Biology subjects

Cheney, K. L.

Publications and source records attributed to Cheney, K. L..

8 recordsLinked to original sources

bioRxiv2026

From deployment to functioning ecosystems: assessing taxonomic richness and community composition on modular shellfish reefs using environmental DNA metabarcoding

Ecological restoration success is commonly assessed against historical reference states that are often altered, poorly defined, or absent, particularly in marine systems. Reliance on taxon richness alone can further obscure changes in community structure, successional trajectories, and the emergence of functionally important taxa at restoration sites. We assessed biodiversity recovery on modular shellfish reef structures using environmental DNA (eDNA) metabarcoding, combining taxon-specific richness models with multivariate community composition analyses across a four-year age gradient (9, 21, and 42 months). Genus richness increased rapidly following reef deployment but differed strongly among taxon groups. Dominant groups, particularly Mollusca, showed similar richness in nine-month-old and 42-month-old reefs; crustaceans and fishes also showed high, consistent richness early in development. Five of nine taxon groups displayed significant richness changes through time, with increasing (flatworms and macroalgae) and decreasing (cnidarians, sponges, and roundworms) trajectories. Community composition showed pronounced age-related structuring: younger reefs were compositionally distinct from older reefs, and within-age variability declined markedly with age, consistent with convergent successional assembly. Trait-based patterns indicated shifts towards non-benthic crustaceans, larger-bodied fish, and free-living flatworms in older reefs. These results show that modular shellfish structures are rapidly colonised by a wide taxonomic range within 9 months, producing early richness gains. However, the identity and relative representation of those taxa continue to change, generating structured compositional shifts undetectable from richness alone. Integrated richness-composition frameworks focused on ecological trajectories provide a more robust basis for evaluating restoration success than strict reference states. Environmental DNA metabarcoding offers a scalable, non-invasive monitoring approach capable of capturing both early richness gains and longer-term community assembly dynamics in data-limited marine systems.

ecology↗

bioRxiv2023

Automated workflows using Quantitative Colour Pattern Analysis (QCPA): A guide to batch processing and downstream data analysis

Animal and plant colouration presents a striking dimension of phenotypic variation, the study of which has driven general advances in ecology, evolution, and animal behaviour. Quantitative Colour Pattern Analysis (QCPA) is a dynamic framework for analysing colour patterns through the eyes of non-human observers. However, its extensive array of user-defined image processing and analysis tools means image analysis is often time-consuming. This hinders the full use of analytical power provided by QCPA and its application to large datasets. Here, we offer a robust and comprehensive batch script, allowing users to automate many QCPA workflows. We further provide a set of useful R scripts for downstream data extraction and analysis. These scripts will empower users to exploit the full analytical power of QCPA and facilitate the development of customised semi-automated workflows. Such quantitatively scaled workflows are crucial for exploring colour pattern space and developing ever-richer frameworks for analysing organismal colouration accounting for the visual perception in animals other than humans. These advances will, in turn, facilitate testing hypotheses on the function and evolution of vision and signals at quantitative and qualitative scales, which are otherwise computationally unfeasible.

animal behavior and cognition↗

bioRxiv2023

Colour patterns are less variable in highly unpalatable nudibranchs

The selective factors that shape phenotypic diversity in prey communities with aposematic animals are diverse and coincide with similar diversity in the strength of underlying secondary defences. However, quantitative assessments of colour pattern variation and the strength of chemical defences in assemblages of aposematic species are lacking. We quantified colour pattern diversity using Quantitative Colour Pattern Analysis (QCPA) in 13 Dorid nudibranch species (Infraorder: Doridoidei) that varied in the strength of their chemical defences. We accounted for the physiological properties of a potential predators visual system (a triggerfish, Rhinecanthus aculeatus) and modelled the appearance of nudibranchs from multiple viewing distances (2cm and 10cm). We identified distinct colour pattern properties associated with the presence and strength of chemical defences. Colour patterns were also less variable among species with chemical defences when compared to undefended species. This confirms correlations between secondary defences and diverse, bold colouration while showing that chemical defences coincide with decreased colour pattern variability among species. Our study suggests that complex spatiochromatic properties of colour patterns perceived by potential predators can be used to make inferences on the presence and strength of chemical defences.

