ArticlePeerJ2015
Nucleotide variation and balancing selection at the Ckma gene in Atlantic cod: analysis with multiple merger coalescent models.
Article in PeerJ, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 48 citations in OpenAlex.
- Interpreting the pervasive observation of U-shaped Site Frequency Spectra.PLoS genetics · 2023Article
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- Multiple Merger Genealogies in Outbreaks of Mycobacterium tuberculosis.Molecular biology and evolution · 2021Article
- Gene flow as a simple cause for an excess of high-frequency-derived alleles.Evolutionary applications · 2020Article
- Identifying loci under positive selection in complex population histories.Genome research · 2019Article
- Codweb: Whole-genome sequencing uncovers extensive reticulations fueling adaptation among Atlantic, Arctic, and Pacific gadids.Science advances · 2019Article
- Phylogeographic mitogenomics of Atlantic codEcology and evolution · 2018Article
- Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography.Genetics · 2018Article
- Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Genetic load in marine animals: a review.Current zoology · 2016Article
- Coalescent inferences in conservation genetics: should the exception become the rule?Biology letters · 2016Review
- Three chromosomal rearrangements promote genomic divergence between migratory and stationary ecotypes of Atlantic cod.Scientific reports · 2016Article
- Evaluating the adaptive potential of the European eel: is the immunogenetic status recovering?PeerJ · 2016Article
- Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees.BMC bioinformatics · 2015Article
- Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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