McQueen, C. | bioRxiv Science

bioRxiv2026

Standardized benthic imaging with small, modular ROVs: an open-source framework developed in temperate kelp forests

(1) Kelp forests support ecologically, commercially, and culturally important species, yet their benthic communities remain difficult to monitor consistently across space and time. Scientific SCUBA surveys provide valuable observations but can be constrained by safety, bottom time, depth, and the spatial extent that divers can efficiently cover, motivating complementary approaches for collecting standardized benthic imagery. (2) We developed and field-tested a standardized, open-source framework for benthic visual-imaging surveys using a small, modular remotely operated vehicle (ROV). Across four cost-scalable hardware configurations, we integrated navigation sensors, custom BlueOS Extensions, and our surftrak contribution to ArduSub, which enables fixed-altitude flight above the seafloor, and developed two open-source desktop applications that streamline field operations (rov_flight_ops) and imagery processing (rov_imagery_processing). We also evaluated power supplies, benthic lighting, camera settings, field protocols, and telemetry-processing workflows over 303 transects conducted on 64 survey days from 2022 to 2026. (3) The ROV operated across soft-sediment and rocky habitats, currents of 0-3 kt, and underwater visibility of 0-10 m. surftrak held the ROV within 0.2 m of its target altitude for 96% of 21 h of survey transects, producing an approximately 1 m^2 standardized image footprint. Sufficient illumination and optimized camera settings yielded high-resolution imagery in visibility below 2 m, while topside power increased endurance and operational flexibility. Combining Doppler velocity log and underwater acoustic positioning data through the vehicle's extended Kalman filter improved navigation and post hoc transect reconstruction. During 2026 surveys, rov_flight_ops and rov_imagery_processing automated flight logging, log retrieval, fault diagnosis, and the sorting, development, and telemetry annotation of survey imagery. Dense kelp canopies nevertheless constrained vehicle operation, and downward-facing imagery provided limited observations of cryptic or obscured organisms. (4) We provide configuration-specific bills of materials, hardware and wiring documentation, software and firmware inventories, camera settings, open-source field and imagery-processing software, step-by-step field protocols, and pre- and post-dive checklists to support replication and adaptation of the framework. Together, these resources provide a field-tested starting point for expanding standardized benthic imaging while complementing diver surveys across kelp forests and other shallow coastal ecosystems.

ecology↗

bioRxiv2023

Fgf signalling triggers an intrinsic mesodermal timer that determines the duration of limb patterning

Complex signalling between the apical ectodermal ridge (AER - a thickening of the distal epithelium) and the mesoderm controls limb patterning along the proximo-distal axis (humerus to digits). However, the essential requirement for AER-Fgf signalling during in vivo development makes it difficult to understand the exact roles that it fulfils. To overcome this barrier, we developed an amenable ex vivo chick wing tissue explant system that faithfully replicates in vivo parameters. Using inhibition experiments and RNA-sequencing, we identify a transient role for Fgfs in triggering the distal patterning phase. Fgfs are then dispensable for the maintenance of an intrinsic mesodermal transcriptome, which controls proliferation/differentiation timing and the duration of patterning. We also uncover additional roles for Fgf signalling in maintaining AER-related gene expression and in suppressing myogenesis. We describe a simple logic for limb patterning duration, which is potentially applicable to other systems, including the main body axis.

developmental biology↗

bioRxiv2019

A positional information gradient of sonic hedgehog is required for flight feather formation in avian wings

Flight is a triumph of evolution that enabled the radiation and success of birds. A crucial step was the development of forelimb flight feathers that may have evolved for courtship or territorial displays in ancestral theropod dinosaurs. Classical tissue recombination experiments performed in the chick embryo provide evidence that signals operating during early limb development specify the position and identity of feathers. Here we show that a positional information gradient of Sonic hedgehog (Shh) signalling in the embryonic chick wing bud specifies the pattern of adult flight feathers in a defined spatial and temporal sequence that reflects their different identities. We reveal that the Shh signalling gradient is interpreted into specific patterns of flight feather-associated gene expression. Our data suggests that flight feather evolution involved the co-option of the pre-existing digit patterning mechanism and therefore uncovers an embryonic process that played a fundamental step in the evolution of avian flight.

developmental biology↗