Biology subjects

Fernandes, A. M.

Publications and source records attributed to Fernandes, A. M..

8 recordsLinked to original sources

bioRxiv2026

Pauses in a fast-paced life: Intermittent hovering in hummingbirds

Hummingbirds are known for sustained hovering powered by rapid and continuous wingbeats. Here, we describe and quantify a novel flight behavior, intermittent hovering, in which hovering hummingbirds momentarily pause their wing motion mid-air but maintain their vertical position in space, keeping their wings fully extended at the end of the upstroke. We present the first systematic account of flap-pauses and wing coloration across hummingbirds, and evaluate potential morphological and ecological correlates, as well as evolutionary patterns in the expression of this behavior. Slow-motion footage from 86 species spanning all nine major hummingbird clades shows that at least 45 species exhibited flap-pauses during sustained hovering. Phylogenetic comparative analyses revealed that hovering pauses are evolutionarily conserved and significantly associated with both greater body mass and longer wings. Furthermore, we found that the 16 species in our study with colored underwings also exhibit significantly longer wings. The convergence of intermittent hovering, wing elongation, and chromatic traits leads us to hypothesize that this flight behavior plays a role in visual and/or auditory communication.

evolutionary biology↗

bioRxiv2025

Temporal patterns of dominance in a hummingbird assemblage

A substantial gap in dominance hierarchies research is understanding how such relationships change over time. Previous studies have generally used a single interaction matrix, assuming that dominance is temporally consistent. Yet food sources can be scarce and temporary, leading to changes in species frequency and assemblage composition. Hummingbird assemblages fluctuate as these tiny birds track seasonal floral resources, with individual movements affecting species composition. Artificial feeders, which may foster a greater number of aggressive interactions, provide a stable environment for studying dominance, unlike ephemeral and shifting wild resources. To assess the temporal stability of dominance relationships, we documented aggressive interactions in a hummingbird assemblage over three months on the western slope of the eastern Cordillera of Colombian Andes. We tracked local changes in species composition and visit frequency, recording interactions among 11 hummingbird species using high-speed cameras at three time scales: hour, day, and month. Dominance relationships and their certainty were analyzed through Perc analyses and interaction networks. Over three months of recording, and perusing over 27 hours of non continuous highspeed videos, we registered 3,907 aggressive interactions and 12,629 visits. Our results revealed substantial temporal variation in dominance relationships, species composition, and visit frequency, even within the constant food source that feeders provide. Dominance hierarchies were generally intransitive, with large species dominating, but also with smaller species occasionally winning interactions. We found high uncertainty in dominance relationships within shorter intervals with fewer interactions (e.g., hourly); and that rank changes between dominant species across months and days were linked to shifts in feeder visits. We recommend that future studies incorporate temporal variation, certainty analyses, and interaction networks to determine whether dominance relationships are stable enough to form reliable hierarchies and to explore the ecological significance of reversals in dominance and associated determinants. HighlightsO_LIDominance fluctuates across temporal scales, with monthly, daily, and hourly variations. C_LIO_LIHierarchies become less stable at finer temporal scales. C_LIO_LIBody size and feeder visitation frequency shape dominance interactions. C_LIO_LISmaller species initiate more aggressive interactions but lose more frequently. C_LIO_LIRelationships among dominant species are less predictable than among subordinates. C_LI

animal behavior and cognition↗

bioRxiv2025

Specialised super-enhancer networks in stem cells and neurons

Super-enhancers (SEs) are clusters of enhancers with high transcriptional activity that play essential roles in defining cell identity through regulation of nearby genes. SEs preferentially form multiway chromatin interactions with other SEs and highly transcribed regions in embryonic stem cells. However, the properties of the interacting SEs and their specific contributions to complex regulatory interactions in differentiated cell types remain poorly understood. Here, we compare the structural and functional properties of SEs between embryonic stem cells (ESCs) and dopaminergic neurons (DNs) by combining Genome Architecture Mapping (GAM), chromatin accessibility, histone modification, and transcriptome data. Most SEs are cell-type specific and establish extensive pairwise and multiway chromatin interactions with other SEs and genes with cell-type specific expression. SE interactions span megabase genomic distances and frequently connect distant topologically associating domains. By applying network centrality analyses, we detected SEs with different hierarchical importance. Highest network centrality SEs contain binding motifs for cell-type specific transcription factors, and are candidate regulatory hubs. The functional heterogeneity of SEs is also highlighted by their organisation into modular sub-networks that differ in structure and spatial scale between ESCs and DNs, with more specific and strongly connected SE modules in post-mitotic neurons. Our results uncover both the high complexity and specificity of SE-based 3D regulatory networks and provide a resource for prioritizing SEs with potential roles in transcriptional regulation and disease.

