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

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.

Links

Authors+Show Affiliations

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Botany and Plant Pathology, Oregon State University Corvallis, OR, USA.

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College of Electrical Engineering and Computer Science, Oregon State University Corvallis, OR, USA.

Botany and Plant Pathology, Oregon State University Corvallis, OR, USA ; Horticultural Crops Research Laboratory, USDA Agricultural Research Service Corvallis, OR, USA.

Source

Frontiers in genetics 6: 2015 pg 208

Pub Type(s)

Journal Article

Language

eng

PubMed ID

26113860

Citation

TY - JOUR T1 - Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality. AU - Kamvar,Zhian N, AU - Brooks,Jonah C, AU - Grünwald,Niklaus J, Y1 - 2015/06/10/ PY - 2015///ecollection PY - 2015/5/08/received PY - 2015/5/29/accepted PY - 2015/6/10/epublish PY - 2015/6/27/entrez PY - 2015/6/27/pubmed PY - 2015/6/27/medline KW - bootstrap KW - clonality KW - hierarchical analysis KW - index of association KW - population genomics KW - sliding window SP - 208 EP - 208 JF - Frontiers in genetics JO - Front Genet VL - 6 N2 - 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. SN - 1664-8021 UR - https://www.unboundmedicine.com/medline/citation/26113860/Novel_R_tools_for_analysis_of_genome_wide_population_genetic_data_with_emphasis_on_clonality_ ER -