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

PeerJ
E Arnason, Katrín Halldórsdóttir

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 coales...Continue Reading

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Citations

Apr 15, 2016·PeerJ·Miguel Baltazar-SoaresChristophe Eizaguirre
Apr 27, 2016·Theoretical Population Biology·Jochen BlathMatthias Hammer
Aug 9, 2017·Proceedings of the National Academy of Sciences of the United States of America·Bastiaan StarJames H Barrett
Aug 1, 2019·Genome Research·Alba Refoyo-MartínezFernando Racimo
Nov 12, 2017·Genetics·Sebastian MatuszewskiJeffrey D Jensen
Dec 1, 2016·Current Zoology·Louis V Plough
Oct 3, 2020·Evolutionary Applications·Nina Marchi, Laurent Excoffier
Jul 16, 2020·Molecular Biology and Evolution·Fabrizio MenardoFabian Freund
Sep 2, 2020·Annual Review of Genetics·Bjarki Eldon

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Datasets Mentioned

BETA
KM624310
KM624437
EX184243

Methods Mentioned

BETA
PCR

Software Mentioned

LDheatmap
MLHKA
seaview
DNAsp
ade4
Ckma
adegenet
R

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