Allelic states of lineages in present

Figure 5.15 A genealogy constructed under the simultaneous processes of coalescence in a single finite population and mutation. Here the infinite sites model of mutation for DNA sequences is assumed to determine the allelic state of each lineage in the genealogy. Arbitrarily assigning the DNA sequence ACTGCTAGCA to the most recent common ancestor (MRCA), each mutational event then alters the DNA sequence of the lineage experiencing the mutation. Each mutation occurs at a random site in the DNA sequence that has not previously experienced a mutation (bases in blue lower-case letters), giving rise to differences in the DNA sequences among the lineages in the present. Here each base is equally likely to be produced by a mutation, although there are numerous models to specify the pattern of nucleotide changes expected by mutation. Under the finite sites model of mutation, each site in the DNA sequence could experience mutation repeatedly.

When a genealogy containing mutations is combined with a mutation model, it results in an explicit prediction of the diversity and types of allelic states expected under the processes that influence the branching patterns. Although the two examples shown here both utilize genealogies resulting from genetic drift in a finite population, mutation could also be combined with processes such as population structure, growing or shrinking population sizes, or natural selection that are used to generate a coalescent genealogy. Chapter 7 covers genealogies expected with natural selection and Chapter 8 explains methods to compare the expected patterns of allelic states in genealogies generated by different population genetic processes.

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