Genetic Incompatibilities are Widespread Within Species

The importance of epistasis — non-additive interactions between alleles — in shaping population fitness has long been a controversial topic, hampered in part by lack of empirical evidence(1,2,3,4). Traditionally, epistasis is inferred based on non-independence of genotypic values between loci for a given trait. However epistasis for fitness should also have a genomic footprint(5,6,7). To capture this signal, we have developed a simple approach that relies on detecting genotype ratio distortion (GRD) as a signal for epistasis, and we confirm experimentally that instances of GRD represent loci with epistatic fitness effects. In applying this method to a large panel of Drosophila melanogaster recombinant inbred lines(8, 9), we conservatively estimate that any two haploid genomes in this study are expected to harbor 1.15 pairs of incompatible alleles. This observation has important implications for speciation genetics, as it indicates that the raw material to drive reproductive isolation is segregating contemporaneously within species and does not necessarily require, as proposed by the Dobzhansky–Muller model, the emergence of incompatible mutations independently derived and fixed in allopatry. The relevance of our result extends beyond speciation, as it demonstrates that epistasis is widespread but that it may often go undetected due to lack of statistical power or lack of genome-wide scope of the experiments.