Biology subjects

Nourani, E.

Publications and source records attributed to Nourani, E..

13 recordsLinked to original sources

bioRxiv2026

Early avoidance of human-dominated landscapes by juvenile Alpine golden eagles

O_LIThe expanding human footprint drives profound transformations in species, including not only morphological trait loss but also behavioural trait extinction. In contrast to behavioural trait extinction, which entails a reduction in genetic variability, behavioural plasticity maintains behavioural trait diversity and the associated genetic variability required for evolutionary adaptation. Yet, while behavioural plasticity shaping non-human capacity to coexist with humans has evolved under past, human-modified, environmental conditions, few studies have examined whether species retain a level of behavioural plasticity after past interactions with humans. C_LIO_LIUsing data from 64 juveniles golden eagles (Aquila chrysaetos) from a population demographically recovering after centuries of persecution, yet still restricted to less human-dominated alpine massifs, we tested whether human avoidance is innate or learned through experience during dispersal or parental influences during the pre-dispersal period. We performed a Principal Component Analysis (PCA) on landscape features used during the pre-dispersal and the first fifteen weeks of the dispersal phase, and used Mahalanobis distance as an indicator for quantifying changes in individual spatial behaviour over time. C_LIO_LIThe lower frequency of use of human-dominated landscape features, compared with the more sparsely populated mid- and high-elevation landscape features, resulted from individuals consistent use of similar landscape features across the pre-dispersal and dispersal periods. Avoidance of humans was therefore better explained by a learning or imprinting process prior to dispersal, which predisposed individuals to use landscape features similar to those experienced during pre-dispersal, rather than by learning during dispersal, or by an innate avoidance. C_LIO_LIImprinting on natal habitat features corroborates the observed limited range expansion of the alpine population beyond the massif borders. Differences among European populations in range recolonisation suggest contrasting histories of persecution, which may have left varying degrees of behavioural plasticity across populations. C_LIO_LIAs a guide for future conservation priorities, these findings underscore the need to reconstruct past conditions and/or to document contemporary animal behaviour in order to build a library of behaviours that can be used in the future to track behavioural changes. C_LI

animal behavior and cognition↗

bioRxiv2025

Overcoming Innate Lateralization Improves Avian Flight Performance

Behavioural lateralization--side-bias or handedness--enhances neurological processing efficiency but creates a dilemma for behaviours requiring symmetry. Flight demands symmetric execution, particularly when optimising energy extraction from atmospheric updrafts during soaring. Using high-resolution biologging of 31 juvenile European honey buzzards from fledging through their first intercontinental migration leg, we show that strong lateralised circling was prevalent immediately after fledging (74%). This proportion declined to parity by migration onset, indicating developmental adjustment with increasing experience. During migration, side-biased circling was linked to wider turns, reduced altitude gain, and daily travel distances shortened by 13%. These findings reveal a direct trade-off between the neurological efficiency of lateralization and the aerodynamic requirements of efficient soaring. Our results challenge the notion that lateralization is universally adaptive and highlight how experience and ontogeny modulate the balance between task difficulty, neural specialization, and ecological performance.

animal behavior and cognition↗

bioRxiv2025

Timing of independence is explained by movement ability, but depends on how independence is defined for a long-lived raptor

Many young animals must gain independence from parental care by acquiring the necessary skills for survival. Thus, the rate of skill acquisition can predict how long juveniles remain with their parents before emigrating from the natal territory. Yet in some systems, young animals acquire adult-like skills and the capacity to be independent long before they emigrate. This raises the question of why the timing of emigration decouples from the rate of skill acquisition, resulting in extended parental care. We addressed this by leveraging GPS tracking data from juvenile golden eagles (Aquila chrysaetos), which learn to fly and to hunt while remaining with their parents for 61-283 days after fledging. Young golden eagles often go on excursions without their parents outside of their natal territories before emigration. We expected flight performance to predict the timing of excursions better than the timing of emigration, which should be more influenced by external factors. In a set of time-to-event models, we predicted the rate of excursions and of emigration using metrics of soaring flight performance or of daily movement. Contrary to our prediction, we found that soaring performance failed to predict the rate of either excursions or emigration, whereas daily movement predicted both rates, but inconsistently. This was likely because those coarser metrics captured motivation and weather in addition to flight skills. Thus external factors seem more likely to explain the timing of independence and internal development--in this case of flight skills--may be completed quickly. Juveniles may delay emigration not due to lack of skill, but because the costs of leaving parental care outweigh the benefits. The difference we discovered between when individuals were capable of independence and when they committed to it may obscure the more general link between skill acquisition and the end of parental care in other systems as well.

