@article{Ha2026d,

title = {Morphology and Distribution of Olfactory Receptor Neurons in Southern Bluefin Tuna,

                    \textit{Thunnus maccoyii}

                    (Teleostei): Implications for Olfactory Hydrodynamics},

author = {Myoung‐Hoon Ha and Lucille Chapuis and Travis L. Dutka and Julian Pepperell and Caroline C. Kerr and Shaun P. Collin},

doi = {10.1002/jmor.70133},

issn = {1097-4687},

year  = {2026},

date = {2026-05-00},

journal = {Journal of Morphology},

volume = {287},

number = {5},

publisher = {Wiley},

abstract = {ABSTRACT

                  

                    Olfactory receptor neurons (ORNs) of teleosts interact with waterborne odorants and serve as a crucial first step in detecting and transmitting the olfactory signal to the brain. Despite the significance of olfaction in feeding among pelagic teleosts, very little is known about the spatial distribution pattern of the density and types of ORNs on the olfactory lamellar surface. A scanning electron microscopy (SEM) investigation was conducted on southern bluefin tuna,

                    Thunnus maccoyii

                    , to quantify the types and density of ORNs in different parts of the olfactory lamellar surface. SEM revealed two types of ORNs: ciliated olfactory receptor neurons (cORNs) and microvillous olfactory receptor neurons (mORNs). The cORNs are dominant over mORNs with mean densities of 84,000 mm

                    −2

                    and 5000 mm

                    −2

                    , respectively. Ciliated non‐sensory cells (cNSs) are present at the periphery of the olfactory epithelium, with a mean density of 800 mm

                    −2

                    . The mORNs display a distinct, heterogeneous spatial distribution, being highly concentrated in the rostral region of the lamellar surface, especially at the entry of the interlamellar space. Based on the hydrodynamics of the incoming flow of seawater within the interlamellar spaces and the topography of the olfactory epithelium, the rostral distribution of mORNs is organised to optimise interactions with water‐borne stimuli. The mean density of ORNs on the lamellar surface of

                    T. maccoyii

                    (90,000 mm

                    −2

                    ) is one of the highest among teleosts reported to date, which may serve as an anatomical indicator of high olfactory ability.

                  },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ha2026c,

title = {Brain Morphology and Quantitative Assessment of Sensory Brain Areas in Southern Bluefin Tuna,

                    \textit{Thunnus maccoyii}

                    (Scombridae, Teleostei)},

author = {Myoung Hoon Ha and Lucille Chapuis and Rebecca Glarin and Bradford Moffat and David K. Wright and Travis L. Dutka and Julian Pepperell and Caroline C. Kerr and Kara E. Yopak and Shaun P. Collin},

doi = {10.1002/cne.70148},

issn = {1096-9861},

year  = {2026},

date = {2026-04-00},

journal = {J of Comparative Neurology},

volume = {534},

number = {4},

publisher = {Wiley},

abstract = {ABSTRACT

                  

                    A quantitative comparison of the absolute and relative volumes of different brain areas is useful for predicting the sensory capabilities and behavior of large pelagic teleosts, which are difficult to study in the field or in vivo. However, the size of pelagic teleost brain regions has only been approximated using the idealized ellipsoid method, which is susceptible to over‐ or underestimation, as it assumes the shape of brain regions to be an idealized ellipsoid or half‐ellipsoid. This study examines the gross morphology and volumes of different sensory brain areas of southern bluefin tuna

                    Thunnus maccoyii

                    using magnetic resonance imaging (MRI). The results show that the optic tectum (568 ± 11 mm

                    3

                    ) has a larger absolute volume compared to the olfactory bulb (50 ± 5 mm

                    3

                    ), eminentia granularis (62 ± 9 mm

                    3

                    ), and cristae cerebelli (47 ± 3 mm

                    3

                    ), suggesting the significance of vision for

                    T. maccoyii

                    . The full segmentation of a

                    T. maccoyii

                    brain allowed the quantification of the integration areas, which reveals that the corpus cerebelli (1299 mm

                    3

                    ) occupies the largest proportion (35%) of total brain volume, whereas the optic tectum only occupies 15% of total brain volume. The corpus cerebelli also exhibits a rostro‐caudal elongation with multiple horizontal sulci, which resemble the corpus cerebelli of some species of sharks. The results reveal that the brain of

                    T. maccoyii

                    is dominated by the locomotive area of the corpus cerebelli and highlight the benefits of using MRI when performing quantitative analyses on the brain volumes of large pelagic teleosts.

                  },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ha2026b,

title = {Novel sensory epithelial topography of the olfactory lamellae in southern bluefin tuna, Thunnus maccoyii (Scombridae)},

author = {Myoung-Hoon Ha and Travis Dutka and Julian Pepperell and Lucille Chapuis and Caroline C. Kerr and Shaun P. Collin},

doi = {10.1007/s10228-026-01058-x},

issn = {1616-3915},

year  = {2026},

date = {2026-03-06},

journal = {Ichthyol Res},

publisher = {Springer Science and Business Media LLC},

abstract = {Abstract

                  

                    The arrangement of the sensory epithelium over the surface of the olfactory lamellae in teleosts is variable, with a diverse pattern ranging from large expanses of continuous epithelium to numerous discrete islets. As the olfactory epithelium is the location where water-borne odorants interact with olfactory receptors, its spatial distribution pattern serves as an important anatomical proxy for olfactory ability. However, nothing is known about the olfactory epithelial pattern in southern bluefin tuna,

                    Thunnus maccoyii

                    . Scanning electron microscopy was used to examine the spatial distribution pattern, area, and number of olfactory epithelial patches over the olfactory lamellar surface within the olfactory rosettes of both juvenile and mature

                    T. maccoyii

                    . Juvenile

                    T. maccoyii

                    exhibit a novel olfactory epithelial topography, where the lamellae in the caudal parts of the olfactory rosette display a combination of Type IV (olfactory epithelium arranged into numerous, small discrete islets) and Type III (olfactory epithelium irregularly intermingled with non-sensory epithelium) topographies. The lamellae in the rostral parts of the olfactory rosettes primarily have Type IV topography. In both arrangement patterns, the olfactory epithelia are smaller and more numerous rostrally. In mature

                    T. maccoyii

                    , the Type IV topography disappears, and lamellae in all parts of the olfactory rosette display exclusively Type III topography. The combined results of this study reveal a new and unique distribution pattern of olfactory sensory epithelia in

                    T. maccoyii

                    , with a striking change in distribution pattern associated with both lamellar location and growth, indicating adaptation to the different hydrodynamic conditions.

                  },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{vonSchuckmann2026,

title = {Global ocean indicators: Marking pathways at the science-policy nexus},

author = {Karina von Schuckmann and Alex Godoy-Faundez and Véronique Garçon and Frank E. Muller-Karger and Karen Evans and Ward Appeltans and Narissa Bax and Lisandro Benedetti Cecchi and Anthony Bernard and Kim Bernard and Jarret Byrnes and Gabrielle Canonico and Lucille Chapuis and Malcolm R. Clark and Audrey M. Darnaude and Claire Davies and Pia Englyst and Agneta Fransson and Samantha Hallam and Emma Heslop and Elisabeth Holland and Maria Hood and Stefan Kern and Aurélien Liné and Ana Lara-Lopez and Nora Loose and Belén Martín Míguez and Clive R. McMahon and Lina Mtwana Nordlund and Joanna Post and Sabrina Speich and Adrienne Sutton and Toste Tanhua and Maciej Telszewski and Dimitris Poursanidis and Weidong Yu},

doi = {10.1016/j.marpol.2025.106922},

issn = {0308-597X},

year  = {2026},

date = {2026-02-00},

journal = {Marine Policy},

volume = {184},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Havlik2026,

title = {Boat noise alters behaviour of two coral reef macroinvertebrates, Lambis lambis and Tridacna maxima},

author = {M.N. Havlik and N.R. Geraldi and L.W. Hopkins and J. Hubert and L. Chapuis and L.P. Gaffney and R.P. Wilson and S.D. Simpson and F.J. Juanes and C.M. Duarte},

