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4,753 results for “SHAPE”
Data and code for: Past and future extinctions shape the body size - fruit size relationship between palms and mammalian frugivores
<p>The dispersal of seeds by mammalian frugivores influences the structure and composition of plant communities, but most ecosystems have undergone defaunation over thousands of years, a process that continues today. Understanding how past defaunation has affected fruit-frugivore interactions will thus provide insights into how ecosystems may respond to future frugivore loss. By integrating palm and mammalian frugivore trait and occurrence data worldwide, we reveal a global positive relationship between fruit size and body size of frugivore assemblages. Global variation in fruit size is better explained by present-day frugivore assemblages compared to those of the Late Pleistocene (including extinct species), suggesting a substantial ecological and evolutionary reorganization after Pleistocene mammal extinctions. Interestingly, the reverse is true for the Neotropics where some large-fruited palm species may have persisted over thousands of years following extinction of their main seed dispersers. Simulations of frugivore extinction over the next 100 years suggest that changes in body size will require up to a 4% assemblage-level decrease in palm fruit sizes to maintain the current global frugivore body size - fruit size relationship. Absolute changes in assemblage-level means of palm fruit size were on average up to two-fold higher than observed species-level estimates of seed size change following defaunation. Overall, our results suggest that while some large-fruited palms may persist after the loss of their main dispersers, many palms may be unable to keep pace with future defaunation through evolutionary changes in fruit size alone. The burden of the impact of the extinction of seed dispersers will probably be disproportionately borne by large-fruited palms, possibly over thousands of years to come.</p>
Winds at departure shape seasonal patterns of nocturnal bird migration over the North Sea
On their migratory journeys, terrestrial birds can come across large inhospitable areas with limited opportunities to rest and refuel. Flight over these areas poses a risk especially when wind conditions en route are adverse, in which case inhospitable areas can act as an ecological barrier for terrestrial migrants. Thus, within the East-Atlantic flyway, the North Sea can function as an ecological barrier. The main aim of this study was to shed light on seasonal patterns of bird migration in the southern North Sea and determine whether departure decisions on nights of intense migration were related to increased wind assistance. We measured migration characteristics with a radar that was located 18 km off the NW Dutch coast and used simulation models to infer potential departure locations of birds on nights with intense nocturnal bird migration. We calculated headings, track directions, airspeeds, groundspeeds on weak and intense migration nights in both seasons and compared speeds between seasons. Moreover, we tested if departure decisions on intense migration nights were associated with supportive winds. Our results reveal that on the intense migration nights in spring, the mean heading was towards E, and birds departed predominantly from the UK. On intense migration nights in autumn, the majority of birds departed from Denmark, Germany and north of the Netherlands with the mean heading towards SW. Prevailing winds from WSW at departure were supportive of a direct crossing of the North Sea in spring. However, in autumn winds were generally not supportive, which is why many birds exploited positive wind assistance which occurred on intense migration nights. This implies that the seasonal wind regimes over the North Sea alter its migratory dynamics which is reflected in headings, timing and intensity of migration.
Data from: Behavioral hypervolumes of predator groups and predator-predator interactions shape prey survival rates and selection on prey behavior
Predator-prey interactions often vary on the basis of the traits of the individual predators and prey involved. Here we examine whether the multidimensional behavioral diversity of predator groups shapes prey mortality rates and selection on prey behavior. We ran individual sea stars (Pisaster ochraceus) through three behavioral assays to characterize individuals' behavioral phenotype along three axes. We then created groups that varied in the volume of behavioral space that they occupied. We further manipulated the ability of predators to interact with one another physically via the addition of barriers. Prey snails (Chlorostome funebralis) were also run through an assay to evaluate their predator avoidance behavior before their use in mesocosm experiments. We then subjected pools of prey to predator groups and recorded the number of prey consumed and their behavioral phenotypes. We found that predator-predator interactions changed survival selection on prey traits: when predators were prevented from interacting, more fearful snails had higher survival rates, whereas prey fearfulness had no effect on survival when predators were free to interact. We also found that groups of predators that occupied a larger volume in behavioral trait space consumed 35% more prey snails than homogeneous predator groups. Finally, we found that behavioral hypervolumes were better predictors of prey survival rates than single behavioral traits or other multivariate statistics (i.e., principal component analysis). Taken together, predator-predator interactions and multidimensional behavioral diversity determine prey survival rates and selection on prey traits in this system.
