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644 results for “Data Visualizations”
Data from: Timing of vegetation sampling does not influence associations between visual obstruction and turkey nest survival in a montane forest
Evaluating relationships between ecological processes that occur concurrently is complicated by the potential for such processes to covary. Ground-nesting birds rely on habitat characteristics that provide concealment from predators; this protection often is provided by vegetation at the nest. Recently, researchers have raised concern that measuring vegetation at nest fate introduces a bias, as vegetation at successful nests is measured later in the growing season. This bias can lead to an erroneous conclusion that plant height is positively associated with nest survival. However, if the features that provide concealment are invariant during the incubation period, no bias should be expected, and the timing of measurement is less influential. We used data collected from 98 nests to evaluate whether there is evidence that such a bias exists in a study of wild turkey (Meleagris gallopavo) nesting in a forest ecosystem. We modelled nest survival as a function of visual obstruction and other covariates of interest. At unsuccessful nests, we collected visual obstruction readings at both the date of nest failure and the projected hatch date and compared survival estimates generated using both sets of vegetation data. In contrast to studies in other systems, we found little evidence that the timing of vegetation sampling influenced conclusions regarding the association between visual obstruction and survival; model selection and estimates of nest survival were similar regardless of when vegetation data were collected. The dominant hiding cover at most of our nests was provided by evergreen shrubs; slow growth of these plants likely prevent appreciable changes in visual obstruction during incubation. When considered with a growing body of literature, our results suggest that the influence of timing of sampling depends on the study system. When designing future studies, investigators should consider the structures that provide nest concealment and whether phenology is confounded with nest survival.
Data files for Corron et al.'s article, "How low can we go? A skeletal maturity threshold for probabilistic visual sex estimation from immature human os coxae".
<p>Data files for Corron et al.'s article, "How low can we go? A skeletal maturity threshold for probabilistic visual sex estimation from immature human <em>os coxae</em>", published in <em>Forensic Science International</em>. doi: <a href="https://doi.org/10.1016/j.forsciint.2021.110854">10.1016/j.forsciint.2021.110854</a>.</p>
data set related to article Preservation of Visual Cortex Plasticity in Retinitis Pigmentosa
<p>This record contains raw data related to article Preservation of Visual Cortex Plasticity in Retinitis Pigmentosa</p>
Supplementary data for "Visual cues of predation risk outweigh acoustic cues: a field experiment in black-capped chickadees"
<p>All data required for the analyses, including R code, presented in the paper "Visual cues of predation risk outweigh acoustic cues: a field experiment in black-capped chickadees" DOI: 10.1098/rspb.2020.2002</p>
CognIDE: A Psychophysiological Data Integrator Approach for Visual Studio Code
<p> Psychophysiological Data Integrator Approach for Visual Studio Code</p>
Data from: Visualizing connectivity of ecological and evolutionary concepts – an exploration of research on plant species rarity
<p>Understanding the ecological and evolutionary factors that influence species rarity has important theoretical and applied implications, yet the reasons why some species are rare while others are common remain unresolved. As a novel exploration of scientific knowledge, we used network analysis conceptually to visualize the foci of a comprehensive base of >800 studies on plant species rarity within the context of ecology and evolution. In doing so, we highlight existing research strengths that could substantiate novel syntheses and gaps that could inspire new research. Our results reveal strong integrated foci on population dynamics with other ecological concepts. In contrast, despite the potential for ecological and evolutionary processes to interact, few studies explored the interplay of environmental factors and microevolutionary patterns. The cellular and molecular biology, physiology, and plasticity of rare plant species within both ecological and evolutionary contexts similarly provide avenues for impactful future investigations.</p>
Data related to the manuscript entitled "Traffic Data Visualization: A Systematic Literature Review"
<p>Data related to the manuscript entitled "Traffic Data Visualization: A Systematic Literature Review"</p>
