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A pairwise relatedness estimator for polyploids

Authors

  • Kang Huang,

    1. Key Laboratory of Resource Biology and Biotechnology in Western China of Ministry of Education, and College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
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  • Kermit Ritland,

    1. Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
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  • Songtao Guo,

    1. Key Laboratory of Resource Biology and Biotechnology in Western China of Ministry of Education, and College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
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  • Milena Shattuck,

    1. Anthropology Department, University of Illinois at Urbana-Champaign, Urbana-Champaign, IL, USA
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  • Baoguo Li

    Corresponding author
    1. Key Laboratory of Resource Biology and Biotechnology in Western China of Ministry of Education, and College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
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Abstract

Studies in genetics and ecology often require estimates of relatedness coefficients based on genetic marker data. Many diploid estimators have been developed using either method-of-moments or maximum-likelihood estimates. However, there are no relatedness estimators for polyploids. The development of a moment estimator for polyploids with polysomic inheritance, which simultaneously incorporates the two-gene relatedness coefficient and various ‘higher-order’ coefficients, is described here. The performance of the estimator is compared to other estimators under a variety of conditions. When using a small number of loci, the estimator is biased because of an increase in ill-conditioned matrices. However, the estimator becomes asymptotically unbiased with large numbers of loci. The ambiguity of polyploid heterozygotes (when balanced heterozygotes cannot be distinguished from unbalanced heterozygotes) is also considered; as with low numbers of loci, genotype ambiguity leads to bias. A software, PolyRelatedness, implementing this method and supporting a maximum ploidy of 8 is provided.

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