Data from: Feeding environment and other traits shape species' roles in marine food webs
Food webs and meso-scale motifs allow us to understand the structure of ecological communities and define species' roles within them. This species-level perspective on networks permits tests for relationships between species' traits and their patterns of direct and indirect interactions. Such relationships could allow us to predict food-web structure based on more easily-obtained trait information. Here we calculated the roles of species (as vectors of motif position frequencies) in six well-resolved marine food webs and identified the motif positions associated with the greatest variation in species' roles. We then tested whether the frequencies of these positions varied with species' traits. Despite the coarse-grained traits we used, our approach identified several strong associations between traits and motifs. Feeding environment was a key trait in our models and may shape species' roles by affecting encounter probabilities. Incorporating environment into future food web models may improve predictions of an unknown network structure.
Data from: Management actions shape dung beetle community structure and functional traits in restored tallgrass prairie
<p>1. Ecosystem restoration often focuses on reestablishing species richness and diversity of native organisms, especially plants. However, effective restoration requires re-establishment of ecosystem functions and processes by all trophic levels. Functional trait descriptions of communities, including decomposer communities, may provide more comprehensive evaluations of restoration activities and management than taxonomic community metrics alone.</p> <p>2. We examined species and functional trait composition of dung beetle (Coleoptera: Scarabaeidae, Geotrupidae) communities across a 3-31 year chronosequence of restored prairies, in which sites varied in the presence of re-introduced bison and prescribed fire. We calculated functional diversity metrics and community-weighted mean trait values using behavioral and morphological measurements. We also performed a dung decomposition experiment to measure an ecosystem function driven by these insects.</p> <p>3. Bison presence doubled beetle abundance and increased richness by 50%. Shannon diversity increased with restoration age, nearly doubling from the youngest to oldest restorations. Functional diversity was unchanged, except functional richness, which was reduced by bison and fire presence. Beetles were, on average, smaller in older restorations, although this pattern was weaker when bison were present.</p> <p>4. Dung decomposition was unaffected by site characteristics but increased with community weighted mean beetle mass. Dung decomposition was better predicted by mean trait values, suggesting that supporting large-bodied species may be more important than species diversity in settings where maximizing decomposition function is a goal.</p> <p>5. Restoration managers should consider dung beetle communities and their functional characteristics when making management decisions, particularly where large grazers are a component of management strategies.</p> <p> </p>
Empirical shapes for the publication "Modifications of the K-Profile parameterization with nondiffusive fluxes for wave effects"
<p>This dataset contains data for the reproduction of the empirical shape functions G_l and g_s introduced in the publication "Modifications of the K-Profile parameterization with nondiffusive fluxes for wave effects".</p>
Seasonality and interspecific competition shape individual niche variation in co-occurring tetra fish in Neotropical streams
The drivers of intraspecific niche variation and its effects on species interactions are still unclear, especially in species-rich Neotropical environments. Here, we investigated how ecological opportunity and interspecific competition affect the degree of individual trophic specialization and the population niche breadth in tetra fish. We studied the four ecologically similar species (Psalidodon aff. gymnodontus, P. aff. paranae, P. bifasciatus, and Bryconamericus ikaa) in subtropical headwater streams (three sites with two co-occurring species and three sites with only one species). We sampled fish in two contrasting seasons (winter/dry and summer/wet), and quantified their trophic niches using gut content analysis. Psalidodon bifasciatus was the only species distributed over all the sampled streams. We observed seasonal differences in population trophic niche breadth of P. bifasciatus just when this species co-occurred with P. aff. gymnodontus. These findings confirm the complex nature of the effects of interspecific competition, depending, for instance, on the identity of the competitor. The degree of individual specialization of P. bifasciatus was higher in the winter, and it was not influenced by the presence of another species. Conversely, the other two Psalidodon species studied presented greater individual specialization in the summer, when fish consumed a higher proportion of allochthonous items (terrestrial insects and seeds), and there were no effects only for B. ikaa. Herein, our results suggest that seasonality in food-resource availability is a major driver of niche variation and it has the potential to play an important role in how these similar tetra species interact and coexist.
