Comparative Biology

■ Abstract Polymorphism, or variation within species, is common in all kinds of data and is the major focus of research on microevolution. However, polymorphism is often ignored by those who study macroevolution: systematists and comparative evolutionary biologists. Polymorphism may have a profound impact on phylogeny reconstruction, species-delimitation, and studies of character evolution. A variety of methods are used to deal with polymorphism in phylogeny reconstruction, and many of these methods have been extremely controversial for more than 20 years. Recent research has attempted to address the accuracy of these methods (their ability to estimate the true phylogeny) and to resolve these issues, using computer simulation, congruence, and statistical analyses. These studies suggest three things: that (a) the exclusion of polymorphic characters (as is commonly done in morphological phylogenetics) is unjustified and may greatly decrease accuracy relative to analyses that include these characters; (b) methods that incorporate frequency information on polymorphic characters tend to perform best, and (c) distance and likelihood methods designed for polymorphic data may often outperform parsimony methods. Although rarely discussed, polymorphism may also have a major impact on comparative studies of character evolution, such as the reconstruction of ancestral character states. Finally, polymorphism is an important issue in the delimitation of species, although this area has been somewhat neglected methodologically. The integration of within-species variation and microevolutionary processes into studies of systematics and comparative evolutionary biology is another example of the benefits of exchange of ideas between the fields of population genetics and systematics.