Biology subjects

Dominoni, D. M.

Publications and source records attributed to Dominoni, D. M..

17 recordsLinked to original sources

bioRxiv2026

Increased stress in early life epigenetically rewires pathways related to aging and longevity

Environmental conditions experienced early in life have profound consequences for vertebrate health, yet the molecular pathways linking developmental stress to aging and reduced lifespan remain poorly understood. Through a novel highly accurate epigenetic clock, developed from RRBS-based blood DNA methylation profiles, we show that experimental lifespan-reducing early-life stress rapidly accelerates epigenetic age in zebra finch chicks (Taeniopygia guttata). Corticosterone-treated 29-day-old chicks share differentially methylated loci with non-treated aged birds and cluster with 6-month-old birds. The transcriptional repressor ZBTB16 emerges as an epigenetically top age-correlated gene and is strongest affected by corticosterone. Elevated developmental corticosterone causes rapid epigenetic remodelling of metabolic pathways well-established in aging and longevity. Our results demonstrate epigenetic rewiring of the aging trajectory through conserved stress-survival mechanisms immediately following elevated early-life stress exposure.

developmental biology↗

bioRxiv2026

Deep learning reveals the individual-level effects of artificial light at night on a wild insect

Artificial light at night (ALAN) is a widespread anthropogenic phenomenon with varied physiological, behavioural, and ecosystem-level effects. Its impacts have been studied extensively at the population level, however less is known about the individual changes that underpin these larger trends. We use a networked video system combined with GryllAI--a deep learning-based system for continuous individual monitoring--to explore this in the field cricket, Gryllus campestris. Applying field-realistic artificial light (10-25lx) or a control treatment to burrows, we continuously track the activity of 144 nymphs across >38,000h of video footage, recording life history outcomes for each individual. Results indicate that ALAN exposure does not influence daily activity timing, total activity duration, predation risk, or nymphal development duration. However, changes in fine-scale behaviour were apparent, with ALAN causing crickets to enter and exit burrows less frequently, especially at night; and spent greater proportion of time outside burrows during daytime. These behavioural adjustments were not evident from broad scale activity trends that could be observed manually. Consequently, our findings suggest that aggregate measures of activity may fail to capture the full scope of ALAN-mediated impacts in nature, and that automated monitoring techniques offer a promising means of addressing this.

ecology↗

bioRxiv2026

Tuning into the city soundscape: Optimizing Convolutional Neural Networks for avian acoustic identification in the neotropics and evaluating their performance against established monitoring approaches.

Convolutional Neural Networks (CNNs) have become increasingly prominent in biodiversity monitoring due to their strong performance in accurately detecting species from sound recordings, overcoming some limitations of traditional methods such as point-counts. Yet, their use in urban ecosystems remains limited, highlighting the need for frameworks that identify modelling strategies to optimize their performance in these complex soundscapes. Here, we evaluated how preprocessing and labelling strategies, detection thresholds, sample size, and architecture affect the performance of CNNs for bird identification in urban tropical ecosystems. We also assessed its potential by comparing CNN-derived biodiversity estimates with those from point-counts and acoustic indices. For this, we used one week of recordings collected along urbanization gradients in five Colombian Andes cities to develop 11 multiclass CNN models varying in spectral representation, labelling strategies, training data source and backbone architecture. The best-performing model, evaluated with F1-scores, combined Log-Mel spectrograms, multispecies labels, ecosystem-specific and XenoCanto recordings, a probability threshold of 0.3 and a ConvNeXt backbone with its performance generally improving with sample size. Although CNNs and point counts detected partially distinct assemblages, CNN-derived species richness was higher to that estimated from point-counts. Additionally, the Normalized Difference Soundscape Index (NDSI) was positively associated with richness, suggesting its potential as a biodiversity proxy in tropical urban soundscapes. Overall, by identifying effective modelling designs and monitoring strategies, our study advances the development of robust biodiversity assessment frameworks in urbanized ecosystems in the Neotropics whilst highlighting the potential of acoustic approaches for avian monitoring and providing methodological guidance for future research and practical insights for wildlife monitoring and conservation.

ecology↗

bioRxiv2026

Parental age at reproduction accelerates offspring pace of life in Gryllus bimaculatus