Data from: Rapid light-induced shifts in opsin expression: finding new opsins, discerning mechanisms of change, and implications for visual sensitivity
Light induced shifts in cone frequency and opsin expression occur in many aquatic species. Yet little is known about how quickly animals can alter opsin expression and, thereby, track their visual environments. Similarly, little is known about whether adult animals can alter opsin expression or whether shifts in opsin expression are limited to critical developmental windows. We took adult wild caught bluefin killifish (Lucania goodei) from three different lighting environments (spring, swamp, variable), placed them under two different lighting treatments (clear vs. tea-stained water), and monitored opsin expression over four weeks. We measured opsin expression for five previously described opsins (SWS1, SWS2B, SWS2A, RH2-1, LWS) as well as RH2-2 which we discovered via 454 sequencing. We used two different metrics of opsin expression. We measured expression of each opsin relative to a housekeeping gene and the proportional expression of each opsin relative to the total pool of opsins. Population and lighting environment had large effects on opsin expression which were present at the earliest time points indicating rapid shifts in expression. The two measures of expression produced radically different patterns. Proportional measures indicated large effects of light on the SWS1 expression whereas relative measures indicated no such effect. Instead, light had large effects on the relative expression of SWS2B, RH2-2, RH2-1, and LWS. We suggest that proportional measures of opsin expression are best for making inferences about color vision, but that measures relative to a house keeping gene are better for making conclusions about which opsins are differentially regulated.
Data from: Differential survival between visual environments supports a role of divergent sensory drive in cichlid fish speciation
Identifying the selective forces that initiate ecological speciation is a major challenge in evolutionary biology. Sensory drive has been implicated in speciation in various taxa, largely based on phenotype-environment correlations and signatures of selection in sensory genes. Here, we present a reciprocal transplant experiment revealing species differences in performance in alternative visual environments, consistent with speciation by divergent sensory drive. The closely related cichlids Pundamilia pundamilia and P. nyererei inhabit different visual environments in Lake Victoria and show associated differences in visual system properties. Mimicking the two light environments in the laboratory, we find a substantial reduction in survival of both species when reared in the other species' visual environment. This implies that the observed differences in Pundamilia colour vision are indeed adaptive, and substantiates the implicit assumption in sensory drive speciation models that divergent environmental selection is strong enough to drive divergence in sensory properties.
Data from: Left cortical specialization for visual letter strings predicts rudimentary knowledge of letter-sound association in preschoolers
Reading, one of the most important cultural inventions of human society, critically depends on posterior brain areas of the left hemisphere in proficient adult readers. In children, this left hemispheric cortical specialization for letter strings is typically detected only after approximately 1 y of formal schooling and reading acquisition. Here, we recorded scalp electrophysiological (EEG) brain responses in 5-y-old (n = 40) prereaders presented with letter strings appearing every five items in rapid streams of pseudofonts (6 items per second). Within 2 min of recording only, letter strings evoked a robust specific response over the left occipito-temporal cortex at the predefined frequency of 1.2 Hz (i.e., 6 Hz/5). Interindividual differences in the amplitude of this electrophysiological response are significantly related to letter knowledge, a preschool predictor of later reading ability. These results point to the high potential of this rapidly collected behavior-free measure to assess reading ability in developmental populations. These findings were replicated in a second experiment (n = 26 preschool children), where familiar symbols and line drawings of objects evoked right-lateralized and bilaterally specific responses, respectively, showing the specificity of the early left hemispheric dominance for letter strings. Collectively, these findings indicate that limited knowledge of print in young children, before formal education, is sufficient to develop specialized left lateralized neuronal circuits, thereby pointing to an early onset and rapid impact of left hemispheric reentrant sound mapping on posterior cortical development.
