DOI: 10.5061/dryad.64482
title: Data from: PolyPatEx: an R package for paternity exclusion in autopolyploids

description: Microsatellite markers have demonstrated their value for performing
 paternity exclusion and hence exploring mating patterns in plants and
 animals. Methodology is well established for diploid species and several
 software packages exist for elucidating paternity in diploids, however
 these issues are not so readily addressed in polyploids due to the
 increased complexity of the exclusion problem and a lack of available
 software. We introduce PolyPatEx, an R package for paternity exclusion
 analysis using microsatellite data in autopolyploid, monoecious or
 dioecious/bisexual species with a ploidy of 4n, 6n or 8n. Given marker
 data for a set of offspring, their mothers, and a set of candidate
 fathers, PolyPatEx uses allele matching to exclude candidates whose marker
 alleles are incompatible with the alleles in each offspring-mother pair.
 PolyPatEx can analyse marker data sets in which allele copy numbers are
 known (genotype data) or unknown (allelic phenotype data) – for data sets
 in which allele copy numbers are unknown, comparisons are made taking into
 account all possible genotypes that could arise from the compared allele
 sets. PolyPatEx is a software tool that provides population geneticists
 with the ability to investigate the mating patterns of autopolyploids
 using paternity exclusion analysis on data from codominant markers having
 multiple alleles per locus.
description: Tetraploid Genotype
 dataset - Salix CinereaExample SSR allele
 (genotype) data from seven loci in a tetraploid, dioecious species, Salix
 cinerea. From: Hopley, T (2011) Reproductive ecology and dispersal
 dynamics of the invasive willow, Salix cinerea, in south-eastern
 Australia. Ph.D. Thesis, The Australian National University,
 Canberra.FR_Genotype.csvHexaploid Allelic Phenotype dataset - Eremophila glabra ssp. glabraExample SSR (allelic phenotype) data from seven loci in a hexaploid, monoecious species, Eremophila glabra ssp. glabra. From: Elliott, CP (2010) Patterns and processes: ecological and genetic function of fragmented Emu bush (Eremophila glabra ssp. glabra) populations. Ph.D. Thesis, The Australian National University, Canberra. Formatted for use with PolyPatEx package.GF_Phenotype.csvR script - PolyPatEx usage example.An R script to perform the example of use of PolyPatEx in the published manuscript. Operates on the Eremophila (allelic phenotype) dataset to obtain IDs and counts of potential fathers that remain after exclusion.Example.RPolyPatEx performance simulation R scriptsR scripts to perform the simulations assessing PolyPatEx performance in the published PolyPatEx manuscript. Unzips to create a folder, "Simulation_scripts" with content.Simulation_scripts.zipEremophila allelic phenotype dataset in COLONY-required formatThe Eremophila glabra spp. glabra allelic phenotype dataset recoded for use with COLONY (Jones OR, Wang J (2002) COLONY: a program for parentage and sibship inference from multilocus genotype data. Molecular Ecology Resources, 10(3), 551–555.). Unzips to create a folder, 'COLONY_data_files', with content.COLONY_data_files.zip