Abstract
The comparative analysis of DNA molecules is a useful means for phylogenetic reconstruction, because different types of genetic elements yield resolution at different levels of taxonomic divergence. A single individual is usually characterized for each operational taxonomic unit (OTU), based on the premise that within-OTU variation can be safely ignored. Whereas that premise is expedient, it may not be generally valid. Sometimes variation within OTUs can affect the analysis. We develop a formal analytic treatment of variation in phylogenetic output as a consequence of intraspecific variation. Using restriction site data from the mitochondria of three species of cyprinid fishes to illustrate, we show that genetic variation within taxa impacts on tree topology
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