genomics↗

bioRxiv2025

Tiny radio-tag backpacks impact, but do not significantly affect, hummingbird time budgets in captivity

BackgroundGiven that wildlife tags have recently become miniaturized enough to work with some of the worlds smallest vertebrates, there is a newfound urgency for affordable, field-accessible biologging ethics studies. We designed a 3-hour time-budget experiment to investigate how radio-transmitter backpacks affect hummingbirds behavior. Using a large flight arena in Colombia, we individually filmed 25 Black-throated Mangoes (Anthracothorax nigricollis) under two randomized treatments, tagged and untagged, to characterize and quantitatively compare their behavior. We analyzed all videos using the Behavioral Observation Research Interactive Software (BORIS), to create time-budget breakdowns of our key behaviors of interest: flying, feeding, preening, and perching. We also designed an aviary-style "entanglement test" (n = 30) to determine if any individuals would snag on vegetation while equipped with the backpack harness, and tested 6 additional birds in this enclosure overnight for any longer-term negative effects. ResultsAcross duration, number of bouts, and bout length, we found no significant differences in the behavior of individuals (flying, feeding, preening, and perching) when they were or were not tagged. However, the additive effects of treatment number (whether the bird was undergoing its first or second 1.5-hour treatment) and treatment type (tagged or untagged) most accurately predicted time spent flying (birds flew significantly more in their second 1.5-hour treatment). The weight of the bird, meanwhile, best predicted feeding duration (lighter birds fed significantly more). Lastly, the additive effects of time of day and treatment type had the highest predictive accuracy of time spent preening (birds preened significantly more in the afternoon than the morning, and significantly more in the evening than the afternoon); here, the effect of treatment type was highly significant. In our aviary tests, no individuals became entangled in vegetation or exhibited any adverse overnight effects from harness wear. ConclusionsIn our captive study, radio-transmitter backpacks did not significantly affect hummingbird behavior when considered independently; however, additional covariates are essential to account for, and the effects of being in a confined space may also be significant. Nonetheless, our experimental model is relatively straightforward to fine-tune to other small taxa and is suitable for remote conditions, providing a useful basis with which to examine species-specific effects of biologging prior to starting field studies.

animal behavior and cognition↗

bioRxiv2024

Estimating wingbeat frequency on hummingbirds by using a no-labeling learning computer vision approach

SynopsisWingbeat frequency estimation is an important aspect for the study of avian flight, energetics, and behavioral patterns, among others. Hummingbirds, in particular, are ideal subjects to test a method for this estimation due to their fast wing motions and unique aerodynamics, which results from their ecological diversification, adaptation to high-altitude environments, and sexually selected displays. Traditionally, wingbeat frequency measurements have been done via "manual" image/sound processing. In this study, we present an automated method to detect, track, classify, and monitor hummingbirds in high-speed video footage, accurately estimating their wingbeat frequency using computer vision techniques and signal analysis. Our approach utilizes a zero-shot learning algorithm that eliminates the need for labeling during training. Results demonstrate that our method can produce automated wingbeat frequency estimations with minimal supervision, closely matching those performed by trained human observers. This comparison indicates that our method can, in some scenarios, achieve low or zero error compared to a human, making it a valuable tool for flight analysis. Automating video analysis can assist wingbeat frequency estimation by reducing processing time and, thus, lowering barriers to analyze biological data on fields such as aerodynamics, foraging behavior, and signaling.

bioinformatics↗

bioRxiv2020

Molecular classification of zebrafish retinal ganglion cells links genes to cell types to behavior