doi = {10.1016/j.marpolbul.2025.118650},

issn = {0025-326X},

year  = {2026},

date = {2026-01-00},

journal = {Marine Pollution Bulletin},

volume = {222},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ha2026,

title = {Hydrodynamic flow in the peripheral olfactory system of pelagic fishes: A comparison between southern bluefin tuna, Thunnus maccoyii and black marlin, Istiompax indica},

author = {Myoung-Hoon Ha and Travis Dutka and Julian Pepperell and Lucille Chapuis and Caroline C. Kerr and Shaun P. Collin},

doi = {10.1016/j.zool.2026.126318},

issn = {0944-2006},

year  = {2026},

date = {2026-01-00},

journal = {Zoology},

volume = {174},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chapuis2025b,

title = {A universal symphony: coral reef fish calls exhibit consistent acoustic characteristics across different bioregions},

author = {Lucille Chapuis and Tzu-Hao Lin and Ben Williams and Timothy A. C. Lamont and Rucha Karkarey and Gabriela G. Nava-Martínez and Aya Maryam Rahil Naseem and Andrew N. Radford and Stephen D. Simpson},

doi = {10.3389/frsen.2025.1522641},

issn = {2673-6187},

year  = {2025},

date = {2025-12-18},

journal = {Front. Remote Sens.},

volume = {6},

publisher = {Frontiers Media SA},

abstract = {Coral reefs host diverse fish communities, many of which produce sounds. Passive acoustic monitoring (PAM) has become an essential tool for studying these ecosystems, yet the variability in fish calls across regions remains poorly understood. In this study, we analysed 144 h of underwater recordings collected from six coral reef locations around the world, automatically detecting more than 120,000 fish calls. Using Geometric Morphometrics Methods (GMM), Principal Component Analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP), we examined both the three-dimensional shape and spectro-temporal properties of these sounds. The GMM analysis revealed that fish calls showed remarkable acoustic similarity across geographical areas, with the first two principal components explaining 33% of the total variance. Typical fish calls consisted of short (<1 s), low-frequency sounds (∼500 Hz). The UMAP embedding, based on five key acoustic parameters, revealed a largely homogeneous distribution of fish calls across geographical locations. These results suggest that coral reef fish calls exhibit a level of global consistency, potentially reflecting the conserved structure of fish communities across different biogeographic realms. This study emphasises the potential of unknown fish call analyses as a non-invasive tool to explore fish diversity and assemblages, with future work required to extend these findings to other marine ecosystems and integrate automated species identification systems.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Robins2025b,

title = {The effects of anthropogenic sound on behaviour and physiology in female Port Jackson sharks Heterodontus portusjacksoni (Elasmobranchii)},

author = {H. Robins and C.C. Kerr and T.L. Dutka and J.A. Donald and A. Macdonald and S.P. Collin and L. Chapuis},

doi = {10.1016/j.marpolbul.2025.118525},

issn = {0025-326X},

year  = {2025},

date = {2025-12-00},

journal = {Marine Pollution Bulletin},

volume = {221},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Veneruso2025,

title = {Tidal flow masks acoustic detections of harbour porpoises (\textit{Phocoena phocoena}): Implications for passive acoustic studies of cetaceans},

author = {Gemma Veneruso and Lucille Chapuis and Gordon D. Hastie and Lewis Le Vay and Line S. Cordes},

doi = {10.1121/10.0039560},

issn = {1520-8524},

year  = {2025},

date = {2025-10-01},

volume = {158},

number = {4},

pages = {2883--2891},

publisher = {Acoustical Society of America (ASA)},

abstract = {Passive acoustics is widely used to detect vocalising cetaceans, yet in tidal environments, strong currents facilitate sediment transport, creating “flow noise” that may mask signals and bias detection ranges. Although detection ranges are known to vary with background noise, the magnitude and spatiotemporal scale of such variation in tidal environments remain poorly quantified. Flow noise may fluctuate within tidal cycles and across small spatial scales, with consequences for estimating cetacean occurrence. To examine this, we tested the effects of flow noise on harbour porpoise (Phocoena phocoena) echolocation click detection, from data collected from an array of moored recorders in a tidal stream environment. Flow noise overlapping with porpoise clicks varied by up to 29 dB in mean sound pressure levels within tidal cycles (∼12 h). Differences between sites <500 m apart were also significant, and modelled relationships between porpoise occurrence and tidal flow speed changed when a fixed detection threshold was applied. These findings show that flow noise in tidal habitats is heterogeneous across space and time, which may bias estimates of cetacean occurrence and distribution. Accounting for flow noise is therefore essential in ecological studies and is particularly relevant in environmental assessments of tidal energy developments.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chapuis2025,

title = {Motorboat sound in shallow waters and implications for mitigation},

author = {Lucille Chapuis and Michael A. Ainslie and Harry R. Harding and James Campbell and Andrew N. Radford and Stephen D. Simpson and Sophie L. Nedelec},

doi = {10.1121/10.0039578},

issn = {1520-8524},

year  = {2025},

date = {2025-10-01},

volume = {158},

number = {4},

pages = {3605--3618},

publisher = {Acoustical Society of America (ASA)},

abstract = {Small motorboats are a pervasive source of underwater noise pollution in many coastal regions of the world. The environmental impacts of motorboat noise include marine life disturbances and ecosystem disruptions. Mitigation strategies may involve speed restrictions in certain areas, on the assumption that slower speeds correspond to lower acoustic energy. We investigate the acoustic footprint of small motorboats navigating at different speeds in shallow water. Sound pressure and particle motion are characterized and the source levels estimated. We find that the acoustic energy (source level) associated with small motorboat noise may be higher at low speed than high speed. Our study therefore suggests that the vessel's optimal cruising speed should be considered while implementing speed limitation as a mitigation strategy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Williams2025b,

title = {Noise from deep-sea mining in the Clarion-Clipperton Zone, Pacific Ocean will impact a broad range of marine taxa},

author = {Rob Williams and Kieran D. Cox and Diva Amon and Erin Ashe and Lucille Chapuis and Christine Erbe and Asha de Vos and Kimberly A. Nielsen and Marena Salerno Collins and Craig Smith and Travis Washburn and Kirsten F. Young and Christopher W. Clark},

doi = {10.1016/j.marpolbul.2025.118135},

issn = {0025-326X},

year  = {2025},

date = {2025-09-00},

journal = {Marine Pollution Bulletin},

volume = {218},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Holmes2025,

title = {Structural and developmental insights into the muscles involved in lionfish (\textit{Pterois} spp.) vocalisations},

author = {Roxanne B. Holmes and Nadia M. Hamilton and Katharine E. Criswell and Keturah Z. Smithson and James E. Herbert‐Read and Lucille Chapuis},

doi = {10.1111/jfb.70183},

issn = {1095-8649},

year  = {2025},

date = {2025-08-28},

journal = {Journal of Fish Biology},

publisher = {Wiley},

abstract = {AbstractVocal signalling is an important mode of communication in fishes. The two species of lionfish in the Pterois complex, the Indo‐Pacific lionfish (Pterois volitans) and the red lionfish (Pterois miles), are both known to produce different types of sounds with sonic muscles attached to the swimbladder. However, the specific mechanism and the functions of these vocalisations in these invasive species are still unknown. We used three‐dimensional bioimaging to describe the anatomy of the sonic muscles of both species. We further quantified the muscles of P. volitans to specifically explore how muscles developed across ontogeny and to test the hypothesis that sonic muscles would show sexual dimorphism if they were a sexually selected trait. Both P. volitans and P. miles showed a physoclistous swimbladder with a bilaterally symmetric pair of extrinsic sonic swimbladder muscles (ESSMs), which have been suggested to control buoyancy and generate vocalisations. Both species also displayed an additional pair of anterior extrinsic muscles, which projected dorsoventrally from the spinal column and inserted onto the anterior wall of the swimbladder, potentially also having a role in sound production. Both types of sonic muscles were present across ontogeny. Quantification of the posterior belly of the ESSMs in P. volitans showed that both the length and mass of these muscles in both mature and immature individuals increased linearly with body size. There were no ontogenetic or sex differences in sonic muscle investment between individuals. Given the primary function of these muscles is to control the swimbladder for buoyancy, this may constrain the modification of these muscles relative to body size, or they may have no differences in their acoustic function between sexes or across ontogeny.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Robins2025,

