The spatial distribution of genetic markers can be useful both in estimating patterns of gene flow and in reconstructing biogeographic history, particularly when gene genealogies can be estimated. Genealogies based on nonrecombining genetic units such as mitochondrial and chloroplast DNA often consist of geographically separated clades that come into contact in narrow regions. Such phylogeographic breaks are usually assumed to be the result of long-term barriers to gene flow. Here I show that deep phylogeographic breaks can form within a continuously distributed species even when there are no barriers to gene flow. The likelihood of observing phylogeographic breaks increases as the average individual dispersal distance and population size decrease. Those molecular markers that are most likely to show evidence of real geographic barriers are also most likely to show phylogeographic breaks that formed without any barrier to gene flow. These results might provide an explanation as to why some species, such as the greenish warblers (Phylloscopus trochiloides), have phylogeographic breaks in mitochondrial or chloroplast DNA that do not coincide with sudden changes in other traits.
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