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The equid locomotor transition is one of the most iconic morphofunctional shifts in terrestrial mammals. Throughout their evolution, equids reduced their side-digits, with different phylogenetic clades exhibiting greater or lesser degrees of digit reduction. Over 80% of equid genera retained side-digits, despite many species coexisting with monodactyl equids for over 7 Ma. In this continuing study, we shed light on the functionality of the side-digits of extinct equids using an extant morphological bracket, comparing toe-ground interception across ecologically diverse ungulates with side-digits. Using high-resolution 3D surface scans, joint range-of-motion was estimated from osteological material of modern and extinct ungulate forelimbs. Distal limb rigs were built and analysed, rotating the third proximal phalange parasagittally at biologically realistic, regularly spaced intervals. Toe-to-ground interception for the side-digits was scored for the varying degrees of central digit extension (simulating high-performance actions), and under increasingly compliant substrates (mimicking different underfoot conditions). Our results demonstrate widespread functionality in the side digits of tridactyl equids, with significant differences found between earlier browsing forms (e.g. Anchitherium) and later grazing forms (e.g. Hipparion). High-performance actions, such as galloping or jumping/landing would have caused the side digits of almost all tridactyl equids to impact the substrate. Our work confidently refutes the notion of functional redundancy in equid side-digits. The extant morphological framework within which this study was conducted also provides a suite of potential extant analogues for verifying simulations of extinct equid locomotion, and thus paves the way for more integrative investigations involving in-vivo and in-silico locomotor kinematics.

SEB Conference 2025

Still using modern ungulate analogues to explore equid side-toe function through an iconic evolutionary transition...

horse

3d scanning

locomotion

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SEB Conference 2024

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Single-toed (monodactyl) equids (horses, zebras, asses) are the only surviving members of the family Equidae, despite living contemporaneously with three-toed (tridactyl) forms for c.15 Ma. Among the tridactyl forms, a trend of side-digit reduction is observed, raising the question about the energetic advantage of digit loss. The inertial load hypothesis describes the reduction (and eventual loss) of side-digits in equids as a means to minimize energetic cost during locomotion, linked to reducing inertial load (or moment of inertia, MOI) of the limbs by minimizing their distal mass. In this study, we tested this hypothesis by estimating and comparing inertial loads of tridactyl equid limbs, both with and without side-digits. Additionally, we compared the results of the tridactyl and monodactyl equids, while accounting for differences in limb size, to investigate the effect of side-digit loss across equid evolution. MOI was calculated on soft tissue limb reconstructions created using 3D models of (fossil) bones. A validation analysis using 3D renders of cadaver specimens verified the predictability of these reconstructions. We demonstrate that the entire limb MOI with regard to the scapular rotation centre is significantly smaller without side-digits. However, the difference is very small, and its functional significance can be questioned.  Size-corrected MOI between monodactyl and tridactyl taxa suggest overall significant differences (monodactyl equids with lower MOI); however, distal limb mass comparisons (e.g. pastern segments) showed no signs of the effect of side-digits. Our results hint at limb segment allometry as a more notable influence on MOI reduction during horse evolution.

Investigating the biomechanical efficiency of horse limbs through their iconic distal limb evolution.

Cranial shape in extinct fossilised species provides a vital puzzle piece to our understanding of their feeding behaviour which cannot be observed in real time. The carnivorous theropod MOR693 Allosaurus jimmadseni fossil offers insight into its feeding function and the palaeo-ecology of the Late Jurassic geological period. A. jimmadseni possesses a distinctive cranial anatomy, displaying large fenestrae and a thin cranio-caudally elongated skull. The skull’s lightweight anatomy has led researchers to hypothesise a “puncture and pull” feeding behaviour, in which an animal captures prey with a puncture bite, and proceeds to tear with a pulling motion. Using 3D scans of the MOR693 skull and applying a finite element analysis, I obtained the maximum, average, and minimum total von Mises stress in the skull during different biting angles. My results report that the 0-30° bites (puncture) exhibited the highest stress values, while the 90° bite (pull) showed the lowest. A consistent decrease from a 0° to a 90° bite in the maximum, average, and minimum stress indicates that the skull experienced the least amount of stress during the pulling aspect of feeding. Low-stress values suggest an evolutionarily advantageous feeding motion in this dinosaur, therefore it is reasonable to conclude that the A. jimmadseni utilised this feeding strategy. The results of this research present that the skull was likely adapted for a pulling dominant feeding behaviour rather than a puncture, further supporting the puncture and pull feeding hypothesis in the A. jimmadseni.

