Maximum-likelihood estimation of a hybrid index based on molecular markers

This paper elaborates on a hybrid index that utilizes information from genetic markers to quantify the genetic contribution of hybridizing species to individuals of unknown ancestry. Dominant markers will only lead to reliable and accurate estimates of hybrid index in later generation hybrids. In contrast, codominant markers can be fully resolved and their use is unproblematic. For both types of markers and allele frequencies that differ substantially between parental species (F-ST >= 0.17), a hybrid index based on 35-45 loci will have a nearly minimal confidence interval. Estimates of hybrid index are robust to modest errors in estimates of parental allele frequencies.