Across invertebrates, it is widely known that older parents produce offspring with abbreviated lifespans (i.e., the Lansing effect). Yet the ecological and evolutionary ramifications of such nongenetic parental age effects remain unclear. Two demographic processes could culminate in a Lansing effect, with different fitness implications: (i) Later-conceived offspring may display greater mortality from conception, constraining fitness from birth. (ii) Alternatively, they may exhibit an increased age-specific mortality (i.e., accelerated senescence), with negative effects that manifest after maturity. If parental age accelerates offspring senescence without affecting initial mortality rate, then later-conceived offspring may maintain fitness by shifting to a faster pace-of-life. We exposed Gryllus bimaculatus parents to one of three experimental temperatures to generate environmental variation in parent mortality. Using a longitudinal within-parent study, we tested whether parental age influenced offspring longevity via increased initial mortality or accelerated senescence, and whether these effects depended on the parents thermal environment. Contrary to our predictions, we found no evidence that parental age reduced offspring longevity. Instead, parental age mediated offspring pace-of-life. Irrespective of the parents thermal environment, the earliest- and latest-conceived offspring were demographically distinct. Later-conceived offspring exhibited accelerated development, a smaller adult mass, and improved reproductive success. Unexpectedly, they also showed extended adult lifespans. This increased adult lifespan did not arise from reduced initial mortality, but from a delayed onset and slower progression of actuarial senescence. The slowed senescence in later-conceived offspring is unlikely to reflect a direct parental age effect, potentially arising indirectly through causal effects on adult size. Our results challenge the universality of the Lansing effect and contribute to a growing recognition that parental age has important life-history consequences. Accelerated life-histories in later-conceived offspring may be adaptive, enabling these individuals to compete over dwindling seasonal resources or overcome seasonal time constraints. Determining whether these demographic parental age effects accumulate across generations, or persist under natural environments, will be essential for establishing their ecological consequences and proximate role in the evolution of ageing. Open research statementData and code are not yet provided but will be made openly and freely available on request during the review process. Data will be uploaded to the Dryad data repository and code will be uploaded to Zenodo open repository on acceptance of the manuscript.

evolutionary biology↗

bioRxiv2025

Artificial light at night consistently impacts avian physiology and behaviour: a meta-analysis

Artificial light at night (ALAN) is a major anthropogenic pressure across the tree of life, driving population declines in insects and reptiles. Avian responses to ALAN defy simple patterns, varying in direction and magnitude, and the consequences of these responses remain unresolved. We conducted a meta-analysis to test how ALAN alters physiological, behavioural and life history traits underpinning avian performance. We analysed 623 effect sizes from 36 studies in 30 species. We found consistent physiological and behavioural shifts under ALAN, while life-history traits were unaffected. ALAN disrupted molecular and endocrine processes, leading to reduced sleep, higher metabolic rate, and accelerated reproductive maturation. Behaviourally, daily activity was extended, with earlier onset, later offset, and increased nocturnal activity and foraging effort. ALAN effects were stronger in migratory species and more pronounced in adults and females than nestlings and males. Higher light intensities amplified activity shifts, ageing, and sleep disruption, whereas exposure below 2 lux had minimal impact. Birds appear to buffer ALAN effects through physiological and behavioural adjustments, minimising impacts on life-history traits, a paradox likely explained by phenotypic plasticity or evolutionary adaptation. We identified light intensity threshold and group-specific vulnerabilities, emphasizing the need for targeted conservation in our increasingly illuminated world.

ecology↗

bioRxiv2025

The impact of microplastics on the mice gut microbiome: a meta-analysis

BackgroundMicroplastics are nearly ubiquitous in the natural environment. There is increasing awareness of the ingestion of microplastics in a wide range of wild animals and humans, but their health and fitness impacts remain poorly understood. Mounting evidence suggests that microplastics could accumulate in the gut, affecting the microbiome and hindering its function. This may constitute a direct pathway through which exposure to microplastics could affect health and disease. However, prior studies on the effects of microplastic exposure on the microbiome show contrasting findings raising the question whether microplastics truly affect the microbiome. Here, we performed the first meta-analysis on the effects of dietary microplastic exposure on the gut microbiome of mice. ResultsOverall, we found support for a significant impact of microplastic exposure on the relative abundance of gut bacteria. More in-depth analysis revealed microplastic exposure significantly increased the relative abundance of Bacillota and Pseudomonadota. In the gut microbiome, Bacillota is associated with carbohydrate metabolism and Pseudomonadota is associated with facultative anaerobes, thus these changes may have functional consequences. ConclusionsOur findings highlight the importance of distinguishing among differing bacterial phyla when assessing the impacts of microplastics on the gut microbiome as the direction and size of the impact varies by phyla.

microbiology↗

bioRxiv2025

Questioning the utility of oxidative stress measurements as biomarkers of physiological condition and fitness

