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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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Global and pairwise outlier patterns in Atlantic cod. Manhattan plots of global and pairwise outlier analyses based on median log10(BF) from ten replicate runs of BAYESCAN. 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respective position within the LGs along the X axis based on the results of a preliminary SNP linkage map (Lien S, unpublished data).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-F4: Global and pairwise outlier patterns in Atlantic cod. Manhattan plots of global and pairwise outlier analyses based on median log10(BF) from ten replicate runs of BAYESCAN. 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respective position within the LGs along the X axis based on the results of a preliminary SNP linkage map (Lien S, unpublished data).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: In the global outlier analyses comprising all four populations, we identified 123 (1.4%) and 114 (1.3%) SNPs as candidates for divergent selection (log10(Bayes factor [BF]) > 1, empirical P < 0.01), using BAYESCAN and LOSITAN, respectively. Pairwise outlier analyses using BAYESCAN, revealed 228 (2.6%) SNPs as candidates for divergent selection (supplementary fig. S3 and table S4, Supplementary Material online). However, the pattern and the number of outliers in each pairwise comparison varied (fig. 4b–g). In total, 266 SNPs (3.0%) were detected as candidates for divergent selection using global or pairwise outlier test. LG2 and 12 had the highest proportion of SNPs potentially under selection (36 and 98, respectively; supplementary table S4, Supplementary Material online). These two LGs contain large LD blocks, where most, but not all, of these outliers reside (fig. 3).Fig. 4.—


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)

Global and pairwise outlier patterns in Atlantic cod. Manhattan plots of global and pairwise outlier analyses based on median log10(BF) from ten replicate runs of BAYESCAN. 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-F4: Global and pairwise outlier patterns in Atlantic cod. Manhattan plots of global and pairwise outlier analyses based on median log10(BF) from ten replicate runs of BAYESCAN. 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: In the global outlier analyses comprising all four populations, we identified 123 (1.4%) and 114 (1.3%) SNPs as candidates for divergent selection (log10(Bayes factor [BF]) > 1, empirical P < 0.01), using BAYESCAN and LOSITAN, respectively. Pairwise outlier analyses using BAYESCAN, revealed 228 (2.6%) SNPs as candidates for divergent selection (supplementary fig. S3 and table S4, Supplementary Material online). However, the pattern and the number of outliers in each pairwise comparison varied (fig. 4b–g). In total, 266 SNPs (3.0%) were detected as candidates for divergent selection using global or pairwise outlier test. LG2 and 12 had the highest proportion of SNPs potentially under selection (36 and 98, respectively; supplementary table S4, Supplementary Material online). These two LGs contain large LD blocks, where most, but not all, of these outliers reside (fig. 3).Fig. 4.—

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