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Multi-locus inference of population structure: a comparison between single nucleotide polymorphisms and
1Laboratory of Genetics, University of Wisconsin, Madison, WI 53706, USA.
Heredity
|March 25, 2010
Summary
Fewer short tandem repeat polymorphisms (STRPs) than single nucleotide polymorphisms (SNPs) are needed to detect recent population structure. STRPs also offer more accurate population number estimation, aiding genetic studies.
Area of Science:
- Population Genetics
- Molecular Ecology
- Bioinformatics
Background:
- Single nucleotide polymorphisms (SNPs) and short tandem repeat polymorphisms (STRPs) are widely used genetic markers for inferring population structure.
- The relative effectiveness and properties of SNPs and STRPs in detecting population structure are not fully understood due to their distinct mutation mechanisms.
- Understanding these differences is crucial for optimizing study design in population genetics.
Purpose of the Study:
- To quantitatively compare the power of SNPs and STRPs in detecting population structure using coalescent simulations.
- To evaluate the influence of biological and practical factors on the performance of these markers in population structure analyses.
- To provide guidance for designing effective multi-locus studies for population structure inference.
Main Methods:
- Utilized coalescent simulations to model the behavior of SNPs and STRPs under various population genetic scenarios.
- Focused on the widely used STRUCTURE analysis framework to assess marker performance.
- Investigated factors including divergence times, gene flow, mutation models, marker ascertainment, and sample composition.
Main Results:
- Fewer unlinked STRPs than SNPs are required to detect population structure at recent divergence times (<0.3 N(e) generations).
- Accurate estimation of the number of populations requires significantly fewer STRPs compared to SNPs.
- Increasing marker numbers largely compensates for power loss due to moderate gene flow (N(e)m=1.0) for both marker types; SNP haplotypes showed power comparable to STRPs; ascertainment schemes selecting highly variable loci improved power but may limit broader inference.
Conclusions:
- STRPs are generally more efficient than SNPs for detecting recent population structure and estimating the number of populations.
- Study design choices, such as marker number and ascertainment strategy, significantly impact the power to detect population structure.
- These findings offer practical recommendations for researchers designing genetic studies to investigate population structure in natural populations.
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