Abstract
Identification of genome-wide patterns of divergence provides insight on how genomes are influenced by selection and can reveal the potential for local adaptation in spatially structured populations. In Atlantic cod – historically a major marine resource – Northeast-Arctic- and Norwegian coastal cod are recognized by fundamental differences in migratory and non-migratory behavior, respectively. However, the genomic architecture underlying such behavioral ecotypes is unclear. Here, we have analyzed more than 8.000 polymorphic SNPs distributed throughout all 23 linkage groups and show that loci putatively under selection are localized within three distinct genomic regions, each of several megabases long, covering approximately 4% of the Atlantic cod genome. These regions likely represent genomic inversions. The frequency of these distinct regions differ markedly between the ecotypes, spawning in the vicinity of each other, which contrasts with the low level of divergence in the rest of the genome. The observed patterns strongly suggest that these chromosomal rearrangements are instrumental in local adaptation and separation of Atlantic cod populations, leaving footprints of large genomic regions under selection. Our findings demonstrate the power of using genomic information in further understanding the population dynamics and defining management units in one of the world’s most economically important marine resources.
Highlights
Identification of genome-wide patterns of divergence provides insight on how genomes are influenced by selection and can reveal the potential for local adaptation in spatially structured populations
Genome-wide single nucleotide polymorphism (SNP) analyses as well as large-scale sequencing of natural populations address this challenge by identifying areas of the genome involved in diversification[1,2,7,8], and sometimes the underlying candidate genes involved in population divergence[4,9,10]
These are all single outliers, not representing any larger outlier blocks and not residing within linked regions of the genome, indicating that a few smaller areas of the genome could play a role in the genomic diversification of the Northeast Arctic cod (NEAC) and Norwegian coastal cod (NCC) populations
Summary
Identification of genome-wide patterns of divergence provides insight on how genomes are influenced by selection and can reveal the potential for local adaptation in spatially structured populations. We have analyzed more than 8.000 polymorphic SNPs distributed throughout all 23 linkage groups and show that loci putatively under selection are localized within three distinct genomic regions, each of several megabases long, covering approximately 4% of the Atlantic cod genome. The clearly observed phenotypic diversity between ecotypes of migrating and non-migrating Atlantic cod populations that spawn in the vicinity of each other, offers an excellent opportunity to identify the potential for local adaptation and investigate its genomic architecture, when both natural selection and gene flow are potentially high, in a major marine resource. We discuss the mechanisms driving the observed patterns of local adaptation and separation in Atlantic cod and in marine fish species in general
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