Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality

To gain a detailed understanding of how plant microbes evolve and adapt to hosts, pesticides, and other factors, knowledge of the population dynamics and evolutionary history of populations is crucial. Plant pathogen populations are often clonal or partially clonal which requires different analytical tools. With the advent of high throughput sequencing technologies, obtaining genome-wide population genetic data has become easier than ever before. We previously contributed the R package poppr specifically addressing issues with analysis of clonal populations. In this paper we provide several significant extensions to poppr with a focus on large, genome-wide SNP data. Specifically, we provide several new…

• UD
  U.S. Department of Agriculture

  Awards: 2011-68004-30154, 5358-22000-039-00D
• NE
  National Evolutionary Synthesis Center
• NI
  National Institute of Food and Agriculture

  Award: 2011-68004-30154
• UF
  U.S. Forest Service
• AR
  Agricultural Research Service

  Award: 5358-22000-039-00D
• AA
  Animal and Plant Health Inspection Service