title = {The inner ear of the Port Jackson shark, Heterodontus portusjacksoni: morphometric analysis using bioimaging and phalloidin staining},

author = {H. Robins and L. Chapuis and C.C. Kerr and T. Dutka and J. Donald and S.P. Collin},

doi = {10.1016/j.heares.2025.109368},

issn = {0378-5955},

year  = {2025},

date = {2025-07-00},

journal = {Hearing Research},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Williams2025c,

title = {Unlocking the soundscape of coral reefs with artificial intelligence: pretrained networks and unsupervised learning win out},

author = {Ben Williams and Santiago M. Balvanera and Sarab S. Sethi and Timothy A.C. Lamont and Jamaluddin Jompa and Mochyudho Prasetya and Laura Richardson and Lucille Chapuis and Emma Weschke and Andrew Hoey and Ricardo Beldade and Suzanne C. Mills and Anne Haguenauer and Frederic Zuberer and Stephen D. Simpson and David Curnick and Kate E. Jones},

editor = {Jason A. Papin},

doi = {10.1371/journal.pcbi.1013029},

issn = {1553-7358},

year  = {2025},

date = {2025-04-28},

journal = {PLoS Comput Biol},

volume = {21},

number = {4},

publisher = {Public Library of Science (PLoS)},

abstract = {Passive acoustic monitoring can offer insights into the state of coral reef ecosystems at low-costs and over extended temporal periods. Comparison of whole soundscape properties can rapidly deliver broad insights from acoustic data, in contrast to detailed but time-consuming analysis of individual bioacoustic events. However, a lack of effective automated analysis for whole soundscape data has impeded progress in this field. Here, we show that machine learning (ML) can be used to unlock greater insights from reef soundscapes. We showcase this on a diverse set of tasks using three biogeographically independent datasets, each containing fish community (high or low), coral cover (high or low) or depth zone (shallow or mesophotic) classes. We show supervised learning can be used to train models that can identify ecological classes and individual sites from whole soundscapes. However, we report unsupervised clustering achieves this whilst providing a more detailed understanding of ecological and site groupings within soundscape data. We also compare three different approaches for extracting feature embeddings from soundscape recordings for input into ML algorithms: acoustic indices commonly used by soundscape ecologists, a pretrained convolutional neural network (P-CNN) trained on 5.2 million hrs of YouTube audio, and CNN’s which were trained on each individual task (T-CNN). Although the T-CNN performs marginally better across tasks, we reveal that the P-CNN offers a powerful tool for generating insights from marine soundscape data as it requires orders of magnitude less computational resources whilst achieving near comparable performance to the T-CNN, with significant performance improvements over the acoustic indices. Our findings have implications for soundscape ecology in any habitat.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chapuis2024,

title = {Bioimaging marine crustacean brain: quantitative comparison of micro-CT preparations in an Alpheid snapping shrimp},

author = {Lucille Chapuis and Cara-Sophia Andres and Dane A. Gerneke and Craig A. Radford},

doi = {10.3389/fnins.2024.1428825},

issn = {1662-453X},

year  = {2024},

date = {2024-11-26},

journal = {Front. Neurosci.},

volume = {18},

publisher = {Frontiers Media SA},

abstract = {Non-invasive bioimaging techniques like X-ray micro-computed tomography (μCT), combined with contrast-enhancing techniques, allow the 3D visualization of the central nervous system in situ, without the destruction of the sample. However, quantitative comparisons of the most common fixation and contrast-enhancing protocols are rare, especially in marine invertebrates. Using the snapping shrimp (Alpheus richardsoni) as a model, we test three common fixation and staining agents combinations to prepare specimens prior to μCT scanning. The contrast ratios of the resulting images are then quantitatively compared. Our results show that a buffered iodine solution on a specimen fixed with 10% formalin offers the best nervous tissue discriminability. This optimal combination allows a semi-automated segmentation of the central nervous system organs from the μCT images. We thus provide general guidance for μCT applications, particularly suitable for marine crustaceans. Species-specific morphological adaptations can then be characterized and studied in the context of evolution and behavioral ecology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ryan2024,

title = {Counterillumination reduces bites by Great White sharks},

author = {Laura A. Ryan and Enrico Gennari and David J. Slip and Shaun P. Collin and Victor M. Peddemors and Charlie Huveneers and Lucille Chapuis and Jan M. Hemmi and Nathan S. Hart},

doi = {10.1016/j.cub.2024.10.042},

issn = {0960-9822},

year  = {2024},

date = {2024-11-00},

journal = {Current Biology},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Collin2024,

title = {Bioimaging of sense organs and the central nervous system in extant fishes and reptiles in situ: A review},

author = {Shaun P. Collin and Kara E. Yopak and Jenna M. Crowe‐Riddell and Victoria Camilieri‐Asch and Caroline C. Kerr and Hope Robins and Myoung Hoon Ha and Annalise Ceddia and Travis L. Dutka and Lucille Chapuis},

doi = {10.1002/ar.25566},

issn = {1932-8494},

year  = {2024},

date = {2024-09-02},

journal = {The Anatomical Record},

publisher = {Wiley},

abstract = {AbstractBioimaging is changing the field of sensory biology, especially for taxa that are lesser‐known, rare, and logistically difficult to source. When integrated with traditional neurobiological approaches, developing an archival, digital repository of morphological images can offer the opportunity to improve our understanding of whole neural systems without the issues of surgical intervention and negate the risk of damage and artefactual interpretation. This review focuses on current approaches to bioimaging the peripheral (sense organs) and central (brain) nervous systems in extant fishes (cartilaginous and bony) and non‐avian reptiles in situ. Magnetic resonance imaging (MRI), micro‐computed tomography (μCT), both super‐resolution track density imaging and diffusion tensor‐based imaging, and a range of other new technological advances are presented, together with novel approaches in optimizing both contrast and resolution, for developing detailed neuroanatomical atlases and enhancing comparative analyses of museum specimens. For MRI, tissue preparation, including choice of fixative, impacts tissue MR responses, where both resolving power and signal‐to‐noise ratio improve as field strength increases. Time in fixative, concentration of contrast agent, and duration of immersion in the contrast agent can also significantly affect relaxation times, and thus image quality. For μCT, the use of contrast‐enhancing stains (iodine‐, non‐iodine‐, or nanoparticle‐based) is critical, where the type of fixative used, and the concentration of stain and duration of staining time often require species‐specific optimization. Advanced reconstruction algorithms to reduce noise and artifacts and post‐processing techniques, such as deconvolution and filtering, are now being used to improve image quality and resolution.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Davidson2024,

title = {Context-dependent multimodal behaviour in a coral reef fish},

author = {Isla Keesje Davidson and Ben Williams and John E. Stratford and Lucille Chapuis and Stephen D. Simpson and Andrew N. Radford},

doi = {10.1098/rsos.240151},

issn = {2054-5703},

year  = {2024},

date = {2024-05-00},

journal = {R. Soc. Open Sci.},

volume = {11},

number = {5},

publisher = {The Royal Society},

abstract = {

            Animals are expected to respond flexibly to changing circumstances, with multimodal signalling providing potential plasticity in social interactions. While numerous studies have documented context-dependent behavioural trade-offs in terrestrial species, far less work has considered such decision-making in fish, especially in natural conditions. Coral reef ecosystems host 25% of all known marine species, making them hotbeds of competition and predation. We conducted experiments with wild Ambon damselfish (

            Pomacentrus amboinensis

            ) to investigate context-dependent responses to a conspecific intruder; specifically, how nest defence is influenced by an elevated predation risk. We found that nest-defending male Ambon damselfish responded aggressively to a conspecific intruder, spending less time sheltering and more time interacting, as well as signalling both visually and acoustically. In the presence of a model predator compared to a model herbivore, males spent less time interacting with the intruder, with a tendency towards reduced investment in visual displays compensated for by an increase in acoustic signalling instead. We therefore provide ecologically valid evidence that the context experienced by an individual can affect its behavioural responses and multimodal displays towards conspecific threats.

