Biology subjects

Elliott, K. H.

Publications and source records attributed to Elliott, K. H..

9 recordsLinked to original sources

bioRxiv2026

The BEAC, an epigenetic clock for birds

Epigenetic clocks are powerful tools for estimating both chronological and biological age, enabling the integration of age information into population monitoring, demographic modelling, and research on the ecophysiology and evolution of ageing. Most epigenetic clocks so far have been developed for mammals: here, we present the Bird Epigenetic Ageing Clock (BEAC) for estimating chronological age in avian species. BEAC was established based on genome-wide enzymatic methylation sequencing data of known-age king penguins (Aptenodytes patagonicus), and validated in nine other bird species. The BEAC collects age-informative signals into a bisulfite amplicon sequencing panel of 24 primer pairs, providing a highly accurate and cost-effective alternative to sequencing-intensive approaches. It achieved strong predictive performance in independent king penguin training (R{superscript 2}=0.88; MAE=1.7 years, n=78) and testing data (R{superscript 2}=0.79; MAE=2.3 years, n=41), with negligible batch effects, high longitudinal consistency, and resilience to reduced sample size or missing loci. Importantly, cross-species validation across 180 samples showed that BEAC reliably captures age-associated methylation signals in nine additional bird species across seven clades, demonstrating that a single set of loci can be predictive of ageing across multiple different bird species. BEAC offers a flexible, empirically validated tool and a transferable framework for developing epigenetic clocks in avian species, providing a highly valuable resource for eco-evolutionary studies of ageing in wild species.

molecular biology↗

bioRxiv2025

Including fitness and health proxies can alter our understanding of habitat selection

Habitat selection analyses, which discern the environmental conditions individuals select, often inform conservation planning. Through a literature review, we demonstrate that recent habitat selection studies rarely include fitness and health information. With a simulation study, we show that ignoring such information could support the protection of sink habitats. Our case studies demonstrate how health and fitness proxies can modify our understanding of habitat selection: (1) incorporating mass gain of thick-billed murres shows the energetic benefit of areas deemed secondary by a naive resource selection function; (2) including number of chicks in a step selection function (SSF) exposes the complex relationships glaucous-winged gulls have with landscapes impacted by humans; and (3) including external signs of trauma in the movement kernel of SSFs demonstrate others ways in which narwhal distribution can be altered. We urge movement ecologists to collect and use health and fitness data to improve ecological inference and conservation action.

ecology↗

bioRxiv2025

IRIS PIGMENTATION IRREGULARITIES FOLLOWING AN AVIAN INFLUENZA OUTBREAK: IMPLICATIONS FOR DISEASE SURVEILLANCE AND POPULATION MONITORING IN A COLONIAL SEABIRD

Emerging infectious diseases can have catastrophic impacts on wildlife populations, yet identifying individuals that survived exposure, especially when external symptoms are absent, remains challenging. Since 2021, a virulent strain of highly pathogenic avian influenza virus (HPAIV H5N1 clade 2.3.4.4b) has caused unprecedented mortality in wild birds across continents. Northern Gannets (Morus bassanus) are among the species that suffered significant population declines in Europe and North America. At North Americas largest gannet colony (Bonaventure Island) dramatic mortality and reproductive failure occurred in 2022. Following this event, researchers noted a subset of gannets displaying irregular iris pigmentation, raising the possibility that this visible change may indicate a lasting effect of infection. Here, we build on earlier observations linking irregular iris pigmentation to HPAIV exposure in gannets using anti-nucleoprotein (NP) and anti-hemagglutinin (H5) antibodies. This provides the first quantitative test of this relationship using serological data and field-based digital photography. Iris irregularities were strongly associated ({rho} = -0.72) with antibodies to NP, supporting the hypothesis that they can indicate past exposure. The likelihood of NP antibody detection increased with iris pigment irregularity--about 50% likelihood at 40% irregularity, 65% at 50%, 77% at 60%, and over 90% above 77% irregularity. Moderate correlations ({rho} = 0.30) were observed for H5 antibodies. Our findings provide quantitative support for the hypothesis that iris pigmentation irregularities may serve as a visible, non-invasive marker of past HPAIV exposure in gannets. If validated across colonies and years, iris assessment could offer a rapid tool for tracking population health and recovery following HPAIV outbreaks, enhancing conservation monitoring and disease surveillance. Lay SummaryOur research shows clear evidence that irregular iris pigmentation in Northern Gannets is strongly linked to past infection with a deadly bird flu strain. This visible marker could allow scientists to rapidly identify surviving birds and monitor population health after outbreaks, helping conservation efforts across affected colonies. HighlightsO_LIIris pigmentation irregularities reveal past avian influenza exposure. C_LIO_LIExtent of iris pigmentation irregularity correlates with antibody levels. C_LIO_LIExposure likelihood increases with degree of iris pigmentation irregularity. C_LIO_LICould provide a rapid, non-invasive tool for wildlife disease and conservation monitoring. C_LI Graphical abstracts O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/685885v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@12fa683org.highwire.dtl.DTLVardef@15d23b1org.highwire.dtl.DTLVardef@1d2425eorg.highwire.dtl.DTLVardef@10367cd_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2025

