Nucleotide variation and balancing selection at the Ckma gene in Atlantic cod: analysis with multiple merger coalescent models

Abstract

High-fecundity organisms, such as Atlantic cod, can withstand substantial natural selection and the entailing genetic load of replacing alleles at a number of loci due to their excess reproductive capacity. High-fecundity organisms may reproduce by sweepstakes leading to highly skewed heavy-tailed offspring distribution. Under such reproduction the Kingman coalescent of binary mergers breaks down and models of multiple merger coalescent are more appropriate. Here we study nucleotide variation at the Ckma (Creatine Kinase Muscle type A) gene in Atlantic cod. The gene shows extreme differentiation between the North (Canada, Greenland, Iceland, Norway, Barents Sea) and the South (Faroe Islands, North-, Baltic-, Celtic-, and Irish Seas) with FST > 0.8 between regions whereas neutral loci show no differentiation. This is evidence of natural selection. The protein sequence is conserved by purifying selection whereas silent and non-coding sites show extreme differentiation. The unfolded site-frequency spectrum has three modes, a mode at singleton sites and two high frequency modes at opposite frequencies representing divergent branches of the gene genealogy that is evidence for balancing selection. Analysis with multiple-merger coalescent models can account for the high frequency of singleton sites and indicate reproductive sweepstakes. Coalescent time scales vary with population size and with the inverse of variance in offspring number. Parameter estimates using multiple-merger coalescent models show that times scales are faster than under the Kingman coalescent.

Keywords: Atlantic cod; Balancing selection; Ckma; Multiple-merger coalescent; Time scales.

Figure 1. Maximum likelihood tree of Ckma variation (A and B alleles) among 122 individual Atlantic cod and 10 individuals of four closely related outgroup O taxa, Boreogadus saida Bsa, Gadus chalcogramma Gch, Gadus macrocephalus Gma, and Gadus ogac Gog.

Localities and color codes for Atlantic cod are the waters of Canada (Nova Scotia and Newfoundland) Can, Greenland Gre, Iceland Ice, Norway Nor, Faroe Islands Far, and from the Barents Sea Bar, White Sea Whi, North Sea Nse, Baltic Sea Bal, Celtic Sea Cel, and Irish Sea Iri.

Figure 2. Heterozygosity per nucleotide site of Ckma locus among A alleles (red A, n = 43), B alleles (blue B, n = 79), and all individuals combined (magenta C, n = 122).

Boxes represent exons, start (red), internal (magenta) and terminal (blue). Green boxes represent sequenced fragments trimmed to Phred score of at least 30. The black circles mark the three SNPs of Moen et al. (2008), Gm366-0514 locus with an F_ST = 0.83, Gm366-1022 locus with an F_ST = 0.82, and Gm366-1073 with an F_ST = 0.82 from left to right respectively. Crosses mark mutant sites relative to outgroup that were fixed or nearly fixed among A alleles. Triangles mark mutant sites relative to outgroup that were fixed or nearly fixed among B alleles. Gadus macrocephalus individual 152047 was used as the outgroup.

Figure 3. Unfolded site frequency spectrum of Atlantic cod Ckma gene.

Gadus macrocephalus was used as the outgroup. Number of individuals n = 122. Theroretical expectation under Kingman coalescent (red dots), Beta(2 − α, α) coalescent (magenta squares), and point-mass coalescent (blue stars).