Markers of oxidative stress are widely used as indicators of physiological state, but their utility for ecological and evolutionary inference remains uncertain due to high intraindividual variation masking associations with environmental conditions, fitness, and other physiological indicators such as telomere length. Although numerous longitudinal studies exist, individual repeatability of oxidative stress measurements is rarely reported explicitly. Here, we present the first meta-analysis assessing individual repeatability of oxidative stress markers, comprising 123 repeatability estimates from 22 studies. Overall, oxidative stress markers exhibited low repeatability on average (Intraclass correlation = 0.164), although repeatability estimates were highly heterogenous across biomarkers, study systems, and ecological contexts. Repeatability was generally low across taxa, sexes, study designs, and environments, although some markers, particularly lipid peroxidation quantified with HPLC, exhibited moderate repeatability in specific contexts. To illustrate the statistical consequences of low repeatability, we used heuristic simulations examining associations between oxidative stress and telomere length under different biological scenarios. These simulations demonstrate how low repeatability substantially reduces statistical power, but this is somewhat mitigated by taking repeated measurements. More broadly, our findings highlight the value of greater cross-disciplinary dialogue, as ecological and biomedical studies often use oxidative stress biomarkers in different ways and may benefit from shared perspectives.

physiology↗

bioRxiv2025

Phenology underlies apparent urbanisation effects on avian malaria in juvenile songbirds

Urbanisation can modify species interactions, including those between parasites and their hosts. In birds, urbanisation can either increase or decrease avian malaria infection, depending on host species, parasite or study location. However, temporal coordination between parasites and hosts, which may impact infection outcomes, has not been studied in urban ecology. To fill this gap, we collected blood samples from wild blue tit nestlings (Cyanistes caeruleus) in urban and forest habitats to examine how their hatch dates affected the prevalence and intensity of malaria infection. To separate parasites and quantify parasite load, we newly developed a species-specific qPCR assay. We found that Leucocytozoon prevalence was strongly affected by urbanisation, but effects depended on study year. This was driven by hatch date: nestlings that hatched earlier in the spring had a lower probability of being infected, independent of habitat type. In the few heavily infected nestlings, intensity of infection was associated with low body weight, suggesting fitness effects of infection. These results highlight the importance of breeding early to avoid early-life infection with malaria parasites, and that apparent urbanisation effects on infection arose from phenological differences between urban and forest habitats. Underappreciated phenological changes may underline other ecological effects of urbanisation.

ecology↗

bioRxiv2024

Urban effects on timing and variability of diel activity differ across passerine species and seasons

1. Life on Earth is adapted to rhythmic cycles in environmental conditions throughout the day and year via diel patterns of behavioural activity. 2. Urban conditions can disrupt such behavioural rhythms of activity. However, most studies so far have investigated urban effects on patterns of activity of single species in a single season. Additionally, we know little about the level of between and within-individual variation in urban and non-urban populations, and whether they differ. 3. Here, we use automated radio telemetry to record patterns of daily activity in six passerine species (blackbird, robin, great tit, blue tit, dunnock and chaffinch) across two urban and two forest populations during the pre-breeding and post-breeding season. We investigate urban effects on five activity-related traits: time of activity onset, time of activity end, duration of diurnal activity, level of diurnal activity and level of nocturnal activity. We employ statistical tools that allow us to estimate urban effects on mean phenotypic values, but also quantify urban versus forest differences in between-individual and within-individual phenotypic variation. 4. We found the strongest urban effects on time of activity onset in blackbirds and robins during the pre-breeding season: urban populations of blackbird and robin started their daily activity earlier than their forest counterparts. We did not find this effect in the other species. Urban populations of all species showed higher levels of nocturnal activity than forest populations, but this effect was not offset by lower diurnal activity, suggesting that urban birds may incur higher daily energetic demands. 5. Lastly, our analysis revealed large and consistent differences in variation in the investigated timing traits. Urban birds were more variable between individuals, implying lower population synchronization, and more variable within individuals, implying less consistent behaviour than their forest counterparts. Conversely, activity levels were more variable in forest birds. 6. We conclude that, for birds, urban life is associated with less rest, less consistency, and lower synchronicity, but that effect sizes depend on species and time of the year. Our results warn against generalising the effects of urbanisation on daily rhythms of birds, and call for future studies to understand the mechanisms behind species and seasonal differences.

animal behavior and cognition↗

bioRxiv2024

Urbanization Affects Nest Material Composition and Use of Anthropogenic Materials in Blue Tit Nests

