Find research datasets worth reusing

opencc-zeroNov 2022View details →

Data from: Geographic and climatic constraints on bioregionalization of European ants

Aim: Biogeographic regionalization is scant for most insect groups due to shortfalls in distribution and phylogenetic information, namely the Wallacean and Darwinian shortfalls respectively. Here, we focused on the European ants and compared new techniques to classical analyses based on regional lists and taxonomic methods. We asked the following: 1) Can grid-based regionalizations using novel distribution data improve biogeographic transitions? and 2) Can phylogenetic approaches reveal new insights regarding ant evolutionary history? Location: Europe and Anatolia. Taxon: Ants (Formicidae). Methods: First, we developed a refined database integrating the occurrences of 747 ant species across 207 regions of Europe and Anatolia, based on newly expert-validated records derived from the existing Global Ant Biodiversity Informatics (GABI) database. Using range estimates for these species derived from polygons and species distribution modelling, we produced species assemblages in 50 × 50 km grid cells. We calculated taxonomic and phylogenetic turnover of ant assemblages, then performed a hierarchical clustering procedure to delineate biogeographic structure. Results: At both the regional list- and grid assemblage-levels, the Mediterranean has higher turnover and more biogeographic regions than northern Europe, both taxonomically and phylogenetically. Delineations based on grid assemblages detected more detailed biogeographic transitions, while those based on regional lists showed stronger insularity in biogeographic structure. The phylogenetic regionalization suggested a very similar spatial structure but varied affinities between assemblages in comparison to the taxonomic approach. Main conclusions: Here, we integrated expert-validated regional lists, species distribution modelling, and a recent phylogeny to tackle Wallacean and Darwinian shortfalls for an important insect group by developing a next-generation map of biogeographic regionalization for European ants. The results of this study suggest strong constraints from geographic barriers and potential effects of climatic history on ant distributions and evolutionary history and also provide baseline spatial information for future investigations of regional insect distributions.

opencc-by-4.0Nov 2022View details →

Sensing a priori constraints in DNNs for solving geophysical problems

Original data and associated results for the paper "Sensing a priori constraints in DNNs for solving geophysical problems" submitted to PNAS on Nov. 16th, 2022.

opencc-by-4.0Nov 2022View details →

Preprocessed EEG data for the experiment reported in "Understanding the effects of constraint and predictability in ERP"

This repository contains intermediate preprocessing files for the above-named paper. Preprocessing scripts are stored at: <a href="http://osf.io/fndk5/">https://osf.io/fndk5/</a> For the raw EEG data, please see <a href="http://zenodo.org/record/6992085">https://zenodo.org/record/6992085</a>. The intermediate preprocessing files are *_ica.rds (R datasets saved after running ICA), and *_prepro.rds (R datasets saved after individual preprocessing complete, before combination with other participants). To use the data with the preprocessing scripts, download and save it in a folder called prepro_EEG_data as explained in the preprocessing script.

opencc-zeroJan 2023View details →

Data: Large old trees increase growth under shifting climatic constraints: Aligning tree longevity and individual growth dynamics in primary mountain spruce forests

In a world of accelerating changes in environmental conditions driving tree growth, tradeoffs between tree growth rate and longevity could curtail the abundance of large, old trees (LOTs), with potentially dire consequences for biodiversity and carbon storage. However, the influence of tree-level tradeoffs on forest structure at landscape scales will also depend on disturbances, which shape tree size and age distribution, and on whether LOTs can benefit from improved growing conditions due to climate warming. We analyzed temporal and spatial variation in radial growth patterns from ~5000 Norway spruce (Picea abies (L.) H. Karst) live and dead trees from the Western Carpathian primary spruce forest stands. We applied mixed-linear modeling to quantify the importance of LOT growth histories and stand dynamics (i.e. competition and disturbance factors) on lifespan. Finally, we assessed regional synchronization in radial growth variability over the 20th century, and modelled the effects of stand dynamics and climate on LOTs recent growth trends. Tree age varied considerably among forest stands, implying an important role of disturbance as an age constraint. Slow juvenile growth and longer period of suppressed growth prolonged tree lifespan, while increasing disturbance severity and shorter time since last disturbance decreased it. The highest age was not achieved only by trees with continuous slow growth, but those with slow juvenile growth followed by subsequent growth releases. Growth trend analysis demonstrated an increase in absolute growth rates in response to climate warming, with late summer temperatures driving the recent growth trend. Contrary to our expectation that LOTs would eventually exhibit declining growth rates, the oldest LOTs (>400 years) continuously increase growth throughout their lives, indicating a high phenotypic plasticity of LOTs for increasing biomass, and a strong carbon sink role of primary spruce forests under rising temperatures, intensifying droughts, and increasing bark beetle outbreaks.

