genepopedit: a simple and flexible tool for manipulating multilocus molecular data in R

Abstract

Advances in genetic sequencing technologies and techniques have made large, genome-wide data sets comprised of hundreds or even thousands of individuals and loci the norm rather than the exception even for nonmodel organisms. While such data present new opportunities for evaluating population structure and demographic processes, the large size of these genomic data sets brings new computational challenges for researchers needing to parse, convert and manipulate data often into a variety of software-specific formats required of genomic analyses. We developed genepopedit as a flexible tool for the manipulation of multilocus molecular data sets. Functionality can be divided among diagnostic-, manipulation-, sampling-, simulation-, and transformation-based tools. Metadata from large genomic data sets can be efficiently extracted, without the need to view data in a text-editing program. genepopedit provides tools to manipulate loci, individual samples and populations included in genomic data sets, in addition to the ability to convert directly to a variety of software formats. Functions are compiled as an R package, which can integrate into existing analysis workflows. Importantly, genepopedit provides a simple yet robust code-based tool for repeatable genomic data manipulation, which has been proven to be stable for data sets in excess of 200 000 SNPs. The latest version of the package and associated documentation are available on Github (github.com/rystanley/genepopedit).

Genomewide evidence of environmentally mediated secondary contact of European green crab (Carcinus maenas) lineages in eastern North America

“…As with LFMM, we combined all outliers for all environmental parameters and then compared the number of overlapping loci between the two methods. Outliers were subset from our full SNP panel using the R package genepopedit (Stanley, Jeffery, Wringe, DiBacco, & Bradbury, ) to generate our outlier panel of SNPs. Linkage disequilibrium r 2 values were calculated among all environmental outliers in PLINK (Purcell et al., ).…”

RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic

“…Only loci identified as outliers by all three methods were considered to reduce the number of false positives, and our putatively neutral panel was comprised only of SNPs that were not detected as outliers by any of these methods (Figure 3). Outlier loci were subset from the full RAD panel using the subset_genepop function in genepopedit (Stanley et al., 2017). Observed ( H o ) and expected ( H e ) heterozygosities were calculated in the package hierfstat (Goudet, 2014) in R (R Core Team 2015) for each population within each SNP panel, as well as the average H o and H e for each panel.…”

Habitat use and hybridisation between the Rocky Mountain sculpin (Cottussp.) and slimy sculpin (Cottus cognatus)

“…NEWHYBRIDS probabilistically classifies individuals based on their 10 locus genotypes into six genotypic classes: the two parental species, first (F1) and second (F2) generation hybrids and backcrosses to one or other parental species (BC 1 and BC2, respectively) (Anderson & Thompson, ). The NEWHYBRIDS model was built using the genepopedit , paralellnewhybrid , and hybriddetective packages in R software (Stanley, Jeffery, Wringe, Dibacco, & Bradbury, ; Wringe, Stanley, Jeffery, Anderson, & Bradbury, ,b). For our NEWHYBRIDS model, we also used a burn‐in of 50,000 generations and 500,000 MCMC generations to produce assignments of pure RMS, SS and hybrids across five simulated data sets.…”