Detecting structure of haplotypes and local ancestry

Genetics. 2014 Mar;196(3):625-42. doi: 10.1534/genetics.113.160697. Epub 2014 Jan 3.


We present a two-layer hidden Markov model to detect the structure of haplotypes for unrelated individuals. This allows us to model 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 of admixed individuals. Our method outperforms competing state-of-the-art methods, particularly for regions of small ancestral track lengths. Applying our method to Mexican samples in HapMap3, we found two regions on chromosomes 6 and 8 that show significant departure of local ancestry from the genome-wide average. A software package implementing the methods described in this article is freely available at

Keywords: admixture; haplotype; linkage disequilibrium (LD); local ancestry; two-layer clustering.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Chromosomes, Human, Pair 6
  • Chromosomes, Human, Pair 8
  • Evolution, Molecular
  • Genetic Variation
  • Genome, Human*
  • Genomics
  • Haplotypes*
  • Humans
  • Linkage Disequilibrium
  • Markov Chains
  • Mexico
  • Models, Genetic
  • Phylogeny*
  • Polymorphism, Single Nucleotide
  • Software