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opencc-by-4.0Apr 2022View details →

Spherical harmonic model of the shape of Mars: MarsTopo719

THIS MODEL IS SUPERSEDED BY <a href="../records/10794059">Spherical harmonic models of the shape of Mars</a>   MarsTopo719.shape is a spherical harmonic model of the shape of the planet Mars. This model makes use of 4-pi normalized spherical harmonic functions that exclude the Condon-Shortley phase factor of (-1)m. The description of how this spherical harmonic model was constructed can be found in Wieczorek (2015). MarsTopo719.shape is a truncated version of MarsTopo2600.shape.

opencc-by-4.0Apr 2022View details →

To what extent naringenin binding and membrane depolarization shape mitoBK channel gating - a machine learning approach (code and dataset)

The dataset consists of dwell-time series (sampling frequency 100 kHz) of the mitoBK ion channel activation modulated by the naringenin binding and membrane depolarization. It also contains the code written in Python, with the use of tslearn and scikit-learn packages, classifying the dwell-time subseries into right categories. The dataset is organized as follows. The mitoBK_ML.zip directory consists of two directories: <ol> <li>dwell times containing 5 subdirectories comprising  groups  of dwell-time subseries obtained at different pipette potentials and naringenin concentration. First number in the name od directory stands for the applied voltage in mV, whilst the second one denotes the naringenin concentration in µmol. For instance, directory named 20_3 means that the obtained dwell-times series were obtained at 20 mV (value of pipette potential) and 3 µmol (concentration of naringenin). These subdirectories are named as follows:</li> </ol> <ul> <li>1group comprising dwell time series 20_3, 40_1, 60_0</li> <li>2group comprising dwell-time series 20_10, 60_1</li> <li>3group comprising dwell-time series 40_10, 60_3</li> <li>naringenina comprising dwell-time series 60_0, 60_10</li> <li>voltage comprising dwell-time series 20_10, 60_10</li> </ul> 1group, 2group and 3group contain the dwell-time series with approximately the same value of open-state probability of the ion channel. The naringenina contains the dwell-time series with the same value of potential (60 mV) and different values of naringenin concentration (0 µmol and 10 µmol).  The voltage contains the dwell-time series with the same value of naringenin concentration (10 µmol) and different values of applied voltage (20 mV and 60 mV).      2. rslt is organized analogously to dwell times. The subdirectories are empty, but they will be filled with the results after launching the Python scripts placed in the  knn_ion_channel.ipynb or shapelet_ion_channel.ipynb files. The Python code is placed in two files: <ol> <li>knn_ion_channel.ipynb containing kNN (k-Nearest Neighbors) algorithm classifying dwell-time series belonging to one of 5 different categories enumerated above: 1group, 2group, 3group, naringenina, voltage. More detailed description of the code can be found inside uploaded Jupyter notebook.</li> <li>shapelet_ion_channel.ipynb containing shapelet-learning algorithm classifying dwell-time series belonging to one of 5 different categories enumerated above. 1group, 2group, 3group, naringenina, voltage. More detailed description of the code can be found inside uploaded Jupyter notebook.</li> </ol>

opencc-zeroMay 2022View details →

Data from: The shape of aroma: Measuring and modeling citrus oil gland distribution

From preventing scurvy to being part of religious rituals, citrus are intrinsically connected to human health and perception. From tiny mandarins to head-sized pummelos, citrus capability of hybridization provides a vastly diverse array of fruit sizes and shapes, which in turn corresponds to a diversity of flavors and aromas. These sensory qualities are tightly linked to oil glands in the citrus skin. The oil glands are also key to understanding fruit development, and the essential oils contained by them are fundamental in the food and perfume industries. We study the shape of citrus based on 3D X-ray CT scan reconstruction of 163 different citrus samples comprising 58 different species and cultivars, including samples of all fundamental citrus species. First, using the power of X-rays and image processing, we are able to compare and contrast size ratios between different tissues, such as the size of the skin compared to the rind or the flesh. Second, we model the fruit shape as an ellipsoidal surface, and later we study and infer possible oil gland distributions on this surface using principles of directional statistics. We finally compare and contrast these overall fruit shape models along their gland distributions across different citrus species. This morphological modeling will allow us later to link genotype with phenotype, furthering our insight on how the physical shape is genetically specified in DNA.

opencc-by-4.0May 2022View details →

Data supporting 'Controls on Greenland moulin geometry and evolution from the Moulin Shape model'

