title: Polypatex: an R package for paternity exclusion in autopolyploids.
abstract: 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.
authors.affiliation: CSIRO Data61, GPO Box 664, Canberra, ACT, 2601, Australia.
authors.forename: Alexander B
authors.initials: AB
authors.lastname: Zwart
authors.affiliation: CSIRO National Facilities and Collections, GPO Box 1600, Canberra, ACT, 2601, Australia.
authors.forename: Carole
authors.initials: C
authors.lastname: Elliott
authors.affiliation: CSIRO National Facilities and Collections, GPO Box 1600, Canberra, ACT, 2601, Australia.
authors.forename: Tara
authors.initials: T
authors.lastname: Hopley
authors.affiliation: Queensland University of Technology (QUT), GPO Box 2434, Brisbane, QLD, 4001, Australia.
authors.forename: David
authors.initials: D
authors.lastname: Lovell
authors.affiliation: CSIRO National Facilities and Collections, GPO Box 1600, Canberra, ACT, 2601, Australia.
authors.forename: Andrew
authors.initials: A
authors.lastname: Young
mesh_terms: D000818:Animals; D056808:Biostatistics / Q000379:methods*; D060005:Genotyping Techniques / Q000379:methods; D018895:Microsatellite Repeats; D010334:Paternity; D010944:Plants; D011123:Polyploidy; D012984:Software
keywords: allele matching; microsatellite; pollen dispersal; polyploid