Retinal ganglion cells (RGCs) form an array of feature detectors, which convey visual information to central brain regions. Characterizing RGC diversity is required to understand the logic of the underlying functional segregation. Using single-cell transcriptomics, we systematically classified RGCs in adult and larval zebrafish, thereby identifying marker genes for at least 33 stable and transient cell types. We used this dataset to engineer transgenic driver lines, enabling experimental access to specific RGC types. Strikingly, expression of one or few transcription factors often predicts dendrite morphologies and axonal projections to specific tectal layers and extratectal targets. In vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuning. Finally, chemogenetic ablation of eomesa+ RGCs, which comprise melanopsin-expressing types with projections to a small subset of central targets, selectively impaired phototaxis. Together, our study establishes a framework for systematically studying the functional architecture of the visual system.

neuroscience↗

bioRxiv2019

Neuronal circuitry for stimulus selection in the visual system

Visual objects naturally compete for the brains attention, and selecting just one of them for a behavioural response is often crucial for the animals survival1. The neural correlate of such stimulus prioritisation might take the form of a saliency map by which responses to one target are enhanced relative to distractors in other parts of the visual field2. Single-cell responses consistent with this type of computation have been observed in the tectum of primates, birds, turtles and lamprey2-7. However, the exact circuit implementation has remained unclear. Here we investigated the underlying neuronal mechanism presenting larval zebrafish with two simultaneous looming stimuli, each of which was able to trigger directed escapes on their own. Behaviour tracking revealed that the fish respond to these competing stimuli predominantly with a winner-take-all strategy. Using brain-wide functional recordings, we discovered neurons in the tectum whose responses to the target stimulus were non-linearly modulated by the saliency of the distractor. When the two stimuli were presented monocularly in different positions of the visual field, stimulus selection was already apparent in the activity of retinal ganglion cell axons, a likely consequence of antagonistic mechanisms operating outside the classical receptive field8,9. When the two stimuli were presented binocularly, i.e., on opposite sides of the fish, our analysis indicates that a loop involving excitatory and inhibitory neurons in the nucleus isthmi (NI) and the tectum weighed stimulus saliencies across hemispheres. Consistent with focal enhancement and global suppression, glutamatergic NI cells branch locally in the tectum, whereas GABAergic NI cells project broadly across both tectal hemispheres. Moreover, holographic optogenetic stimulation confirmed that glutamatergic NI neurons can modulate visual responses in the tectum. Together, our study shows, for the first time, context-dependent contributions of retinotectal and isthmotectal circuits to the computation of the visual saliency map, a prerequisite for stimulus-driven, bottom-up attention.

neuroscience↗

bioRxiv2018

Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements

Advances in high-throughput sequencing techniques now allow relatively easy and affordable sequencing of large portions of the genome, even for non-model organisms. Many phylogenetic studies reduce costs by focusing their sequencing efforts on a selected set of targeted loci, commonly enriched using sequence capture. The advantage of this approach is that it recovers a consistent set of loci, each with high sequencing depth, which leads to more confidence in the assembly of target sequences. High sequencing depth can also be used to identify phylogenetically informative allelic variation within sequenced individuals, but allele sequences are infrequently assembled in phylogenetic studies.\n\nInstead, many scientists perform their phylogenetic analyses using contig sequences which result from the de novo assembly of sequencing reads into contigs containing only canonical nucleobases, and this may reduce both statistical power and phylogenetic accuracy. Here, we develop an easy-to-use pipeline to recover allele sequences from sequence capture data, and we use simulated and empirical data to demonstrate the utility of integrating these allele sequences to analyses performed under the Multispecies Coalescent (MSC) model. Our empirical analyses of Ultraconserved Element (UCE) locus data collected from the South American hummingbird genus Topaza demonstrate that phased allele sequences carry sufficient phylogenetic information to infer the genetic structure, lineage divergence, and biogeographic history of a genus that diversified during the last three million years. The phylogenetic results support the recognition of two species, and suggest a high rate of gene flow across large distances of rainforest habitats but rare admixture across the Amazon River. Our simulations provide evidence that analyzing allele sequences leads to more accurate estimates of tree topology and divergence times than the more common approach of using contig sequences.

evolutionary biology↗