Specimen alignment with limited point-based homology: 3D morphometrics of disparate bivalve shells (Mollusca: Bivalvia)

Comparative morphology fundamentally relies on the orientation and alignment of specimens. In the era of geometric morphometrics, point-based homologies are commonly deployed to register specimens and their landmarks in a shared coordinate system. However, the number of point-based homologies commonly diminishes with increasing phylogenetic breadth. These situations invite alternative, often conflicting, approaches to alignment. The bivalve shell (Mollusca: Bivalvia) exemplifies a homologous structure with few universally homologous points—only one can be identified across the Class, the shell ‘beak.’ Here, we develop an axis-based framework, grounded in the homology of shell features, to orient shells for landmark-based, comparative morphology. As the choice of homologous points for alignment can affect shape differences among specimens, so can the choice of orientation axes. Analysis of forty-five possible alignment schemes finds general conformity among the shape differences of ‘typical’ equilateral shells, but the shape differences among atypical shells can change considerably, particularly those with distinctive modes of growth. Each alignment implies a hypothesis about the ecological, developmental, or evolutionary basis of morphological differences, but we recognize one alignment in particular as a continuation of the historical approaches to morphometrics of shell form: orientation via the hinge line. Beyond bivalves, this axis-based approach to aligning specimens facilitates the comparison of continuous differences in shape among many other phylogenetically broad and morphologically disparate samples. ### Competing Interest Statement The authors have declared no competing interest.