Data from: Developmental effects of visual environment on species-assortative mating preferences in Lake Victoria cichlid fish
Local adaptation can be a potent force in speciation, with environmental heterogeneity leading to niche specialization and population divergence. However, local adaption often requires non-random mating in order to generate reproductive isolation. Population divergence in sensory properties can be particularly consequential in speciation, affecting both ecological adaptation and sexual communication. Pundamilia pundamila and Pundamilia nyererei are two closely related African cichlid species that differ in male coloration, blue vs. red. They co-occur at rocky islands in southern Lake Victoria, but inhabit different depth ranges with different light environments. The species differ in colour vision properties and females exert species-specific preferences for blue vs. red males. Here, we investigated the mechanistic link between colour vision and preference, which could provide a rapid route to reproductive isolation. We tested the behavioural components of this link by experimentally manipulating colour perception – we raised both species and their hybrids under light conditions mimicking shallow and deep habitats - and tested female preference for blue and red males under both conditions. We found that rearing light significantly affected female preference: shallow-reared females responded more strongly to P. pundamilia males and deep-reared females favored P. nyererei males - implying that visual development causally affects mate choice. These results are consistent with sensory-drive predictions, suggesting that the visual environment is key to behavioural isolation of these species. However, the observed plasticity could also make the species barrier vulnerable to environmental change: species-assortative preferences were weaker in females that were reared in the other species' light condition.
Data from: Sensory limitations and the maintenance of color polymorphisms: viewing the 'alba' female polymorphism through the visual system of male Colias butterflies
Although color polymorphisms are a widespread and conspicuous component of extant biodiversity, the selective pressures that act to maintain multiple morphs within populations remain poorly understood in most cases. In particular, the role that visual system limitations may play in maintaining multiple color morphs is not well explored. We used a female-limited color polymorphism common to the butterfly genus Colias, called the 'alba' polymorphism, to investigate the hypotheses that mate-searching males may struggle to discriminate pale 'alba' females from co-occurring heterospecific white butterflies and/or heterospecific 'alba' females, or that 'alba' females may be more difficult to detect than non-'alba' females in natural scenes. Such perceptual limitations may influence the relative mating rates of 'alba' versus non-'alba' females, contributing to the evolutionary persistence of both morphs. Based on receptor-noise-limited modeling of the male Colias visual system, we find that 'alba' females exhibit chromatic and luminance contrasts against background foliage that are most similar to the 'alba' females of other co-occurring Colias species and females of the co-occurring white butterfly Pieris rapae. When compared to other co-flying butterflies including non-'alba' females, 'alba' females are consistently lower in chromatic contrast against background, but higher in luminance contrast. When viewed side-by-side, we estimate that male Colias should be able to discriminate 'alba' females from other co-occurring heterospecific butterflies, including heterospecific 'albas'. However, under field conditions that involve larger distances in space or time, males are likely to face challenges discriminating between conspecific 'alba' females and co-occurring heterospecific white butterflies, particularly heterospecific 'alba' females. Our results suggest that constraints arising from male visual function may be involved in the maintenance of this color polymorphism, particularly in populations that co-occur with other 'alba'-polymorphic Colias species. We argue that such visual system constraints may play a larger role in the maintenance of color polymorphism than has been empirically appreciated to date.
Data from: Social group signatures in hummingbird displays provide evidence of co-occurrence of vocal and visual learning
Vocal learning, in which animals modify their vocalizations based on social experience, has evolved in several lineages of mammals and birds, including humans. Despite much attention, the question of how this key cognitive trait has evolved remains unanswered. The motor theory for the origin of vocal learning posits that neural centers specialized for vocal learning arose from adjacent areas in the brain devoted to general motor learning. One prediction of this hypothesis is that visual displays that rely on complex motor patterns may also be learned in taxa with vocal learning. While learning of both spoken and gestural languages is well-documented in humans, the occurrence of learned visual displays has rarely been examined in non-human animals. We tested for geographic variation consistent with learning of visual displays in long-billed hermits (Phaethornis longirostris), a lek-mating hummingbird that, like humans, has both learned vocalizations and elaborate visual displays. We found lek-level signatures in both vocal parameters and visual display features, including element proportions, sequence syntax, and fine-scale parameters of elements. This variation was not associated with genetic differentiation between leks. In the absence of genetic differences, geographic variation in vocal signals at small scales is most parsimoniously attributed to learning, suggesting a significant role of social learning in visual display ontogeny. The co-occurrence of learning in vocal and visual displays would be consistent with a parallel evolution of these two signal modalities in this species.
