Whole-genome sequencing uncovers cryptic and hybrid species among Atlantic and Pacific cod-fish

Speciation often involves the splitting of a lineage and the adaptation of daughter lineages to different environments. It may also involve the merging of divergent lineages, thus creating a stable homoploid hybrid species1 that constructs a new ecological niche by transgressing2 the ecology of the parental types. Hybrid speciation may also contribute to enigmatic and cryptic biodiversity in the sea.3,4 The enigmatic walleye pollock, which is not a pollock at all but an Atlantic cod that invaded the Pacific 3.8 Mya,5 differs considerably from its presumed closest relatives, the Pacific and Atlantic cod. Among the Atlantic cod, shallow-water coastal and deep-water migratory frontal ecotypes are associated with highly divergent genomic islands;6,7 however, intermediates remain an enigma.8 Here, we performed whole-genome sequencing of over 200 individuals using up to 33 million SNPs based on genotype likelihoods9 and showed that the evolutionary status of walleye pollock is a hybrid species: it is a hybrid between Arctic cod and Atlantic cod that transgresses the ecology of its parents. For the first time, we provide decisive evidence that the Atlantic cod coastal and frontal ecotypes are separate species that hybridized, leading to a true-breeding hybrid species that differs ecologically from its parents. We refute monophyly and dichotomous branching of these taxa, and stress the importance of looking beyond branching trees at admixture and hybridity. Our study demonstrates the power of whole-genome sequencing and population genomics in providing deep insights into fundamental processes of speciation. Our study was a starting point for further work aimed at examining the criteria of hybrid speciation,10 selection, sterility and structural chromosomal variation11 among cod-fish, which are among the most important fish stocks in the world. The hybrid nature of both the walleye pollock and Atlantic cod raises the question concerning the extent to which very profitable fisheries12,13 depend on hybrid vigour. Our results have implications for management of marine resources in times of rapid climate change.14,15