Biology subjects

Brown, T. M.

Publications and source records attributed to Brown, T. M..

13 recordsLinked to original sources

bioRxiv2026

Artificial light at night and concealment level affect detection probability of stranded seabirds: a study with 3D-printed puffin decoys

Fledglings of burrow-nesting seabirds are vulnerable to disorientation by artificial light at night (ALAN) and grounding in coastal human settlements, where most individuals presumably perish if not rescued. Accurate estimates of the effects of stranding on seabird populations remain elusive due to several levels of uncertainty, such as the number of stranded seabirds estimated to remain undiscovered by rescuers. One species subjected to stranding is the Atlantic puffin (Fratercula arctica). We hypothesized that the detection probability of puffin fledglings by the Puffin Patrol rescue program, operating in Newfoundland, Canada, is affected by light level, concealment level, and search effort. We deployed realistic puffin decoys in locations of varying light and concealment levels throughout two sites that are searched nightly by rescuers and measured the amount of time and search effort required until each decoy was found. Approximately 78% more search effort was required to find a decoy in darkness (32.0 min) compared with illuminated conditions (18.0 min), and up to 100% more search effort was required to find a decoy placed in concealed conditions (35.5 min) than one in the open (17.5 min). After two hours of searching, on average over 10% of decoys were still not found, although each additional minute of search effort increased detection rate of an individual decoy by 0.6%. In combination with recent advances in our knowledge of seabird post-stranding behaviour, our study offers a first step in the development of correction factors which can be adapted to site- and species-specific requirements of other rescue programs around the world that rely on volunteers to search for stranded birds. Application of such correction factors will hopefully result in better estimation of mortality rates and their resultant effects on populations.

zoology↗

bioRxiv2026

Parallel visual processing in the suprachiasmatic region of a diurnal mammal.

Light shapes mammalian physiology and behaviour through hypothalamic pathways, yet how these pathways process visual information in day-active species remains poorly understood. Based largely on work in nocturnal rodents, the suprachiasmatic nucleus (SCN) is classically viewed as a retinal target that encodes ambient illumination for circadian entrainment. We combine anatomical tracing, light-evoked c-Fos mapping and high-density silicon-probe electrophysiology to define visual processing in the suprachiasmatic region of the diurnal murid Rhabdomys pumilio. We find that retinal input and light-evoked activity extend beyond the SCN into rostral and lateral peri-SCN hypothalamus. Within the SCN, neurons encode irradiance with graded changes in maintained firing broadly similar to those observed in parallel recordings of nocturnal Mus domesticus. Across the wider suprachiasmatic region, Rhabdomys neurons show selectivity for more dynamic visual stimuli, including luminance transitions, contrast and temporal structure. Unsupervised clustering identifies five functionally distinct hypothalamic visual response classes with different anatomical distributions. These findings reveal an expanded hypothalamic visual network in a diurnal mammal, placing SCN irradiance coding within a broader system for processing dynamic visual features.

neuroscience↗

bioRxiv2026

Loss of Adaptive Capacity Drives Climate Vulnerability Across Taxonomic Scales in an Alpine Specialist Species Complex

Accelerated warming at high elevations is having a disproportionate impact on alpine species. While assessments of climate vulnerability require quantifying the ecological and evolutionary components of adaptive capacity, such assessments are rare, especially in alpine systems. We leverage recent advances in population and landscape genomics to assess how variation in spatial heterogeneity and population connectivity across alpine systems influences adaptive capacity, using the North American Rosy-Finch species complex as a model system. In doing so, we clarify taxonomic relationships across the complex and identify one new ESU, the Sierra Nevada Rosy-Finch, based on its combined ecological and evolutionary distinctiveness. We then illustrate how combining genomic analyses with ecological data can improve estimates of adaptive capacity, sensitivity, and exposure and ultimately clarify climate vulnerability. Overall, our integrative analyses revealed that more isolated lineages, such as the Sierra Nevada Rosy-Finch, have lower adaptive capacity and face disproportionately high risks from climate change. This work highlights how conservation strategies that account for the multidimensional aspects of adaptive capacity can improve estimates of climate vulnerability.

evolutionary biology↗

bioRxiv2026

Co-limitation by stable, dynamic and directional habitat features shapes climate vulnerability in an alpine specialist

