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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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Distribution of maximum CLR values in 1-Mb windows. Simulations based on the standard neutral model (constant population size) for southern Sweden (a) and northern Sweden (b). Simulations based on the secondaryContact6 model for southern Sweden (c) and northern Sweden (d). The dashed line indicates the 99% statistical cutoff (223, 303, 110, and 1,667 in a, b, c, and d, respectively).
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msu247-F5: Distribution of maximum CLR values in 1-Mb windows. Simulations based on the standard neutral model (constant population size) for southern Sweden (a) and northern Sweden (b). Simulations based on the secondaryContact6 model for southern Sweden (c) and northern Sweden (d). The dashed line indicates the 99% statistical cutoff (223, 303, 110, and 1,667 in a, b, c, and d, respectively).

Mentions: We determine the neutral CLR distribution for northern and southern Sweden under the best-fitting demographic model (secondaryContact6). As it turns out, this model mimics the observed shifts in the CLR distribution that we observed for northern and southern Sweden (fig. 5), with the distribution for the North being more skewed and having a higher median than that for the South (table 3). The strong skew in our model is a consequence of the secondary contact scenario: Neither a 100-fold increase in migration, that is, a quasi-panmictic population, where CLR-differences must be due to sample size, nor a scenario without migration can produce a long tail similar to the observed one (supplementary fig. S7, Supplementary Material online). Similar shifts in the CLR distribution, although not as pronounced, were also observed for the two other models we tested: splitMig5 and splitMigBottleneck8 (supplementary fig. S6, Supplementary Material online).Fig. 5.


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

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

Distribution of maximum CLR values in 1-Mb windows. Simulations based on the standard neutral model (constant population size) for southern Sweden (a) and northern Sweden (b). Simulations based on the secondaryContact6 model for southern Sweden (c) and northern Sweden (d). The dashed line indicates the 99% statistical cutoff (223, 303, 110, and 1,667 in a, b, c, and d, respectively).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

msu247-F5: Distribution of maximum CLR values in 1-Mb windows. Simulations based on the standard neutral model (constant population size) for southern Sweden (a) and northern Sweden (b). Simulations based on the secondaryContact6 model for southern Sweden (c) and northern Sweden (d). The dashed line indicates the 99% statistical cutoff (223, 303, 110, and 1,667 in a, b, c, and d, respectively).
Mentions: We determine the neutral CLR distribution for northern and southern Sweden under the best-fitting demographic model (secondaryContact6). As it turns out, this model mimics the observed shifts in the CLR distribution that we observed for northern and southern Sweden (fig. 5), with the distribution for the North being more skewed and having a higher median than that for the South (table 3). The strong skew in our model is a consequence of the secondary contact scenario: Neither a 100-fold increase in migration, that is, a quasi-panmictic population, where CLR-differences must be due to sample size, nor a scenario without migration can produce a long tail similar to the observed one (supplementary fig. S7, Supplementary Material online). Similar shifts in the CLR distribution, although not as pronounced, were also observed for the two other models we tested: splitMig5 and splitMigBottleneck8 (supplementary fig. S6, Supplementary Material online).Fig. 5.

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