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Controlling Population Evolution in the Laboratory to Evaluate Methods of Historical Inference

By Patrick Mardulyn, Marie-Anne Vaesen and Michel C. Milinkovitch

Abstract

Natural populations of known detailed past demographic history are extremely valuable to evaluate methods of historical inference, yet are extremely rare. As an alternative approach, we have generated multiple replicate microsatellite data sets from laboratory-cultured populations of a gonochoric free-living nematode, Caenorhabditis remanei, that were constrained to pre-defined demographic histories featuring different levels of migration among populations or bottleneck events of different magnitudes. These data sets were then used to evaluate the performances of two recently developed population genetics methods, BayesAss+, that estimates recent migration rates among populations, and Bottleneck, that detects the occurrence of recent bottlenecks. Migration rates inferred by BayesAss+ were generally over-estimates, although these were often included within the confidence interval. Analyses of data sets simulated in-silico, using a model mimicking the laboratory experiments, produced less biased estimates of the migration rates, and showed increased efficiency of the program when the number of loci and sampled genotypes per population was higher. In the replicates for which the pre-bottleneck laboratory-cultured populations did not significantly depart from a mutation/drift equilibrium, an important assumption of the program Bottleneck, only a portion of the bottleneck events were detected. This result was confirmed by in-silico simulations mirroring the laboratory bottleneck experiments. More generally, our study demonstrates the feasibility, and highlights some of the limits, of the approach that consists in generating molecular genetic data sets by controlling the evolution of laboratory-reared nematode populations, for the purpose of validating methods inferring population history

Topics: Research Article
Publisher: Public Library of Science
OAI identifier: oai:pubmedcentral.nih.gov:2491900
Provided by: PubMed Central
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    1. (2002). Approximate Bayesian computation in population genetics.
    2. (2005). Arlequin ver. 3.0: An integrated software package for population genetics data analysis.
    3. (2003). Bayesian inference of recent migration rates using multilocus genotypes.
    4. (2004). Beyond Fst: Analysis of population genetic data for conservation.
    5. (1999). Bottleneck: a computer program for detecting recent reductions in the effective population size using allele frequency data.
    6. (2004). Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss.
    7. (2005). Comparison of methods for detecting bottlenecks from microsatellite loci.
    8. (2006). Computer programs for population genetics data analysis: a survival guide.
    9. (1996). Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data.
    10. (1999). Detecting population expansion and decline using microsatellites.
    11. (2002). Distinguishing between selection and population expansion in an experimental lineage of bacteriophage T7.
    12. (2003). Estimating effective population size and migration rates from genetic samples over space and time.
    13. (1984). Estimating F-statistics for the analysis of population structure.
    14. (2007). Evaluating the performance of a multilocus Bayesian method for the estimation of migration rates.
    15. (2004). Evaluating the performance of likelihood methods for detecting population structure and migration.
    16. (1931). Evolution in Mendelian populations.
    17. (1992). Experimental phylogenetics: generation of a known phylogeny.
    18. (1985). Gene flow in natural populations.
    19. (1995). Genepop (Version-1.2)-Population-Genetics Software for Exact Tests and Ecumenicism.
    20. (2006). High nucleotide polymorphism and rapid decay of linkage disequilibrium in wild populations of Caenorhabditis remanei.
    21. (2007). Inbreeding and outbreeding depression in Caenorhabditis nematodes.
    22. (1999). Indirect measures of gene flow and migration:
    23. (1998). Laboratory cultivation of Caenorhabditis elegans and other free-living nematodes.
    24. (2006). LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters.
    25. (2002). Levels of DNA polymorphism vary with mating system in the nematode genus caenorhabditis.
    26. (2001). Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach.
    27. (1994). Modelling problems in conservation genetics using Drosophila: consequences of fluctuating population sizes.
    28. (1989). Molecular cloning: a laboratory manual.
    29. (1987). Molecular evolutionary genetics.
    30. (2004). Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis.
    31. (1992). Reproductive isolation in Rhabditidae (Nematoda: secernentea); mechanisms that isolate six species of three genera.
    32. (1999). Resolving conceptual issues in conservation genetics: the roles of laboratory species and meta-analyses.

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