Performing Parentage Analysis in the Presence of Inbreeding and Null Alleles

Genetics: A Periodical Record of Investigations Bearing on Heredity and Variation

article

Kang Huang¹  Rui Mi¹  Derek W. Dunn¹  Tongcheng Wang¹  Baoguo Li¹ 

[1] Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China;Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China

关键词: Parentage analysis;    inbreeding;    population subdivision;    null alleles;    LOD score;    negative amplification;   

DOI  :  10.1534/genetics.118.301592

学科分类：医学（综合）

来源: Genetics Society of America

【 摘 要 】

Parentage analysis is an important method that is used widely in zoological and ecological studies. Current mathematical models of parentage analyses usually assume that a population has a uniform genetic structure and that mating is panmictic. In a natural population, the geographic or social structure of a population, and/or nonrandom mating, usually leads to a genetic structure and results in genotypic frequencies deviating from those expected under the Hardy-Weinberg equilibrium (HWE). In addition, in the presence of null alleles, an observed genotype represents one of several possible true genotypes. The true father of a given offspring may thus be erroneously excluded in parentage analyses, or may have a low or negative LOD score. Here, we present a new mathematical model to estimate parentage that includes simultaneously the effects of inbreeding, null alleles, and negative amplification. The influences of these three factors on previous model are evaluated by Monte-Carlo simulations and empirical data, and the performance of our new model is compared under controlled conditions. We found that, for both simulated and empirical data, our new model outperformed other methods in many situations. We make available our methods in a new, free software package entitled parentage . This can be downloaded via http://github.com/huangkang1987/parentage .

【 授权许可】

CC BY