Alpine ecosystems are among the most climate sensitive on Earth, yet logistical challenges and detection biases often impede robust assessment of alpine dependent species. We investigated habitat associations and density patterns of the Sierra Nevada subspecies of the Gray-crowned Rosy-Finch (Leucosticte tephrocotis dawsoni), an alpine obligate and regional endemic, over five breeding seasons from 2018 to 2022 using hierarchical distance sampling and mark-recapture distance sampling to explicitly account for imperfect detection and spatial heterogeneity. Density estimates tracked annual snowpack variation, ranging from 4.77 individuals/km{superscript 2} in a low snow year to 12.08 individuals/km{superscript 2} in a high snow year. Abundance was highest near persistent snow patches that provide foraging habitat and near cliffs that provide nesting substrate, and declined sharply above approximately 10% woody cover, with densities approaching zero beyond approximately 25%, indicating a steep ecological threshold. In contrast, the proportion of surveyed blocks with detections remained relatively stable across years. Together, these patterns indicate a three timescale co-limitation framework in which breeding habitat is shaped by static features (cliffs), dynamic annual drivers (snowpack), and longer-term directional change (woody encroachment). By linking population density to climate sensitive habitat features, this study provides a high-resolution abundance-based baseline for long term monitoring and offers a framework for evaluating climate vulnerability in alpine and other resource-limited systems. Open Research StatementData necessary to replicate the analyses and results presented in this manuscript will be archived in the Dryad Digital Repository upon acceptance, with no embargo on the material. The R code associated with this manuscript is not novel. All analyses use publicly available packages and functions without modification, including mrds (v2.3.0), unmarked (v1.2.5), tidyverse (v2.0.0), MuMIn (v1.47.5), and standard ggplot2 visualization tools. All code is properly cited within the manuscript and publicly available through CRAN. Complete analysis scripts will be archived in Dryad alongside the data upon acceptance to facilitate full reproducibility of results.

ecology↗

bioRxiv2026

Identifying adaptive variation in spatially structured populations using low-coverage whole-genome sequencing data

Successful implementation of evolutionary programs to rescue climatically threatened species requires identification of adaptive variation. Although many genotype-environment association methods have been successful in identifying adaptive variation, current approaches can be improved in two important aspects. First, most existing methods do not account for genotype uncertainty in widely available low-coverage whole-genome sequencing data. Researchers often restrict analysis to loci for which genotypes can be inferred reliably or call the most probable genotype, allowing the use of genotype-based methods. However, discarding data and false genotype calls increase the uncertainty in estimates of genetic variation and can introduce systematic biases. Second, most methods use phenomenological approaches, such as logistic regression, to partition estimated variation into adaptive and non-adaptive components. Consequently, current approaches may fail to account for evolutionary processes, such as migration-selection balance. Structured migration between climatically disparate locations can produce deviations from a smooth S-shape response curve, which can be difficult to accommodate using generalized linear models. To overcome these challenges, we developed a method that accounts for genotype uncertainty in sequencing data and propagates this uncertainty to inform the parameters of an evolutionary model. A key feature of this model is that it describes mechanistically how genetic variation arises from joint interactions between local adaptation, structured migration, mutation, and drift. Our synthetic simulation tests reveal that accounting for genotype uncertainty and structured migration substantially reduces false negatives. We also applied our approach to analyze data on North American rosy-finches (3.7 million SNPs), a high-alpine, climatically threatened clade of bird species.

genomics↗

bioRxiv2024

Under Cover of Darkness: Refuge from Artificial Light at Night may Mitigate Risks to Stranded Seabirds

