  We present a two-layer hidden Markov model to detect structure of haplotypes
for unrelated individuals. This allows modeling two scales of linkage
disequilibrium (one within a group of haplotypes and one between groups),
thereby taking advantage of rich haplotype information to infer local ancestry
for admixed individuals. Our method outperforms competing state-of-art methods,
particularly for regions of small ancestral track lengths. Applying our method
to Mexican samples in HapMap3, we found five coding regions, ranging from $0.3
-1.3$ megabase (Mb) in lengths, that exhibit excessive European ancestry
(average dosage > 1.6). A particular interesting region of 1.1Mb (with average
dosage 1.95) locates on Chromosome 2p23 that harbors two genes, PXDN and MYT1L,
both of which are associated with autism and schizophrenia. In light of the low
prevalence of autism in Hispanics, this region warrants special attention. We
confirmed our findings using Mexican samples from the 1000 genomes project. A
software package implementing methods described in the paper is freely
available at \url{http://bcm.edu/cnrc/mcmcmc}