Avian nests are complex structures that protect eggs and nestlings. Nest-building behaviour varies between species and habitats, and recent work has highlighted that in areas with high human activity and low availability of natural nest material, birds may use anthropogenic material to construct nests. However, we still know relatively little about how nest composition is affected by human presence, including along urban gradients. Here we present the results of a study where we examined how nest composition differed between an urban and a forest population of blue tits, and the impact that variation in nest composition had on reproductive success. We found a significant decrease in the amount of natural materials and an increase in anthropogenic materials in urban compared to forest nests. Earlier urban nests showed a higher amount of anthropogenic materials compared to late urban nests. The amount of moss incorporated in a nest was the strongest predictor of fledgling success, suggesting that the use of anthropogenic material by urban birds might be a maladaptation, and/or that urban birds are constrained in the amount of moss they can use to build their nests. Future studies should aim at quantifying the availability of natural materials to distinguish between these two hypotheses.

ecology↗

bioRxiv2023

The effects of artificial light at night (ALAN) on the gaping activity and feeding of mussels

Artificial light at night (ALAN) is one of the most widespread forms of environmental pollution. Studies on terrestrial organisms have shown that the effects of ALAN can be pervasive, and importantly, can depend on the colour (i.e., wavelength) of light. ALAN also affects marine environments as it is present in more than 22% of the worlds coastlines and can reach depths of up to 100m. However, the impact of different colour ALAN on coastal marine organisms is under-investigated. In this study, we tested the effects of different ALAN colours on Mytilus edulis, a widespread coastal bivalve known for its high phytoplankton clearance capacity amongst other valuable ecosystem services. Using a lab-based valvometry system, we recorded the impact of red, green, and white ALAN on gaping activity patterns and phytoplankton clearance capacity of individual mussels and compared these to dark night control. Mussels exhibited a semi-diel activity pattern in both proportion of time open and gaping frequency. Although ALAN did not have significant effects on the proportion of time open it did significantly affect the gaping frequency. This effect was colour-specific with red and white ALAN resulting in lower activity compared to the dark night control but there were no effects on the phytoplankton consumption. Under green light, however, mussels showed a higher gaping frequency and reduced phytoplankton consumption with increasing time spent open compared to the other ALAN treatments and the dark control. Our findings suggest that ALAN does have colour-specific effects on mussels and indicate the importance of further investigating the physiological mechanisms behind these patterns, and their potential ecological consequences.

ecology↗

bioRxiv2023

Environmental constraints can explain clutch size differences between urban and forest blue tits (Cyanistes caeruleus): insights from an egg removal experiment

Urban environments present novel ecological challenges to wild species. Understanding whether species responses to urban living are adaptive or maladaptive is critical to predicting the impacts of urbanisation on biodiversity. In birds, urban populations generally exhibit reduced reproductive investment (clutch size) compared to forest populations. However, whether smaller clutches are adaptive, or a result of environmental constraints is unclear. Here, to investigate these two hypotheses, we quantified the ability of urban and forest blue tits (Cyanistes caeruleus) to lay new eggs upon egg removal. Consistent with the constraint hypothesis, our results suggest that urban females do not lay new eggs, at least to the same extent as forest birds. Meanwhile, forest birds laid approximately two additional eggs. As urban blue tits did not lay replacement eggs, our experiment resulted in a brood reduction and nestlings from urban experimental nests had higher survival than those from urban control nests, suggesting that females may be misjudging urban habitat quality and produce a clutch too large to be sustained. Taken together, our results suggest that urban females may experience constraints that limit egg formation and/or exacerbate the trade-off between female survival and egg production. This has important implications for urban green space management.

ecology↗

bioRxiv2022

Part-night exposure to artificial light at night has more detrimental effects on aphid colonies than fully lit nights

Artificial light at night (ALAN) threatens natural ecosystems globally. While ALAN research is increasing, little is known about how ALAN affects plants and interactions with other organisms. We explored the effects of ALAN on plant defence and plant-insect interactions using barley (Hordeum vulgare) and the English grain aphid (Sitobion avenae). Plants were exposed to full or part nights of 15-20 lux ALAN, or no ALAN control nights, to test the effects of ALAN on plant growth and defence. Although plant growth was only minimally affected by ALAN, aphid colony growth and aphid maturation were reduced significantly by ALAN treatments. Importantly, we found strong differences between full-night and part-night ALAN treatments. Contrary to our expectations, part ALAN had stronger negative effects on aphid colony growth than full ALAN. Defence-associated gene expression was affected in some cases by ALAN, but also positively correlated with aphid colony size, suggesting that the effects of ALAN on plant defences are indirect, and regulated via direct disruption of aphid colonies, rather than via ALAN-induced upregulation of defences. Mitigating ecological side effects of ALAN is a complex problem, as reducing exposure to ALAN increased its negative impact on insect herbivores.