Artificial light at night is an anthropogenic pollutant that has wide-ranging effects on wildlife. Fledgling seabirds of the order Procellariiformes exhibit phototaxis toward artificial lights on their first flights from the nest, causing them to become grounded in human settlements where they are subject to increased risk of predation. Limited evidence suggests that certain light types may be less attractive than others, yet there is also evidence for an aversion to light under certain circumstances. We investigated differences in phototactic behaviour, activity level, and shelter-seeking behaviour of grounded Hydrobates leucorhous (Leachs storm-petrel) fledglings exposed to artificial light in three experiments: a Y-maze choice experiment, an open field test, and a modified open field test with a hide box provided ("Safe Haven test"). When provided with combinations of different light types in the Y-maze, storm-petrels typically remained stationary in the darkest part of the apparatus and exhibited no response toward one light type over another. This was consistent with results from the open field test, in which individuals were less active in darkness than when exposed to two out of three light conditions (Warm White Light-Emitting Diode and High Pressure Sodium). More than half of birds entered the hide box in light conditions, compared to none in the dark. Considered together, our results indicate Leachs storm-petrel fledglings exhibit photophobic behaviour after stranding, which may be part of a behavioural strategy to avoid predation. Further, we demonstrate the utility of providing hide boxes to protect stranded seabird fledglings in locations where lighting cannot be eliminated or where rescue efforts may be limited in spatial or temporal coverage. However, hide boxes would have limited utility in dark locations. Hide boxes constitute a novel mitigation measure that merits future testing for its ability to reduce stranding-induced mortality, especially in imperiled procellariiform species. LAY SUMMARYO_LIGlobally, fledglings of many seabird species become stranded in towns and at industrial sites near their breeding colonies C_LIO_LIStrandings are thought to be caused by attraction to lights, although some species appear to avoid light C_LIO_LIWe tested behavioural responses and activity levels of Leachs storm-petrel fledglings toward several different light types C_LIO_LIWhen presented with different types of light in a choice experiment, most birds remained stationary C_LIO_LIFledglings were more active in warm-hued lights than in darkness C_LIO_LIBirds sought shelter when it was provided in light conditions, but not when provided in darkness C_LIO_LIOur results suggest that rescue programs targeting Leachs storm-petrels should include searches in dark, hidden locations where fledglings are likely to hide, and support the use of small shelters to protect stranded seabirds when lights cannot be turned off C_LI

animal behavior and cognition↗

bioRxiv2024

Navigating the Night: Effects of Artificial Light on the Behaviour of Atlantic Puffin Fledglings

Every year in Newfoundland, young Atlantic Puffins (Fratercula arctica) departing their nests at night for the first time become stranded in towns near their breeding colonies, a phenomenon thought to be caused by attraction toward artificial light. To test this hypothesis, we conducted three behavioural experiments. First, we illuminated beaches near a breeding colony to determine whether more fledglings would become stranded in illuminated versus dark conditions. Next, we conducted a Y-maze experiment to test stranded fledglings for phototactic behaviour in general and for preferences among High Pressure Sodium (HPS), Warm White Light-Emitting Diode (LED), Cool White LED, Blue LED, and Orange LED light. Lastly, we quantified activity levels of stranded fledglings in an open field test during exposure to several different light types. We found significantly more fledglings stranded when beaches were illuminated, and fledglings significantly preferred light over darkness in the Y-maze, supporting our hypothesis that Atlantic Puffin fledglings become stranded due to light attraction. Fledglings displayed no preferences for certain light types over others in the Y-maze, potentially suggesting that strandings in this species may not be mitigable by changing the streetlight type in stranding-prone towns. Interestingly, fledglings exhibited higher activity levels in darkness and HPS light than in LED light, potentially holding implications for rescue, rehabilitation, and husbandry programs. Overall, our findings demonstrate that the only evidence-based strategy for the reduction of Atlantic Puffin strandings remains to be the reduction of coastal artificial lighting; however, further research is needed to determine if aspects of artificial light besides bulb type may be altered to effectively reduce light attraction in this species.

animal behavior and cognition↗

bioRxiv2023

Beyond Lux: Methods for Species and Photoreceptor-Specific Quantification of Ambient Light for Mammals

BackgroundLight is a key environmental regulator of physiology and behaviour. Mistimed or insufficient light disrupts circadian rhythms and is associated with impaired health and well-being across mammals. Appropriate lighting is therefore crucial for indoor housed mammals. The most commonly used measurement for lighting is lux. However, this employs a spectral weighting function based on human perceived brightness and is not suitable for non-visual effects of light or use across species. In humans, a photoreceptor-specific (-opic) metrology system has been proposed as a more appropriate way of measuring light. ResultsHere we establish technology to allow this -opic measurement approach to be readily extended to any mammalian species, accounting for differences in photoreceptor types, photopigment spectral sensitivities, and eye anatomy. Since measuring photopigment spectral sensitivity can be hard to derive for novel animals and photoreceptors, we developed a high-throughput, easy-to-use, method to derive spectral sensitivities for recombinantly expressed melanopsins and use it to establish the spectral sensitivity of melanopsin from 12 non-human mammals. We further address the need for simple measurement strategies for species-specific -opic measures by developing an accessible online toolbox for calculating these units and validating an open hardware, low-cost, multichannel light sensor for point and click measurement. We finally demonstrate that species-specific -opic measurements are superior to photopic lux as predictors of physiological responses to light in mice and allow ecologically relevant comparisons of photosensitivity between species. ConclusionOur study demonstrates that measuring light more accurately using species-specific -opic units is superior to the existing unit of photopic lux and holds the promise of improvements to the health and welfare of animals, scientific research reproducibility, agricultural productivity, and energy usage.

