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Double reduction estimation and equilibrium tests in natural autopolyploid populations

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  • David Gerard

Abstract

Many bioinformatics pipelines include tests for equilibrium. Tests for diploids are well studied and widely available, but extending these approaches to autopolyploids is hampered by the presence of double reduction, the comigration of sister chromatid segments into the same gamete during meiosis. Though a hindrance for equilibrium tests, double reduction rates are quantities of interest in their own right, as they provide insights about the meiotic behavior of autopolyploid organisms. Here, we develop procedures to (i) test for equilibrium while accounting for double reduction, and (ii) estimate the double reduction rate given equilibrium. To do so, we take two approaches: a likelihood approach, and a novel U‐statistic minimization approach that we show generalizes the classical equilibrium χ2 test in diploids. For small sample sizes and uncertain genotypes, we further develop a bootstrap procedure based on our U‐statistic to test for equilibrium. We validate our methods on both simulated and real data.

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  • David Gerard, 2023. "Double reduction estimation and equilibrium tests in natural autopolyploid populations," Biometrics, The International Biometric Society, vol. 79(3), pages 2143-2156, September.
    • Handle: RePEc:bla:biomet:v:79:y:2023:i:3:p:2143-2156
    DOI: 10.1111/biom.13722
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    References listed on IDEAS

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    1. Oliver Serang & Marcelo Mollinari & Antonio Augusto Franco Garcia, 2012. "Efficient Exact Maximum a Posteriori Computation for Bayesian SNP Genotyping in Polyploids," PLOS ONE, Public Library of Science, vol. 7(2), pages 1-13, February.
    2. Hansen, Lars Peter, 1982. "Large Sample Properties of Generalized Method of Moments Estimators," Econometrica, Econometric Society, vol. 50(4), pages 1029-1054, July.
    3. Newey, Whitney K & West, Kenneth D, 1987. "Hypothesis Testing with Efficient Method of Moments Estimation," International Economic Review, Department of Economics, University of Pennsylvania and Osaka University Institute of Social and Economic Research Association, vol. 28(3), pages 777-787, October.
    4. Honore, Bo E. & Powell, James L., 1994. "Pairwise difference estimators of censored and truncated regression models," Journal of Econometrics, Elsevier, vol. 64(1-2), pages 241-278.
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