opencc-by-4.0Jan 2023View details →

Data files for Constraints on axionlike particles from a combined analysis of three flaring Fermi flat-spectrum radio quasars

In this repository, we provide data files in connection to our publication “Constraints on axionlike particles from a combined analysis of three flaring Fermi flat-spectrum radio quasars” submitted for publication in Physical Review D and available on the Arxiv: <a href="https://arxiv.org/abs/2211.03414">https://arxiv.org/abs/2211.03414</a> In the paper, we analyze data from the Fermi Large Area Telescope (LAT) of three flat spectrum radio quasars (FSRQs): 3C454.3, 3C279, and CTA102, to search for signatures of oscillations between photons and axion-like particles (ALPs). In this repository, we provide the following data: <ul> <li>Files ending on *_data_seds.npy contain the spectral energy distributions (SEDs) measured with the Fermi LAT and extracted using the fermipy software</li> <li>Files ending on *_LLs.npy contain the log-likelihood values of our fits over a grid of ALP masses and photon-ALP couplings</li> <li>Files ending on *_Lambdas.npy contain the log-likelihood ratio test values of our fits over a grid of ALP masses and photon-ALP couplings</li> <li>Files ending on *_LL_thresh.npy contain the threshold values for the log-likelihood ratio test for which we can claim an exclusion at the 95% confidence level over a grid of ALP masses and photon-ALP couplings</li> <li>Files ending on*_contours.npy contain the upper limit contours.</li> </ul> Files starting with "ALL" contain the likelihoods combined over all sources We also provide a minimal jupyter notebook, analysis_arrays.ipynb, that demonstrates how to read in the files.

opencc-by-4.0Mar 2023View details →

Supplemental Materials for "Convective boundary mixing in main-sequence stars: theory and empirical constraints"

MESA inlists and data products used for generating the figures of the review paper: "Convective boundary mixing in main-sequence stars: theory and empirical constraints".

opencc-zeroMar 2023View details →

Data for: Drought impairs herbivore-induced volatiles, but not through constraints on newly assimilated carbon

Volatile terpenes serve multiple biological roles including tree resistance against herbivores. The increased frequency and severity of drought stress observed in forests across the globe may hinder trees from producing defense-related volatiles in response to biotic stress. To assess how drought-induced physiological stress alters volatile emissions alone and in combination with a biotic challenge, we monitored pre-dawn water potential, gas exchange, needle terpene concentrations, and terpene volatile emissions of ponderosa pine (Pinus ponderosa) saplings during three periods of drought and in response to simulated herbivory via methyl jasmonate application. Although three-, six-, and seven-week drought treatments reduced net photosynthetic rates by 20%, 89%, and 105%, respectively, the magnitude of volatile fluxes remained generally resistant to drought. Herbivore-induced emissions, however, exhibited threshold-like behavior; saplings were unable to induce emissions above constitutive levels when pre-dawn water potentials were below the approximate zero-assimilation point. By comparing compositional shifts in emissions to needle terpene concentrations, we found evidence that drought effects on constitutive and herbivore-induced volatile flux and composition are primarily via constraints on the de novo fraction, suggesting that reduced photosynthesis during drought limits the carbon substrate available for de novo volatile synthesis. However, results from a subsequent 13CO2 pulse-chase labeling experiment then confirmed that both constitutive (<3% labeled) and herbivore-induced (<8% labeled) de novo emissions from ponderosa pine are synthesized predominantly from older carbon sources with little contribution from new photosynthates. Taken together, we provide evidence that in ponderosa pine, drought does not constrain herbivore-induced de novo emissions through substrate limitation via reduced photosynthesis, but rather, through more sophisticated molecular and/or biophysical mechanisms that manifest as saplings reach the zero-assimilation point. These results highlight the importance of considering drought severity when assessing impacts on the herbivore-induced response and suggest that drought-altered volatile metabolism constrains induced emissions once a physiological threshold is surpassed.

opencc-zeroMar 2023View details →

Data for: Is the hyoid a constraint on innovation? A study in convergence driving feeding in fish-shaped marine tetrapods