ecology↗

bioRxiv2022

Reproductive fitness is associated with female chronotype in a songbird

Research on biological rhythms has revealed widespread variation in diel timing within populations. Repeatable individual chronotypes have been linked to performance in humans but, in free-living species, benefits of chronotype are poorly understood. To address this gap, we investigated fitness correlates of incubation patterns in female songbirds (great tit, Parus major) at urban and forest sites. We confirm repeatable chronotypes (r [≥] 0.31) and show novel links between chronotype and reproductive success. In both habitats, females that started activity earlier in the day raised more fledglings. We also observed that forest females started their day at a similar time throughout the breeding season, whereas urban females tied their onset of activity closely to sunrise. Our study points to possible mechanisms that underlie chronotype variation and provides sought-after evidence for its relevance to fitness.

animal behavior and cognition↗

bioRxiv2021

A global meta-analysis reveals more variable life histories in urban birds compared to their non-urban neighbours

Cities pose a major ecological challenge for wildlife worldwide. Phenotypic variation, which can result from underlying genetic variation or plasticity, is an important metric to understand eco-evolutionary responses to environmental change. Recent work suggests that urban populations might have higher levels of phenotypic variation than non-urban counterparts. This prediction, however, has never been tested across species nor over a broad geographical range. Here, we conduct a meta-analysis of the avian literature to compare urban versus non-urban means and variation in phenology (i.e., lay date) and reproductive effort (i.e., clutch size, number of fledglings). First, we show that urban populations reproduce earlier and have smaller broods than non-urban conspecifics. Second, we show that urban populations have higher phenotypic variation in laying date than non-urban populations. This result arises from differences between populations within breeding seasons, conceivably due to higher landscape heterogeneity in urban habitats. These findings reveal a novel effect of urbanisation on animal life-histories with potential implications for species adaptation to urban environments (which will require further investigation). Higher variation in phenology in birds subjected to urban disturbance could result from plastic responses to a heterogeneous environment, or from higher genetic variation in phenology, possibly linked to higher evolutionary potential.

evolutionary biology↗

bioRxiv2021

Wavelength-dependent effects of artificial light at night on phytoplankton growth and community structure

Artificial light at night (ALAN) is increasingly recognised as a disruptive form of environmental pollution, impacting many physiological and behavioural processes that may scale up to population and community-level effects. Mounting evidence from animal studies show that the severity and type of the impact depends on the wavelength and intensity of ALAN. This knowledge has been instrumental for informing policy-making and planning for wildlife-friendly illumination. However, most of this evidence comes from terrestrial habitats, while research testing alternative wavelength illumination in marine environments is lagging behind. In this study we investigated the effect of such alternative ALAN colours on marine primary producers. Specifically, we tested the effect of green, red, and natural white LED illumination at night, compared to a dark control, on the growth of a green microalgae as well as the biomass, diversity and composition of a phytoplankton assemblage. Our findings show that green ALAN boosted chlorophyll production at the exponential growth stage, resulting in higher biomass production in the green algae Tetraselmis suesica. All ALAN wavelengths affected the biomass and diversity of the assemblage with the red and green ALAN having the stronger effects, leading to higher overall abundance and selective dominance of specific diatom species compared to white ALAN and the dark control. SynthesisOur work indicates that the wavelength of artificial light sources in marine areas should be carefully considered in management and conservation plans. In particular, green and red light should be used with caution in coastal areas, where there might be a need to strike a balance between the strong effects of green and red light on marine primary producers with the benefit they bring to other organisms.

ecology↗

bioRxiv2020

Artificial light at night shifts the circadian system but still leads to physiological disruption in a wild bird

Globally increasing levels of artificial light at night (ALAN) are associated with shifts in circadian rhythms of behaviour in many wild species. However, it is still unclear whether changes in behavioural timing are underlined by parallel shifts in the molecular clock, and whether such internal shifts may differ between different tissues and physiological pathways, which could highlight circadian disruption. We tackled these questions in a comprehensive study that integrated behavioural, gene expression and metabolomic analyses. We exposed captive male great tits (Parus major) to three ALAN intensities or to dark nights, recorded their activity rhythms and obtained mid-day and midnight samples of brain, liver, spleen and blood. ALAN advanced wake-up time, and this shift was paralleled by an advance in the expression of the clock gene BMAL1 in all tissues, suggesting close links of brain and peripheral clock gene expression with activity rhythms. However, several metabolic and immune genes were desynchronised the shifted BMAL1 expression, suggesting circadian disruption of behaviour and physiology. This result was reinforced by untargeted metabolomic profiling, which showed that only 9.7% of the 755 analysed metabolites followed the behavioural shift. We suggest circadian as a key mediator of the health impacts of ALAN on wild animals.

zoology↗