Figure 1.

The sequentially Markovian coalescent. The colored circles represent nucleotide states belonging to the alleles at each locus. Double gray lines denote recombination breakpoints, which separate the loci along the genome. The time to the most recent common ancestor of the two alleles at each locus is reflected in the local tree. (a) In PSMC, there are only two haplotypes. Thus, the topology of the local tree is fixed, but the time to the most recent common ancestor differs among loci. (b) In MSMC, there are multiple haplotypes. MSMC ignores most of the local tree topology, focusing only on the most recent coalescence event at each locus