Revised Calculation of Kalinowski’s Ancestral and New Inbreeding Coefficients

• Main Authors: Harmen P. Doekes, Ino Curik, István Nagy, János Farkas, György Kövér, Jack J. Windig
• Format: Article
• Language: English
• Published: MDPI AG 2020-04-01
• Series: Diversity
• Subjects: ancestral inbreeding; new inbreeding; purging; gene dropping; inbreeding depression
• Online Access: https://www.mdpi.com/1424-2818/12/4/155
• ISSN: 1424-2818

To test for the presence of purging in populations, the classical pedigree-based inbreeding coefficient (<i>F</i>) can be decomposed into Kalinowski’s ancestral (<i>F_ANC</i>) and new (<i>F_NEW</i>) inbreeding coefficients. The <i>F_ANC</i> and <i>F_NEW</i> can be calculated by a stochastic approach known as gene dropping. However, the only publicly available algorithm for the calculation of <i>F_ANC</i> and<i> F_NEW</i>, implemented in GRain v 2.1 (and also incorporated in the PEDIG software package), has produced biased estimates. The <i>F_ANC</i> was systematically underestimated and consequently, <i>F_NEW</i> was overestimated. To illustrate this bias, we calculated <i>F_ANC</i> and <i>F_NEW</i> by hand for simple example pedigrees. We revised the GRain program so that it now provides unbiased estimates. Correlations between the biased and unbiased estimates of <i>F_ANC</i> and <i>F_NEW</i>, obtained for example data sets of Hungarian Pannon White rabbits (22,781 individuals) and Dutch Holstein Friesian cattle (37,061 individuals), were high, i.e., >0.96. Although the magnitude of bias appeared to be small, results from studies based on biased estimates should be interpreted with caution. The revised GRain program (v 2.2) is now available online and can be used to calculate unbiased estimates of <i>F_ANC</i> and<i> F_NEW</i>.