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Allelic states of lineages in the present

Figure 5.14 A genealogy constructed under the simultaneous processes of coalescence in a single finite population and mutation. Here the infinite alleles model of mutation is assumed to determine the allelic state of each lineage in the genealogy. Arbitrarily assigning allelic state A to the most recent common ancestor (MRCA), each mutational event then alters the state of the lineage experiencing the mutation. Each mutation changes the allelic state of the lineage to a new allele not present in the population, giving rise to a variety of allelic states among the lineages in the present.

model. Each mutation event is an instance where the current state of a lineage changes to an allelic state not currently present in the population. Because of mutational changes to the ancestral allelic state, the six lineages in the present represent four allelic states. Two of the alleles have a frequency of 2/6 = 33% while the remaining two alleles have a frequency of 1/6 = 16.6%. The lineages sharing B or C alleles are identical in state and therefore can be considered identical by descent. Figure 5.15 shows a third version of the genealogy with mutations, this time representing each allele as a DNA sequence and employing the infinite sites mutation model. Each mutational event alters a randomly picked site in the DNA sequence under the constraint that a site can only experience mutation a single time. The result is a set of DNA sequences that differ at three of 10 nucleotide sites. As with the infinite alleles model, DNA sequences in the present that are identical in state are therefore identical by descent.

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