Using the Allosaurus jimmadseni Skull Structure as a Puzzle Piece to Feeding Function

In extinct and extant species, some insights on joint function can be gained using bone morphology. Models of joints tend to use tendons to control joint function, often giving little or no insight on the role of ligaments in controlling the range of motion of a joint. This study presents an algorithm to automatically compute ligament attachment sites for a flexion-extension joint using optimisation, given bone morphology and required range of motion. To start with, the focus is on the collateral ligaments of the human finger Distal Inter-Phalangeal (DIP) joint.
The algorithm takes bone profiles and the required maximum flexion and extension angles as inputs. First, a grid of possible attachment sites is generated from the bone profiles. Using this grid, a discrete stage determines the best combination of attachment sites by minimising an objective function subject to a set of geometric constraints. This seeds the second stage– a continuous domain local optimisation which refines the attachment coordinates by minimising the error between required and computed range of motion. The algorithm’s outputs are attachment site coordinates of the two edges of a band of collateral ligaments capable of achieving the required range of motion. The outputs were verified by adding ligaments computed by the algorithm to an OpenSim simulation model and confirming that the required range of motion was achieved.
In contrast to other published research, the algorithm presented here computes ligament attachment sites based on range of motion - deriving form from function rather than relating form to function.

From Function to Form : Computing Collateral Ligament Attachments

Trap-jaw ants are recognized for their generally elongated mandibles that snap at remarkable speeds, having evolved among nine genera and three subfamilies. Despite superficial similarities, mandible morphology varies considerably, potentially affecting bite performance. To investigate these effects, we measured functional traits — mechanical advantage, cuticle thickness, and second moment of area (I) — and conducted finite element analysis (FEA) simulating a strike bite on 3D mandible reconstructions of 25 species from eight genera and two subfamilies of trap-jaw ants. We performed Principal Component Analysis with the functional traits and FEA-derived stress values and hypothesized that species distribution in this multivariate space would reflect their phylogenetic relationships. Species mostly grouped with their generic relatives, except Anochetus and Orecthognathus, which showed broader distributions. The distribution of trap-jaw genera also resembled their phylogenetic relatedness, but Myrmicinae and Ponerinae subfamilies did not form distinct clusters, as was initially anticipated. FEA stress data were relevant for grouping species with more elongated mandibles, such as Acantognathus spp. and Strumigenys denticulata. Odontomachus spp. and Daceton armigerum clustered due to their higher values ofI normalised by cross-section shape. Strumigenys spp. with shorter mandibles grouped due to their high mechanical advantage, I corrected by mandible length, cuticle thickness, and the low-stress values they exhibited under bite loading. Although our results only partially support the hypothesis that mandible function aligns with the phylogenetic relationships of trap-jaw ants, they highlight the functional consequences of mandible morphological variation in the context of the outstanding strike impacts these ants are submitted to.

Morphology drives functional performance variation: the case of trap-jaw ant mandibles

The arboreal environment is a complex three-dimensional environment that presents functional challenges. Despite these challenges, many clades of tetrapods have colonised this environment independently. So far, only a handful of studies investigate the impact of living in trees on the morphology in a large macroevolutionary sample. Here, we investigate whether there is an effect of degree of arboreality on radius shape. To do so, we compared radius shape across arboreal and terrestrial species of carnivorans and primates. Radius shape is an interesting structure as it influences forearm movement and hand position, which are vital in arboreal environments. Our sample comprises 239 specimens belonging to 160 species and, is representative of the locomotor diversity of carnivorans and primates. We used 3D geometric morphometrics to quantify the shape of the radius. Comparative phylogenetic methods were applied to understand the influence of size, locomotion and evolutionary history of each clade on radial shape. Our results showed a significant impact of the locomotion and morphological similarities in the radial shape among species with similar arboreal locomotion. Furthermore, the morphological diversity of radial shapes in carnivorans and primates is low, in contrast to the high diversity observed in terrestrial species. This suggests that arboreal environments impose greater constraints on the radial morphology in carnivorans and primates, which is consistent with results obtained in other vertebrates.

Arboreal adaptations constrain the morphological evolution of the radius bone in primates and carnivorans.

Legs can perform many functions, but fundamentally their ‘purpose’ is to support body weight while the body travels.  To do this effectively, the structures, mechanisms and actions of the legs should 1) avoid avoidable mechanical work demand, 2) allow economical supply of mechanical work, while 3) be simple and robust to control. Recent work considering ‘legs as linkages’ focuses on these roles. Sequences of isometric muscle actions result in a work-avoiding ‘sliding’ motion of the body over the foot (role 1); in the human, this would account for gluteus, then vastus, then rectus femoris (forming a 4-bar linkage) tensions. Given a limited peak muscle power, and a cost to muscle activation, work is provided economically (role 2) with muscles that contract over the entire stance; in running humans this would be the hamstrings that provide mechanical power without altering the work-avoiding geometries of role 1. And the sequence of linkages resulting in sliding (role 1) engage muscles through simple changes in geometry (role 3). Early application of these principles to a range of toy and human-scale models will be presented. These demonstrate the potential for bio-convergent linkages to facilitate work-avoidance, powering economy, and simplified control in engineered leg design.

Legs as linkages, legs as machines, legs as toys… and for robots?