The hyoid apparatus is essential for underwater feeding in marine tetrapods, but it is unclear whether this complex has evolved as convergently as other traits, such as dentition or locomotion. Here we compare the ossified hyoid elements in ophthalmosaurid ichthyosaurs and odontocete cetaceans, two groups with an overall similar body shape, to understand whether the hyoid elements show any signs of convergence in the context of feeding. We examined three types of data (size, morphology, and internal bone microstructure) in ophthalmosaurid and odontocete taxa in which these elements are preserved. Our data show that ichthyosaurs never experienced a shift in feeding mode, which might indicate that their hyoid apparatus never adapted to suction feeding. Also, the internal microstructure of the two animal groups differs, where the odontocetes have an overall less compact structure, ophthalmosaurid ichthyosaurs have cancellous inner cones in an outer, more compact sheath. These differences are likely explained as biomechanical adaptations to different feeding modes. Thus, the hyoid changed less, and acted more as a constraint for feeding innovation in ichthyosaurs compared to cetaceans, and through a much longer time span (over 150 million years).

opencc-zeroMay 2023View details →

Physiological constraints and cognitive chunking in Zebra Finch songs: Data and R script

Learned bird songs often have a hierarchical organization. In the case of zebra finches, each bird's song is made up of a string of notes delivered in a stereotyped sequence to form a "motif", and motifs are repeated to form a song bout. During song learning, young males copy "chunks" of two or more consecutive notes from their tutors' songs. These chunks are represented as distinct units within memory (during learning) and within motor systems (during song production). During song performance, motifs may deviate from the learned sequence by stopping short, starting late, or by skipping, inserting or repeating notes. We measured acoustic and temporal variables related to the respiratory and vocal physiology of song production and asked how they related to deviations from each bird's "canonical" sequence. The best predictor of deviations from that sequence was the duration of the silent interval between notes, when inspiration normally occurs. Deviations from the canonical motif occurred less often after higher-pitched notes, perhaps because a high-low sequence forms a prosodic unit. Premature stops often followed louder and longer notes, suggesting that respiratory and muscular physiology influence the location of such stops. Boundaries between the learned chunks of a male's motif predicted where and how often non-canonical starts occurred. Physiological and cognitive elements also interacted to define the segmentation of zebra finch song sequences. Long silent intervals between notes were associated both with physiology (inspirations) and with the cognitive boundaries of learned chunks – and hence with deviations from the canonical motif.

opencc-zeroJun 2023View details →

Raw data for: Over-eruption in marsupial carnivore teeth: compensation for a constraint

Pronounced over-eruption of the canine teeth, much greater than in eco-morphologically equivalent placental carnivores, occurs with age and growth in Australian marsupial carnivores. Suppression of functional tooth replacement is a characteristic of marsupials and is frequent among diverse placentals, where the primitive therian pattern is two generations of incisor, canine and premolar teeth. Rapid determinate growth is one among multiple hypotheses proposed to explain the loss of tooth replacement in mammals. In this line of reasoning, the animal reaches a sufficient body or jaw size to accommodate adult-sized teeth by the time it requires functional dentition. Marsupial carnivores have a full set of adult anterior teeth at weaning, which erupt into a juvenile jaw that is 25 to 30 % adult size, compared with well grown in placental carnivores. Indeterminate over-eruption of the canine teeth in marsupial carnivores results in increasing canine height and diameter with increasing body size with age, suggesting this is a compensatory mechanism for the constraint of a single generation of anterior teeth. Patterns of over-eruption in different tooth types of marsupial carnivores are consistent with two non-exclusive mechanisms that operate in other mammals, a response to tooth wear and lack of an occlusal partner.

opencc-by-4.0Jul 2023View details →

Data for "Chasing rainbows and ocean glints: Inner working angle constraints for the Habitable Worlds Observatory"

Data for the paper on "Chasing rainbows and ocean glints: Inner working angle constraints for the Habitable Worlds Observatory"

opencc-by-4.0Jul 2023View details →

Data for "Climatic Constraints of Spring Phenology and its Variability on the Mongolian Plateau from 1982 to 2021"

The files named "SOSmean_Mongolia Plateau", derived from the GIMMS NDVI3g dataset (1982-2015) and the extended GIMMS NDVI (2016-2021) (i.e., NDVI for 40-year).

opencc-zeroJul 2023View details →

Geographical trends of soil-associated biodiversity changes due to tree plantations in South America: biome and climate constraints revealed through meta-analysis