Data from: Climate-related environmental variation in a visual signalling device: the male and female dewlap in Anolis sagrei lizards
Animals communicate using a variety of signals that differ dramatically among and within species. The astonishing dewlap diversity in anoles has attracted considerable attention in this respect. Yet, the evolutionary processes behind it remain elusive and have mostly been explored for males only. Here, we considered Anolis sagrei males and females to study signal divergence among populations. First, we assessed the degree of variation in dewlap design (size, pattern, colour) and displays by comparing 17 populations distributed across the Caribbean. Second, we assessed whether the observed dewlap diversity is associated to variation in climate-related environmental conditions. Results showed that populations differed in all dewlap characteristics, with the exception of display rate in females. We further found that males and females occurring in 'xeric' environments had a higher proportion of solid dewlaps with higher UV-reflectance. In addition, lizards inhabiting 'mesic' environments had primarily marginal dewlaps showing high reflectance in red. For dewlap display, a correlation with environment was only observed in males. Our study provides evidence for a strong relationship between signal design and prevailing environmental conditions, which may result from differential selection on signal efficacy. Moreover, our study highlights the importance of including females when studying dewlaps in an evolutionary context.
Data from: Visual obstruction and vigilance: a natural experiment
Visual obstructions can cause an increase in antipredator vigilance in prey animals by making predator detection more difficult. However, visual obstructions can also skew the perception of group size and inter-individual distances and impair the detection of alarm signals by conspecifics. These changes within the group alone can cause an increase in vigilance. To disentangle the contribution of these various factors to changes in vigilance, I documented vigilance in a gregarious species, the semipalmated sandpiper Calidris pusilla, foraging in a habitat where a naturally-occurring visual barrier partially prevented predator detection without altering the transfer of information about predation risk within the group. I used a matched sampling design to collect vigilance data for birds using adjacent areas with and without the visual barrier. In the visually-obstructed area, sandpipers maintained a higher level of vigilance, occurred farther away from cover and in smaller flocks, and preferentially scanned the area of danger with one eye in particular. All these changes suggest that visual obstruction increased perceived predation risk. I conclude that it is the inability to get a good view of any approaching predator, rather than changes in intra-group communication that caused the increase in vigilance in the visually-obstructed area.
Data from: Disentangling visual and olfactory signals in mushroom-mimicking Dracula orchids using realistic three-dimensional printed flowers
Flowers use olfactory and visual signals to communicate with pollinators. Disentangling the relative contributions and potential synergies between signals remains a challenge. Understanding the perceptual biases exploited by floral mimicry illuminates the evolution of these signals. Here, we disentangle the olfactory and visual components of Dracula lafleurii, which mimics mushrooms in size, shape, color and scent, and is pollinated by mushroom-associated flies. To decouple signals, we used three-dimensional printing to produce realistic artificial flower molds that were color matched and cast using scent-free surgical silicone, to which we could add scent. We used GC-MS to measure scents in co-occurring mushrooms, and related orchids, and used these scents in field experiments. By combining silicone flower parts with real floral organs, we created chimeras that identified the mushroom-like labellum as a source of volatile attraction. In addition, we showed remarkable overlap in the volatile chemistry between D. lafleurii and co-occurring mushrooms. The characters defining the genus Dracula – a mushroom-like, 'gilled' labellum and a showy, patterned calyx – enhance pollinator attraction by exploiting the visual and chemosensory perceptual biases of drosophilid flies. Our techniques for the manipulation of complex traits in a nonmodel system not conducive to gene silencing or selective breeding are useful for other systems.
