DICAROS: Diffeomorphic Ancestral Shape Reconstruction on Phylogenies

Abstract

Reconstructing ancestral morphologies on a phylogenetic tree is a central task in evolutionary morphometrics. Established reconstruction methods, including multivariate Brownian-motion approaches, rely on linear assumptions and do not directly model the correlations between landmarks within a shape, which can oversimplify the reconstructed morphology. The DICAROS method (Diffeomorphic Independent Contrasts for Ancestral Reconstruction of Shapes; Severinsen et al., 2026) instead fuses sibling shapes along branches with large-deformation diffeomorphic (LDDMM) landmark dynamics that model these correlations, so that ancestors remain on the shape manifold. DICAROS was shown to outperform ordinary least-squares, Brownian-motion, and penalized-likelihood reconstruction, particularly on non-symmetric trees. The dicaros package repackages that pipeline as a documented, pip-installable tool that runs on arbitrary landmark datasets from a single command. It handles 2D and 3D landmarks, Newick and NEXUS trees, a choice of Euclidean or Frechet species means, optional anchor-based alignment, and tips backed by a single specimen, and it returns the reconstructed shapes for all nodes together with the tree relabelled at its internal nodes. We demonstrate dicaros on two new datasets: a 2D leaf dataset (217 species) and a 3D guenon skull dataset (22 species).