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Sequence mismatch (number of nucleotide sites)

Figure 8.21 The basis of the mismatch distribution. (a) A neutral genealogy that bears multiple mutation events. Each mutation event is represented by a circle and the number of the random nucleotide site that mutated assuming the infinite sites mutation model. The six lineages in the present can be separated into two groups (called A and B) based on their ancestral lineage when there were only two lineages in the population. (b) The DNA sequences for each lineage are shown based on the 30 base-pair sequence assigned to the most recent common ancestor (MRCA) with mutations shown in lower-case letters. (c) The number of nucleotide sites that are different or mismatched between pairs of DNA sequences. (d) The mismatch distribution shown is a histogram of the mismatches for the 15 pairs of DNA sequences compared. Neutral genealogies from populations with constant Ne through time tend to show bimodal mismatch distributions. The cluster of observations with few mismatches results from sequence comparisons between recently related lineages (comparisons within group A or group B). In contrast, sequences from distantly related lineages that do not share the same ancestor when k = 2 (comparisons between groups A and B) tend to have more mismatches.

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