Biology subjects

Drage, H. B.

Publications and source records attributed to Drage, H. B..

6 recordsLinked to original sources

bioRxiv2026

TaxonMatch: taxonomic integration and tree construction from heterogeneous biological databases

Integrating taxonomic data across heterogeneous biological databases remains a major challenge in biodiversity research due to non-standardized nomenclature, incomplete synonym annotation, and inconsistencies in taxonomic hierarchies. These issues limit interoperability between key resources such as the Global Biodiversity Information Facility (GBIF), the National Center for Biotechnology Information (NCBI), and citizen science platforms such as iNaturalist. Here, we present TaxonMatch, a scalable and reproducible framework for taxonomic reconciliation and cross-database integration. The workflow combines string-based candidate generation using TF-IDF vectorization, supervised machine learning for match classification, and lineage-aware synonym resolution to align taxonomic entities across multiple sources. By integrating both declared and implicit equivalences, TaxonMatch resolves typographical variation, synonymy, and structural inconsistencies in taxonomic data. The framework produces a unified taxonomic structure in which equivalent entities are reconciled while preserving source-specific identifiers, provenance information, and hierarchical relationships. We evaluate its robustness across multiple classifiers and demonstrate its effectiveness in resolving ambiguous taxonomic cases that are not handled by traditional matching approaches. We illustrate the applicability of TaxonMatch through three use cases: the construction of a unified arthropod taxonomy integrating GBIF, NCBI, and iNaturalist data; the identification of closest extant relatives of fossil taxa with molecular information; and the integration of genomic resources with conservation data from the IUCN Red List. These applications highlight the ability of the workflow to support the integration of ecological, genomic, and paleontological datasets. TaxonMatch provides a flexible and generalizable solution for taxonomic data integration, enabling the construction of coherent and interoperable biodiversity datasets for downstream analyses in ecology, evolution, and conservation biology.

evolutionary biology↗

bioRxiv2026

Morphological characterization of moulting in the Atlantic horseshoecrab Limulus polyphemus: phylogenetic conservation amongchelicerates and evolutionary convergence of ecdysis linked to headshield patterns

Arthropods must periodically moult their exoskeleton to permit growth, a conserved developmental process whose morphological and behavioural execution varies widely among lineages. Horseshoe crabs (Limulidae) are members of Xiphosura, a chelicerate lineage with a fossil record extending as far back as the Ordovician and provide a valuable comparative framework for studying the evolution of moulting strategies in Arthropoda. Despite their importance, detailed morphological characterization of moulting in horseshoe crabs remains scarce, limiting developmental studies and broader comparative analyses. Here, we provide a detailed morphological characterization of the moulting process in the Atlantic horseshoe crab Limulus polyphemus. Morphological changes in specific anatomical structures, including the anterior margin of the prosoma, lateral spines and dorsal spinous process of the opisthosoma, were observed during the moulting process. By tracking these morphological markers, such as retraction of the epidermis from the cuticle and degree of corrugation of the epidermis, we were able to identify individuals in the early and late pre-moult stage, predict the onset of ecdysis, and distinguish post-moult and intermoult stages. We compare ecdysis patterns in L. polyphemus with other arthropod taxa, both extant and fossil. We find that, despite differences in behavioural execution, ecdysis in L. polyphemus shares features with other chelicerates, and that both phylogenetic signal and convergent patterns are evident across Arthropoda. This study offers a robust, non-invasive method for determining moult stages in juvenile horseshoe crabs and provides insights into the diversity and constraints of ecdysis in Arthropoda.

evolutionary biology↗

bioRxiv2025

Hierarchical importance of factors impacting trilobite cephalic disparity

1Trilobite cephala show high disparity owing to their supporting of key functional ecological structures, such as sensory and feeding structures, and those enabling important behaviours like enrollment and exoskeleton moulting. Previous studies analysed associations between cephalic morphometry, trends through time and with diversity, and these behaviours. However, no studies have yet quantitatively compared the importance of these different varied factors on cephalic morphometry. Here, we explore the association between trilobite cephalic morphometry and taxonomic variables, moulting behaviour, and facial suture type in Principal Components Analysis morphospace, and assess whether these variables can predict cephalic morphometry using Linear Discriminant Analyses. We employed Linear Mixed-Effects Models (LMMs) to quantify the hierarchical importance of these variables for determining cephalic disparity. The dataset used comprises cephalon outlines for 762 species of trilobites from across the globe and through the entire Palaeozoic. We found that variation in cephalic morphometry is not clearly associated with moulting behaviour, nor is moulting behaviour linked to facial suture type. Trilobite moulting behaviour is evidently too phenotypically plastic, and/or preservationally impacted, to produce clear signals across broad datasets. Results demonstrate the utility of LMMs for palaeontological datasets; we found that family-level assignment overall well explains cephalic morphometry, more so than order-level assignment which shows significant overlap in morphospace. Geological Period, facial suture type, and moulting behaviour had little impact on cephalic morphometry. We thereby demonstrate that trilobite cephalic outline morphometry is generally in accordance with trilobite family-level systematics and highlight the use of LMMs for interrogating broad-scale fossil morphological data.

paleontology↗

bioRxiv2024

Hydrodynamic function of genal prolongations in trinucleimorph trilobites revealed by computational fluid dynamics

