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

Severinsen, Michael1; Pedersen, Morten Akhøj1; Nielsen, Rasmus2; Sommer, Stefan1; Hipsley, Christy Anna1

Published Apr 08, 2026 on Dryad. https://doi.org/10.5061/dryad.41ns1rnr7

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Apr 08, 2026 version files 1.37 GB

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Abstract

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.