Low levels of hybridization between sympatric cold-water-adapted Arctic cod and Polar cod in the Beaufort Sea confirm genetic distinctiveness

Abstract

As marine ecosystems respond to climate change and other stressors, it is necessary to evaluate current and past hybridization events to gain insight on the outcomes and drivers of such events. Ancestral introgression within the gadids has been suggested to allow cod to inhabit a variety of habitats. Little attention has been given to contemporary hybridization especially within cold-water adapted cod (Boreogadus saida and Arctogadus glacialis). We used whole-genome, restriction-site associated, and mitochondrial sequence data to explore the degree and direction of hybridization between these species where previous hybridization had not been reported. Although nearly identical morphologically at certain life stages, we detected very distinct nuclear and mitochondrial lineages. We detected one potential hybrid with a Arctogadus mitochondrial haplotype and Boreogadus nuclear genotype, but no early generational hybrids. The presence of a late generation hybrid suggests that at least some hybrids survive to maturity and reproduce. However, a historical introgression event could not be excluded. Contemporary gene flow appears asymmetrical from Arctogadus into Boreogadus which may be due to overlap in timing of spawning, environmental heterogeneity, or differences in population size. This study provides important baseline information for the degree of potential hybridization between these species within Alaska marine environments.

Reference genome bias in light of species-specific chromosomal reorganization and translocations

“…Additionally, a difference in how the two species clustered along the PC2 axis was detected, with Arctic cod exhibiting minimal intraspecific variation, whereas polar cod displayed intraspecific variability along the PC2 axis (Figure 3d-f), explained by 3.75-3.81% of the variation in the datasets, depending on the reference used. Taken together, these findings indicate that polar cod has a larger standing genetic variation compared to Arctic cod, which could be linked to the difference in female Ne observed between the species (Figure S4 and Hoff et al 27 ) as well as documented by others 37,56,57 .…”

“…Both Arctic cod and polar cod represent important sympatric species inhabiting the Arctic, one of the world's most rapidly changing environments that is undergoing warming at a pace almost four times faster than the global average 30 . Until now, there are only a few studies that have looked into the population genetic structuring of Arctic cod and polar cod using a handful of genetic markers [31][32][33][34][35][36] and even fewer that have used whole genome sequencing approaches 28,37 , and by such, this study will advance our insight into the genomic composition and potential within these species in the light of the ongoing climatic changes.…”

Chromosomal fusions and large-scale inversions are key features for adaptation in Arctic codfish species

“…The quartet frequency analysis for the BUSCO phylogeny demonstrated discordance among the gene trees in the placement of Arctic cod and polar cod as sister lineage Gadus (Figure 6C). The uncertainty in the placement of Arctic cod in the BUSCO phylogeny could be due to several factors affecting phylogenetic inference, e.g., introgressive hybridization [10,92], incomplete lineage sorting, and/or large amounts of highly linked genomic regions leading to an altered recombination landscape [93]. For the latter, quantification of BUSCOs within and outside identified chromosomal inversions in polar cod and Arctic cod revealed some BUSCOs to be localized within these regions, possibly contributing to uncertainties in the phylogenetic placement of the species.…”