Novel R Tools for Analysis of Genome-wide Population Genetic Data with Emphasis on Clonality

Overview

Journal Front Genet

Date 2015 Jun 27

PMID 26113860

Citations 265

Authors

Zhian N Kamvar

Jonah C Brooks

Niklaus J Grunwald

Affiliations

Soon will be listed here.

Abstract

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 functionalities including the new function mlg.filter to define clone boundaries allowing for inspection and definition of what is a clonal lineage, minimum spanning networks with reticulation, a sliding-window analysis of the index of association, modular bootstrapping of any genetic distance, and analyses across any level of hierarchies.

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