Molecular Ecology Notes (2004) doi: 10.1111/j.1471-8286.2004.00779.x © 2004 Blackwell Publishing Ltd Blackwell Publishing, Ltd. PROGRAM NOTE matesoft: a program for deducing parental genotypes and estimating mating system statistics in haplodiploid species ATTE MOILANEN,* LISELOTTE SUNDSTRÖM* and JES SØE PEDERSEN†‡ *Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland; †Department of Ecology and Evolution, Bâtiment de Biologie, University of Lausanne, Lausanne, Switzerland; ‡ Department of Population Biology, Institute of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark Abstract With the advent of sophisticated genetic markers, studies on mating systems and reproductive apportionment have become increasingly feasible. In particular, paternity analyses in haplodiploid species have gained in power as hemizygous paternal genotypes allow maternal and paternal genotypes to be directly inferred from offspring genotypes. The computer program MATESOFT offers both newly developed algorithms for inferring maternal and paternal genotypes, and integrated estimation and correction procedures for calculating mating frequency statistics. Standard data are offspring genotypes of male-haplodiploid organisms, including social Hymenoptera. Keywords: breeding system, mating system, parentage analysis, paternity assignment, polyandry, social insects Received 6 May 2004; revision accepted 23 July 2004 The study of breeding systems and female mating fre- quencies in natural populations of hymenopteran social insects (Ross 2001; Strassmann 2001) usually relies on offspring genotypes and, occasionally, maternal genotypes, whereas paternal genotypes normally have to be inferred. Limitations in the number of offspring genotypes scored may lead to nonsampling errors because some patrilines fail to be included in the sample. Furthermore, nondetection errors may occur due to identical multilocus genotypes of fathers or paternal alleles being identical to those of heterozygous mothers. Corrections for these errors have been developed (Pamilo 1993; Boomsma & Ratnieks 1996; Pedersen & Boomsma 1999; Nielsen et al . 2003), but manual calculations are cumbersome. Here we present the computer package matesoft , which implements the procedures developed by Pedersen & Boomsma (1999) for estimating the absolute and effective mating frequencies in male-haplodiploid organisms, the degree of paternity skew and the corrections for these with respect to nondetection and nonsampling errors (cf. Boomsma & Ratnieks 1996). In addition, we develop new algorithms for deducing: (i) maternal genotypes from gen- otypes of female offspring, (ii) paternal genotypes based on offspring genotypes and inferred or observed maternal genotypes, and (iii) the number of sires in single-female broods. matesoft infers maternity and paternity for any mating frequency. However, general procedures for estimating the effective mating frequencies and associated statistics are not available for systems in which a female may have more than two mates, each contributing an unknown proportion to the brood. Although matesoft has been designed for social Hymenoptera, it can also be used to study mating frequen- cies in other haplodiploid species such as mites, thrips and nonsocial bees and wasps where clutches of single females may be sired by multiple males (Choe & Crespi 1997). Estimations done by matesoft are based on the assump- tion that: (i) marker loci are codominant, neutral and unlinked; (ii) population allele frequencies are the same for males and females; (iii) females are unrelated to their mates (i.e. no inbreeding); and (iv) multiple mates of the same female are not related. For all procedures the population- wide allele frequencies are entered so that gene similarities owing to a common genetic background are taken into account. The input data may be: (i) the genotypes of off- spring sorted into groups of sisters; (ii) the genotypes of offspring and mothers; (iii) the genotypes of offspring, Correspondence: J. S. Pedersen, Department of Population Biology. Fax: +45 3532-1250; E-mail: JSPedersen@bi.ku.dk