Revising how the computer program <scp>cervus</scp> accommodates genotyping error increases success in paternity assignment

TLDR

Genotypes are widely used for parentage testing, but the analysis is highly susceptible to genotyping error, a problem that has sparked debate and is addressed by programs such as cervus. The study demonstrates that cervus versions 1.0 and 2.0 miscalculate the probability of observing an erroneous genotype when accommodating genotyping error. Simulation and reanalysis of Rum red deer paternity demonstrate that correcting the miscalculation improves assignment success, and a new cervus 3.0 version implementing the corrected equations is available online.

Abstract

Abstract Genotypes are frequently used to identify parentage. Such analysis is notoriously vulnerable to genotyping error, and there is ongoing debate regarding how to solve this problem. Many scientists have used the computer program cervus to estimate parentage, and have taken advantage of its option to allow for genotyping error. In this study, we show that the likelihood equations used by versions 1.0 and 2.0 of cervus to accommodate genotyping error miscalculate the probability of observing an erroneous genotype. Computer simulation and reanalysis of paternity in Rum red deer show that correcting this error increases success in paternity assignment, and that there is a clear benefit to accommodating genotyping errors when errors are present. A new version of cervus (3.0) implementing the corrected likelihood equations is available at http://www.fieldgenetics.com .