neuroscience↗

bioRxiv2023

A FRET-based excitatory luminopsin with improved efficacy of bioluminescence-driven activation

SignificanceBioluminescent optogenetics (BL-OG) offers a unique and powerful approach to manipulate neural activity both opto- and chemogenetically using a single actuator molecule (a LuMinOpsin, LMO). AimTo further enhance the utility of BL-OG by improving the efficacy of chemogenetic (bioluminescence- driven) LMO activation. ApproachWe developed novel luciferases optimized for Forster resonance energy transfer (FRET) when fused to the fluorescent protein mNeonGreen, generating bright bioluminescent (BL) emitters spectrally tuned to Volvox Channelrhodopsin 1 (VChR1). ResultsA new LMO generated from this approach (LMO7) showed significantly stronger BL-driven opsin activation compared to previous and other new variants. We extensively benchmarked LMO7 against LMO3 (current standard), and found significantly stronger neuronal activity modulation ex vivo and in vivo, and efficient modulation of behavior. ConclusionsWe report a robust new option for achieving multiple modes of control in a single actuator, and a promising engineering strategy for continued improvement of BL-OG.

neuroscience↗

bioRxiv2020

Daily electrical activity in the master circadian clock of a diurnal mammal

Daily or circadian rhythms in mammals are orchestrated by a master circadian clock within the hypothalamic suprachiasmatic nuclei (SCN). Here, cell-autonomous oscillations in gene expression, intrinsic membrane properties, and synaptic communication shape the electrical landscape of the SCN across the circadian day, rendering SCN neurons overtly more active during the day than at night. This well-accepted hallmark bioelectrical feature of the SCN has overwhelmingly emerged from studies performed on a small number of nocturnal rodent species. Therefore, for the first time, we investigate the spontaneous and evoked electrical activity of SCN neurons in a diurnal mammal. To this end, we measured the electrical activity of individual SCN neurons during the day and at night in brain slices prepared from the diurnal murid rodent Rhabdomys pumilio and then developed cutting-edge data assimilation and mathematical modelling approaches to uncover the underlying ionic mechanisms. We find that R. pumilio SCN neurons were more excited in the day than at night, recapitulating the prototypical pattern of SCN neuronal activity previously observed in nocturnal rodents. By contrast, the evoked activity of R. pumilio neurons included a prominent suppressive response that is not present in the SCN of nocturnal rodents. Our computational modelling approaches reveal transient subthreshold A-type potassium channels as the primary determinant of the suppressive response and highlight a key role for this ionic mechanism in tuning excitability of clock neurons and optimising SCN function to accommodate R. pumilios diurnal niche.

neuroscience↗

bioRxiv2020

Daytime light enhances the amplitude of circadian output in a diurnal mammal

Mammalian circadian rhythms are orchestrated by a master pacemaker in the hypothalamic suprachiasmatic nuclei (SCN), which receives information about the 24 h light:dark cycle from the retina. The accepted function of this light signal is to reset circadian phase in order to ensure appropriate synchronisation with the celestial day. Here, we ask whether light also impacts another key property of the circadian oscillation, its amplitude. To this end, we measured rhythms in behavioural activity and body temperature, and SCN electrophysiological activity in the diurnal murid rodent Rhabdomys pumilio following stable entrainment to 12:12 light:dark cycles at 4 different daytime intensities (ranging from 12.77 to 14.80 log melanopsin effective photons/cm2/s). Rhabdomys showed strongly diurnal activity and body temperature rhythms in all conditions, but measures of rhythm robustness were positively correlated with daytime irradiance under both entrainment and subsequent free run. Whole-cell and extracellular recordings of electrophysiological activity in ex vivo SCN revealed substantial differences in electrophysiological activity between dim and bright light conditions. At lower daytime irradiance, daytime peaks in SCN spontaneous firing rate and membrane depolarisation were substantially depressed, leading to an overall marked reduction in the amplitude of circadian rhythms in spontaneous activity. Our data reveal a previously unappreciated impact of daytime light intensity on SCN physiology and the amplitude of circadian rhythms, and highlight the potential importance of daytime light exposure for circadian health.

neuroscience↗

bioRxiv2020

Infra-slow modulation of fast beta/gamma oscillations in the mouse visual system.

