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Figure 3. Result of the analysis of the genes D3, D8, and Id1 (data from Remington et al., 2001) using our Hidden Markov Model (HMM)-based algorithm. The haplotypes are sorted according to their leaf position in a neighbor-joining tree based on their euclidean distance matrix. For each gene the left part of the figure depicts the pattern of mutation in the raw data set and the right part the ancestral origins of marker along the gene. At the top of each figure, the inferred ancestral haplotypes are displayed (i.e., four for D3 and Id1, and three for D8). The average diversity between ancestral haplotypes for D3, Id1, and D8 are 0.50, 0.48, and 0.61, respectively. The extra spaces between single nucleotide polymorphism (SNP) sites are based on a block structure of the haplotype inferred by the HMM-based algorithm of Anderson and Novembre (2003). If some ancestral fragments line up with the block boundaries (for D8 the block structure and our model give a similar pattern), for D3 and Id1 some recombination events detected by our model occur within blocks.