          },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chapuis2023,

title = {From the morphospace to the soundscape: Exploring the diversity and functional morphology of the fish inner ear, with a focus on elasmobranchs},

author = {L. Chapuis and K. E. Yopak and C. A. Radford},

doi = {10.1121/10.0020850},

issn = {0001-4966},

year  = {2023},

date = {2023-09-01},

volume = {154},

number = {3},

pages = {1526--1538},

publisher = {Acoustical Society of America (ASA)},

abstract = {Fishes, including elasmobranchs (sharks, rays, and skates), present an astonishing diversity in inner ear morphologies; however, the functional significance of these variations and how they confer auditory capacity is yet to be resolved. The relationship between inner ear structure and hearing performance is unclear, partly because most of the morphological and biomechanical mechanisms that underlie the hearing functions are complex and poorly known. Here, we present advanced opportunities to document discontinuities in the macroevolutionary trends of a complex biological form, like the inner ear, and test hypotheses regarding what factors may be driving morphological diversity. Three-dimensional (3D) bioimaging, geometric morphometrics, and finite element analysis are methods that can be combined to interrogate the structure-to-function links in elasmobranch fish inner ears. In addition, open-source 3D morphology datasets, advances in phylogenetic comparative methods, and methods for the analysis of highly multidimensional shape data have leveraged these opportunities. Questions that can be explored with this toolkit are identified, the different methods are justified, and remaining challenges are highlighted as avenues for future work.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1002/rse2.249,

title = {HydroMoth: Testing a prototype low-cost acoustic recorder for aquatic environments},

author = {Timothy A. C. Lamont and Lucille Chapuis and Ben Williams and Sasha Dines and Tess Gridley and Guilherme Frainer and Jack Fearey and Permas B. Maulana and Mochyudho E. Prasetya and Jamaluddin Jompa and David J. Smith and Stephen D. Simpson},

url = {https://zslpublications.onlinelibrary.wiley.com/doi/abs/10.1002/rse2.249},

doi = {https://doi.org/10.1002/rse2.249},

year  = {2022},

date = {2022-01-05},

journal = {Remote Sensing in Ecology and Conservation},

volume = {n/a},

number = {n/a},

abstract = {Abstract Passive acoustic monitoring (PAM) involves recording the sounds of animals and environments for research and conservation. PAM is used in a range of contexts across terrestrial, marine and freshwater environments. However, financial constraints limit applications within aquatic environments; these costs include the high cost of submersible acoustic recorders. We quantify this financial constraint using a systematic literature review of all ecoacoustic studies published in 2020, demonstrating that commercially available autonomous underwater recording units are, on average, five times more expensive than their terrestrial equivalents. This pattern is more extreme at the low end of the price range; the cheapest available aquatic autonomous units are over 40 times more expensive than their terrestrial counterparts. Following this, we test a prototype low-cost, low-specification aquatic recorder called the ‘HydroMoth’: this device is a modified version of a widely used terrestrial recorder (AudioMoth), altered to include a waterproof case and customisable gain settings suitable for a range of aquatic applications. We test the performance of the HydroMoth in both aquaria and field conditions, recording artificial and natural sounds, and comparing outputs with identical recordings taken with commercially available hydrophones. Although the signal-to-noise ratio and the recording quality of HydroMoths are lower than commercially available hydrophones, the recordings with HydroMoths still allow for the identification of different fish and marine mammal species, as well as the calculation of ecoacoustic indices for ecosystem monitoring. Finally, we outline the potential applications of low-cost, low-specification underwater sound recorders for bioacoustic studies, discuss their likely limitations, and present important considerations of which users should be aware. Several performance limitations and a lack of professional technical support mean that low-cost devices cannot meet the requirements of all PAM applications. Despite these limitations, however, HydroMoth facilitates underwater recording at a fraction of the price of existing hydrophones, creating exciting potential for diverse involvement in aquatic bioacoustics worldwide.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.1007/s11160-022-09698-8,

title = {The auditory system of cartilaginous fishes},

author = {Lucille Chapuis and Shaun P. Collin},

doi = {10.1007/s11160-022-09698-8},

issn = {0960-3166},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Reviews in Fish Biology and Fisheries},

pages = {1--34},

abstract = {Cartilaginous fishes (Chondrichthyes), including sharks, skates, rays, elephant fishes and chimaeras, have been in existence for over 400 million years and represent early stages of the evolution of extant jawed vertebrates. The sensory systems of cartilaginous fishes, including their hearing apparatus, have adapted to a diverse range of ecosystems, from the deep ocean to freshwater rivers, revealing high levels of morphological diversity. Since sound travels such long distances underwater, this environmental cue may represent an important signal in the behavior and survival of this group of fishes but there are still many gaps in our understanding of their hearing system. Based on current knowledge, cartilaginous fishes are most sensitive to low frequency sounds (< 1500 Hz) and there is abundant support that their inner ears use only particle displacement detection rather than the detection of sound pressure, but further studies are needed to corroborate the observations of long distance detection of sound sources that might be based on the detection of pressure oscillations. This review investigates the diversity and functional significance of the inner ear of chondrichthyans from a range of habitats and explores what is known about their hearing capabilities. How underwater sounds are processed by the central nervous system, the impacts of sound on acoustic ecology and behavior, and the potential effects of anthropogenic sound are also examined. Some suggestions for future work are presented to fill the large gaps in our knowledge of the hearing abilities of this important group of vertebrates.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1111/1365-2664.14089,

title = {The sound of recovery: Coral reef restoration success is detectable in the soundscape},

author = {Timothy A. C. Lamont and Ben Williams and Lucille Chapuis and Mochyudho E. Prasetya and Marie J. Seraphim and Harry R. Harding and Eleanor B. May and Noel Janetski and Jamaluddin Jompa and David J. Smith and Andrew N. Radford and Stephen D. Simpson},

url = {https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1365-2664.14089},

doi = {https://doi.org/10.1111/1365-2664.14089},

year  = {2022},

date = {2022-01-01},

journal = {Journal of Applied Ecology},

volume = {59},

number = {3},

pages = {742-756},

abstract = {Abstract Pantropical degradation of coral reefs is prompting considerable investment in their active restoration. However, current measures of restoration success are based largely on coral cover, which does not fully reflect ecosystem function or reef health. Soundscapes are an important aspect of reef health; loud and diverse soundscapes guide the recruitment of reef organisms, but this process is compromised when degradation denudes soundscapes. As such, acoustic recovery is a functionally important component of ecosystem recovery. Here, we use acoustic recordings taken at one of the world's largest coral reef restoration projects to test whether successful restoration of benthic and fish communities is accompanied by a restored soundscape. We analyse recordings taken simultaneously on healthy, degraded (extensive historic blast fishing) and restored reefs (restoration carried out for 1–3 years on previously degraded reefs). We compare soundscapes using manual counts of biotic sounds (phonic richness), and two commonly used computational analyses (acoustic complexity index [ACI] and sound-pressure level [SPL]). Healthy and restored reef soundscapes exhibited a similar diversity of biotic sounds (phonic richness), which was significantly higher than degraded reef soundscapes. This pattern was replicated in some automated analyses but not others; the ACI exhibited the same qualitative result as phonic richness in a low-frequency, but not a high-frequency bandwidth, and there was no significant difference between SPL values in either frequency bandwidth. Furthermore, the low-frequency ACI and phonic richness scores were only weakly correlated despite showing a qualitatively equivalent overall result, suggesting that these metrics are likely to be driven by different aspects of the reef soundscape. Synthesis and applications. These data show that coral restoration can lead to soundscape recovery, demonstrating the return of an important ecosystem function. They also suggest that passive acoustic monitoring (PAM) might provide functionally important measures of ecosystem-level recovery—but only some PAM metrics reflect ecological status, and those that did are likely to be driven by different communities of soniferous animals. Recording soundscapes represents a potentially valuable tool for evaluating restoration success across ecosystems, but caution must be exercised when choosing metrics and interpreting results.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{WILLIAMS2022108986,

title = {Enhancing automated analysis of marine soundscapes using ecoacoustic indices and machine learning},

author = {Ben Williams and Timothy A. C. Lamont and Lucille Chapuis and Harry R. Harding and Eleanor B. May and Mochyudho E. Prasetya and Marie J. Seraphim and Jamaluddin Jompa and David J. Smith and Noel Janetski and Andrew N. Radford and Stephen D. Simpson},

