Best Practices for Population Genetic Analyses

Phytopathology
N J GrünwaldZ N Kamvar

Abstract

Population genetic analysis is a powerful tool to understand how pathogens emerge and adapt. However, determining the genetic structure of populations requires complex knowledge on a range of subtle skills that are often not explicitly stated in book chapters or review articles on population genetics. What is a good sampling strategy? How many isolates should I sample? How do I include positive and negative controls in my molecular assays? What marker system should I use? This review will attempt to address many of these practical questions that are often not readily answered from reading books or reviews on the topic, but emerge from discussions with colleagues and from practical experience. A further complication for microbial or pathogen populations is the frequent observation of clonality or partial clonality. Clonality invariably makes analyses of population data difficult because many assumptions underlying the theory from which analysis methods were derived are often violated. This review provides practical guidance on how to navigate through the complex web of data analyses of pathogens that may violate typical population genetics assumptions. We also provide resources and examples for analysis in the R programming envi...Continue Reading

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Citations

Feb 17, 2018·Molecular Plant-microbe Interactions : MPMI·Javier F TabimaNiklaus J Grünwald
Jan 16, 2019·The New Phytologist·Shiv D Kale
May 30, 2019·Plant Disease·Nicholas C CarlesonNiklaus J Grünwald
Aug 27, 2019·Plant Disease·Christopher R WymanRobert N Trigiano
Jun 20, 2019·Phytopathology·Andrew S TaylorTreena Burgess
Jan 2, 2020·Evolutionary Applications·Richard C Hamelin, Amanda D Roe
Dec 19, 2021·Molecular Plant Pathology·Hervé Van der HeydenOdile Carisse

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