animal behavior and cognition↗

bioRxiv2024

Golden eagles regularly use gravity waves to soar in the Alps: new insights from high-resolution weather data

1Soaring flight developed as a result of behavioural and morphological adaptations that allow birds to reduce the metabolic cost of flight by harnessing the energy available in the atmosphere. Despite an increased attention given in the last decades to the physics and ecology that allow soaring flight, its study has been limited by the generally low spatio-temporal resolution of available atmospheric data. This constrained our ability to quantify the atmospheric conditions that allow soaring, and limited our understanding of its flexibility in different uplift conditions. While the use of updraughts such as thermals and orographic lifting are well described in the literature (albeit only quantified through atmospheric proxies), the use of others, such as gravity waves, was hypothesised but largely undocumented. Recent advancements in high-resolution atmospheric modelling, with hourly output available at the kilometer-scale grid spacing, offer new opportunities to investigate the flexibility of soaring flight in response to complex atmospheric dynamics. In this study, we used a combination of a high-resolution atmospheric analysis and high-resolution GPS tracking data to characterise the updraught sources used by golden eagles, Aquila chrysaetos, in the European Alps. We document that golden eagles in this region repeatedly use gravity waves, and that while thermals were still the main updraught source used for soaring, gravity waves were involved in at least 19% of the inspected soaring segments. In winter, when thermals were more scarce, the quasi-totality of soaring events were powered by gravity waves or orographic lifting, largely expanding the environmental energy available to soaring birds and therefore the landscape connectivity in topographically complex regions. Our results also emphasise the difficulty to distinguish between convective (thermals) and dynamic updraught sources, as these co-occur within the boundary layer over complex terrain.

ecology↗

bioRxiv2024

Lifestyle factors in the biomedical literature: comprehensive resources for named entity recognition

MotivationDespite lifestyle factors (LSFs) being increasingly acknowledged in shaping individual health trajectories, particularly in chronic diseases, they have still not been systematically described in the biomedical literature. This is in part because no named entity recognition (NER) system exists, which can comprehensively detect all types of LSFs in text. The task is challenging due to their inherent diversity, lack of a comprehensive LSF classification for dictionary-based NER, and lack of a corpus for deep learning-based NER. ResultsWe present a novel Lifestyle Factor Ontology (LSFO), which we used to develop a dictionarybased system for recognition and normalization of LSFs. Additionally, we introduce a manually annotated corpus for LSFs (LSF200) suitable for training and evaluation of NER systems, and use it to train a transformer-based system. Evaluating the performance of both NER systems on the corpus revealed an F-score of 64% for the dictionary-based system and 76% for the transformer-based system. Largescale application of these systems on PubMed abstracts and PMC Open Access articles identified over 300 million mentions of LSF in the biomedical literature. AvailabilityLSFO, the annotated LSF200 corpus, and the detected LSFs in PubMed and PMC-OA articles using both NER systems, are available under open licenses via the following GitHub repository: https://github.com/EsmaeilNourani/LSFO-expansion. This repository contains links to two associated GitHub repositories and a Zenodo project related to the study. LSFO is also available at BioPortal: https://bioportal.bioontology.org/ontologies/LSFO. Contactkaterina.nastou@cpr.ku.dk, soren.brunak@cpr.ku.dk, lars.juhl.jensen@cpr.ku.dk Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2023

Experience reduces reliance on conspecifics for route selection by a collectively migrating soaring bird

Migration can be an energetically costly behavior with strong fitness consequences in terms of mortality and reproduction 1-11. Migrants should select migratory routes to minimize their costs, but both costs and benefits may change with experience 12-14. This raises the question of whether experience changes how individuals select their migratory routes. Here we investigate the effect of age on route selection criteria in a collectively migrating soaring bird, the white stork (Ciconia ciconia). We perform step selection analysis on a longitudinal data set tracking 158 white storks over up to nine years to quantify how they select their routes based on the social and atmospheric environments, and to examine how this selection changes with age. We find clear ontogenetic shifts in route selection criteria. Juveniles choose routes that have good atmospheric conditions and high conspecific densities. Yet, as they gain experience storks selection on the availability of social information reduces--after their fifth migration experienced birds also choose routes with low conspecific densities. Thus, our results suggest that as individuals age, they gradually replace information gleaned from other individuals with information gained from experience, allowing them to shift their migration timing and increasing the time scale at which they select their routes.

