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Analyzing Autopolyploid Genetic Data Using GenoDive

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Polyploidy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2545))

Abstract

Analyzing autopolyploid genetic data still presents numerous challenges due to, e.g., missing dosage information of genotypes and the presence of multiple ploidy levels within species or populations, but also because the choice of software is limited when compared to what is available for diploid data. However, over the last years, the number of software programs that can deal with polyploid data is slowly increasing. The software GenoDive is one of the most widely used programs for the analysis of polyploid genetic data, presenting a wide array of different methods. In this chapter, I outline several frequently used types of population genetic analyses and explain how these apply to polyploid data, including possible pitfalls and biases. I then explain how GenoDive approaches these analyses and whether and how it can overcome possible biases. Specifically, I focus on analyses of genetic diversity, Hardy-Weinberg equilibrium, quantifying population differentiation, clustering, and calculation of genetic distances. GenoDive can be downloaded freely from http://www.patrickmeirmans.com/software.

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Authors and Affiliations

  1. Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands

    Patrick G. Meirmans

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  1. Patrick G. Meirmans
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Correspondence to Patrick G. Meirmans .

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  1. Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium

    Yves Van de Peer

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Meirmans, P.G. (2023). Analyzing Autopolyploid Genetic Data Using GenoDive. In: Van de Peer, Y. (eds) Polyploidy. Methods in Molecular Biology, vol 2545. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2561-3_14

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  • DOI: https://doi.org/10.1007/978-1-0716-2561-3_14

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2560-6

  • Online ISBN: 978-1-0716-2561-3

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