of a transspecies color polymorphism"

Assortative mating based on color polymorphisms, should theoretically facilitate speciation even in sympatry. Yet some polymorphisms persist unexpectedly long without speciation. We investigated the origin, genetic basis, evolutionary trajectory, and maintenance of a transspecific dark/gold color polymorphism in Midas cichlids by integrating genomics with ecology and mate-choice experiments. A pangenome uncovered novel transposon-derived structural variants, as single- or duplicated/inverted alleles, in gold but not dark fish that mate strongly assortatively color-based. These alleles act dosage-dependently during the ontogenetic dark-to-gold transition, potentially producing phenotype–genotype adult mismatches. Some mature genetically gold individuals retaining juvenile dark mated according to their dark phenotype rather than their gold genotype. This temporal phenotype–genotype mismatch thereby leads to gene flow across genetic color-morphs preventing build-up of genetic differences and speciation.