Limits...
Keeping it local: evidence for positive selection in Swedish Arabidopsis thaliana.

Huber CD, Nordborg M, Hermisson J, Hellmann I - Mol. Biol. Evol. (2014)

Bottom Line: The model plant Arabidopsis thaliana exemplifies this problem: In spite of the large amounts of data, little evidence for classic selective sweeps has been found.Moreover, it affects the power differently for northern Sweden (more false positives) as compared with southern Sweden (more false negatives).This study demonstrates the necessity of combining demographic analyses and sweep scans for the detection of selection, particularly when selection acts predominantly local.

View Article: PubMed Central - PubMed

Affiliation: Mathematics and BioSciences Group, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria.

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CLR and FST behavior under global and local selection. (a) and (b) are results of a strong sweep (s = 0.01) starting in northern Sweden, (b) and (d) are results of a weak sweep (s = 0.0025) starting in southern Sweden. Green points indicate results under global selection, cyan points indicate results under local selection. The blue and red circles show the CLR and FST values of the significant sweep regions in northern and southern Sweden, respectively. A single sweep region (violet circle) is significant in both northern and southern Sweden. The colored lines are 95% confidence contours. Upper 99% confidence cutoffs for FST and CLR are calculated from 2,400 neutral simulations of 1 Mb sequence and are indicated by the dashed lines. The pointed line indicates the lower 99% cutoff of FST. The msms code for all simulations can be found in supplementary table S5, Supplementary Material online.
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msu247-F6: CLR and FST behavior under global and local selection. (a) and (b) are results of a strong sweep (s = 0.01) starting in northern Sweden, (b) and (d) are results of a weak sweep (s = 0.0025) starting in southern Sweden. Green points indicate results under global selection, cyan points indicate results under local selection. The blue and red circles show the CLR and FST values of the significant sweep regions in northern and southern Sweden, respectively. A single sweep region (violet circle) is significant in both northern and southern Sweden. The colored lines are 95% confidence contours. Upper 99% confidence cutoffs for FST and CLR are calculated from 2,400 neutral simulations of 1 Mb sequence and are indicated by the dashed lines. The pointed line indicates the lower 99% cutoff of FST. The msms code for all simulations can be found in supplementary table S5, Supplementary Material online.

Mentions: Furthermore, we simulated a scenario of global selection with different average selection strength and local selection. As before, we assume that the same allele is under selection with s = 0.01 in the North, but weaker selection in the South with s = 0.0025. We have chosen a selection coefficient in the South to match the observed CLR values of sweep regions in southern Sweden (table 4). The power of detecting a global, but weaker sweep in southern Sweden is still at 60–70%. Hence, it seems highly unlikely that the five northern sweeps are global, because we should have also seen some of them in the South (fig. 6a).Fig. 6.


Keeping it local: evidence for positive selection in Swedish Arabidopsis thaliana.

Huber CD, Nordborg M, Hermisson J, Hellmann I - Mol. Biol. Evol. (2014)

CLR and FST behavior under global and local selection. (a) and (b) are results of a strong sweep (s = 0.01) starting in northern Sweden, (b) and (d) are results of a weak sweep (s = 0.0025) starting in southern Sweden. Green points indicate results under global selection, cyan points indicate results under local selection. The blue and red circles show the CLR and FST values of the significant sweep regions in northern and southern Sweden, respectively. A single sweep region (violet circle) is significant in both northern and southern Sweden. The colored lines are 95% confidence contours. Upper 99% confidence cutoffs for FST and CLR are calculated from 2,400 neutral simulations of 1 Mb sequence and are indicated by the dashed lines. The pointed line indicates the lower 99% cutoff of FST. The msms code for all simulations can be found in supplementary table S5, Supplementary Material online.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4209139&req=5

msu247-F6: CLR and FST behavior under global and local selection. (a) and (b) are results of a strong sweep (s = 0.01) starting in northern Sweden, (b) and (d) are results of a weak sweep (s = 0.0025) starting in southern Sweden. Green points indicate results under global selection, cyan points indicate results under local selection. The blue and red circles show the CLR and FST values of the significant sweep regions in northern and southern Sweden, respectively. A single sweep region (violet circle) is significant in both northern and southern Sweden. The colored lines are 95% confidence contours. Upper 99% confidence cutoffs for FST and CLR are calculated from 2,400 neutral simulations of 1 Mb sequence and are indicated by the dashed lines. The pointed line indicates the lower 99% cutoff of FST. The msms code for all simulations can be found in supplementary table S5, Supplementary Material online.
Mentions: Furthermore, we simulated a scenario of global selection with different average selection strength and local selection. As before, we assume that the same allele is under selection with s = 0.01 in the North, but weaker selection in the South with s = 0.0025. We have chosen a selection coefficient in the South to match the observed CLR values of sweep regions in southern Sweden (table 4). The power of detecting a global, but weaker sweep in southern Sweden is still at 60–70%. Hence, it seems highly unlikely that the five northern sweeps are global, because we should have also seen some of them in the South (fig. 6a).Fig. 6.

Bottom Line: The model plant Arabidopsis thaliana exemplifies this problem: In spite of the large amounts of data, little evidence for classic selective sweeps has been found.Moreover, it affects the power differently for northern Sweden (more false positives) as compared with southern Sweden (more false negatives).This study demonstrates the necessity of combining demographic analyses and sweep scans for the detection of selection, particularly when selection acts predominantly local.

View Article: PubMed Central - PubMed

Affiliation: Mathematics and BioSciences Group, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria.

Show MeSH