url = {https://www.sciencedirect.com/science/article/pii/S1470160X22004575},

doi = {https://doi.org/10.1016/j.ecolind.2022.108986},

issn = {1470-160X},

year  = {2022},

date = {2022-01-01},

journal = {Ecological Indicators},

volume = {140},

pages = {108986},

abstract = {Historically, ecological monitoring of marine habitats has primarily relied on labour-intensive, non-automated survey methods. The field of passive acoustic monitoring (PAM) has demonstrated the potential of this practice to automate surveying in marine habitats. This has primarily been through the use of ‘ecoacoustic indices’ to quantify attributes from natural soundscapes. However, investigations using individual indices have had mixed success. Using PAM recordings collected at one of the world’s largest coral reef restoration programmes, we instead apply a machine-learning approach across a suite of ecoacoustic indices to improve predictive power of ecosystem health. Healthy and degraded reef sites were identified through live coral cover surveys, with 90–95% and 0–20% cover respectively. A library of one-minute recordings were extracted from each. Twelve ecoacoustic indices were calculated for each recording, in up to three different frequency bandwidths (low: 0.05–0.8 kHz, medium: 2–7 kHz and broad: 0.05–20 kHz). Twelve of these 33 index-frequency combinations differed significantly between healthy and degraded habitats. However, the best performing single index could only correctly classify 47% of recordings, requiring extensive sampling from each site to be useful. We therefore trained a regularised discriminant analysis machine-learning algorithm to discriminate between healthy and degraded sites using an optimised combination of ecoacoustic indices. This multi-index approach discriminated between these two habitat classes with improved accuracy compared to any single index in isolation. The pooled classification rate of 1000 cross-validated iterations of the model had a 91.7% 0.8, mean SE) success rate at correctly classifying individual recordings. The model was subsequently used to classify recordings from two actively restored sites, established >24 months prior to recordings, with coral cover values of 79.1% (±3.9) and 66.5% (±3.8). Of these recordings, 37/38 and 33/39 received a classification as healthy respectively. The model was also used to classify recordings from a newly restored site established <12 months prior with a coral cover of 25.6% (±2.6), from which 27/33 recordings were classified as degraded. This investigation highlights the value of combining PAM recordings with machine-learning analysis for ecological monitoring and demonstrates the potential of PAM to monitor reef recovery over time, reducing the reliance on labour-intensive in-water surveys by experts. As access to PAM recorders continues to rapidly advance, effective automated analysis will be needed to keep pace with these expanding acoustic datasets.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ryan2021,

title = {A shark's eye view: testing the ‘mistaken identity theory’ behind shark bites on humans},

author = {Laura A. Ryan and David J. Slip and Lucille Chapuis and Shaun P. Collin and Enrico Gennari and Jan M. Hemmi and Martin J. How and Charlie Huveneers and Victor M. Peddemors and Louise Tosetto and Nathan S. Hart},

doi = {10.1098/rsif.2021.0533},

issn = {1742-5662},

year  = {2021},

date = {2021-10-00},

journal = {J. R. Soc. Interface.},

volume = {18},

number = {183},

publisher = {The Royal Society},

abstract = {Shark bites on humans are rare but are sufficiently frequent to generate substantial public concern, which typically leads to measures to reduce their frequency. Unfortunately, we understand little about why sharks bite humans. One theory for bites occurring at the surface, e.g. on surfers, is that of mistaken identity, whereby sharks mistake humans for their typical prey (pinnipeds in the case of white sharks). This study tests the mistaken identity theory by comparing video footage of pinnipeds, humans swimming and humans paddling surfboards, from the perspective of a white shark viewing these objects from below. Videos were processed to reflect how a shark's retina would detect the visual motion and shape cues. Motion cues of humans swimming, humans paddling surfboards and pinnipeds swimming did not differ significantly. The shape of paddled surfboards and human swimmers was also similar to that of pinnipeds with their flippers abducted. The difference in shape between pinnipeds with abducted versus adducted flippers was bigger than between pinnipeds with flippers abducted and surfboards or human swimmers. From the perspective of a white shark, therefore, neither visual motion nor shape cues allow an unequivocal visual distinction between pinnipeds and humans, supporting the mistaken identity theory behind some bites.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Duarte_2021,

title = {The soundscape of the Anthropocene ocean},

author = {Carlos M. Duarte and Lucille Chapuis and Shaun P. Collin and Daniel P. Costa and Reny P. Devassy and Victor M. Eguiluz and Christine Erbe and Timothy A. C. Gordon and Benjamin S. Halpern and Harry R. Harding and Michelle N. Havlik and Mark Meekan and Nathan D. Merchant and Jennifer L. Miksis-Olds and Miles Parsons and Milica Predragovic and Andrew N. Radford and Craig A. Radford and Stephen D. Simpson and Hans Slabbekoorn and Erica Staaterman and Ilse C. Van Opzeeland and Jana Winderen and Xiangliang Zhang and Francis Juanes},

url = {https://doi.org/10.1126%2Fscience.aba4658},

doi = {10.1126/science.aba4658},

year  = {2021},

date = {2021-02-04},

journal = {Science},

volume = {371},

number = {6529},

pages = {eaba4658},

abstract = {BACKGROUND

Sound is the sensory cue that travels farthest through the ocean and is used by marine animals, ranging from invertebrates to great whales, to interpret and explore the marine environment and to interact within and among species. Ocean soundscapes are rapidly changing because of massive declines in the abundance of sound-producing animals, increases in anthropogenic noise, and altered contributions of geophysical sources, such as sea ice and storms, owing to climate change. As a result, the soundscape of the Anthropocene ocean is fundamentally different from that of preindustrial times, with anthropogenic noise negatively impacting marine life.



ADVANCES

We find evidence that anthropogenic noise negatively affects marine animals. Strong evidence for such impacts is available for marine mammals, and some studies also find impacts for fishes and invertebrates, marine birds, and reptiles. Noise from vessels, active sonar, synthetic sounds (artificial tones and white noise), and acoustic deterrent devices are all found to affect marine animals, as are noise from energy and construction infrastructure and seismic surveys. Although there is clear evidence that noise compromises hearing ability and induces physiological and behavioral changes in marine animals, there is lower confidence that anthropogenic noise increases the mortality of marine animals and the settlement of their larvae.



OUTLOOK

Anthropogenic noise is a stressor for marine animals. Thus, we call for it to be included in assessments of cumulative pressures on marine ecosystems. Compared with other stressors that are persistent in the environment, such as carbon dioxide emitted to the atmosphere or persistent organic pollutants delivered to marine ecosystems, anthropogenic noise is typically a point-source pollutant, the effects of which decline swiftly once sources are removed. The evidence summarized here encourages national and international policies to become more ambitious in regulating and deploying existing technological solutions to mitigate marine noise and improve the human stewardship of ocean soundscapes to maintain a healthy ocean. We provide a range of solutions that may help, supported by appropriate managerial and policy frameworks that may help to mitigate impacts on marine animals derived from anthropogenic noise and perturbations of soundscapes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{CHAPUIS2021107957,

title = {Low-cost action cameras offer potential for widespread acoustic monitoring of marine ecosystems},

author = {Lucille Chapuis and Ben Williams and Timothy A C Gordon and Stephen D Simpson},

url = {https://www.sciencedirect.com/science/article/pii/S1470160X21006221},

doi = {https://doi.org/10.1016/j.ecolind.2021.107957},

issn = {1470-160X},

year  = {2021},

date = {2021-01-01},

journal = {Ecological Indicators},

volume = {129},

pages = {107957},

abstract = {Underwater passive acoustic monitoring (PAM) is of growing importance for monitoring the health of aquatic environments. Standard practices use expensive hydrophones to sample soundscapes. They must either be linked to surface recording rigs or use autonomous instrumentation which comes at a premium cost. Although citizen science projects could be of great value to PAM by increasing the number of underwater recordings collected around the world, there is a lack of available low-cost and user-friendly recording hardware. However, consumer-grade action cameras potentially offer an accessible alternative to traditional hydrophones, capable of capturing underwater acoustic recordings. We evaluated the performance of two models of GoPro underwater action cameras deployed as PAM recorders. We tested these cameras against a research-grade hydrophone in a range of shallow tropical sea environments. First, in a sandy area away from reef habitat, we took simultaneous recordings of loudspeaker playbacks of known acoustic signals using all three instruments. We then performed repeated deployments on different coral reef sites in which all three instruments were placed side-by-side to record simultaneously the same natural reef soundscapes. We calculated eight of the most commonly used ecoacoustic indices used in marine soundscape ecology, and assessed the reliability and quantitative accuracy of these compared to the hydrophone. Although not calibrated, GoPros captured recordings from which selected ecoacoustic indices could be calculated reliably, including temporal variability, the acoustic complexity index and acoustic richness. Metrics derived from GoPros can be valuably compared between recordings taken using the same model, but are not directly comparable with hydrophone-derived values. We outline the best settings for collecting soundscape data with GoPros. Underwater action cameras are used frequently by marine scientists, sports enthusiasts and tourists around the world. Their capacity to capture soundscape recordings represents a valuable approach for the global expansion of PAM through citizen science.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{mccloskey2020assessing,

