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.

Show MeSH

Related in: MedlinePlus

Population recombination rates  for the data and the model. ρ is estimated in 1-Mb windows by fitting a curve to the decay of r2 with distance according to Hill and Weir (1988). On average, there is an about 8-fold smaller effective recombination rate in northern compared with southern Sweden in the data. Simulations from the secondaryContact6 model predict a similar ratio.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4209139&req=5

msu247-F3: Population recombination rates for the data and the model. ρ is estimated in 1-Mb windows by fitting a curve to the decay of r2 with distance according to Hill and Weir (1988). On average, there is an about 8-fold smaller effective recombination rate in northern compared with southern Sweden in the data. Simulations from the secondaryContact6 model predict a similar ratio.

Mentions: Additional evidence in support of this model comes from comparing linkage disequilibrium (LD) between the data and coalescent simulations under the secondaryContact6 demography. This model recapitulates the ratio of LD between South and North very well (fig. 3): The estimated population recombination rate is 7.9-fold larger in southern Sweden than in northern Sweden and the simulations predict a comparable ratio of 8.3. For this reason, all subsequent simulation results are based on the secondary contact model.Fig. 3.


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

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

Population recombination rates  for the data and the model. ρ is estimated in 1-Mb windows by fitting a curve to the decay of r2 with distance according to Hill and Weir (1988). On average, there is an about 8-fold smaller effective recombination rate in northern compared with southern Sweden in the data. Simulations from the secondaryContact6 model predict a similar ratio.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

msu247-F3: Population recombination rates for the data and the model. ρ is estimated in 1-Mb windows by fitting a curve to the decay of r2 with distance according to Hill and Weir (1988). On average, there is an about 8-fold smaller effective recombination rate in northern compared with southern Sweden in the data. Simulations from the secondaryContact6 model predict a similar ratio.
Mentions: Additional evidence in support of this model comes from comparing linkage disequilibrium (LD) between the data and coalescent simulations under the secondaryContact6 demography. This model recapitulates the ratio of LD between South and North very well (fig. 3): The estimated population recombination rate is 7.9-fold larger in southern Sweden than in northern Sweden and the simulations predict a comparable ratio of 8.3. For this reason, all subsequent simulation results are based on the secondary contact model.Fig. 3.

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
Related in: MedlinePlus