Biology subjects

Bever, G. S.

Publications and source records attributed to Bever, G. S..

4 recordsLinked to original sources

bioRxiv2026

Muscle Loss as a Foundational Step in the Development and Evolution of the Turtle Shell

Modern biodiversity is built on a series of disparate body plans whose origins are obscured by deep time. Our most direct source of clarifying data is the fossilized skeleton, where morphology reflects an evolving functionality realized through the development of associated tissues. We apply this dualistic perspective to the shelled body plan of turtles whose Paleozoic initiation is marked by a derived relationship between ribs and dermis (Lyson & Bever, 2020). Current developmental models remain in conflict with an increasingly informative fossil record, suggesting critical steps remain unrecognized. Here we explore the hypothesis that the breakdown of rib-spanning muscles--an evolutionary transformation mirrored in embryogenesis--is one such step. Multi-modal imaging of turtle embryos, including a novel application of histology-based deep learning (Kiemen et al., 2022; Matos-Romero et al., 2025; Forjaz et al., 2026), establishes intercostal muscle degradation as preceding turtle-specific rib development and highlights the heuristic power of 3D, whole-embryo analysis (Forjaz et al., 2026). Quantified divergence from mouse pinpoints the timing and tempo of this organized, apoptotic breakdown. Initial evidence suggests an associated non-pathological inflammatory response, which has been shown capable of driving evolutionarily stable hyperossification (Rashid et al., 2023). These patterns support trunk muscles as a critical signalling centre whose ontogenetic loss set the phylogenetic stage for a morphogenetic transformation remarkable in a non-metamorphic species.

evolutionary biology↗

bioRxiv2026

Whole organism 3D mapping reveals universal branching topology and biophysical optimization governs vascular and nervous system development

The vascular and nervous systems are transport networks essential for life, yet whether universal geometric and topological principles govern their formation remains unclear. The organism-wide molecular and biophysical coordination required to build and maintain these networks during embryonic development has inspired decades of theoretical work, offering predictions about their expected organization. However, the lack of complete three-dimensional (3D) data has limited validation to isolated structures, leaving whole-organism networks unexplored. Here, we developed a computational pipeline for whole-organism 3D imaging to reconstruct the complete vascular and nervous systems of rhesus macaque, mouse, and turtle embryos. Our analysis reveals that both networks share structural principles, including binary branching and scale-invariant bifurcation geometry, maintained across species and throughout development. Yet, from these shared rules emerge fundamentally different architectures. Vasculature exhibits fractal topology with a fractal dimension [~]3, forming space-filling trees that prioritize proximity to every cell in the body. Nervous system networks exhibit a fractal dimension [~]2, forming sheet-like arbors that prioritize electrical signal transmission. This architectural divergence originates from distinct biophysical constraints operating in bifurcations, where vascular junctions minimize energy expenditure while conserving fluid flow and nerve junctions maximize conduction velocity while conserving electrical current. These local optimization rules, iterated across generations, construct organism-wide networks governed by distinct physical constraints, revealing how evolution generated different solutions for fluid versus electrical transport.

developmental biology↗

bioRxiv2024

Reconstructing the deep phylogeny of the MAPK signaling network: functional specialization via multi-tier coevolutionary expansion

The mitogen-activated protein kinase (MAPK) signaling network is a three-tier cascade that regulates key cellular responses in eukaryotes. However, the evolutionary origins of its complex interactions and functional diversity remain poorly understood. Here, we conducted a comprehensive phylogenetic analysis of MAPK components across Eukarya to delineate divergences of non-human orthologs of human paralogs along the human evolutionary backbone. We identified two major pulses of coevolutionary expansion: one predating the divergence of fungi and animals, and another predating the origin of animals. Our reconstruction also infers a polyphyletic origin for the atypical MAPKs. Integrating functional literature across eukaryotic taxa with our reconstructed trees reveals that the two clades of MAP3K, Sterile-like (STE) and tyrosine kinase-like (TKL), had distinct evolutionary trajectories and influences on downstream pathway diversification. STEs that function as MAP3Ks are conserved across extant eukaryotes. Despite the absence of TKL MAP3Ks in many early diverging eukaryotes, the expansion of TKL MAP3Ks aligns phylogenetically and functionally with that of the downstream MAP2Ks and MAPKs. We thus propose that the MAPK network originated as a STE-regulated pathway, and that subsequent radiations of the TKLs drove the diversification of downstream components and top-down finetuning of pathway specificity. We thus provide an evolutionary framework for generating novel hypotheses on the functional diversity of this key signaling network, including potential insights into the evolution of animal multicellularity. Our study demonstrates that phylogenetics can offer new perspectives towards understanding complex cellular physiology. SignificanceThe mitogen-activated protein kinase (MAPK) signaling network responds to various signals and regulates basic cell physiology including proliferation and apoptosis. This three-tier network is universal in eukaryotes, but there is great functional diversity among different homologs as well as different taxa. Here we compared amino acid sequences to reconstruct MAPK evolutionary history as a network. We found that the three levels expand in parallel, showcasing a special case of coevolution. Two distinct pulses of network expansion predate the origin of animals, indicating that the functional diversity of human MAPK network proteins originate from ancient evolutionary radiations. Together, our study provides a critical look at the deep history of this important network.

evolutionary biology↗

bioRxiv2019

CaMKII oxidation is a performance/disease trade-off in vertebrate evolution

Reactive oxygen species (ROS) contribute to health and disease. CaMKII is a widely expressed enzyme whose activation by oxidation of regulatory domain methionines (ox-CaMKII) contributes to cardiovascular disease, asthma, and cancer. Here we integrate comparative genomic and experimental data to show that CaMKII activation by ROS arose more than half-a-billion years ago on the vertebrate stem lineage where it constituted a bridge between ROS and increased intracellular Ca2+ release, exercise responsive gene transcription, and improved performance in skeletal muscle. These enhancements to fight-or-flight physiology were likely key in facilitating a well-evidenced shift in the behavioural ecology of our immediate chordate ancestors, and, in turn, the evolutionary success of vertebrates. Still, the ox-CaMKII innovation for augmenting performance must be considered a critical evolutionary trade-off, as it rendered us more susceptible to common and often fatal diseases linked to excessive ROS.

evolutionary biology↗