Data from: Visual effects in great bowerbird sexual displays and their implications for signal design
It is often assumed that the primary purpose of a male's sexual display is to provide information about quality, or to strongly stimulate prospective mates, but other functions of courtship displays have been relatively neglected. Male great bowerbirds (Ptilonorhynchus nuchalis) construct bowers that exploit the female's predictable field of view (FOV) during courtship displays by creating forced perspective illusions, and the quality of illusion is a good predictor of mating success. Here, we present and discuss two additional components of male courtship displays that use the female's predetermined viewpoint: (i) the rapid and diverse flashing of coloured objects within her FOV and (ii) chromatic adaptation of the female's eyes that alters her perception of the colour of the displayed objects. Neither is directly related to mating success, but both are likely to increase signal efficacy, and may also be associated with attracting and holding the female's attention. Signal efficacy is constrained by trade-offs between the signal components; there are both positive and negative interactions within multicomponent signals. Important signal components may have a threshold effect on fitness rather than the often assumed linear relationship.
Data from: In the eye of the beholder: visual mate choice lateralization in a polymorphic songbird
Birds choose mates on the basis of colour, song and body size, but little is known about the mechanisms underlying these mating decisions. Reports that zebra finches prefer to view mates with the right eye during courtship, and that immediate early gene expression associated with courtship behaviour is lateralized in their left hemisphere suggest that visual mate choice itself may be lateralized. To test this hypothesis, we used the Gouldian finch, a polymorphic species in which individuals exhibit strong, adaptive visual preferences for mates of their own head colour. Black males were tested in a mate-choice apparatus under three eye conditions: left-monocular, right-monocular and binocular. We found that black male preference for black females is so strongly lateralized in the right-eye/left-hemisphere system that if the right eye is unavailable, males are unable to respond preferentially, not only to males and females of the same morph, but also to the strikingly dissimilar female morphs. Courtship singing is consistent with these lateralized mate preferences; more black males sing to black females when using their right eye than when using their left. Beauty, therefore, is in the right eye of the beholder for these songbirds, providing, to our knowledge, the first demonstration of visual mate choice lateralization.
Data from: Zebrafish differentially process colour across visual space to match natural scenes
Animal eyes have evolved to process behaviorally important visual information, but how retinas deal with statistical asymmetries in visual space remains poorly understood. Using hyperspectral imaging in the field, in vivo 2-photon imaging of retinal neurons, and anatomy, here we show that larval zebrafish use a highly anisotropic retina to asymmetrically survey their natural visual world. First, different neurons dominate different parts of the eye and are linked to a systematic shift in inner retinal function: above the animal, there is little color in nature, and retinal circuits are largely achromatic. Conversely, the lower visual field and horizon are color rich and are predominately surveyed by chromatic and color-opponent circuits that are spectrally matched to the dominant chromatic axes in nature. Second, in the horizontal and lower visual field, bipolar cell terminals encoding achromatic and color-opponent visual features are systematically arranged into distinct layers of the inner retina. Third, above the frontal horizon, a high-gain UV system piggybacks onto retinal circuits, likely to support prey capture.
Data from: Visual adaptation and microhabitat choice in Lake Victoria cichlid fish
When different genotypes choose different habitats to better match their phenotypes, adaptive differentiation within a population may be promoted. Mating within those habitats may subsequently contribute to reproductive isolation. In cichlid fish, visual adaptation to alternative visual environments is hypothesised to contribute to speciation. Here, we investigated whether variation in visual sensitivity causes different visual habitat preferences, using two closely related cichlid species that occur at different but overlapping water depths in Lake Victoria and that differ in visual perception (Pundamilia sp.). In addition to species differences, we explored potential effects of visual plasticity, by rearing fish in two different light conditions: broad-spectrum (mimicking shallow water) or red-shifted (mimicking deeper waters). Contrary to expectations, fish did not prefer the light environment that mimicked their typical natural habitat. Instead, we found an overall preference for the broad-spectrum environment. We also found a transient influence of the rearing condition, indicating that assessment of microhabitat preference requires repeated testing to control for familiarity effects. Together, our results show that cichlid fish exert visual habitat preference, but do not support straightforward visual habitat matching.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.