COLONY: a program for parentage and sibship inference from multilocus genotype data

TLDR

Pedigree reconstruction is essential in many fields, and while molecular markers enable inference in species lacking observable relationships, existing software is often limited by rigid assumptions such as monogamous diploid, codominant markers, no genotyping error, and reliance on pairwise comparisons rather than full‑pedigree likelihood approaches. We present COLONY, a program that simultaneously infers parentage and sibship using a full‑pedigree likelihood framework on multilocus genotype data. COLONY accommodates diploid and haplodiploid species, accepts dominant or codominant markers, estimates locus‑specific genotyping error, handles monoecious and dioecious systems, and is available as a Windows GUI or a Macintosh R‑based interface.

Abstract

Pedigrees, depicting genealogical relationships between individuals, are important in several research areas. Molecular markers allow inference of pedigrees in wild species where relationship information is impossible to collect by observation. Marker data are analysed statistically using methods based on Mendelian inheritance rules. There are numerous computer programs available to conduct pedigree analysis, but most software is inflexible, both in terms of assumptions and data requirements. Most methods only accommodate monogamous diploid species using codominant markers without genotyping error. In addition, most commonly used methods use pairwise comparisons rather than a full-pedigree likelihood approach, which considers the likelihood of the entire pedigree structure and allows the simultaneous inference of parentage and sibship. Here, we describe colony, a computer program implementing full-pedigree likelihood methods to simultaneously infer sibship and parentage among individuals using multilocus genotype data. colony can be used for both diploid and haplodiploid species; it can use dominant and codominant markers, and can accommodate, and estimate, genotyping error at each locus. In addition, colony can carry out these inferences for both monoecious and dioecious species. The program is available as a Microsoft Windows version, which includes a graphical user interface, and a Macintosh version, which uses an R-based interface.