We describe a novel method for analysis of marker genotype data from admixed populations,
based on a hybrid of Bayesian and frequentist approaches in which the posterior distribution is
generated by Markov chain simulation and score tests are obtained from the missing-data likelihood.
We analysed data on unrelated individuals from eight African-American populations, genotyped at
ten marker loci of which two (FY and AT3) are linked (22 cM apart). Linkage between these two loci
was detected by testing for association of ancestry conditional on parental admixture. The strength
of this association was consistent with European gene flow into the African-American population
between five and nine generations ago. To mimic the mapping of an unknown gene in an ‘affecteds-
only’ analysis, a binary trait was constructed from the genotype at the AT3 locus and a score test
was shown to detect linkage of this ‘trait’ with the FY locus. Mis-specification of the ancestry-specific
allele frequencies – the probabilities of each allelic state given the ancestry of the allele – was
detected at three of the ten marker loci. The methods described here have wide application to the
analysis of data from admixed populations, allowing the effects of linkage and population structure
(variation of admixture between individuals) to be distinguished. With more markers and a more
complex statistical model, genes underlying ethnic differences in disease risk could be mapped by this
approach.