Data from: Metabolic rate shapes phenotypic covariance among physiological, behavioural, and life history traits in honeybees
<p>Metabolic rate is often cited as the fundamental rate that determines the rate of all biological processes by shaping energetic availability for the various behavioral and life history traits that contribute to performance. It has therefore been suggested that metabolic rate drives the widely observed covariance among these different levels of phenotypic traits. However, much of the work on this topic has relied on pairwise correlational analysis, thereby leaving an important gap in our understanding regarding the functional links that shape this phenotypic covariance, often referred to as pace-of-life. Using honeybees as an experimental model, we measured a large number of behavioural, life history and physiological traits in individual bees and used a structural equation model to characterize the phenotypic covariance structure among these traits. Following this with a path analysis, we demonstrate that variation in metabolic rate plays a fundamental proximate role in driving this phenotypic covariance structure in honeybees. We discuss the importance of these findings in the context of how interindividual variation in terms of slow-fast phenotypes may drive the phenotype of a group and the functional role metabolic rate might play in shaping division of labour and social evolution.</p>
Landscape heterogeneity shapes bird phylogenetic responses at forest-matrix interfaces in Atlantic Forest, Brazil
<p>Agricultural intensification is one of the major factors driving biodiversity loss. However, most studies in human-dominated landscapes have used taxonomic diversity in their analysis, ignoring evolutionary relationships. Consequently, the relationship between landscape structure and phylogenetic diversity is not well understood. Here, we tested the hypothesis that landscape heterogeneity is positively related to bird phylogenetic indexes of diversity and structure, leading to over-dispersed phylogenies in very heterogeneous landscapes. We analyzed phylogenetic responses in interfaces between forest edges and anthropogenic matrices (forest-pasture and forest-eucalyptus) using generalized linear mixed models. We also compared these indexes between land covers to assess which one best preserves the phylogenetic history of communities. We used both traditional phylogenetic indexes and those corrected for species richness. Our results showed that phylogenetic diversity varied significantly between land cover types, but this did not occur when we removed effects associated with species richness, suggesting that all land covers preserve similar levels of evolutionary history. Additionally, our best models showed a positive relationship between landscape heterogeneity and bird phylogenetic indexes of diversity and structure, but the strength of these relationships may be land-cover dependent. In summary, our work highlights the influence of landscape heterogeneity on the phylogenetic diversity and structure of bird communities, reinforcing the need for its incorporation into conservation-based studies.</p>
Detecting phylogenetic signal and adaptation in papionin cranial shape by decomposing variation at different spatial scales
<p>Phylogenetic reconstruction based on morphometric data is hampered by homoplasies. For example, many similarities in cranial form between primate taxa more strongly reflect ecological similarities rather than phylogenetic relatedness. However, the way in which the different cranial bones constitute cranial form is, if at all, of less functional relevance and thus largely hidden from selection. We propose that these "constructional details" are better indicators of phylogenetic history than any large-scale shape feature or raw form variable. Within a geometric morphometric context, we show how to analyze the relative extent of bones independently of differences in overall shape. We also show how to decompose total shape variation into small-scale and large-scale shape variation. We apply both methods to the midsagittal cranial morphology of papionin monkeys, which are well known for the discrepancy between morphological similarities and phylogenetic relationships. We study phylogenetic signal and functional adaptation using a molecular phylogeny and contextual data on feeding ecology and locomotor behavior. As expected, total cranial shape, bone outline shape, and large-scale shape features were only weakly associated with phylogenetic distance. But the relative bone contributions and small-scale shape features were both highly correlated with phylogenetic distances. By contrast, the association with ecological and behavioral variables was strongest for the outline shape and large-scale shape features. Studies of morphological adaptation and phylogenetic history thus profit from a decomposition of shape variation into different spatial scales.</p>
Vertebral pneumaticity is correlated with serial variation in vertebral shape in storks