Grain yield is a key determinant of cereal crop productivity, with spike morphology playing a crucial role in its assessment. Traditional spike characterization methods are often labor-intensive and time-consuming, limiting their scalability for large-scale breeding programs. To address this challenge, we present an advanced image-based tool leveraging deep learning methodologies for non-invasive, high-throughput spike phenotyping. The system utilizes a U-Net model trained on 200 annotated spike images, incorporating data augmentation techniques such as rotation and scaling to enhance robustness. With the Dice coefficient as the loss function and the Adam optimizer, the model was trained for 60 epochs with early stopping to prevent overfitting. Additionally, adaptive thresholding and the Segment Anything Model (SAM) were evaluated, achieving Dice coefficients of 0.95 and 0.98, respectively, demonstrating the effectiveness of automated spike segmentation. The post processing of segmented grains extracts key morphological traits, including spike length, grain number, grain width, grain length, and grain area, facilitating precise yield analysis. This innovation enhances the efficiency of crop breeding research by providing an accurate, non-destructive, and scalable solution for spike trait analysis.

Automated X-ray-Based Spike Analysis for Grain Characterization

The maize plastochron1 (pla1) mutant exhibits a shortened plastochron (accelerated leaf initiation) and reduced plant growth. This remarkable phenotype suggests a role for PLA1 in regulating leaf initiation and growth in the maize shoot apical meristem (SAM). The SAM is a highly complex structure where stem cells gradually differentiate into plant organs in a spatially coordinated manner. However, the transcriptional mechanisms by which PLA1 influences these developmental processes remain unclear. To investigate how PLA1 affects plant architecture at the molecular level, we applied spatial transcriptomics to visualize the expression of 500 genes in wild-type and pla1 mutant shoot apices. Our analysis showed that PLA1 is expressed at the boundary between undifferentiated and differentiated cells, suggesting a role in regulating cell division and organ initiation. Developmental trajectory analysis tracing transcriptional changes from stem cells to differentiated cells revealed overlaps of PLA1 with stem cell markers such as Knotted1 and differentiation markers such as YABBY14, further supporting its regulatory function. Comparisons between wild-type and pla1 mutants revealed significant transcriptional changes, particularly in auxin metabolism, indicating an important role for PLA1 in (hormonal) regulation of the SAM. These findings provide novel insights into the transcriptional regulation of the maize meristem SAM and plastochron regulation, showcasing spatial transcriptomics and its downstream data-analysis as a valuable tool for studying plant development.

Plastochron regulation in maize: spatial transcriptomics reveals transcriptional changes in the plastochron1 mutant.

Overall plant architecture (consisting of the number, spacing and angle of secondary root and shoot branches) determines the efficiency of crops to capture essential resources such as water and nutrients below-ground, and light above-ground. Plant architecture is critically regulated by gravitropic growth, and recently, members of the highly conserved LAZYgene family have been demonstrated to play crucial roles in regulation of branching angle, a key determinant of plant architecture. Our previous work identified a novel dominant point mutation in LAZY4, (described as lazy4D) through an EMS mutagenesis screen in the model plant, Arabidopsis. Lateral roots in the lazy4Dmutant demonstrate steeper rooting, a highly desirable trait, that maximises nitrogen uptake, drought tolerance and carbon sequestration in cereal crops, making LAZY4 (and related LAZY genes) attractive targets for gene-editing to engineer deeper rooting in crop plants. However, the mechanistic basis for LAZY4dependent-regulation of root angle remains uncharacterised. Using live cell bioimaging and molecular genetic techniques, we determined that lazy4Dinfluences root growth angle in a dose-dependent manner, and further, that root LAZYs interact with D6PK proteins to regulate PIN polarisation and/or activity to regulate  lateral root growth angle.  Further we show that an MKK-MPK31,2  phosphorylation module is required forLAZY4, but notlazy4d dependent regulation of growth angle. Collectively, our work sheds novel insights into the molecular mechanisms that underpin thelazy4D (and more broadly,LAZY) dependent regulation of root and shoot branching angle in flowering plants.

LAZY but effective: The role ofLAZYgenes in regulating lateral root gravitropic setpoint angle (GSA)

Ectopic expression of a cytochrome P450 enzyme-encoding gene PLASTOCHRON1(PLA1/ZmCYP78A1) leads to increased biomass and seed yield potential by extending the duration of cell division, as demonstrated by multi-year and multi-location field trials. The expression pattern of PLA1 in the maize shoot apical meristem resembles a boundary region between meristematic and differentiated cells, where cells divide more rapidly and begin transitioning. We refer to these PLA1-expressing cells as transit amplifying cells (TACs), in analogy with similar cell types in animal systems. However, the precise mechanism of enzymatic reaction of PLA1 and its surrounding gene network in TACs remain unclear. To address these gaps, we utilize targeted spatial transcriptomics in the maize shoot apex to spatially map gene distribution and apply multiplex genome editing to investigate the genetic interactions of PLA1 co-expressing genes in TACs. Additionally, we use a cell-free protein expression system to stably and purely synthesize PLA1 for target binding assays to identify its substrate-product pair. These findings will advance both fundamental and applied research, deepening our understanding of growth, cell differentiation, and leaf initiation in the shoot apical meristem; and they will facilitate the fine-tuning of key growth genes through genetic engineering and the utilization of enzymatic characteristics to enhance crop traits.

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Investigating the biomechanical efficiency of horse limbs through their iconic distal limb evolution.

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Using modern ungulate analogues to explore equid side-toe function through an iconic evolutionary transition

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