ORIGINAL ARTICLE A priori assumptions about characters as a cause of incongruence between molecular and morphological hypotheses of primate interrelationships Matthew A. Tornow • Randall R. Skelton Received: 11 April 2011 / Accepted: 18 October 2011 / Published online: 8 November 2011 Ó Japan Monkey Centre and Springer 2011 Abstract When molecules and morphology produce incongruent hypotheses of primate interrelationships, the data are typically viewed as incompatible, and molecular hypotheses are often considered to be better indicators of phylogenetic history. However, it has been demonstrated that the choice of which taxa to include in cladistic anal- ysis as well as assumptions about character weighting, character state transformation order, and outgroup choice all influence hypotheses of relationships and may posi- tively influence tree topology, so that relationships between extant taxa are consistent with those found using molecular data. Thus, the source of incongruence between morphological and molecular trees may lie not in the morphological data themselves but in assumptions sur- rounding the ways characters evolve and their impact on cladistic analysis. In this study, we investigate the role that assumptions about character polarity and transformation order play in creating incongruence between primate phylogenies based on morphological data and those sup- ported by multiple lines of molecular data. By releasing constraints imposed on published morphological analyses of primates from disparate clades and subjecting those data to parsimony analysis, we test the hypothesis that incon- gruence between morphology and molecules results from inherent flaws in morphological data. To quantify the difference between incongruent trees, we introduce a new method called branch slide distance (BSD). BSD mitigates many of the limitations attributed to other tree comparison methods, thus allowing for a more accurate measure of topological similarity. We find that releasing a priori constraints on character behavior often produces trees that are consistent with molecular trees. Case studies are pre- sented that illustrate how congruence between molecules and unconstrained morphological data may provide insight into issues of polarity, transformation order, homology, and homoplasy. Keywords Primate phylogeny Á Congruence Á A priori assumptions Á Branch slide distance Introduction Phylogenetic analysis of primate interrelationships is an important aspect of primatological research. In addition to providing a rationale for primate classification (e.g., Szalay 1976; Skelton and McHenry 1992; Strait et al. 1997; Tor- now 2008), hypotheses of primate phylogeny provide avenues for the study of adaptation (Kay and Ungar 1997; Robson-Brown 1999; Lockwood and Fleagle 1999), bio- geography (Ford 2005), and ecology (Fleagle and Reed 1999; Lockwood and Fleagle 1999;), as well as data from which to establish conservation protocol (Mittermeier et al. 2008; Nijman and Meijaard 2008). Whereas any of the aforementioned endeavors can be contextualized within any phylogenetic tree, changes in tree topology may alter interpretations; thus, phylogenetic accuracy may be essential to our broader understanding of primate biology. Whereas evolutionary relationships between taxa can never be known with certainty, taxonomic congruence between trees constructed using different data sets is often viewed as support for congruent clades (Allard and M. A. Tornow (&) Anthropology Program, Saint Cloud State University, 720 Fourth Avenue South, Saint Cloud, MN 56301-4498, USA e-mail: matornow@stcloudstate.edu M. A. Tornow Á R. R. Skelton Department of Anthropology, University of Montana, Missoula, MT 59812, USA 123 Primates (2012) 53:83–96 DOI 10.1007/s10329-011-0282-2