Effects of intraspecific variation on phylogenetic inference: A likelihood analysis of mtdna restriction site data in cyprinid fishes

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. Genetic variation among populations is most important; that within populations is small. Genetic variation should be expected within any taxon, and it is generally useful to sample (replicate) one taxonomic level below that of interest.