<p class="Body"><span><span><span><span><span><span><span><span><span><span>Birds and their ornithodiran ancestors are unique among vertebrates in exhibiting air-filled sinuses in their postcranial bones, a phenomenon called postcranial skeletal pneumaticity. The factors that account for serial and interspecific variation in postcranial skeletal pneumaticity are poorly understood, although body size, ecology, and bone biomechanics have all been implicated as influencing the extent to which pneumatizing epithelia invade the skeleton and induce bone resorption. Here, I use high-resolution computed-tomography to holistically quantify vertebral pneumaticity in members of the neognath family Ciconiidae (storks), with pneumaticity measured as the relative volume of internal air space. These data are used to describe serial variation in extent of pneumaticity and to assess whether and how pneumaticity varies with the size and shape of a vertebra. Pneumaticity increases dramatically from the middle of the neck onwards, contrary to previous predictions that cervical pneumaticity should decrease towards the thorax to maintain structural integrity as the mass and bending moments of the neck increase. Although the largest vertebrae sampled are also the most pneumatic, vertebral size cannot on its own account for serial or interspecific variation in extent of pneumaticity. Vertebral shape, as quantified by three-dimensional geometric morphometrics, is found to be significantly correlated with extent of pneumaticity, with elongate vertebrae being less pneumatic than craniocaudally short and dorsoventrally tall vertebrae. Considered together, the results of this study are consistent with the hypothesis that shape- and position-specific biomechanics influence the amount of bone loss that can be safely tolerated. These results have potentially important implications for the evolution of vertebral morphology in birds and their extinct relatives.</span></span></span></span></span></span></span></span></span></span></p>
MicroED datasets from 3 proteinase K wedge-shaped lamellae
<p>Plunge-frozen grids containing crystals of proteinase K with approximate dimensions of 12 x 10 x 10 µm were coated with a layer of organoplatinum using the in situ gas injection system of the Scios DualBeam cryoFIB instrument (Thermo Fisher Scientific). A series of initial milling steps produced lamellae of approximately 0.5 µm thickness. Wedged lamellae were then generated by tilting the stage through a defined angle away from the initial milling position before further milling from the underside only. The defined angle was calculated to produce a lamella where the leading edge measured approximately 200 nm and the back edge of the crystal within the lamella measured approximately 400 nm.</p> <p>Electron diffraction data were collected using a Thermo Fisher Scientific Talos Arctica transmission electron microscope equipped with a Ceta-D camera. The microscope was operated at an accelerating voltage of 200 kV using gun lens 8, a spot size of 11 and a 50 µm C2 aperture. These conditions gave a beamsize of 1.3 µm and an approximate electron dose of 0.04 e/Å<sup>2</sup>/s at the sample position.</p> <p>Diffraction images can be read in DIALS using the <a href="https://github.com/dials/dxtbx_ED_formats/blob/master/FormatMRC.py">FormatMRC</a> plug-in, after renaming the files to conform to a standard serial number template.</p>
In the Shape of Europe Through the Islamic Lens: Circulation and Use of Turko-Mongol Textiles in Christian Context (ISETIL)
<p>5<sup>th</sup> Project Presentation</p>
Absolute and arbitrary orientation of single molecule shapes
<p>All software for the kinetic, thermodynamic, and EM simulations associated with the journal paper are presented here. Additionally the AFM images and codes for analyzing the orientation of right triangles as well as e-beam and DNA origami design files associated with the paper is included.</p>
Interspecific allometry for sexual shape dimorphism: macroevolution of multivariate sexual phenotypes with application to Rensch's rule
<p>Allometric trends in the degree of sexual dimorphism with body size have long fascinated evolutionary biologists. Many male-biased clades display more prominent sexual dimorphism in larger taxa (Rensch's rule), with most examples documenting this pattern for body size dimorphism. While sexual dimorphism in traits other than body size is equally functionally relevant, characterizing allometric patterns of sexual dimorphism in such traits is hampered by lack of an analytical framework that can accommodate multivariate phenotypes. In this paper we derive a multivariate equivalency for investigating trends in sexual dimorphism – relative to overall body size – across taxa and provide a generalized test to determine whether such allometric patterns correspond with Rensch's rule. For univariate linear traits like body size, our approach yields equivalent results to those from standard procedures, but our test is also capable of detecting trends in multivariate datasets like shape. Computer simulations reveal the method displays appropriate statistical properties, and an empirical example in Mediterranean lizards provides the first demonstration of Rensch's rule in a multivariate phenotype (head shape). Our generalized procedure substantially extends the analytical toolkit for investigating macroevolutionary patterns of sexual dimorphism and seeking a better understanding of the processes that underlie them.</p>
