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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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Model diagrams. (a) General model setup. (b) Model scheme and parameter estimates of backward migration rates , times (in units of ) and population sizes (in units of N0) for the best fitting model (secondaryContact6).
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msu247-F2: Model diagrams. (a) General model setup. (b) Model scheme and parameter estimates of backward migration rates , times (in units of ) and population sizes (in units of N0) for the best fitting model (secondaryContact6).

Mentions: Within the two-deme framework, we modeled a number of potential evolutionary histories. All models begin with the split of the ancestral population and allow for the exchange of migrants. We allow for variable and asymmetric migration, secondary contact after a phase of separation, different deme sizes, population size changes (including bottlenecks) either at the split time or afterwards, and variable split times from the common ancestor. In addition, we model three different admixture scenarios in order to simulate two postglacial waves of expansion (François et al. 2008). In total, we tested 14 models with 4–9 parameters using (Gutenkunst et al. 2009). A summary of the tested models is given in table 1 and figure 2.Fig. 2.


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

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

Model diagrams. (a) General model setup. (b) Model scheme and parameter estimates of backward migration rates , times (in units of ) and population sizes (in units of N0) for the best fitting model (secondaryContact6).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

msu247-F2: Model diagrams. (a) General model setup. (b) Model scheme and parameter estimates of backward migration rates , times (in units of ) and population sizes (in units of N0) for the best fitting model (secondaryContact6).
Mentions: Within the two-deme framework, we modeled a number of potential evolutionary histories. All models begin with the split of the ancestral population and allow for the exchange of migrants. We allow for variable and asymmetric migration, secondary contact after a phase of separation, different deme sizes, population size changes (including bottlenecks) either at the split time or afterwards, and variable split times from the common ancestor. In addition, we model three different admixture scenarios in order to simulate two postglacial waves of expansion (François et al. 2008). In total, we tested 14 models with 4–9 parameters using (Gutenkunst et al. 2009). A summary of the tested models is given in table 1 and figure 2.Fig. 2.

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