Mutations are the fundamental source of biological variation, and their rate is a crucial parameter for evolutionary and medical studies. Here we used whole-genome sequence data from 753 Icelandic males, grouped into 274 patrilines, to estimate the point mutation rate for 21.3 Mb of male-specific Y chromosome (MSY) sequence, on the basis of 1,365 meioses (47,123 years). The combined mutation rate for 15.2 Mb of X-degenerate (XDG), X-transposed (XTR) and ampliconic excluding palindromes (rAMP) sequence was 8.71 × 10(-10) mutations per position per year (PPPY). We observed a lower rate (P = 0.04) of 7.37 × 10(-10) PPPY for 6.1 Mb of sequence from palindromes (PAL), which was not statistically different from the rate of 7.2 × 10(-10) PPPY for paternally transmitted autosomes. We postulate that the difference between PAL and the other MSY regions may provide an indication of the rate at which nascent autosomal and PAL de novo mutations are repaired as a result of gene conversion.

Marine environments are home to a significant portion of fish and other organisms' biodiversity. However, our knowledge and empirical evidence of speciation in the marine realm is quite limited. Here we use genomics and study population differentiation and speciation in the Atlantic cod, a marine teleost of biological and economic importance. We show that the non-inversion part of the genome separates individuals into five clusters. At the four chromosomes carrying large inversions that define ecotypic variation, individuals also cluster into the same five clusters in conjunction with individuals' inversion genotypes. Within each cluster, individuals homozygous or heterozygous for the inversions are divergent, and there is an adaptive divergence of each type of inversion homozygote among groups. These interchromosomal correlations imply the reproductive isolation of five cryptic species. We show that the inversion haplotypes are ancient trans-species balanced polymorphisms that would evolve towards homozygous lethality under Muller's ratchet and recombination suppression of inversions. However, gene flux from gene conversion rescues homozygous fitness, and recombination and selection lead to the evolution of habitat specialists through ecological speciation. The specialized genotypes actively seek out their preferred habitat resulting in a widespread but patchy distribution that contradicts the traditional geographical speciation model and the stock concept in fisheries biology. Our results highlight the power of genomics in studying selection and speciation while informing conservation and management of essential fisheries resources.

Chromosomal structural rearrangements such as inversions are large scale genomic mutations. Inversions suppress recombination in heterozygotes and are often referred to as supergenes if they combine adaptive gene complexes within their genomic islands of differentiation. Such islands are known in the Atlantic cod (Gadus morhua), maintaining genomic divergence that define known ecotypes. Little is known about the genome architecture of the related polar cod (Boreogadus saida) although its panmictic distribution suggests small, if any, genetic diversity and population divergence. However, previous observations show seasonal and spatial variation in biological and ecological characteristics that strongly indicate distinct populations, although genetic analyses have not yet been conclusive. Here we use four approaches and find genomic evidence for inversions in a sample of polar cod from north-eastern Greenland at the same chromosomal locations as are found in Atlantic cod. The inversions on chromosomes 1 and 7 in the Atlantic cod, both linked to temperature adaptation, are also present in the polar cod. There is a geographical separation among these different inversions. The polar cod is a key player in the Arctic food-web, transferring a large share of energy from plankton to mammals and birds. With warming temperatures, cold adapted gadid species such as the polar cod are under threat, as is the whole Arctic ecosystem. As the habitat of polar cod is already shrinking, these results may aid our understanding of polar cod’s future success or demise.

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.