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. 2012 Jan 26;8(1):e1002453. doi: 10.1371/journal.pgen.1002453

Figure 1. Illustration of the painting process to create the coancestry matrix.

Figure 1

We show the process by which a haplotype (haplotype 1, black) is painted using the others. A) True underlying genealogies for eight simulated sequences at three locations along a genomic segment, produced using the program ‘ms’ [52] and showing coalescence times between haplotypes at each position. B) The Time to the Most Recent Common Ancestor (TMRCA) between haplotype 1 and each other haplotype, as a function of sequence position. Note multiple haplotypes can share the same TMRCA and changes in TMRCA correspond to historical recombination sites. C) True distribution of the ‘nearest neighbour’ haplotype. D) Sample ‘paintings’ of the Li & Stephens algorithm. E) Expectation of the painting process, estimating the nearest neighbour distribution. F) Resulting row of the coancestry matrix, based on the expectation of the painting.