animal behavior and cognition↗

bioRxiv2023

Gaining proficiency in flight transforms energy landscapes during ontogeny

The heterogeneity of the physical environment determines the cost of transport for animals, shaping their energy landscape. Animals respond to this energy landscape by adjusting their distribution and movement to maximize gains and reduce costs. Much of our knowledge about energy landscape dynamics focuses on factors external to the animal, particularly the spatio-temporal variations of the environment. However, an animals internal state can significantly impact its ability to perceive and utilize available energy, creating a distinction between the "fundamental" and the "realized" energy landscapes. Here we show that the realized energy landscape varies along the ontogenetic axis. Locomotor and cognitive capabilities of individuals change over time, especially during the early life stages. We investigate the development of the realized energy landscape in the Central European Alpine population of the golden eagle Aquila chrysaetos, a large predator that requires negotiating the atmospheric environment to achieve energy-efficient soaring flight. We quantified weekly energy landscapes using environmental features for 55 juvenile golden eagles, demonstrating that energetic costs of traversing the landscape decreased with age. Consequently, the potentially flyable area within the Alpine region increased 2,170-fold during their first three years of independence. Our work contributes to a predictive understanding of animal movement by presenting ontogeny as a mechanism shaping the realized energy landscape.

animal behavior and cognition↗

bioRxiv2022

Extreme tolerable winds for seabirds are determined by morphology

Storms can cause widespread seabird strandings and wrecking1,2,3,4,5, yet little is known about the maximum wind speeds that birds are able to tolerate or the conditions they avoid. We analyzed > 300,000 hours of tracking data from 18 seabird species, including flapping and soaring fliers, to assess how flight morphology affects wind selectivity, both at fine scales (hourly movement steps) and across the breeding season. We found no general preference or avoidance of particular wind speeds within foraging tracks. This suggests seabird flight morphology is adapted to a "wind niche", with higher wing loading being selected for in windier environments. In support of this, wing loading was positively related to the median wind speeds on the breeding grounds, as well as the maximum wind speeds in which birds flew. Yet globally, the highest wind speeds occur in the tropics (in association with tropical cyclones) where birds are morphologically adapted to low median wind speeds. Tropical species must therefore show behavioral responses to extreme winds, including long-range avoidance of wind speeds that can be twice their operable maxima. In contrast, procellariiformes flew in almost all wind speeds they encountered at a seasonal scale. Despite this, we describe a small number of cases where albatrosses avoided strong winds at close-range, including by flying into the eye of the storm. Extreme winds appear to pose context- dependent risks to seabirds, and more information is needed on the factors that determine the hierarchy of risk, given the impact of global change on storm intensity 6,7.

animal behavior and cognition↗

bioRxiv2022

Experience does not change the importance of wind support for migratory route selection by a soaring bird

Migration is a complex behavior that is costly in terms of time, energy, and risk of mortality. Thermal soaring birds rely on airflow, specifically wind support and uplift, to offset their energetic costs of flight. Their migratory routes are a record of movement decisions to negotiate the atmospheric environment and achieve efficiency. Because thermal soaring is a complex flight type that young birds need to learn, we expected that, as individuals gain more experience, their movement decisions will also increasingly favor the best thermal uplift conditions. We quantified how route choice during autumn migration of young European honey buzzards (Pernis apivorus) was adjusted to wind support and uplift over up to four years of migration and compared this to the choices of adult birds. We found that wind support was important in all migrations. However, we did not find an increase in the use of thermal uplifts, which could be an artifact of the uplift proxies that we used. Age-specific variations in response to airflow might occur at a smaller spatio-temporal scale than we investigated.

animal behavior and cognition↗

bioRxiv2021

Tapping into non-English-language science for the conservation of global biodiversity

