How reliable are empirical genomic scans for selective sweeps?
Kosuke M Teshima1, Graham Coop, Molly Przeworski
1Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA. kteshima@uchicago.edu
Genome Research
|May 12, 2006
Summary
Empirical approaches to detect positive selection in genetic data can miss many adaptive loci. The reliability of these methods depends on selection mode and population history, impacting adaptation studies.
Area of Science:
- Population Genetics
- Evolutionary Biology
- Genomics
Background:
- Beneficial allele substitutions drive genetic variation patterns at linked sites.
- Identifying adaptations relies on detecting directional selection signatures in polymorphism data.
- Accurate demographic history and selection effect characterization are crucial but challenging.
Purpose of the Study:
- To evaluate the reliability of empirical approaches for detecting positive selection.
- To assess the impact of selection mode and demographic history on empirical method performance.
- To understand limitations in identifying adaptive loci using polymorphism data.
Main Methods:
- Simulated coalescent models of directional selection.
- Incorporated selection on standing variation and new mutations.
- Analyzed human and maize genomic data to assess empirical methods.
Main Results:
- Empirical approaches identify some adaptive loci but miss many others.
- False discovery rates increase with recessive alleles, selection on standing variation, and population bottlenecks.
- Detection power is influenced by allele dominance and population size changes.
Conclusions:
- Genomic scans using empirical approaches may yield unrepresentative subsets of adaptive loci.
- Understanding selection mode and demographic history is vital for accurate adaptation mapping.
- The limitations of empirical methods necessitate careful interpretation of genomic scan results.
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