Predation risk shapes the degree of placentation in natural populations of live-bearing fish
<p class="manuscriptABSATZ"><span>The placenta is a complex life-history trait that is ubiquitous across the tree of life. Theory proposes that the placenta evolves in response to high performance-demanding conditions by shifting maternal investment from pre- to post-fertilization, thereby reducing a female's reproductive burden during pregnancy. We test this hypothesis by studying populations of the fish species <i>Poeciliopsis retropinna</i> in Costa Rica. We found substantial variation in the degree of placentation among natural populations associated with predation risk: females from high predation populations had significantly higher degrees of placentation compared to low predation females, while number, size and quality of offspring at birth remained unaffected. Moreover, a higher degree of placentation correlated with a lower reproductive burden and hence likely an improved swimming performance during pregnancy. Our study advances an adaptive explanation for why the placenta evolves by arguing that an increased degree of placentation offers a selective advantage in high predation environments. </span></p>
Encoding and control of airflow orientation by a set of Drosophila fan-shaped body neurons
<p class="Body"><span><span><span><span><span><span><span><span><span><span>The insect Central Complex (CX) is thought to underlie goal-oriented navigation but its organization is still not fully understood. We recorded from genetically-identified CX cell types in <i>Drosophila</i> and presented directional visual, olfactory, and airflow cues known to elicit orienting behavior. We found that a group of neurons targeting the ventral fan-shaped body (ventral P-FNs) are robustly tuned for airflow direction. Ventral P-FNs did not generate a "map" of airflow direction. Instead, cells in each hemisphere were tuned to 45° ipsilateral, forming a pair of orthogonal bases. Imaging experiments suggest that ventral P-FNs inherit their airflow tuning from neurons that provide input from the lateral accessory lobe (LAL) to the noduli (NO). Silencing ventral P-FNs prevented flies from selecting appropriate corrective turns following changes in airflow direction. Our results identify a group of central complex neurons that robustly encode airflow direction and are required for proper orientation to this stimulus.</span></span></span></span></span></span></span></span></span></span></p>
Data used in 'The joint role of coevolutionary selection and network structure in shaping trait complementarity in mutualisms' manuscript
<p>The files in this repository correspond to the raw and processed data described in the 'The joint role of coevolutionary selection and network structure in shaping trait complementarity in mutualisms' manuscript.</p> <p>Once expanded, the zip files contains two directories and one documentation file, named data_documentation. Please refer to this file for a thorough description of the organization and contents of raw and processed data files.</p>
Introductory gestures before songbird vocal displays are shaped by learning and biological predispositions
<p>Numerous animal displays begin with introductory gestures. For example, lizards start their head-bobbing displays with introductory push-ups and many songbirds begin their vocal displays by repeating introductory notes (INs) before producing their learned song. Among songbirds, the acoustic structure and the number of INs produced before song vary considerably between individuals in a species. While similar variation in songs between individuals is a result of learning, whether variation in INs are also due to learning remains poorly understood. Here, using natural and experimental tutoring with male zebra finches, we show that mean IN number and IN acoustic structure are learned from a tutor. Interestingly, IN properties and how well INs were learned, was not correlated with the accuracy of song imitation and only weakly correlated with some features of songs that followed. Finally, birds artificially tutored with songs lacking INs still repeated vocalizations that resembled INs, before their songs, suggesting biological predispositions in IN production. These results demonstrate that INs, just like song elements, are shaped both by learning and biological predispositions. More generally, our results suggest mechanisms for generating variation in introductory gestures between individuals while still maintaining the species-specific structure of complex displays like birdsong.</p>
Metabolic rate data and code for: Intra-specific differences in metabolic rates shape carbon stable isotope trophic discrimination factors of muscle tissue in the common teleost Eurasian perch (Perca fluviatilis)
<p>Metabolic rate data and code for: Intra-specific differences in metabolic rates shape carbon stable isotope trophic discrimination factors of muscle tissue in the common teleost Eurasian perch (Perca fluviatilis)</p> <p> </p> <p>The raw data and R-code used to calculate SMR used in the analysis. </p>
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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.