title = {Assessing and mitigating impacts of motorboat noise on nesting damselfish},

author = {Kieran P McCloskey and Katherine E Chapman and Lucille Chapuis and Mark I McCormick and Andrew N Radford and Stephen D Simpson},

doi = {10.1016/j.envpol.2020.115376},

year  = {2020},

date = {2020-01-01},

journal = {Environmental Pollution},

volume = {266},

pages = {115376},

publisher = {Elsevier},

abstract = {Motorboats are a pervasive, growing source of anthropogenic noise in marine environments, with known impacts on fish physiology and behaviour. However, empirical evidence for the disruption of parental care remains scarce and stems predominantly from playback studies. Additionally, there is a paucity of experimental studies examining noise-mitigation strategies. We conducted two field experiments to investigate the effects of noise from real motorboats on the parental-care behaviours of a common coral-reef fish, the Ambon damselfish Pomacentrus amboinensis, which exhibits male-only egg care. When exposed to motorboat noise, we found that males exhibited vigilance behaviour 34% more often and spent 17% more time remaining vigilant, compared to an ambient-sound control. We then investigated nest defence in the presence of an introduced conspecific male intruder, incorporating a third noise treatment of altered motorboat-driving practice that was designed to mitigate noise exposure via speed and distance limitations. The males spent 22% less time interacting with the intruder and 154% more time sheltering during normal motorboat exposure compared to the ambient-sound control, with nest-defence levels in the mitigation treatment equivalent to those in ambient conditions. Our results reveal detrimental impacts of real motorboat noise on some aspects of parental care in fish, and successfully demonstrate the positive effects of an affordable, easily implemented mitigation strategy. We strongly advocate the integration of mitigation strategies into future experiments in this field, and the application of evidence-based policy in our increasingly noisy world.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{camilieri2020volumetric,

title = {Volumetric analysis and morphological assessment of the ascending olfactory pathway in an elasmobranch and a teleost using diceCT},

author = {Victoria Camilieri-Asch and Jeremy A Shaw and Kara E Yopak and Lucille Chapuis and Julian C Partridge and Shaun P Collin},

doi = {10.1007/s00429-020-02127-1},

year  = {2020},

date = {2020-01-01},

journal = {Brain Structure and Function},

pages = {1-29},

publisher = {Springer Berlin Heidelberg},

abstract = {The size (volume or mass) of the olfactory bulbs in relation to the whole brain has been used as a neuroanatomical proxy for olfactory capability in a range of vertebrates, including fishes. Here, we use diffusible iodine-based contrast-enhanced computed tomography (diceCT) to test the value of this novel bioimaging technique for generating accurate measurements of the relative volume of the main olfactory brain areas (olfactory bulbs, peduncles, and telencephalon) and to describe the morphological organisation of the ascending olfactory pathway in model fish species from two taxa, the brownbanded bamboo shark Chiloscyllium punctatum and the common goldfish Carassius auratus. We also describe the arrangement of primary projections to the olfactory bulb and secondary projections to the telencephalon in both species. Our results identified substantially larger olfactory bulbs and telencephalon in C. punctatum compared to C. auratus (comprising approximately 5.2% vs. 1.8%, and 51.8% vs. 11.8% of the total brain volume, respectively), reflecting differences between taxa, but also possibly in the role of olfaction in the sensory ecology of these species. We identified segregated primary projections to the bulbs, associated with a compartmentalised olfactory bulb in C. punctatum, which supports previous findings in elasmobranch fishes. DiceCT imaging has been crucial for visualising differences in the morphological organisation of the olfactory system of both model species. We consider comparative neuroanatomical studies between representative species of both elasmobranch and teleost fish groups are fundamental to further our understanding of the evolution of the olfactory system in early vertebrates and the neural basis of olfactory abilities.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{egeberg2019not,

title = {Not all electric shark deterrents are made equal: Effects of a commercial electric anklet deterrent on white shark behaviour},

author = {Channing A Egeberg and Ryan M Kempster and Nathan S Hart and Laura Ryan and Lucille Chapuis and Caroline C Kerr and Carl Schmidt and Enrico Gennari and Kara E Yopak and Shaun P Collin},

doi = {10.1371/journal.pone.0212851},

year  = {2019},

date = {2019-01-01},

journal = {PLoS one},

volume = {14},

number = {3},

pages = {e0212851},

publisher = {Public Library of Science San Francisco, CA USA},

abstract = {Personal shark deterrents offer the potential of a non-lethal solution to protect individuals from negative interactions with sharks, but the claims of effectiveness of most deterrents are based on theory rather than robust testing of the devices themselves. Therefore, there is a clear need for thorough testing of commercially available shark deterrents to provide the public with information on their effectiveness. Using a modified stereo-camera system, we quantified behavioural interactions between Carcharodon carcharias (white sharks) and a baited target in the presence of a commercially available electric anklet shark deterrent, the Electronic Shark Defense System (ESDS). The stereo-camera system enabled accurate assessment of the behavioural responses of C. carcharias when approaching an ESDS. We found that the ESDS had limited meaningful effect on the behaviour of C. carcharias, with no significant reduction in the proportion of sharks interacting with the bait in the presence of the active device. At close proximity (< 15.5 cm), the active ESDS did show a significant reduction in the number of sharks biting the bait, but this was countered by an increase in other, less aggressive, interactions. The ESDS discharged at a frequency of 7.8 Hz every 5.1 s for 2.5 s, followed by an inactive interval of 2.6 s. As a result, many sharks may have encountered the device in its inactive state, resulting in a reduced behavioural response. Consequently, decreasing the inactive interval between pulses may improve the overall effectiveness of the device, but this would not improve the effective deterrent range of the device, which is primarily a factor of the voltage gradient rather than the stimulus frequency. In conclusion, given the very short effective range of the ESDS and its unreliable deterrent effect, combined with the fact that shark-bite incidents are very rare, it is unlikely that the current device would significantly reduce the risk of a negative interaction with C. carcharias.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chapuis2019effect,

title = {The effect of underwater sounds on shark behaviour},

author = {Lucille Chapuis and Shaun P Collin and Kara E Yopak and Robert D McCauley and Ryan M Kempster and Laura A Ryan and Carl Schmidt and Caroline C Kerr and Enrico Gennari and Channing A Egeberg and others},

doi = {10.1038/s41598-019-43078-w},

year  = {2019},

date = {2019-01-01},

journal = {Scientific reports},

volume = {9},

number = {1},

pages = {1--11},

publisher = {Nature Publishing Group},

abstract = {The effect of sound on the behaviour of sharks has not been investigated since the 1970s. Sound is, however, an important sensory stimulus underwater, as it can spread in all directions quickly and propagate further than any other sensory cue. We used a baited underwater camera rig to record the behavioural responses of eight species of sharks (seven reef and coastal shark species and the white shark, Carcharodon carcharias) to the playback of two distinct sound stimuli in the wild: an orca call sequence and an artificially generated sound. When sounds were playing, reef and coastal sharks were less numerous in the area, were responsible for fewer interactions with the baited test rigs, and displayed less ‘inquisitive’ behaviour, compared to during silent control trials. White sharks spent less time around the baited camera rig when the artificial sound was presented, but showed no significant difference in behaviour in response to orca calls. The use of the presented acoustic stimuli alone is not an effective deterrent for C. carcharias. The behavioural response of reef sharks to sound raises concern about the effects of anthropogenic noise on these taxa.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chapuis2019underwater,

