title: Long distance linkage disequilibrium and limited hybridization suggest cryptic speciation in atlantic cod.
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.
authors.affiliation: Department of Fisheries and Oceans, St. John's, Newfoundland, Canada; Ocean Sciences Center, Memorial University of Newfoundland, St. John's, Newfoundland, Canada.
authors.forename: Ian R
authors.initials: IR
authors.lastname: Bradbury
authors.affiliation: The Atlantic Genome Centre, Halifax, Nova Scotia, Canada.
authors.forename: Sharen
authors.initials: S
authors.lastname: Bowman
authors.affiliation: The Atlantic Genome Centre, Halifax, Nova Scotia, Canada.
authors.forename: Tudor
authors.initials: T
authors.lastname: Borza
authors.affiliation: Ocean Sciences Center, Memorial University of Newfoundland, St. John's, Newfoundland, Canada.
authors.forename: Paul V R
authors.initials: PV
authors.lastname: Snelgrove
authors.affiliation: Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, Halifax, Nova Scotia.
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Hutchings
authors.affiliation: Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, Oslo, Norway.
authors.forename: Paul R
authors.initials: PR
authors.lastname: Berg
authors.affiliation: AZTI-Tecnalia, Marine Research Division, Txatxarramendi ugartea z/g, Sukarrieta, Spain.
authors.forename: Naiara
authors.initials: N
authors.lastname: Rodríguez-Ezpeleta
authors.affiliation: Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, Halifax, Nova Scotia.
authors.forename: Jackie
authors.initials: J
authors.lastname: Lighten
authors.affiliation: Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, Halifax, Nova Scotia.
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Ruzzante
authors.affiliation: Department of Oceanography, Dalhousie University, Halifax, Nova Scotia, Canada.
authors.forename: Christopher
authors.initials: C
authors.lastname: Taggart
authors.affiliation: Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, Halifax, Nova Scotia.
authors.forename: Paul
authors.initials: P
authors.lastname: Bentzen
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D002875:Chromosomes; D048389:Gadus morhua / Q000235:genetics*; D005787:Gene Frequency; D005828:Genetics, Population; D016678:Genome; D006824:Hybridization, Genetic; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D060047:Reproductive Isolation