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Adaptation to Low Salinity Promotes Genomic Divergence in Atlantic Cod (Gadus morhua L.).

Berg PR, Jentoft S, Star B, Ring KH, Knutsen H, Lien S, Jakobsen KS, André C - Genome Biol Evol (2015)

Bottom Line: Combining outlier analyses with a landscape genomic approach, we identified a set of directionally selected loci that are strongly correlated with habitat differences in salinity, oxygen, and temperature.We report a suite of outlier single nucleotide polymorphisms within or closely located to genes associated with osmoregulation, as well as genes known to play important roles in the hydration and development of oocytes.These genes are likely to have key functions within a general osmoregulatory framework and are important for the survival of eggs and larvae, contributing to the buildup of reproductive isolation between the low-salinity adapted Baltic cod and the adjacent cod populations.

View Article: PubMed Central - PubMed

Affiliation: Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway.

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SNPs associated with environmental variables in Atlantic cod. Manhattan plots of SNP association with salinity, temperature, and oxygen level (all at surface and at spawning depth, see table 1) based on median log10(BF) from 32 independent runs of BAYENV. The SNPs are plotted according to LG and their respective position within the LGs along the X axis, based on the results of a preliminary SNP linkage map (Lien S, unpublished data). LG nomenclature follows Hubert et al. (2010). The dotted line at log10(BF) = 1 indicates strong association and the solid line at 2 indicates decisive association according to Jeffreys (1961).
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evv093-F5: SNPs associated with environmental variables in Atlantic cod. Manhattan plots of SNP association with salinity, temperature, and oxygen level (all at surface and at spawning depth, see table 1) based on median log10(BF) from 32 independent runs of BAYENV. The SNPs are plotted according to LG and their respective position within the LGs along the X axis, based on the results of a preliminary SNP linkage map (Lien S, unpublished data). LG nomenclature follows Hubert et al. (2010). The dotted line at log10(BF) = 1 indicates strong association and the solid line at 2 indicates decisive association according to Jeffreys (1961).

Mentions: Correlations between allele frequencies and salinity (‰), temperature (°C) and oxygen concentration at surface and at spawning depth (table 3) were investigated using a landscape genomic approach (BAYENV 2.0). Significant association (median log10(BF) > 1 and q < 0.01) with at least one environmental variable was detected in 234 (2.6%) of the 8,809 examined SNP loci, distributed across all LGs except LG6 (supplementary fig. S3 and table S4, Supplementary Material online). The pattern and the number of SNPs with correlation to each environmental variable varied (fig. 5a–f). An association with salinity and oxygen level at spawning depth is clearly observed at a genome-wide scale, and in particular toward the end of LG2, whereas temperature shows a weak correlation in LG12 (fig. 5). There is a strong correlation between SNPs associated with salinity and oxygen, whereas SNPs associated with temperature are not strongly correlated with salinity or oxygen SNPs (fig. 5).Fig. 5.—


Adaptation to Low Salinity Promotes Genomic Divergence in Atlantic Cod (Gadus morhua L.).

Berg PR, Jentoft S, Star B, Ring KH, Knutsen H, Lien S, Jakobsen KS, André C - Genome Biol Evol (2015)

SNPs associated with environmental variables in Atlantic cod. Manhattan plots of SNP association with salinity, temperature, and oxygen level (all at surface and at spawning depth, see table 1) based on median log10(BF) from 32 independent runs of BAYENV. The SNPs are plotted according to LG and their respective position within the LGs along the X axis, based on the results of a preliminary SNP linkage map (Lien S, unpublished data). LG nomenclature follows Hubert et al. (2010). The dotted line at log10(BF) = 1 indicates strong association and the solid line at 2 indicates decisive association according to Jeffreys (1961).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4494048&req=5

evv093-F5: SNPs associated with environmental variables in Atlantic cod. Manhattan plots of SNP association with salinity, temperature, and oxygen level (all at surface and at spawning depth, see table 1) based on median log10(BF) from 32 independent runs of BAYENV. The SNPs are plotted according to LG and their respective position within the LGs along the X axis, based on the results of a preliminary SNP linkage map (Lien S, unpublished data). LG nomenclature follows Hubert et al. (2010). The dotted line at log10(BF) = 1 indicates strong association and the solid line at 2 indicates decisive association according to Jeffreys (1961).
Mentions: Correlations between allele frequencies and salinity (‰), temperature (°C) and oxygen concentration at surface and at spawning depth (table 3) were investigated using a landscape genomic approach (BAYENV 2.0). Significant association (median log10(BF) > 1 and q < 0.01) with at least one environmental variable was detected in 234 (2.6%) of the 8,809 examined SNP loci, distributed across all LGs except LG6 (supplementary fig. S3 and table S4, Supplementary Material online). The pattern and the number of SNPs with correlation to each environmental variable varied (fig. 5a–f). An association with salinity and oxygen level at spawning depth is clearly observed at a genome-wide scale, and in particular toward the end of LG2, whereas temperature shows a weak correlation in LG12 (fig. 5). There is a strong correlation between SNPs associated with salinity and oxygen, whereas SNPs associated with temperature are not strongly correlated with salinity or oxygen SNPs (fig. 5).Fig. 5.—

Bottom Line: Combining outlier analyses with a landscape genomic approach, we identified a set of directionally selected loci that are strongly correlated with habitat differences in salinity, oxygen, and temperature.We report a suite of outlier single nucleotide polymorphisms within or closely located to genes associated with osmoregulation, as well as genes known to play important roles in the hydration and development of oocytes.These genes are likely to have key functions within a general osmoregulatory framework and are important for the survival of eggs and larvae, contributing to the buildup of reproductive isolation between the low-salinity adapted Baltic cod and the adjacent cod populations.

View Article: PubMed Central - PubMed

Affiliation: Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway.

Show MeSH
Related in: MedlinePlus