Independent molecular and morphological phylogenetic analyses have often produced discordant results for certain groups which, for fossil-rich groups, raises the possibility that morphological data might mislead in those groups for which we depend upon morphology the most. Rhynchonellide brachiopods, with more than 500 extinct genera but only 19 extant genera represented today, provide an opportunity to explore the factors that produce contentious phylogenetic signal across datasets, as previous phylogenetic hypotheses generated from molecular sequence data bear little agreement with those constructed using morphological characters. Using a revised matrix of 66 morphological characters, and published ribosomal DNA sequences, we performed a series of combined phylogenetic analyses to identify conflicting phylogenetic signals. We completed a series of parsimony-based and Bayesian analyses, varying the data used, the taxa included, and the models used in the Bayesian analyses. We also performed simulation-based sensitivity analyses to assess whether the small size of the morphological data partition relative to the molecular data influenced the results of the combined analyses. In order to compare and contrast a large number of phylogenetic analyses and their resulting summary trees, we developed a measure for the incongruence between two topologies and simultaneously ignore any differences in phylogenetic resolution. Phylogenetic hypotheses generated using only morphological characters differed among each other, and with previous analyses, whereas molecular-only and combined Bayesian analyses produced extremely similar topologies. Characters historically associated with traditional classification in the Rhynchonellida have very low consistency indices on the topology preferred by the combined Bayesian analyses. Overall, this casts doubt on the use of morphological systematics to resolve relationships among the crown rhynchonellide brachiopods. However, expanding our dataset to a larger number of extinct taxa with intermediate morphologies is necessary to exclude the possibility that the morphology of extant taxa is not dominated by convergence along long branches.

Crura, the calcareous support structures of the lophophore in rhynchonellide brachiopods, have historically been used to justify higher-level rhynchonellide classification and reveal major evolutionary lineages within rhynchonellides. Seventeen crural types have been described and categorized into four groups based on variation in overall structure and cross-sectional shape, but not evaluated in a quantitative or comprehensive manner. Heterochrony has been hypothesized to play a role in the evolutionary transitions among some types, but the structural, developmental, and phylogenetic context for testing these hypotheses has not yet been established. In this study, we use three-dimensional geometric morphometric techniques to quantify morphological disparity among all six crural morphs in Recent adult rhynchonellides, with the goal of delineating more objective criteria for identifying and comparing crural morphs, ultimately to test hypotheses explaining morphological transformations in ontogeny and phylogeny. We imaged the crura of seven Recent rhynchonellide species, using X-ray computed microtomography. We used landmarks and semi-landmarks to define the dimensions and curvature of the crura and the surrounding hinge area. Procrustes-standardized landmark coordinates were analyzed using a principal component analysis to test the discreteness of the individual crural morphs and named groups of morphs, and to identify features that vary most among the crural configurations. Our results demonstrate that microCT imaging techniques provide novel ways to investigate the morphology of small features that may be otherwise impossible to quantify using more conventional imaging techniques. Although we predicted overlap among crural morphs in the 3-D shape space, the principal component analyses suggest that five of the six crural morphs differ distinctly from one another. Some but not all previously designated crural groups appear to exhibit morphological cohesion. This study establishes a quantitative morphological foundation necessary to begin an investigation of the phylogenetic significance of ontogenetic changes in crura, which will allow hypotheses of heterochrony to be tested.