animal behavior and cognition↗

bioRxiv2022

Signal detectability and boldness are not the same: the function of defensive colouration in nudibranchs is distant-dependent

Aposematic signals advertise underlying defences in many species. They should be detectable (highly contrasting against the background) and bold (high internal pattern contrast) to enhance predator recognition, learning and memorisation. However, the signalling function of aposematic colour patterns may be distance-dependent: signals may be undetectable from a distance to reduce costs of increased attacks from naive predators but bold when viewed up close. To test this hypothesis, we quantified the chromatic and achromatic detectability and boldness of colour patterns in 13 nudibranch species that varied in the strength of their chemical defences, in terms of unpalatability and toxicity, using Quantitative Colour Pattern Analysis (QCPA) and data on the visual perception of a triggerfish (Rhinecanthus aculeatus). When viewed from larger distances, there were no differences in detectability and boldness between well-defended and undefended species. However, when viewed at close distances, well-defended species were more detectable and bolder than undefended species. The detectability of defended species decreased more significantly with increased viewing distances compared to boldness but remained relatively consistent over viewing distances for undefended species. We provide evidence for distance-dependent signalling in aposematic nudibranchs and highlight the importance of distinguishing between signal detectability and boldness in studies of aposematism.

ecology↗

bioRxiv2022

Anemonefish have finer color discrimination in the ultraviolet

In many animals, ultraviolet (UV) vision guides navigation, foraging, and communication, but few studies have addressed the contribution of UV vision to color discrimination, or behaviorally assessed UV discrimination thresholds. Here, we tested UV-color vision in an anemonefish (Amphiprion ocellaris) using a novel five-channel (RGB-V-UV) LED display designed to test UV perception. We first determined that the maximal sensitivity of the A. ocellaris UV cone was at [~]386 nm using microspectrophotometry. Three additional cone spectral sensitivities had maxima at [~]497, 515, and [~]535 nm, which together informed the modelling of the fishs color vision. Anemonefish behavioral discrimination thresholds for nine sets of colors were determined from their ability to distinguish a colored target pixel from grey distractor pixels of varying intensity. We found that A. ocellaris used all four cones to process color information and is therefore tetrachromatic, and fish were better at discriminating colors (i.e., color discrimination thresholds were lower, or more acute) when targets had UV chromatic contrast elicited by greater stimulation of the UV cone relative to other cone types. These findings imply that a UV component of color signals and cues improves their detectability, that likely increases the salience of anemonefish body patterns used in communication and the silhouette of zooplankton prey.

animal behavior and cognition↗

bioRxiv2020

More than noise: context-dependant luminance contrast discrimination in a coral reef fish (Rhinecanthus aculeatus)

Achromatic (luminance) vision is used by animals to perceive motion, pattern, space and texture. Luminance contrast sensitivity thresholds are often poorly characterised for individual species and are applied across a diverse range of perceptual contexts using over-simplified assumptions of an animal’s visual system. Such thresholds are often estimated using the Receptor Noise Limited model (RNL) using quantum catch values and estimated noise levels of photoreceptors. However, the suitability of the RNL model to describe luminance contrast perception remains poorly tested.Here, we investigated context-dependent luminance discrimination using triggerfish (Rhinecanthus aculeatus) presented with large achromatic stimuli (spots) against uniform achromatic backgrounds of varying absolute and relative contrasts. ‘Dark’ and ‘bright’ spots were presented against relatively dark and bright backgrounds. We found significant differences in luminance discrimination thresholds across treatments. When measured using Michelson contrast, thresholds for bright spots on a bright background were significantly higher than for other scenarios, and the lowest threshold was found when dark spots were presented on dark backgrounds. Thresholds expressed in Weber contrast revealed increased contrast sensitivity for stimuli darker than their backgrounds, which is consistent with the literature. The RNL model was unable to estimate threshold scaling across scenarios as predicted by the Weber-Fechner law, highlighting limitations in the current use of the RNL model to quantify luminance contrast perception. Our study confirms that luminance contrast discrimination thresholds are context-dependent and should therefore be interpreted with caution.Competing Interest StatementThe authors have declared no competing interest.View Full Text

animal behavior and cognition↗

bioRxiv2019

Quantitative Colour Pattern Analysis (QCPA): A Comprehensive Framework for the Analysis of Colour Patterns in Nature

