Gene trees, species trees, and systematics: A cladistic perspective

The proliferation of molecular data in systematics has opened a Pandora's box of alternate approaches to inferring hierarchical patterns of relationship among taxa. In this review, we examine practical and theoretical reasons for employing some methods and avoiding others. We offer a philosophical overview of the relationship between systematics patterns and evolutionary processes, and we discuss the differential emphasis given to each of these areas by opposing methodological camps. We review the sources and types of incongruence between data partitions from different sources and recommend a specific procedure for contending with incongruence. We then focus on inference of relationships among closely related taxa, with particular emphasis on mtDNA as a source of characters, its advantages and potential pitfalls. We conclude with a review of several widely cited empirical studies and suggest that the gene tree-species tree problem may be less severe than its prevalence in the literature would suggest.