Widespread but spotty: Atlantic cod is a complex of five species through ecological speciation

Marine environments are home to a significant portion of fish and other organisms’ biodiversity. However, our knowledge and empirical evidence of speciation in the marine realm is quite limited. Here we use genomics and study population differentiation and speciation in the Atlantic cod, a marine teleost of biological and economic impor-tance. We show that the non-inversion part of the genome separates individuals into five clusters. At the four chromosomes carrying large inversions that define ecotypic variation, individuals also cluster into the same five clusters in conjunction with individuals’ inversion geno-types. Within each cluster, individuals homozygous or heterozygous for the inversions are divergent and there is an adaptive divergence of each type of inversion homozygote among clusters. These interchromoso-mal correlations imply the reproductive isolation of five cryptic species. We show that the inversion haplotypes are ancient trans-species bal-anced polymorphisms that would evolve towards homozygous lethality under Muller’s ratchet and recombination suppression of inversions. How-ever, gene flux from gene conversion rescues homozygous fitness, and recombination and selection lead to the evolution of habitat special-ists through ecological speciation. The specialized genotypes actively seek out their preferred habitat resulting in a widespread but patchy distribution that contradicts the traditional geographical speciation model and the stock concept in fisheries biology. Our results high-light the power of genomics in studying selection and speciation while informing conservation and management of essential fisheries resources. ### Competing Interest Statement The authors have declared no competing interest.