A SNP/microsatellite genetic linkage map of the Atlantic cod (<i>Gadus morhua</i>)

Moen, Thomas; Delghandi, Madjid; Wesmajervi, Mette Serine; Westgaard, Jon‐Ivar; Fjalestad, Kjersti Turid

doi:10.1111/j.1365-2052.2009.01938.x

Cited by 28 publications

(21 citation statements)

References 12 publications

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“…Of particular importance would be the integration of genomic variation and additive genetic trait variance (Kawecki & Ebert 2004, Jensen et al 2008, and ultimately fitness variation in the wild (Wiehe et al 2007, Andersen et al 2008, Mäkinen et al 2008, Stinchcombe & Hoekstra 2008. Rapid developments in cod genomics, such as full genome sequencing and linkage map construction (Johansen et al 2009, Moen et al 2009, Hubert et al 2010, greatly enhance the potential for pursuing such approaches in cod and related non-model species. …”

Section: Discussionmentioning

confidence: 99%

Microgeographical population structure and adaptation in Atlantic cod Gadus morhua: spatio-temporal insights from gene-associated DNA markers

Poulsen¹,

Hemmer‐Hansen²,

Loeschcke³

et al. 2011

Mar. Ecol. Prog. Ser.

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Recent technical advances have stimulated studies on spatial scales of adaptive genetic variation in marine fishes. However, very few studies have combined spatial and temporal sampling to investigate adaptive genetic structuring at local and microgeographical scales, i.e. scales at which neutral genetic markers have typically revealed very limited levels of population structure. In the present study we analyzed 92 gene-associated single-nucleotide polymorphism (SNP) markers in Atlantic cod Gadus morhua from several sampling sites within the North Sea and adjacent areas. To test for temporal stability, we included long-and short-term (i.e. from 24 to 38 and from 8 to 11 yr, respectively) temporally replicated samples from a subset of populations. As expected, we found very low levels of neutral genetic population structure (F ST = 0.003). Three specific loci, however, showed highly elevated levels of genetic differentiation. Interestingly, these loci were identical to loci previously found to display signals of adaptive evolution on larger spatial scales. Analysis of historical samples revealed long-term temporally stable patterns of both neutral and adaptive divergence between some populations, indicating long-term temporal adaptive stability driven by strong local selection. In an environmentally dynamic area, on the other hand, patterns of genetic structuring were more variable. Overall, our results not only suggest separation of populations under both evolutionary and ecological paradigms, but also illustrate the usefulness of the spatio-temporal approach for making inferences about the dynamics and geographical distribution of adaptive genetic variation in natural populations.

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Section: Discussionmentioning

confidence: 99%

Microgeographical population structure and adaptation in Atlantic cod Gadus morhua: spatio-temporal insights from gene-associated DNA markers

Poulsen¹,

Hemmer‐Hansen²,

Loeschcke³

et al. 2011

Mar. Ecol. Prog. Ser.

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“…The genomic resources in this species were soon after dramatically enhanced by the discovery of a larger panel of 440,817 SNPs after genomic sequence reads were aligned to an exome assembly built from a muscle transcriptome (Lamichhaney et al, 2012). In Atlantic cod (Gadus morhua), the discovery of about 300 genetic variants (Moen et al, 2009) was quickly followed by the publication of more than 1600 markers (Borza et al, 2010;Hubert et al, 2010). The completion of the Atlantic cod genome sequence (Star et al, 2011) and the availability of high-throughput sequencing technology have now facilitated genome resequencing and the associated discovery of more than 900,000 variants in this species (Karlsen et al, 2013).…”

Section: Marine Fishes As Study Systems For Understanding Evolutionmentioning

confidence: 99%

Population Genomics of Marine Fishes: Next-Generation Prospects and Challenges

Hemmer‐Hansen

Therkildsen

Pujolar

2014

The Biological Bulletin

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“…Such variation is likely to have built up over some time by selection (see time scales below). This is in face of considerable gene flow implied by lack of differentiation of neutral loci (Moen et al, 2009; Bradbury et al, 2010; Eiríksson & Árnason, 2013; Hemmer-Hansen et al, 2014). Similarly, the wide distribution of variants within both the A and B alleles of Ckma implies gene flow among localities within South and within North areas.…”

Section: Discussionmentioning

confidence: 99%

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

Árnason

Halldórsdóttir

2015

PeerJ

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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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A SNP/microsatellite genetic linkage map of the Atlantic cod (Gadus morhua)

Cited by 28 publications

References 12 publications

Microgeographical population structure and adaptation in Atlantic cod Gadus morhua: spatio-temporal insights from gene-associated DNA markers

Microgeographical population structure and adaptation in Atlantic cod Gadus morhua: spatio-temporal insights from gene-associated DNA markers

Population Genomics of Marine Fishes: Next-Generation Prospects and Challenges

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

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