O_LITo understand the function of colour signals in nature, we require robust quantitative analytical frameworks to enable us to estimate how animal and plant colour patterns appear against their natural background as viewed by ecologically relevant species. Due to the quantitative limitations of existing methods, colour and pattern are rarely analysed in conjunction with one another, despite a large body of literature and decades of research on the importance of spatiochromatic colour pattern analyses. Furthermore, key physiological limitations of animal visual systems such as spatial acuity, spectral sensitivities, photoreceptor abundances and receptor noise levels are rarely considered together in colour pattern analyses.\nC_LIO_LIHere, we present a novel analytical framework, called the Quantitative Colour Pattern Analysis (QCPA). We have overcome many quantitative and qualitative limitations of existing colour pattern analyses by combining calibrated digital photography and visual modelling. We have integrated and updated existing spatiochromatic colour pattern analyses, including adjacency, visual contrast and boundary strength analysis, to be implemented using calibrated digital photography through the Multispectral Image Analysis and Calibration (MICA) Toolbox.\nC_LIO_LIThis combination of calibrated photography and spatiochromatic colour pattern analyses is enabled by the inclusion of psychophysical colour and luminance discrimination thresholds for image segmentation, which we call Receptor Noise Limited Clustering, used here for the first time. Furthermore, QCPA provides a novel psycho-physiological approach to the modelling of spatial acuity using convolution in the spatial or frequency domains, followed by Receptor Noise Limited Ranked Filtering to eliminate intermediate edge artefacts and recover sharp boundaries following smoothing. We also present a new type of colour pattern analysis, the Local Edge Intensity Analysis (LEIA) as well as a range of novel psycho-physiological approaches to the visualisation of spatiochromatic data.\nC_LIO_LIQCPA combines novel and existing pattern analysis frameworks into what we hope is a unified, user-friendly, free and open source toolbox and introduce a range of novel analytical and data-visualisation approaches. These analyses and tools have been seamlessly integrated into the MICA toolbox providing a dynamic and user-friendly workflow.\nC_LIO_LIQCPA is a framework for the empirical investigation of key theories underlying the design, function and evolution of colour patterns in nature. We believe that it is compatible with, but more thorough than, other existing colour pattern analyses.\nC_LI

animal behavior and cognition↗

bioRxiv2018

An Ishihara-style test of animal colour vision

O_LIColour vision mediates ecologically relevant tasks for many animals, such as mate choice, foraging and predator avoidance. However, our understanding of animal colour perception is largely derived from human psychophysics, even though animal visual systems differ from our own. Behavioural tests of non-human animals are required to understand how colour signals are perceived by them.\nC_LIO_LIHere we introduce a novel test of colour vision in animals inspired by the Ishihara colour charts, which are widely used to identify human colour deficiencies. These charts consist of dots that vary in colour, brightness and size, and are designed so that a numeral or letter is distinguishable from distractor dots for humans with normal colour vision. In our method, distractor dots have a fixed chromaticity (hue and saturation) but vary in luminance. Animals can be trained to find single target dots that differ from distractor dots in chromaticity. We provide Matlab code for creating these stimuli, which can be modified for use with different animals.\nC_LIO_LIWe demonstrate the success of this method with triggerfish, Rhinecanthus aculeatus, and highlight behavioural parameters that can be measured, including success of finding the target dot, time to detect dot and error rate. Triggerfish quickly learnt to select target dots that differed from distractors dots regardless of the particular hue or saturation, and proved to use acute colour vision. We measured discrimination thresholds by testing the detection of target colours that were of increasing colour distances ({Delta}S) from distractor dots in different directions of colour space. At least for some colours, thresholds indicated better discrimination than expected from the Receptor Noise Limited (RNL) model assuming 5% Weber fraction for the long-wavelength cone.\nC_LIO_LIThis methodology seems to be highly effective because it resembles natural foraging behavior for the triggerfish and may well be adaptable to a range of other animals, including mammals, birds, bees and freshwater fish. Other questions may be addressed using this methodology, including luminance thresholds, sensory bias, effects of sensory noise in detection tasks, colour categorization and saliency.\nC_LI

animal behavior and cognition↗