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Clonal reproduction and linkage disequilibrium in diploids: a simulation study
Thierry de Meeûs1, François Balloux
1Génétique et Evolution des Maladies Infectieuses, Equipe Evolution des Systèmes Symbiotiques, UMR 2724 CNRS-IRD, BP 64501, 911 Av. Agropolis, 34394 Montpellier Cedex 5, France. demeeus@mpl.ird.fr
Summary
Estimating clonal reproduction rates in diploid organisms is challenging. Computer simulations show that no single linkage disequilibrium (LD) estimator accurately measures clonal or sexual reproduction proportions alone.
Area of Science:
- Population genetics
- Molecular ecology
- Evolutionary biology
Background:
- Estimating clonal reproduction in natural diploid populations is difficult.
- Detecting strictly clonal populations is often controversial.
- Non-random associations between loci (linkage disequilibrium) are a signature of clonal reproduction.
Purpose of the Study:
- To investigate the impact of clonal reproduction rates on linkage disequilibrium (LD) estimates.
- To evaluate the performance of different LD estimators in clonal populations.
- To provide tools for studying clonal diploid organisms using molecular markers.
Main Methods:
- Computer simulations were used to model clonal reproduction.
- A comprehensive parameter range was explored.
- Various linkage disequilibrium estimators were analyzed.
Main Results:
- None of the studied LD estimators accurately measured the proportion of clonal or sexual reproduction independently.
- Estimators exhibited significant bias, incoherent behavior, or large variances.
- The effectiveness of LD estimators varied with the rate of clonal reproduction.
Conclusions:
- A single LD estimator is insufficient for accurately quantifying clonal reproduction rates.
- The joint use of multiple statistical measures is recommended for reliable estimation.
- This research offers valuable tools for studying clonal diploids, including medically important parasites.