The widely held assumption that any important scientific information would be available in English underlies the underuse of non-English-language science across disciplines. However, non-English-language science is expected to bring unique and valuable scientific information, especially in disciplines where the evidence is patchy, and for emergent issues where synthesising available evidence is an urgent challenge. Yet such contribution of non-English-language science to scientific communities and the application of science is rarely quantified. Here we show that non-English-language studies provide crucial evidence for informing global biodiversity conservation. By screening 419,680 peer-reviewed papers in 16 languages, we identified 1,234 non-English-language studies providing evidence on the effectiveness of biodiversity conservation interventions, compared to 4,412 English-language studies identified with the same criteria. Relevant non-English-language studies are being published at an increasing rate, and can expand the geographical (by 12-25%) and taxonomic (by 5-32%) coverage of English-language evidence, especially in biodiverse regions, albeit often based on less robust study designs. Our results show that synthesising non-English-language studies is key to overcoming the widespread lack of local, context-dependent evidence and facilitating evidence-based conservation globally. We urge wider disciplines to rigorously reassess the untapped potential of non-English-language science in informing decisions to address other global challenges.

scientific communication and education↗

bioRxiv2020

Sea-crossing along migratory flyways is limited more strongly by wind than by lack of uplift

Flying over the open sea is energetically costly for terrestrial birds. Despite this, over-water journeys of many birds, sometimes hundreds of kilometers long, are uncovered by bio-logging technology. To understand how these birds afford their flights over the open sea, we investigated the role of atmospheric conditions, specifically wind and uplift, in subsidizing over-water flight at the global scale. We first established that {Delta}T, the temperature difference between sea surface and air, is a meaningful proxy for uplift over water. Using this proxy, we showed that the spatio-temporal patterns of sea-crossing in terrestrial migratory birds is associated with favorable uplift conditions. We then analyzed route selection over the open sea for five facultative soaring species, representing all major migratory flyways. The birds maximized wind support when selecting their sea-crossing routes and selected higher uplift when suitable wind support was available. They also preferred routes with low long-term uncertainty in wind conditions. Our findings suggest that, in addition to wind, uplift may play a key role in the energy seascape for bird migration that in turn determines strategies and associated costs for birds crossing ecological barriers such as the open sea.

animal behavior and cognition↗

bioRxiv2020

TripletProt: Deep Representation Learning of Proteins based on Siamese Networks

We introduce TripletProt, a new approach for protein representation learning based on the Siamese neural networks. We evaluate TripletProt comprehensively in protein functional annotation tasks including sub-cellular localization (14 categories) and gene ontology prediction (more than 2000 classes), which are both challenging multi-class multi-label classification machine learning problems. We compare the performance of TripletProt with the state-of-the-art approaches including recurrent language model-based approach (i.e., UniRep), as well as protein-protein interaction (PPI) network and sequence-based method (i.e., DeepGO). Our TripletProt showed an overall improvement of F1 score in the above mentioned comprehensive functional annotation tasks, solely relying on the PPI network. TripletProt and in general Siamese Network offer great potentials for the protein informatics tasks and can be widely applied to similar tasks.

bioinformatics↗

bioRxiv2019

Age-specific migration timing affects the energy seascape over an ecological barrier

Thermal soaring birds extract energy from the atmosphere to achieve energetically low-cost movement. When encountering regions that are energetically costly to fly over, such as open seas, they attempt to adjust the spatio-temporal pattern of their passage to maximize energy extraction from the atmosphere over these ecological barriers. We apply the concept of energy landscapes to investigate the spatio-temporal dynamics of energy availability over the open sea for soaring flight. We specifically investigated how the \"energy seascape\" may shape age-specific sea-crossing behaviour of European honey buzzards Pernis apivorus over the Mediterranean Sea in autumn. We found uplift potential over the sea to be the main determinant of sea-crossing length, rather than wind conditions. Considering this variable as a proxy for available energy over the sea, we constructed the energy seascape for the autumn migration season using forty years of temperature data. Our results indicate that early-migrating adult buzzards are likely to encounter adverse energy subsidence over the Mediterranean, whereas late-migrating juveniles face less adverse flight conditions, and even conditions conducive to soaring flight. Our study provides evidence that the dynamics of the energy landscape can explain intra-specific variation in migratory behaviour also at sea.

ecology↗