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Measuring population differentiation using GST or D? A simulation study with microsatellite DNA markers under a finite island model and nonequilibrium conditions.

Abstract

The genetic differentiation of populations is a key parameter in population genetic investigations. Wright's F(ST) (and its relatives such as G(ST) ) has been a standard measure of differentiation. However, the deficiencies of these indexes have been increasingly realized in recent years, leading to some new measures being proposed, such as Jost's D (Molecular Ecology, 2008; 17, 4015). The existence of these new metrics has stimulated considerable debate and induced some confusion on which statistics should be used for estimating population differentiation. Here, we report a simulation study with neutral microsatellite DNA loci under a finite island model to compare the performance of G(ST) and D, particularly under nonequilibrium conditions. Our results suggest that there exist fundamental differences between the two statistics, and neither G(ST) nor D operates satisfactorily in all situations for quantifying differentiation. D is very sensitive to mutation models but G(ST) noticeably less so, which limits D's utility in population parameter estimation and comparisons across genetic markers. Also, the initial heterozygosity of the starting populations has some important effects on both the individual behaviours of G(ST) and D and their relative behaviours in early differentiation, and this effect is much greater for D than G(ST) . In the early stages of differentiation, when initial heterozygosity is relatively low (<0.5, if the number of subpopulations is large), G(ST) increases faster than D; the opposite is true when initial heterozygosity is high. Therefore, the state of the ancestral population appears to have some lasting impacts on population differentiation. In general, G(ST) can measure differentiation fairly well when heterozygosity is low whatever the causes; however, when heterozygosity is high (e.g. as a result of either high mutation rate or high initial heterozygosity) and gene flow is moderate to strong, G(ST) fails to measure differentiation. Interestingly, when population size is not very small (e.g. N ≥ 1000), G(ST) measures differentiation quite linearly with time over a long duration when gene flow is absent or very weak even if mutation rate is not low (e.g. μ = 0.001). In contrast, D, as a differentiation measure, performs rather robustly in all these situations. In practice, both indexes should be calculated and the relative levels of heterozygosities (especially H(S) ) and gene flow taken into account. We suggest that a comparison of the two indexes can generate useful insights into the evolutionary processes that influence population differentiation.

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  • Publisher Full Text
  • Authors+Show Affiliations

    ,

    State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101.

    Source

    Molecular ecology 20:12 2011 Jun pg 2494-509

    MeSH

    Biological Evolution
    Computer Simulation
    Gene Flow
    Genetic Markers
    Genetic Variation
    Genetics, Population
    Heterozygote
    Microsatellite Repeats
    Models, Genetic
    Mutation
    Population Dynamics
    Software
    Statistics as Topic

    Pub Type(s)

    Journal Article
    Research Support, Non-U.S. Gov't

    Language

    eng

    PubMed ID

    21557781

    Citation

    TY - JOUR T1 - Measuring population differentiation using GST or D? A simulation study with microsatellite DNA markers under a finite island model and nonequilibrium conditions. AU - Leng,Liang, AU - Zhang,D E-Xing, Y1 - 2011/05/09/ PY - 2011/5/9/aheadofprint PY - 2011/5/12/entrez PY - 2011/5/12/pubmed PY - 2011/10/15/medline SP - 2494 EP - 509 JF - Molecular ecology JO - Mol. Ecol. VL - 20 IS - 12 N2 - The genetic differentiation of populations is a key parameter in population genetic investigations. Wright's F(ST) (and its relatives such as G(ST) ) has been a standard measure of differentiation. However, the deficiencies of these indexes have been increasingly realized in recent years, leading to some new measures being proposed, such as Jost's D (Molecular Ecology, 2008; 17, 4015). The existence of these new metrics has stimulated considerable debate and induced some confusion on which statistics should be used for estimating population differentiation. Here, we report a simulation study with neutral microsatellite DNA loci under a finite island model to compare the performance of G(ST) and D, particularly under nonequilibrium conditions. Our results suggest that there exist fundamental differences between the two statistics, and neither G(ST) nor D operates satisfactorily in all situations for quantifying differentiation. D is very sensitive to mutation models but G(ST) noticeably less so, which limits D's utility in population parameter estimation and comparisons across genetic markers. Also, the initial heterozygosity of the starting populations has some important effects on both the individual behaviours of G(ST) and D and their relative behaviours in early differentiation, and this effect is much greater for D than G(ST) . In the early stages of differentiation, when initial heterozygosity is relatively low (<0.5, if the number of subpopulations is large), G(ST) increases faster than D; the opposite is true when initial heterozygosity is high. Therefore, the state of the ancestral population appears to have some lasting impacts on population differentiation. In general, G(ST) can measure differentiation fairly well when heterozygosity is low whatever the causes; however, when heterozygosity is high (e.g. as a result of either high mutation rate or high initial heterozygosity) and gene flow is moderate to strong, G(ST) fails to measure differentiation. Interestingly, when population size is not very small (e.g. N ≥ 1000), G(ST) measures differentiation quite linearly with time over a long duration when gene flow is absent or very weak even if mutation rate is not low (e.g. μ = 0.001). In contrast, D, as a differentiation measure, performs rather robustly in all these situations. In practice, both indexes should be calculated and the relative levels of heterozygosities (especially H(S) ) and gene flow taken into account. We suggest that a comparison of the two indexes can generate useful insights into the evolutionary processes that influence population differentiation. SN - 1365-294X UR - https://www.unboundmedicine.com/medline/citation/21557781/Measuring_population_differentiation_using_GST_or_D_A_simulation_study_with_microsatellite_DNA_markers_under_a_finite_island_model_and_nonequilibrium_conditions_ L2 - http://onlinelibrary.wiley.com/resolve/openurl?genre=article&amp;sid=nlm:pubmed&amp;issn=0962-1083&amp;date=2011&amp;volume=20&amp;issue=12&amp;spage=2494 ER -