title = {Underwater hearing in sea snakes (Hydrophiinae): first evidence of auditory evoked potential thresholds},

author = {Lucille Chapuis and Caroline C Kerr and Shaun P Collin and Nathan S Hart and Kate L Sanders},

doi = {10.1242/jeb.198184},

year  = {2019},

date = {2019-01-01},

journal = {Journal of Experimental Biology},

volume = {222},

number = {14},

pages = {jeb198184},

publisher = {The Company of Biologists Ltd},

abstract = {The viviparous sea snakes (Hydrophiinae) are a secondarily aquatic radiation of more than 60 species that possess many phenotypic adaptations to marine life. However, virtually nothing is known of the role and sensitivity of hearing in sea snakes. This study investigated the hearing sensitivity of the fully marine sea snake Hydrophis stokesii by measuring auditory evoked potential (AEP) audiograms for two individuals. AEPs were recorded from 40 Hz (the lowest frequency tested) up to 600 Hz, with a peak in sensitivity identified at 60 Hz (163.5 dB re. 1 µPa or 123 dB re. 1 µm s−2). Our data suggest that sea snakes are sensitive to low-frequency sounds but have relatively low sensitivity compared with bony fishes and marine turtles. Additional studies are required to understand the role of sound in sea snake life history and further assess these species' vulnerability to anthropogenic noise.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{crowe2019ultrastructural,

title = {Ultrastructural evidence of a mechanosensory function of scale organs (sensilla) in sea snakes (Hydrophiinae)},

author = {Jenna M Crowe-Riddell and Ruth Williams and Lucille Chapuis and Kate L Sanders},

doi = {10.1098/rsos.182022},

year  = {2019},

date = {2019-01-01},

journal = {Royal Society open science},

volume = {6},

number = {4},

pages = {182022},

publisher = {The Royal Society},

abstract = {The evolution of epidermal scales was a major innovation in lepidosaurs, providing a barrier to dehydration and physical stress, while functioning as a sensitive interface for detecting mechanical stimuli in the environment. In snakes, mechanoreception involves tiny scale organs (sensilla) that are concentrated on the surface of the head. The fully marine sea snakes (Hydrophiinae) are closely related to terrestrial hydrophiine snakes but have substantially more protruding (dome-shaped) scale organs that often cover a larger portion of the scale surface. Various divergent selection pressures in the marine environment could account for this morphological variation relating to detection of mechanical stimuli from direct contact with stimuli and/or indirect contact via water motion (i.e. ‘hydrodynamic reception’), or co-option for alternate sensory or non-sensory functions. We addressed these hypotheses using immunohistochemistry, and light and electron microscopy, to describe the cells and nerve connections underlying scale organs in two sea snakes, Aipysurus laevis and Hydrophis stokesii. Our results show ultrastructural features in the cephalic scale organs of both marine species that closely resemble the mechanosensitive Meissner-like corpuscles that underlie terrestrial snake scale organs. We conclude that the scale organs of marine hydrophiines have retained a mechanosensory function, but future studies are needed to examine whether they are sensitive to hydrodynamic stimuli.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ryan2018effects,

title = {Effects of auditory and visual stimuli on shark feeding behaviour: the disco effect},

author = {Laura A Ryan and Lucille Chapuis and Jan M Hemmi and Shaun P Collin and Robert D McCauley and Kara E Yopak and Enrico Gennari and Charlie Huveneers and Ryan M Kempster and Caroline C Kerr and others},

doi = {10.1007/s00227-017-3256-0},

year  = {2018},

date = {2018-01-01},

journal = {Marine biology},

volume = {165},

number = {1},

pages = {11},

publisher = {Springer Berlin Heidelberg},

abstract = {Sensory systems play a central role in guiding animal behaviour. They can be manipulated to alter behavioural outcomes to limit negative interactions between humans and animals. Sharks are often seen as a threat to humans and there has been increasing interest in developing shark mitigation devices. Previous research has concentrated on stimulating the electrosensory and olfactory systems of sharks, whereas the influence of light and sound on their behaviour has received little attention. In this study, the effects of an intense strobe light and a loud, artificial sound composed of mixed frequencies and intensities on shark behaviour were assessed. We tested these stimuli individually and in combination on wild-caught captive Port Jackson (Heterodontus portusjacksoni) and epaulette (Hemiscyllium ocellatum) sharks in aquaria and on wild great white sharks (Carcharodon carcharias) in the field. When presented alone and in combination with sound, the lights reduced the number of times that the bait was taken by both H. portusjacksoni and H. ocellatum in captivity. The strobe light alone, however, did not affect the behaviour of white sharks, but when presented in combination with sound, white sharks spent significantly less time in proximity to the bait. As the lights and sound presented in this study did not show a pronounced deterrent effect on C. carcharias, we do not advise their use as a strategy for mitigating shark–human interactions. However, due to the potential effectiveness of strobe lights in deterring other species of sharks, there may be applications for this approach in the reduction of fisheries bycatch.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kelley2018sensory,

title = {Sensory system responses to human-induced environmental change},

author = {Jennifer L Kelley and Lucille Chapuis and Wayne IL Davies and Shaun P Collin},

doi = {10.3389/fevo.2018.00095},

year  = {2018},

date = {2018-01-01},

journal = {Frontiers in Ecology and Evolution},

volume = {6},

pages = {95},

publisher = {Frontiers},

abstract = {Sensory input to the central nervous system is the primary means by which animals respond to variation in their physical and biological environments. It is well established that key threats such as habitat destruction, the introduction of non-native species, and climate change are imposing significant pressures on natural ecosystems, yet surprisingly few studies have examined how these threats impact the senses or determine species' responses to environmental change. This review focuses on how anthropogenic impacts on aquatic ecosystems can have a detrimental effect on the sensory systems of aquatic organisms and how these modalities can act to influence genetic and non-genetic (e.g., developmental) responses to environmental change, which in turn can cause knock-on effects in a range of other biological systems. Species often exhibit unique sensory specializations that are suited to their behavioral requirements; at present it is unclear whether and how sensory systems have the capacity to respond to environmental change through genetic adaptation and/or sensory plasticity, and on what timescale this might occur. Sensory systems lie at the forefront of how various species respond to environmental perturbation. As such, determining the important role they play in determining fitness is critical for understanding the effects of external processes such as habitat degradation and climate change. Given the current consensus that human impacts and environmental changes are potentially highly detrimental to the delicate balance of the biome, knowing how organisms respond, and to what degree adaptation is physiologically and behaviorally limited, warrants urgent attention.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kempster2016close,

title = {How close is too close? The effect of a non-lethal electric shark deterrent on white shark behaviour},

author = {Ryan M Kempster and Channing A Egeberg and Nathan S Hart and Laura Ryan and Lucille Chapuis and Caroline C Kerr and Carl Schmidt and Charlie Huveneers and Enrico Gennari and Kara E Yopak and others},

doi = {10.1371/journal.pone.0157717},

year  = {2016},

date = {2016-01-01},

journal = {PLoS One},

volume = {11},

number = {7},

pages = {e0157717},

publisher = {Public Library of Science San Francisco, CA USA},

abstract = {Sharks play a vital role in the health of marine ecosystems, but the potential threat that sharks pose to humans is a reminder of our vulnerability when entering the ocean. Personal shark deterrents are being marketed as the solution to mitigate the threat that sharks pose. However, the effectiveness claims of many personal deterrents are based on our knowledge of shark sensory biology rather than robust testing of the devices themselves, as most have not been subjected to independent scientific studies. Therefore, there is a clear need for thorough testing of commercially available shark deterrents to provide the public with recommendations of their effectiveness. Using a modified stereo-camera system, we quantified behavioural interactions between white sharks (Carcharodon carcharias) and a baited target in the presence of a commercially available, personal electric shark deterrent (Shark Shield Freedom7™). The stereo-camera system enabled an accurate assessment of the behavioural responses of C. carcharias when encountering a non-lethal electric field many times stronger than what they would naturally experience. Upon their first observed encounter, all C. carcharias were repelled at a mean (± std. error) proximity of 131 (± 10.3) cm, which corresponded to a mean voltage gradient of 9.7 (± 0.9) V/m. With each subsequent encounter, their proximity decreased by an average of 11.6 cm, which corresponded to an increase in tolerance to the electric field by an average of 2.6 (± 0.5) V/m per encounter. Despite the increase in tolerance, sharks continued to be deterred from interacting for the duration of each trial when in the presence of an active Shark Shield™. Furthermore, the findings provide no support to the theory that electric deterrents attract sharks. The results of this study provide quantitative evidence of the effectiveness of a non-lethal electric shark deterrent, its influence on the behaviour of C. carcharias, and an accurate method for testing other shark deterrent technologies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{zottl2013strategic,

