Closed form maximum-likelihood estimates of ancestry and heterozygosity for diagnostic markers
For hybrid individuals genotyped with diagnostic markers (one allele fixed in each parental lineage), the ancestry index and interclass heterozygosity are calculated using closed form estimators using allele counts.
HIC(G)
G |
Data matrix of individual genotypes (individuals in rows, markers in columns), coded as 0, 1, or 2 for the number of alleles inherited from parental lineage 1. |
Data must be coded as allele counts and markers must be assumed diagnostic. The MLE of the ancestry index is S=∑(x_i)/(2n), where x_i is the allele count for locus i. The MLE of interclass heterozygosity is simply the observed fraction of markers that are heterozygous.
A matrix with three named columns is returned.
S |
The ancestry index for each individual |
H |
The interclass heterozygosity for each individual |
logLik |
The log-likelihood of the joint estimate, given the data for each individual |
Ben Fitzpatrick
Fitzpatrick, B. M. 2008. Hybrid dysfunction: Population genetic and quantitative genetic perspectives. American Naturalist 171:491-198.
Fitzpatrick, B. M. 2012. Estimating ancestry and heterozygosity of hybrids using molecular markers. BMC Evolutionary Biology 12:131. http://www.biomedcentral.com/1471-2148/12/131
Lynch, M. 1991. The genetic interpretation of inbreeding depression and outbreeding depression. Evolution 45:622-629.
HIest finds maximum likelihood estimates for non-diagnostic markers.
## A random set of allele counts for 10 loci and 10 individuals G <- matrix(rbinom(100,2,.5),nrow=10) HIC(G)
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