A dual role for GLI3 signaling in neural crest development

Neural crest cells (NCCs) are a multipotent cell population that undergo specification, epithelial-to-mesenchymal transition, migration, and differentiation into a plethora of cell types. A wealth of studies across various embryonic model systems have established dogma as to the molecular mechanisms and signaling cascades that contribute to NCC development. While Wnt, FGF, and BMP signaling pathways have well-established and essential roles in several aspects of NCC development, the Hedgehog (HH) signaling pathway has received limited attention for any specific role in this process. Herein, we propose two distinct, temporal roles for the transcription factor GLI3 in NCC development. Gli3, and other members of the HH pathway, were robustly co-expressed with established NCC induction and specification markers in chick, mouse, and human embryonic stem cell derived NCCs. Early knock-down of GLI3 reduced expression of key markers of NCC specification and conditional knock-out of Gli3 post-specification specifically impaired the ability of cranial NCCs to differentiate into ectomesenchymal derivatives. Together, these results demonstrate dual, novel roles for GLI3 in early NCC specification and later in cranial NCC differentiation. Summary StatementGLI3 plays distinct temporal roles in neural crest specification and differentiation into ectomesenchymal derivatives.

developmental biology↗

bioRxiv2023

Snow Buntings, an arctic cold-specialist passerine, risk overheating under intense activity even at low air temperatures

Birds maintain some of the highest body temperatures (Tb) among endothermic animals. Often deemed a selective advantage for heat tolerance, high Tb also limits the capacity to increase Tb before reaching lethal levels. Recent thermal modelling suggests that sustained effort in Arctic birds might be restricted at mild air temperatures (Ta) during energetically demanding life history stages, which may force reductions in activity to avoid overheating, with expected negative impacts on reproductive performance. Consequently, understanding how Arctic birds will cope with increasing Ta has become an urgent concern. We examined within-individual changes in Tb in response to an experimental increase in activity in outdoor captive Arctic cold-specialised snow buntings (Plectrophenax nivalis), exposed to naturally varying Ta from -15 to 36 {degrees}C. Calm buntings exhibited a modal Tb range from 39.9 - 42.6 {degrees}C. However, we detected a dramatic increase in Tb within minutes of shifting birds to active flight, with strong evidence for a positive effect of Ta on Tb (slope = 0.04 {degrees}C/{degrees}C). Importantly, by Ta of 9 {degrees}C, flying buntings were already generating Tb [≥] 45{degrees}C, approaching the upper thermal limits of organismal performance (i.e., Tb = 45 - 47 {degrees}C). Under scenarios of elevated Tb, buntings must increase rates of evaporative water loss and/or reduce activity to avoid overheating. With known limited evaporative heat dissipation capacities, we argue buntings operating at peak energy levels will increasingly rely on behavioral thermoregulatory strategies (i.e., reducing activity) to regulate Tb, at the potential detriment to nestling growth and survival.

ecology↗

bioRxiv2022

The role of wingbeat frequency and amplitude in flight power

Body-mounted accelerometers provide a new prospect for estimating power use in flying birds, as the signal varies with the two major kinematic determinants of aerodynamic power: wingbeat frequency and amplitude. Yet wingbeat frequency is sometimes used as a proxy for power output in isolation. There is therefore a need to understand which kinematic parameter birds vary and whether this is predicted by flight mode (e.g., accelerating, ascending/descending flight), speed or morphology. We investigate this using high-frequency acceleration data from (i) 14 species flying in the wild, (ii) two species flying in controlled conditions in a wind tunnel and (iii) a review of experimental and field studies. While wingbeat frequency and amplitude were positively correlated, R2 values were generally low, supporting the idea that parameters can vary independently. Indeed, birds were more likely to modulate wingbeat amplitude for more energy-demanding flight modes, including climbing and take-off. Nonetheless, the striking variability even within species and flight types, highlights the complexity of describing the kinematic relationships, which appear sensitive to both the biological and physical context. Notwithstanding this acceleration metrics that incorporate both kinematic parameters should be more robust proxies for power than wingbeat frequency alone.

