Abstract
Hybrid zones provide unprecedented opportunity for the study of the evolution of reproductive isolation, and the extent of hybridization across individuals and genomes can illuminate the degree of isolation. We examine patterns of interchromosomal linkage disequilibrium (ILD) and the presence of hybridization in Atlantic cod, Gadus morhua, in previously identified hybrid zones in the North Atlantic. Here, previously identified clinal loci were mapped to the cod genome with most (∼70%) occurring in or associated with (<5 kb) coding regions representing a diverse array of possible functions and pathways. Despite the observation that clinal loci were distributed across three linkage groups, elevated ILD was observed among all groups of clinal loci and strongest in comparisons involving a region of low recombination along linkage group 7. Evidence of ILD supports a hypothesis of divergence hitchhiking transitioning to genome hitchhiking consistent with reproductive isolation. This hypothesis is supported by Bayesian characterization of hybrid classes present and we find evidence of common F1 hybrids in several regions consistent with frequent interbreeding, yet little evidence of F2 or backcrossed individuals. This work suggests that significant barriers to hybridization and introgression exist among these co-occurring groups of cod either through strong selection against hybrid individuals, or genetic incompatibility and intrinsic barriers to hybridization. In either case, the presence of strong clinal trends, and little gene flow despite extensive hybridization supports a hypothesis of reproductive isolation and cryptic speciation in Atlantic cod. Further work is required to test the degree and nature of reproductive isolation in this species.
Highlights
Understanding the complex contributions of ecological factors and genomic architecture to the formation of reproductive isolation is central to an understanding of speciation [1,2,3]
The goal of the present paper is to examine the nature of the trends observed previously (e.g., [16,24]) and in particular to explore patterns of interchromosomal linkage disequilibrium (ILD) and the presence of hybridization between wild Atlantic cod N and S types in the previously identified hybrid zone in the northwest Atlantic
The levels of linkage disequilibrium (LD) among outlier genes observed here and the lack of extensive gene flow are consistent with a hypothesis of two sympatric forms of Atlantic cod (N and S types) and support the hypothesis that these genomic regions are associated with reductions in hybrid survival and reproductive isolation
Summary
Understanding the complex contributions of ecological factors and genomic architecture to the formation of reproductive isolation is central to an understanding of speciation [1,2,3]. Study of the early stages of speciation where hybridization is common can reveal genome features involved, as well as the dominant isolating mechanisms (e.g., [5,7,8]) These processes are apparent in hybrid zones and among ecological species where admixture commonly occurs and selection or barriers to hybridization maintain reproductive isolation [9,10,11]. Speciation or isolation with gene flow is hypothesized to involve a progression of increasing isolation leading from selection at a few isolated genomic regions to genome wide divergence [1] During this process, islands of genomic divergence may grow in size via divergence hitchhiking. These genome wide patterns of divergence (i.e. frequency and size of islands of divergence, and LD among islands) may directly reflect the degree of reproductive isolation present between intraspecific groups
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