title: orchard: Paternity program for autotetraploid species.
abstract: Advances in molecular marker technology have provided new opportunities to study the population genetics of polyploid taxa. Paternity analysis using microsatellite markers can be used in detection of gene flow between individuals and populations, in mating system analysis, to identify factors that influence fecundity and fertility, to identify behaviour of parent-offspring relationships and in the analysis of the reproductive success of different ecological groups. As there is no specific program for carrying out paternity analysis in tetraploid species, specialized software was designed for the assignment of paternity for autotetraploid species. orchard is a novel implementation of exclusion and likelihood statistics for carrying out paternity analysis of autotetraploids. First, the program performs an exclusion method, and then, a likelihood statistic is used with nonexcluded candidate fathers. Optional features include estimation of allele dosage of known mother trees and the estimation of pollen flow distances. orchard was tested using a data set of microsatellite data of Dipteryx odorata, a tetraploid Amazonian tree species.
authors.affiliation: St Edmund Hall, Oxford, OX1 4AR, UK.
authors.forename: A
authors.initials: A
authors.lastname: Spielmann
authors.affiliation: Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
authors.forename: S A
authors.initials: SA
authors.lastname: Harris
authors.affiliation: Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
authors.forename: D H
authors.initials: DH
authors.lastname: Boshier
authors.affiliation: Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
authors.forename: C C
authors.identifier: http://orcid.org/0000-0001-8779-8075
authors.initials: CC
authors.lastname: Vinson
mesh_terms: D019295:Computational Biology / Q000379:methods*; D016172:DNA Fingerprinting; D046914:Dipteryx / Q000235:genetics* / Q000502:physiology*; D051456:Gene Flow; D018895:Microsatellite Repeats; D012098:Reproduction; D012984:Software
keywords: autotetraploid; paternity; pollen flow; tetraploid