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

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 o...

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Main Authors: Einar Árnason, Katrín Halldórsdóttir
Format: Article
Language:English
Published: PeerJ Inc. 2015-02-01
Series:PeerJ
Subjects:
Online Access:https://peerj.com/articles/786.pdf
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spelling doaj-f468526fccbf4b21abf3126d9739509d2020-11-24T20:58:47ZengPeerJ Inc.PeerJ2167-83592015-02-013e78610.7717/peerj.786786Nucleotide variation and balancing selection at the Ckma gene in Atlantic cod: analysis with multiple merger coalescent modelsEinar Árnason0Katrín Halldórsdóttir1Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, IcelandInstitute of Life and Environmental Sciences, University of Iceland, Reykjavík, IcelandHigh-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.https://peerj.com/articles/786.pdfBalancing selectionMultiple-merger coalescentAtlantic codTime scales Ckma
collection DOAJ
language English
format Article
sources DOAJ
author Einar Árnason
Katrín Halldórsdóttir
spellingShingle Einar Árnason
Katrín Halldórsdóttir
Nucleotide variation and balancing selection at the Ckma gene in Atlantic cod: analysis with multiple merger coalescent models
PeerJ
Balancing selection
Multiple-merger coalescent
Atlantic cod
Time scales
Ckma
author_facet Einar Árnason
Katrín Halldórsdóttir
author_sort Einar Árnason
title Nucleotide variation and balancing selection at the Ckma gene in Atlantic cod: analysis with multiple merger coalescent models
title_short Nucleotide variation and balancing selection at the Ckma gene in Atlantic cod: analysis with multiple merger coalescent models
title_full Nucleotide variation and balancing selection at the Ckma gene in Atlantic cod: analysis with multiple merger coalescent models
title_fullStr Nucleotide variation and balancing selection at the Ckma gene in Atlantic cod: analysis with multiple merger coalescent models
title_full_unstemmed Nucleotide variation and balancing selection at the Ckma gene in Atlantic cod: analysis with multiple merger coalescent models
title_sort nucleotide variation and balancing selection at the ckma gene in atlantic cod: analysis with multiple merger coalescent models
publisher PeerJ Inc.
series PeerJ
issn 2167-8359
publishDate 2015-02-01
description 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.
topic Balancing selection
Multiple-merger coalescent
Atlantic cod
Time scales
Ckma
url https://peerj.com/articles/786.pdf
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