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Allele genealogies can inform us about the effects of microevolutionary forces on organismal and population lineages. However, as has become well established in the last decade, a gene tree is far from equivalent to the population lineages through which it is transmitted (see review in Avise, 2000). Therefore, caution must be used in drawing inferences about population-level processes from genealogical data. The hypothetical allele genealogy in Fig. 2 illustrates the potential incongruity that can exist between a gene tree and the populations in which it exists. After two populations have become isolated from each other (and barring subsequent gene flow), the populations will diverge genetically until eventually all of the alleles within each population are more closely related to each other than to those from the other population (Fig. 2). At this point, the alleles show reciprocal monophyly with respect to the two populations and accurately reflect the history of population divergence. Before reaching reciprocal monophyly, however, alleles are expected to be poly-

FIGURE 2. Hypothetical allele genealogy in populations A and B that became isolated from each other at time t0. At time t1, genealogical relationships show paraphyly with respect to the two populations. At time t2, alleles show reciprocal monophyly and are congruent with the history of population divergence.

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