Trilobites, a diverse clade of Palaeozoic arthropods, repeatedly converged on the trinucleimorph morphology. Trinucleimorphs possessed vaulted cephala with a broad anterior fringe and prominent posteriorly orientated genal prolongations. Various functional hypotheses have been proposed for the fringe, however the possible function of the genal prolongations has received less attention. Here we use a computational fluid dynamics approach to test whether these prolongations served a hydrodynamic function: generating negative lift to allow trinucleimorphs to remain in place on the seafloor and prevent overturning within fast flowing water. We simulated the performance of cephala with broad, narrow, and absent genal prolongations in a benthic environment with flow speeds ranging from 0.05-0.5 m s-1, in two cephalic postures. The first posture had the anterior of the cephalon parallel to the seafloor, while for the second the genal prolongations were parallel to the seafloor. Posture and presence of genal prolongations were found to be important for generating negative lift, with performance improving under faster flow speeds. No significant difference between narrow and broad genal prolongations was detected. This study provides support for genal prolongations serving a hydrodynamic function, similar to the femurs of some insect larvae, however, it does not preclude prolongations also serving additional functions as snowshoes or antipredatory deterrents.

paleontology↗

bioRxiv2024

Distinct causes underlie double-peaked trilobite morphological disparity

Trilobite cephalic morphology impacted the autecology of individuals, and is critical for high- and low-level taxonomic assignments. Disparity in trilobite cephalon shape varied through time and was integral to the occupation of a diversity of ecological niches. To fully appreciate trilobite cephalic evolution, we must understand how this disparity varies, and what factors control cephalon morphometry. We explore the disparity of trilobite cephala through the Palaeozoic, and analyse the associations between cephalic morphometry and taxonomic assignment and geological Period, using a dataset of 983 2D trilobite cephalon outlines. Elliptical Fourier transformation visualised as a Principal Components Analysis suggests significant differences in morphospace occupation for order and Period groups, and comparisons of disparity measures also suggest significantly different disparities between the groups. Trilobite cephalic disparity peaks in the Ordovician and Devonian. The Cambrian-Ordovician expansion of morphospace occupation appears a result of radiation to new niches, and thus all trilobite orders were established by the late Ordovician. In comparison, the morphospace expansion from the Silurian to Devonian seems solely a result of within-niche diversification rather than novel niche occupation. However, analyses interrogating the regions of morphospace occupied, including centroid distances, average pairwise shape comparisons and Linear Discriminant Analysis demonstrate that, except for the order Harpida and the Cambrian and Ordovician Periods, order and geological Period could not be robustly predicted for an unknown trilobite. Further, Kmeans clustering analyses suggest the total dataset naturally subdivides into only seven groups that do not correspond with taxonomic orders, though Kmeans clusters do decrease in number through the Palaeozoic, aligning with findings of decreasing disparity.

paleontology↗

bioRxiv2022

Trilobite moulting behaviour variability had little association with morphometry

Trilobite moult assemblages preserved in the fossil record show high variability in moulting behaviour and their resulting moult configurations. The reasons for this variability, and the impacts it might have had on their evolutionary trajectories, are unknown and have rarely been investigated quantitatively. A large dataset of trilobite moult morphometric measurements is presented and statistically analysed for associations between moulting behaviour and morphometry. Results indicate little significant statistical association between the two; only between moulting behaviour (usually generalised moult configuration) and the variances and means of thoracic tergite number, thorax length, and pygidium width. Anterior cranidium width, cranidium length, cephalothoracic joint width, thorax width, pygidium length, and total body length all have non-significant associations with moulting behaviour. Moult specimens showing inversion of the librigenae generally have more thoracic tergites, a correspondingly longer thorax, and a narrower pygidium. Thoracic tergite count and pygidium measurements may have multimodal distributions. Principal Components Analyses and Non-Metric Multidimensional Scaling analyses suggest minor differences in the extent of morphometric variation for specimens showing different moulting behaviours, but little difference in the region of morphospace they occupy. This may indicate that trilobite species using Salters mode of moulting had more constrained morphologies, potentially related to facial suture fusion in some groups. Overall, these results do not suggest a strong association between moulting behaviour variation and morphometry in trilobites, leaving open for further study the mystery of why trilobites were so variable in their moulting, and whether this contributed to their long evolutionary reign or ultimate extinction. PLAIN LANGUAGE SUMMARYTrilobites were an important and globally abundant group of arthropods (animals with an exoskeleton and jointed limbs) that lived ~521-251 million years ago. The exoskeletons of arthropods are crucial because they provide protection against predators and parasites, but also restrict their growth. All living and extinct arthropods must therefore periodically moult (shed) their exoskeletons; an incredibly risky event during which many individuals die. Due to its importance, it is presumed that exoskeleton moulting impacted the broad-scale evolution of arthropod morphology (their physical characteristics), behaviour, and ecology. Trilobite moults are preserved in great number in the fossil record, and this can tell us much about their moulting behaviour. Additionally, trilobites appear to be unique in showing many different moulting behaviours. However, we do not know why trilobites were so variable in their moulting behaviour, or what impact this had on their evolution. In this study, a large dataset of trilobite moulting behaviours and their body proportion (morphometry) measurements is presented and analysed to answer: Was variability in trilobite moulting behaviour related to differences in their morphometry? The results suggest that there was little association between the moulting behaviours shown by trilobites and their morphometry. Species showing the different moulting behaviours had overall similar morphologies, although for one moulting behaviour this seemed more limited. Only thorax length and segmentation (the central part of the body), and pygidium ( tail) width, significantly differed between species showing the different moulting behaviours. This study does not indicate a strong relationship between moulting behaviour and morphology in trilobites. This is unexpected, and leaves open the mystery of trilobite moulting variability.

paleontology↗