Aim Evaluate the interaction between climate and biome structure when explaining changes in species richness of soil-associated communities due to tree plantations developed in different biomes. Compare the response of plants, soil invertebrates, and soil microorganisms, and test whether they should be considered sensitive-coupled biotas. Location Continental South America. Time period 1996–2023 Major taxa studied Plants, soil invertebrates and soil microorganisms Methods Through a meta-analysis, the change in species richness (i.e., response ratio) associated with tree plantations was evaluated in 127 points of study across South America, considering soil-associated communities of plants, invertebrates and microorganisms. The influence of biome structure (open vs. closed habitats) on the response ratio and its interaction with the actual evapotranspiration (AET) and temperature seasonality was evaluated. Differentiated responses of different taxa were tested by comparing models with and without an interaction term referring to the taxon studied. The regional agricultural cover and plantation age were considered as anthropogenic variables. Results Models containing the AET were better at explaining the trend of change in species richness than those with temperature seasonality. The response to the change in species richness was oppositely related to the AET in open and closed biomes. Plants presented a higher loss in species richness than soil invertebrates and microorganisms. The three taxa were positively associated with AET, while seasonality was not relevant in any case. Both anthropogenic variables significantly lessened the change in species richness in all models. Main conclusions The structural contrast between the anthropogenic habitat and the biome where it is developed is a key factor influencing the response of soil-associated communities to tree plantations. Nevertheless, its influence must be assessed together with climatic and anthropogenic variables given that their interaction can explain different geographical trends in the change in species richness across regions.

opencc-by-4.0Jul 2023View details →

Oxygen isotope constraints on the ventilation of the modern and glacial Pacific: Water fractions and the associated errors

There is two associated datasets linked to the study: Oxygen isotope constraints on the ventilation of the modern and glacial Pacific. One whch contains the values of the 4 end-memebrs defined in the study, and the other one represent the error associated to the reconstruction of each parameter based on the fractions calculated.

opencc-by-4.0Aug 2023View details →

Demand-Side Constraints in Development: The Role of Market Size, Trade, and (In)Equality

Data and replication code package for the paper "Demand-Side Constraints in Development: The Role of Market Size, Trade, and (In)Equality"

opencc-by-4.0Aug 2023View details →

Experimental constraints on isotopic resetting: synkinematic 40Ar loss from crystal-plastically deformed muscovite

Supporting analytical Ar/Ar data and mineral compositional data for the paper: "Experimental constraints on isotopic resetting: synkinematic 40Ar loss from crystal-plastically deformed muscovite" by: Alexane Legeay, Stéphane Scaillet, Jacques Précigout, Holger Stünitz, Angelo Mottolese, and Florian Duval submitted to to Geochimica et Cosmochimica Acta.

Data from: Global variation in the relationship between avian phylogenetic diversity and functional distance is driven by environmental context and constraints

Aim: If evolutionary distance is akin to evolutionary chance, then it follows that species assemblages that are distantly related will also be more disparate in terms of their traits, features and the niches they occupy. Yet, studies have found that the total phylogenetic distance of an assemblages, known as phylogenetic diversity, is an unreliable surrogate for functional diversity. We investigate global variation in the relationship between Faith's Phylogenetic Diversity (PD) and Mean Pairwise Functional Distance (MPFD) across latitude and the influence of migratory species on both these aspects of diversity. Location: Global. Time period: Present day. Major taxa studied: Birds. Methods: We measure PD and MPFD for over 9,000 species of bird across more than 17,000 globally distributed assemblages. We obtain standardised effect sizes for both indices by simulating assemblage composition under an ecologically informed null model. We employ path analysis to characterise variation in the relationship between PD's and MPFD across latitude, elevation and with proportion of migratory species. Results: Globally, assemblages that were phylogenetically diverse tended to be less functionally dispersed than expected; however this relationship showed considerable variation across latitude decreasing with distance from the equator. The proportion of migratory species in an assemblage was found to be an important predictor of functional diversity, with migrant rich assemblages generally showing less functional diversity than expected. We identify the Andes and Hengduan Mountains as regions of exceptional bird functional diversity. Main conclusions: The relationship between phylogenetic diversity and function diversity is context specific, varying across environmental gradients such as latitude, and influenced by ecological phenomena such a migration. Thus, care should be taken using phylogenetic diversity as a proxy for functional diversity, particularly in clades with sparse functional data. Instead we recommend that studies consider how phylogenetic diversity's surrogacy for functional diversity may be impacted by environmental context and evaluate empirical observations against biogeographically constrained and ecological informed null models.