biophysics↗

bioRxiv2021

Warming in the land of the midnight sun: breeding birds may suffer greater heat stress at high- vs low-Arctic sites

Rising global temperatures are expected to increase reproductive costs for wildlife as greater thermoregulatory demands interfere with essential breeding activities such as parental care. However, predicting the temperature threshold where reproductive performance is negatively impacted remains a significant hurdle. Using a novel thermoregulatory polygon approach, we predicted the threshold temperature at which an Arctic songbird-the snow bunting (Plectrophenax nivalis)-would need to reduce activity and perform below the 4-times basal metabolic rate (BMR) required to sustain nestling provisioning to avoid overheating. We then compared this threshold to operative temperatures recorded at high (82{degrees}N) and low (64{degrees}N) Arctic sites to estimate how heat constraints translate into site-specific impacts on sustained activity level. We predict buntings would become behaviourally constrained at operative temperatures above 11.7{degrees}C, whereupon they must reduce provisioning rates to maintain thermal balance. Low Arctic sites had larger fluctuations in solar radiation, producing consistent daily periods when operative temperatures exceeded 11.7{degrees}C. However, high-latitude birds faced entire, consecutive days where parents would not be able to sustain required provisioning rates. These data indicate that Arctic warming is likely already disrupting the breeding performance of cold-specialist birds, but also suggests counterintuitive and severe negative impacts of warming at high-latitude breeding locations.

ecology↗

bioRxiv2021

Ecological inference using data from accelerometers needs careful protocols

O_LIAccelerometers in animal-attached tags have proven to be powerful tools in behavioural ecology, being used to determine behaviour and provide proxies for movement-based energy expenditure. Researchers are collecting and archiving data across systems, seasons and device types. However, in order to use data repositories to draw ecological inference, we need to establish the error introduced according to sensor type and position on the study animal and establish protocols for error assessment and minimization. C_LIO_LIUsing laboratory trials, we examine the absolute accuracy of tri-axial accelerometers and determine how inaccuracies impact measurements of dynamic body acceleration (DBA), as the main acceleration-based proxy for energy expenditure. We then examine how tag type and placement affect the acceleration signal in birds using (i) pigeons Columba livia flying in a wind tunnel, with tags mounted simultaneously in two positions, (ii) back- and tail-mounted tags deployed on wild kittiwakes Rissa tridactyla. Finally, we (iii) present a case study where two generations of tag were deployed using different attachment procedures on red-tailed tropicbirds Phaethon rubricauda foraging in different seasons. C_LIO_LIBench tests showed that individual acceleration axes required a two-level correction (representing up to 4.3% of the total value) to eliminate measurement error. This resulted in DBA differences of up to 5% between calibrated and uncalibrated tags for humans walking at different speeds. Device position was associated with greater variation in DBA, with upper- and lower back-mounted tags in pigeons varying by 9%, and tail- and back-mounted tags varying by 13% in kittiwakes. Finally, DBA varied by 25% in tropicbirds between seasons, which may be attributable to tag attachment procedures. C_LIO_LIAccelerometer accuracy, tag placement, and attachment details critically affect the signal amplitude and thereby the ability of the system to detect biologically meaningful phenomena. We propose a simple method to calibrate accelerometers that should be used prior to deployments and archived with resulting data, suggest a way that researchers can assess accuracy in previously collected data, and caution that variable tag placement and attachment can increase sensor noise and even generate trends that have no biological meaning. C_LI

animal behavior and cognition↗

bioRxiv2020

Gli3 utilizes Hand2 to synergistically regulate tissue-specific transcriptional networks

Despite a common understanding that Gli TFs are utilized to reiterate a Hh morphogen gradient, genetic analyses suggest craniofacial development does not completely fit this paradigm. We demonstrated that rather than being driven by a Hh threshold, robust Gli3 transcriptional activity during skeletal and glossal development required interaction with the bHLH TF Hand2. Not only did genetic and expression data support a co-factorial relationship, but genomic analysis further revealed that Gli3 and Hand2 were enriched at regulatory elements for genes essential for mandibular patterning and development. Interestingly, motif analysis at sites co-occupied by Gli3 and Hand2 uncovered mandibular-specific, low-affinity, divergent Gli binding motifs (dGBMs). Functional validation revealed these dGBMs conveyed synergistic activation of Gli targets essential for mandibular patterning and development. In summary, this work elucidates a novel, sequence-dependent mechanism for Gli transcriptional activity within the craniofacial complex that is independent of a graded Hh signal.

developmental biology↗