Infra-slow (<0.02 Hz) and fast beta/gamma (20 - 100 Hz) oscillations in neurophysiological activity have been widely found in the subcortical visual system. While it is well established that fast beta/gamma oscillations are involved in visual processing, the role (if any) of infra-slow oscillations is currently unknown. One possibility is that infra-slow oscillations exert influence by modulating the amplitude of fast oscillations, yet the extent to which these different oscillations arise independently and interact remains unknown. We addressed these questions by recording in vivo spontaneous activity from subcortical visual system of visually intact mice, and animals whose retinal network was disrupted by advanced rod/cone degeneration (rd/rd cl) or melanopsin loss (Opn4-/- We found many neurons expressing only one type of oscillation, and indeed fast oscillations were absent in rd/rd cl. Conversely, neurons co-expressing the two oscillations were also common, and were encountered more often than expected by chance in visually intact but not Opn4-/- mice. Finally, where they co-occurred we found that beta/gamma amplitude was modulated by the infra-slow rhythm. Our data thus reveal that: 1.) infra-slow and beta-gamma oscillations are separable phenomena; and 2.) that they actively co-occur in a subset of neurones in which the phase of infra-slow oscillations define beta-gamma oscillation amplitude. These findings suggest that infra-slow oscillations could influence vision by modulating beta-gamma oscillations, and raise the possibility that disruptions in these oscillatory behaviours contribute to vision dysfunction in retinal dystrophy. KEY POINTS SUMMARYO_LINeurophysiological activity in the subcortical visual system fluctuates in both infra-slow and fast oscillatory ranges, however the level of co-occurrence and potential functional interaction of these rhythms is unknown. C_LIO_LIAnalyzing dark-adapted spontaneous activity in the mouse subcortical visual system, we find that these two types of oscillation interact uniquely through a population of neurons expressing both rhythms. C_LIO_LIGenetic ablation of rod/cone signaling potentiates infra-slow and abolishes fast beta/gamma oscillations while genetic ablation of melanopsin substantially diminishes the interaction between these two rhythms. C_LIO_LIOur results indicate that in an intact visual system the phase of infra-slow modulates fast beta/gamma oscillations. C_LIO_LIThus one possible impact of infra-slow oscillations in vision is to guide visual processing by interacting with fast narrowband oscillations. C_LI

neuroscience↗

bioRxiv2019

Patterns of Treatment in Patients with Heart Failure with Preserved Ejection Fraction: the REasons for Geographic And Racial Differences in Stroke study

PurposeWe described medication use patterns among REasons for Geographic And Racial Differences in Stroke (REGARDS) participants hospitalized for heart failure with preserved ejection fraction (HFpEF) (152 hospitalizations, 101 unique individuals).\n\nMethodsMedication data were obtained from medical record review and Medicare Part D pharmacy claims. We compared discharge medication prescriptions between patients with and without chronic kidney disease (CKD), coronary heart disease (CHD), chronic obstructive pulmonary disease (COPD), and diabetes.\n\nResultsThe mean age was 74.8 years, 53.3% were black and 73.7% were female. Hypertension (97.2%), diabetes (65.1%), COPD (51.3%), CKD (41.1%) and history of CHD (60.9%) were common. On admission and discharge, respectively, beta-blockers (66.4%, 72.7%), angiotensin converting enzyme inhibitors or angiotensin receptor blockers (42.8%, 51.7%), diuretics (61.2%, 80.9%), loop diuretics (55.9%, 78.3%), calcium channel blockers (41.0%, 41.2%) and statins (44.7%, 50.3%) were commonly used. Spironolactone, digoxin, hydralazine plus isosorbide dinitrate (HISDN), isosorbide dinitrate alone and aldosterone receptor antagonists were used by <20%. For each medication, prescriptions were more common at discharge than admission. Many participants did not have Medicare claims for filled prescriptions in the year following discharge. A higher percentage of patients with versus without CKD, CHD, and diabetes had discharge prescriptions statins. Participants with CKD were also more likely to receive prescriptions for HISDN.\n\nConclusionBeta-blockers and diuretics were commonly prescribed at admission and discharge among HFpEF, but pharmacy claims for these medications within one-year were substantially less common. The comorbidities CHD, CKD, and diabetes were associated with prescriptions of statins at discharge.

epidemiology↗