Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

Abstract

Many microbial, fungal, or oomcyete populations violate assumptions for population genetic analysis because these populations are clonal, admixed, partially clonal, and/or sexual. Furthermore, few tools exist that are specifically designed for analyzing data from clonal populations, making analysis difficult and haphazard. We developed the R package poppr providing unique tools for analysis of data from admixed, clonal, mixed, and/or sexual populations. Currently, poppr can be used for dominant/codominant and haploid/diploid genetic data. Data can be imported from several formats including GenAlEx formatted text files and can be analyzed on a user-defined hierarchy that includes unlimited levels of subpopulation structure and clone censoring. New functions include calculation of Bruvo's distance for microsatellites, batch-analysis of the index of association with several indices of genotypic diversity, and graphing including dendrograms with bootstrap support and minimum spanning networks. While functions for genotypic diversity and clone censoring are specific for clonal populations, several functions found in poppr are also valuable to analysis of any populations. A manual with documentation and examples is provided. Poppr is open source and major releases are available on CRAN: http://cran.r-project.org/package=poppr. More supporting documentation and tutorials can be found under 'resources' at: http://grunwaldlab.cgrb.oregonstate.edu/.

Keywords: Bootstrap; Bruvo’s distance; Clonality; Clone correction; Genotypic diversity; Hierarchy; Index of association; Minimum spanning networks; Permutation; Population genetics.

Figure 1. Multilocus genotype histogram.

Distribution of 12 multilocus genotypes from the Finland population of the H3N2 SNP data set (Jombart, 2008).

Figure 2. Linkage disequilibrium.

Visualizations of tests for linkage disequilibrium, where observed values (blue dashed lines) of I_A and ${\overline{r}}_d$ are compared to histograms showing results of 999 permutations using method 1 in Table 1. Results are shown for the sexual population 5 of the nancycats data set (Jombart, 2008) (A) and for the clonal Athena population of the Aeut data set (Grünwald et al., 2003) (B).

Figure 3. Minimum spanning network.

Example minimum spanning network using Bruvo’s distance on a simulated partially clonal data set with 50 individuals genotyped over 10 microsatellite loci produced with the software SimuPOP v.1.0.8 (Peng & Amos, 2008). Each node represents a unique multilocus genotype. Node shading (colors) represent population membership, while edge widths and shading represent relatedness. Edge length is arbitrary.

Figure 4. Dendrogram based on genetic distance.

UPGMA tree produced from Bruvo’s distance with 1000 bootstrap replicates (node values greater than 50% are shown). Data from population 9 of the nancycats data set (Jombart, 2008).