Data and code from: Diffeomorphic independent contrasts for ancestral reconstruction of shapes

Ancestral reconstruction is a fundamental challenge in evolutionary
biology, requiring methods that can capture complex morphological changes
while accounting for phylogenetic relationships. Current approaches are
based on linear assumptions that often oversimplify the spatial
relationships between anatomical features and fail to account for landmark
correlations within shapes. Here, we introduce a novel method that
combines the ability of Large Deformation Diffeomorphic Metric Mapping
(LDDMM) to model smooth, invertible transformations between shapes while
preserving the relationships between landmarks with Felsenstein's
Independent Contrasts (IC) to iteratively reconstruct ancestral shapes
along the branches of a phylogenetic tree. We call this method
Diffeomorphic Independent Contrasts for Ancestral Reconstruction of Shapes
(DICAROS). We validate DICAROS against two existing methods: (1) Linear
predictors using Ordinary Least Squares and (2) Ancestral character
estimation using maximum likelihood under Brownian Motion, and apply
DICAROS to a dataset of swallowtail butterfly species (Family Papilonidae,
Order Lepidoptera) to reconstruct the ancestral shape and visualize
evolutionary trajectories in a phylomorphospace from the contrasts. We
conclude that DICAROS outperforms the existing methods in terms of
accuracy and provides a more accurate reconstruction of the ancestral
shape for non-symmetric phylogenetic trees. With DICAROS, we show a
transition between untailed and tailed papilinodae species while also
illustrating how images of modern species would look under the DICAROS
ancestral reconstruction.