Paleomagnetic constraint on the Age of the Shyok Suture Zone

The India-Eurasia collision is a key case study for understanding the influence of plate tectonic processes on Earth's crust, atmosphere, hydrosphere and biosphere. However, the timing of the final India-Eurasia continental collision is debated due to significant uncertainty in the age of the collision between the Kohistan-Ladakh arc and Eurasia along the Shyok suture zone. Here we present paleomagnetic results that constrain the Karakoram terrane in northwest India to a paleolatitude of 19.9 ± 8.9 °N between 93 – 75 million years ago (Ma). Our results show that the Karakoram terrane was situated on the southern margin of Eurasia in the Late Cretaceous. Our results indicate that the Kohistan-Ladakh arc and Eurasian continent had not converged until < 61.6 Ma, placing a Paleocene older limit on the age of final closure of the Shyok suture zone. This suggests that the India-Eurasia collision in northwestern India likely occurred after the closure of the oceanic basin between the Kohistan-Ladakh arc and Eurasia. The Paleocene collision event affecting India that has been widely interpreted to represent the final India-Eurasia collision instead records the arc-continent collision between the Kohistan-Ladakh arc and the northern edge of India prior to the final India-Eurasia collision. The final India-Eurasia collision in northwest India most likely occurred after the closure of the oceanic basin between the Kohistan-Ladakh arc and Eurasia.

Beach recreationists perceive a lack of knowledge about shorebirds' needs as a constraint to walking around shorebird flocks

<div>Walking through shorebird flocks can have negative impacts on shorebird populations. Understanding human behavior is essential for minimizing disturbance. As such, we used a mixed-methods approach consisting of phone interviews and a survey to explore 1) recreationists' perceived benefits and constraints to voluntarily walking around shorebird flocks, 2) recreationists' intentions to walk around shorebird flocks, 3) differences in behavioral intention by sociodemographic variables, and 4) differences in norms, benefits, and constraints among recreationists who intend to walk around flocks and recreationists who do not intend to walk around flocks. From the interviews and survey, we found that recreationists' perceived benefits to walking around flocks were maintaining undisturbed conditions for shorebirds and reducing harm to people and their dogs. Recreationists perceived constraints to walking around flocks related to knowledge about shorebirds' needs. The majority of recreationists were willing to walk around flocks, rather than through them. Intention to walk around flocks can vary by sociodemographic groups. Recreationists who intended to walk around flocks had stronger personal and social norms than recreationists who did not intend to walk around flocks. Recreationists who intended to walk around flocks generally agreed more strongly that maintaining undisturbed conditions for shorebirds and reduced harm to people and their dogs were benefits, compared to participants who did not intend to walk around flocks. Recreationists who did not intend to walk around flocks agreed more strongly that knowledge was a constraint compared to participants who intended to walk around flocks. Our findings could be used in the strategy development phase of a community-based social marketing campaign (CBSM) aimed at encouraging recreationists to voluntarily walk around shorebird flocks. Using behavior change techniques, benefits uncovered in this study can be emphasized and constraints uncovered in this study can be reduced for the purpose of promoting less disturbance to shorebirds.</div>

Molecular constraints on tolerance-resistance trade-offs: Is there a cost?

Plants possess myriad defenses against their herbivores, including constitutive and inducible chemical compounds and regrowth strategies known as tolerance. Recent studies have shown that plant tolerance and resistance are positively associated given they are co-localized in the same molecular pathway, the oxidative pentose phosphate pathway. However, given that both defensive strategies utilize carbon skeletons from a shared resource pool in the oxidative pentose phosphate pathway there are likely costs in maintaining both resistance-tolerance strategies. Here we investigate fitness costs in maintaining both strategies by utilizing a double knockout of cyp79B2 and cyp79B3, key enzymes in the biosynthetic process of indole glucosinolates, which convert tryptophan to indole-3-acetaldoxime (IAOx) and is further used to produce indole glucosinolates. These mutant plants are devoid of any indole glucosinolates thus reducing plant resistance. Results show that knocking out indole glucosinolate production and thus one of the resistance pathways leads to an approximate 46% increase in fitness compensation shifting the undercompensating wild-type Columbia-0 to an overcompensating genotype following damage. We discuss the potential mechanistic basis for the observed patterns.