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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 outlier pattern and LD in Atlantic cod. The extent of pairwise LD among loci within 23 LGs, measured as r2, is estimated using all individuals and populations. A color bar on the right hand side denotes the strength of the r2 values. A global outlier pattern (underneath each LD plot) based on the same SNP data is visualized using a moving average of the median log10(BF), calculated using the global BAYESCAN outlier analyses (see text for details). The SNPs are plotted according to LG and their respective position within the LGs, based on the results of a preliminary SNP linkage map (Lien S, unpublished data). LG nomenclature follows Hubert et al. (2010).
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evv093-F3: Global outlier pattern and LD in Atlantic cod. The extent of pairwise LD among loci within 23 LGs, measured as r2, is estimated using all individuals and populations. A color bar on the right hand side denotes the strength of the r2 values. A global outlier pattern (underneath each LD plot) based on the same SNP data is visualized using a moving average of the median log10(BF), calculated using the global BAYESCAN outlier analyses (see text for details). The SNPs are plotted according to LG and their respective position within the LGs, based on the results of a preliminary SNP linkage map (Lien S, unpublished data). LG nomenclature follows Hubert et al. (2010).

Mentions: LD was evaluated among all 8,809 SNPs, independent of LG localization to detect both inter- and intrachromosomal LD. As expected, we find SNPs with high r 2 values (>0.75) within all LGs (supplementary table S3, Supplementary Material online). The distributions of the intrachromosomal r 2 values among the different LGs show that SNPs with high r 2 values often reside within the same scaffolds and hence are physically close. However, for LG2, 7 and 12, an extensive number of SNPs with high LD (fig. 3) covers multiple scaffolds including 15 and 5 scaffolds in two close but separated blocks in LG2, 14 scaffolds in LG7, and 31 scaffolds in LG12 (supplementary table S3, Supplementary Material online). The LD pattern (fig. 3) also shows less distinct blocks of elevated r 2 values in LG4, 10, and 17. Interestingly, relatively high levels of r 2 values (>0.3) also occur between SNPs on different LGs, particularly between LG1 and 2 and between LG2 and 4 (supplementary table S3, Supplementary Material online).Fig. 3.—


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 outlier pattern and LD in Atlantic cod. The extent of pairwise LD among loci within 23 LGs, measured as r2, is estimated using all individuals and populations. A color bar on the right hand side denotes the strength of the r2 values. A global outlier pattern (underneath each LD plot) based on the same SNP data is visualized using a moving average of the median log10(BF), calculated using the global BAYESCAN outlier analyses (see text for details). The SNPs are plotted according to LG and their respective position within the LGs, based on the results of a preliminary SNP linkage map (Lien S, unpublished data). LG nomenclature follows Hubert et al. (2010).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv093-F3: Global outlier pattern and LD in Atlantic cod. The extent of pairwise LD among loci within 23 LGs, measured as r2, is estimated using all individuals and populations. A color bar on the right hand side denotes the strength of the r2 values. A global outlier pattern (underneath each LD plot) based on the same SNP data is visualized using a moving average of the median log10(BF), calculated using the global BAYESCAN outlier analyses (see text for details). The SNPs are plotted according to LG and their respective position within the LGs, based on the results of a preliminary SNP linkage map (Lien S, unpublished data). LG nomenclature follows Hubert et al. (2010).
Mentions: LD was evaluated among all 8,809 SNPs, independent of LG localization to detect both inter- and intrachromosomal LD. As expected, we find SNPs with high r 2 values (>0.75) within all LGs (supplementary table S3, Supplementary Material online). The distributions of the intrachromosomal r 2 values among the different LGs show that SNPs with high r 2 values often reside within the same scaffolds and hence are physically close. However, for LG2, 7 and 12, an extensive number of SNPs with high LD (fig. 3) covers multiple scaffolds including 15 and 5 scaffolds in two close but separated blocks in LG2, 14 scaffolds in LG7, and 31 scaffolds in LG12 (supplementary table S3, Supplementary Material online). The LD pattern (fig. 3) also shows less distinct blocks of elevated r 2 values in LG4, 10, and 17. Interestingly, relatively high levels of r 2 values (>0.3) also occur between SNPs on different LGs, particularly between LG1 and 2 and between LG2 and 4 (supplementary table S3, Supplementary Material online).Fig. 3.—

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