Testing and Quantifying Phylogenetic Signals and Homoplasy in Morphometric Data

The relationship between morphometrics and phylogenetic analysis has long been controversial. Here we propose an approach that is based on mapping morphometric traits onto phylogenies derived from other data and thus avoids the pitfalls encountered by previous studies. This method treats shape as a single, multidimensional character. We propose a test for the presence of a phylogenetic signal in morphometric data, which simulates the null hypothesis of the complete absence of phylogenetic structure by permutation of the shape data among the terminal taxa. We also propose 2 measures of the fit of morphometric data to the phylogeny that are direct extensions of the consistency index and retention index used in traditional cladistics. We apply these methods to a small study of the evolution of wing shape in the Drosophila melanogaster subgroup, for which a very strongly supported phylogeny is available. This case study reveals a significant phylogenetic signal and a relatively low degree of homoplasy. Despite the low homoplasy, the shortest tree computed from landmark data on wing shape is inconsistent with the well-supported phylogenetic tree from molecular data, underscoring that morphometric data may not provide reliable information for inferring phylogeny.