Biology subjects

Hipsley, C. A.

Publications and source records attributed to Hipsley, C. A..

4 recordsLinked to original sources

bioRxiv2026

DICAROS: Diffeomorphic Ancestral Shape Reconstruction on Phylogenies

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).

evolutionary biology↗

bioRxiv2026

3D shell asymmetry of Testudines as a potential biomarker for environmental stress

Turtles and tortoises (Order Testudines) possess a unique bony shell that varies in shape across ecological niches. Previous studies have linked turtle shell abnormalities to the presence of environmental stress, leading to asymmetry in shell shape. Here we present the first large-scale geometric morphometric analysis of shell asymmetry in preserved museum specimens from 92 turtle species, using high-resolution 3D scans and (semi)landmark-based methods. We quantified fluctuating asymmetry (FA) and directional asymmetry (DA) in the whole shell, carapace, and plastron, and tested for ecological and phylogenetic influences on shell shape. Our results reveal significant ecological effects on both symmetric and asymmetric components of shell morphology, with aquatic and marine species exhibiting higher FA than their terrestrial counterparts. The carapace showed higher asymmetry and integration than the plastron, suggesting different developmental constraints. Phylogenetic signal was present but weak, indicating convergence in shell shape among ecologically similar but distantly related species. Partial least squares analysis revealed strong covariation between symmetric and asymmetric components, supporting the shell as an integrated morphological unit. These findings highlight the utility of FA as a non-invasive indicator of developmental instability, with implications for conservation monitoring using preserved and living specimens.

evolutionary biology↗

bioRxiv2025

Diffeomorphic Independent Contrasts for Ancestral Reconstruction of Shapes

AO_SCPLOWBSTRACTC_SCPLOWAncestral 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 Felsensteins 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 Lepiodetra) 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 un-tailed and tailed papilinodae species while also illustrating how images of modern species would look under the DICAROS ancestral reconstruction

evolutionary biology↗

bioRxiv2020

High throughput micro-CT scanning of small fossils: preparation, packing, parameters and post-processing

High-resolution X-ray microcomputed tomography, or microCT (CT), enables the digital imaging of whole objects in three dimensions. The power of CT to visualise internal features without disarticulation makes it particularly valuable for the study of museum collections, which house millions of physical specimens documenting the spatio-temporal patterns of life. Despite its potential for comparative analyses, most CT studies include limited numbers of museum specimens, due to the challenges of digitising numerous individuals within a project scope. Here we describe a method for high-throughput CT scanning of hundreds of small (< 2 cm) specimens in a single container, followed by individual labelling and archival storage. We also explore the effects of various packing materials and multiple specimens per capsule to minimize sample movement that can degrade image quality, and hence CT investment. We demonstrate this protocol on vertebrate fossils from Queensland Museum, Australia, as part of an effort to track community responses to climate change over evolutionary time. This system can be easily modified for other types of wet and dry material amenable to X-ray attenuation, including geological, botanical and zoological samples, providing greater access to large-scale phenotypic data and adding value to global collections.

evolutionary biology↗