title = {Strategic reduction of help before dispersal in a cooperative breeder},

author = {Markus Zöttl and Lucille Chapuis and Manuel Freiburghaus and Michael Taborsky},

doi = {10.1098/rsbl.2012.0878},

year  = {2013},

date = {2013-01-01},

journal = {Biology Letters},

volume = {9},

number = {1},

pages = {20120878},

publisher = {The Royal Society},

abstract = {In cooperative breeders, sexually mature subordinates can either queue for chances to inherit the breeding position in their natal group, or disperse to reproduce independently. The choice of one or the other option may be flexible, as when individuals respond to attractive dispersal options, or they may reflect fixed life-history trajectories. Here, we show in a permanently marked, natural population of the cooperatively breeding cichlid fish Neolamprologus pulcher that subordinate helpers reduce investment in territory defence shortly before dispersing. Such reduction of effort is not shown by subordinates who stay and inherit the breeding position. This difference suggests that subordinates ready to leave reduce their investment in the natal territory strategically in favour of future life-history perspectives. It seems to be part of a conditional choice of the dispersal tactic, as this reduction in effort appears only shortly before dispersal, whereas philopatric and dispersing helpers do not differ in defence effort earlier in life. Hence, cooperative territory defence is state-dependent and plastic rather than a consistent part of a fixed life-history trajectory.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{letessier2013assessing,

title = {Assessing pelagic fish populations: The application of demersal video techniques to the mid-water environment},

author = {Tom B Letessier and Jessica J Meeuwig and Matthew Gollock and Lloyd Groves and Phil J Bouchet and Lucille Chapuis and Gabriel MS Vianna and Kirsty Kemp and Heather J Koldewey},

doi = {10.1016/j.mio.2013.11.003},

year  = {2013},

date = {2013-01-01},

journal = {Methods in Oceanography},

volume = {8},

pages = {41--55},

publisher = {Elsevier},

abstract = {In the open ocean, the movements and habitat use of large mobile predators are driven by dynamic interactions between biological and physical variables and complex predator–prey relationships. Understanding the spatial and temporal distributions of pelagic fishes and sharks is a critical component of conservation and fisheries management. Here, we report on a novel non-extractive method for the study of pelagic wildlife, based on baited stereo-camera rigs. The mid-water rigs were derived from existing methodology commonly used in demersal fish surveys. We present new data from 66 moored deployments in Shark Bay, Western Australia (26°10′S, 113°06E) in seabed depths of up to 60 m as a demonstration of the rigs’ ability to resolve spatial variability in pelagic fish and shark assemblages, and to make accurate stereo-measurements of animal lengths. We observed 248 pelagic fishes and sharks from 27 species and 10 families and were able to distinguish between assemblages based nominally on location. We make some general recommendations on optimal deployment protocols and sampling effort regimes, based upon species accumulation rates and times of MaxN (maximum number of individuals of a given species in a single video frame). Regression analyses between high quality and low quality stereo-measurements of fish fork-lengths and range were highly significant, indicating that body lengths and distance estimates were consistent even when stereo-measurements were deemed of low quality. Mid-water stereo-video camera rigs represent an efficient tool for the rapid and non-extractive monitoring of pelagic fish and shark populations, with particular relevance for application in no-take marine protected areas.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chapuis2010signalling,

title = {Signalling by the cleaner shrimp Periclimenes longicarpus},

author = {Lucille Chapuis and Redouan Bshary},

doi = {10.1016/j.anbehav.2009.12.012},

year  = {2010},

date = {2010-01-01},

journal = {Animal Behaviour},

volume = {79},

number = {3},

pages = {645--647},

publisher = {Academic Press},

abstract = {Signals increase the fitness of a sender by altering the behaviour of receivers. For cooperative interactions biological market theory proposes that signalling strength may be linked to supply and demand. In this context, a recent laboratory experiment demonstrated that cleaner shrimps may advertise their service to client reef fish and that the advertisement is linked to hunger levels. We investigated signalling by the cleaner shrimp Periclimenes longicarpus in the field to test more detailed predictions of biological market theory. Shrimps often clapped with their pair of claws in response to approaching clients. In line with both theory and the previous study, the probability of clapping increased when the shrimps had been food deprived and clapping shrimps were more likely to clean than nonclapping individuals. However, we found no evidence for the market theory prediction that signalling was targeted specifically to visiting client species with the option to choose other cleaning stations. Instead, shrimps signalled more frequently towards predatory clients than towards nonpredatory clients. We conclude that the signal does not serve primarily to attract the choosy clients but to convey information about identity as preconflict management to avoid predation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chapuis2009strategic,

title = {Strategic adjustment of service quality to client identity in the cleaner shrimp, Periclimenes longicarpus},

author = {Lucille Chapuis and Redouan Bshary},

doi = {10.1016/j.anbehav.2009.06.001},

year  = {2009},

date = {2009-01-01},

journal = {Animal Behaviour},

volume = {78},

number = {2},

pages = {455--459},

publisher = {Academic Press},

abstract = {Cleaning mutualism, in which cleaning organisms remove ectoparasites from cooperating ‘clients’, is widespread among marine animals. Until now, research has focused on fishes as cleaners, whereas cleaner shrimps have received little attention. The aim of this study was to investigate the cleaning behaviour of the cleaner shrimp, Periclimenes longicarpus, and to compare the results directly to data on the sympatric and well-studied cleaner wrasse, Labroides dimidiatus. We first compared the time spent cleaning and client diversity as indicators of the potential importance of the cleaner shrimp to client health and found strong similarities between shrimp and wrasse. We further looked at three correlates of service quality: duration of interactions, tactile stimulation of clients, and jolt rates as correlates of mucus feeding (=cheating). We specifically predicted that shrimps would cheat clients less frequently than the wrasses because they should be more vulnerable to aggressive responses by clients. Although the results partly support our hypothesis, they also suggest that both species strategically adjust cheating rates according to risk, as predatory clients jolted less frequently than nonpredatory clients. In conclusion, the results suggest that the shrimps play an important role in client health but that nonpredatory clients have to control the shrimps' behaviour to receive a good service.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{schwander2008maternal,

title = {Maternal effect on female caste determination in a social insect},

author = {Tanja Schwander and Jean-Yves Humbert and Colin S Brent and Sara Helms Cahan and Lucille Chapuis and Emanuela Renai and Laurent Keller},

doi = {10.1016/j.cub.2008.01.024},

year  = {2008},

date = {2008-01-01},

journal = {Current Biology},

volume = {18},

number = {4},

pages = {265--269},

publisher = {Cell Press},

abstract = {Caste differentiation and division of labor are the hallmarks of social insect colonies 1, 2. The current dogma for female caste differentiation is that female eggs are totipotent, with morphological and physiological differences between queens and workers stemming from a developmental switch during the larval stage controlled by nutritional and other environmental factors (e.g., 3, 4, 5, 6, 7, 8). In this study, we tested whether maternal effects influence caste differentiation in Pogonomyrmex harvester ants. By conducting crossfostering experiments we identified two key factors in the process of caste determination. New queens were produced only from eggs laid by queens exposed to cold. Moreover, there was a strong age effect, with development into queens occurring only in eggs laid by queens that were at least two years old. Biochemical analyses further revealed that the level of ecdysteroids was significantly lower in eggs developing into queens than workers. By contrast, we found no significant effect of colony size or worker exposure to cold, suggesting that the trigger for caste differentiation may be independent of the quantity and quality of resources provided to larvae. Altogether these data demonstrate that the developmental fate of female brood is strongly influenced by maternal effects in ants of the genus Pogonomyrmex.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}