The data included here are MouSh model results generated as part of the following publication: Andrews, L. C., Poinar., K, Trunz, C. (2022). Controls on Greenland moulin geometry and evolution from the Moulin Shape model. The Cryosphere.  Nearly all meltwater from glaciers and ice sheets is routed englacially through moulins. Therefore, the geometry and evolution of moulins has the potential to influence subglacial water pressure variations, ice motion, and the runoff hydrograph delivered to the ocean. We develop the Moulin Shape (MouSh) model, a time-evolving model of moulin geometry. MouSh models ice deformation around a moulin using both viscous and elastic rheologies and melting within the moulin through heat dissipation from turbulent water flow, both above and below the water line. We force MouSh with idealized and realistic surface melt inputs. Our results show that variations in surface melt change the geometry of a moulin by approximately 10% daily and over 100% seasonally. These size variations cause observable differences in moulin water storage capacity and moulin water levels compared to a static, cylindrical moulin. Our results suggest that moulins are storage reservoirs for meltwater, with storage capacity and water levels varying over multiple timescales. Representing moulin geometry within subglacial hydrologic models may therefore improve the representation of subglacial pressures, especially over seasonal periods or in regions where overburden pressures are high. These data are also accessible at: https://ubir.buffalo.edu/xmlui/handle/10477/82587 The development of the MouSh model was funded by NASA Cryosphere grant 80NSSC19K0054 to Lauren Andrews and Kristin Poinar.

Patch quality and genotype-by-environment interactions shape dispersal and post-settlement survival in a butterfly metapopulation

Active dispersal is driven by extrinsic and intrinsic factors at the three stages of departure, transfer, and settlement. Most empirical studies capture only one stage of this complex process, and knowledge of how much can be generalized from one stage to another remains unknown. Here we use genetic assignment tests to reconstruct dispersal across five years and 232 patches of a butterfly metapopulation. We link individual dispersal events to weather, landscape structure, size and quality of patches, and individual genotype to identify the factors that influence the three stages of dispersal and post-settlement survival. We found that nearly all tested factors strongly affected departure probabilities, but that the same factors explained very little variation in realized dispersal distances. Surprisingly, we found no effect of dispersal distance on post-settlement survival. Rather, survival was influenced by weather conditions, carry-over effects of natal patch quality, and a strong interaction between genotype and occupancy status of the settled patch, with more mobile genotypes having higher survival as colonists rather than as immigrants. Our work highlights the multicausality of dispersal and that some dispersal costs can only be understood by considering extrinsic and intrinsic factors and their interaction across the entire dispersal process.

Data from: Pace and shape of senescence in three species of duckweed

Senescence is progressive bodily deterioration associated with declines in survival and fecundity in older age classes. There is great diversity in patterns of senescence across species, but these patterns can be difficult to compare formally due to variation in the absolute time scales in which species live and die: members of some species live for a matter of days, others for millennia. To address this issue, the 'pace-shape' approach was developed to decouple absolute time from analyses and instead standardize life history traits in terms of average life expectancy, facilitating intra- and interspecific comparisons. Here, we use this approach to distinguish the generic form of demographic trajectories (shape) from the time scale on which the trajectories occurred (pace) in three species of tiny, free-floating aquatic plants known as duckweeds (Lemna gibba L., L. minor L., and L. turionifera Landolt), which have mean lifespans of less than a month under typical lab conditions, and exhibit age-related declines in survivorship and reproduction. Using a randomized block design in which we tracked a final total of 430 individuals, we report differences in pace and shape among the three species. Specifically, the largest, least-fecund, and typically longest-lived species, L. gibba, tended to exhibit more rapid decreases in time-standardized survivorship and fecundity compared to the other two species. This study emphasizes variation in aging patterns that can be found among plant species, including those in the same genus, and provides further validation for the utility of applying the pace and shape approach in interspecific comparisons.

opencc-by-4.0Apr 2021View details →

Spherical harmonic models of the gravitational field and shape of (101955) Bennu

Provided are (i) three types of spherical harmonic models of the gravitational field of Bennu, (ii) reference gravitational data and (iii) a spherical harmonic model of Bennu's shape.  The gravitational field models and the reference data were obtained by gravity forward modelling using a degree-15 spherical harmonic expansion of Bennu's shape and a constant mass density. The datasets have been published in Bucha, B., Sanso, F., 2021.  Gravitational field modelling near irregularly shaped bodies using spherical harmonics: a case study for the asteroid (101955) Bennu.  Journal of Geodesy, 95, 56, <a href="https://link.springer.com/article/10.1007/s00190-021-01493-w">https://link.springer.com/article/10.1007/s00190-021-01493-w</a>

Data from: Plant richness, land use and temperature differently shape invertebrate leaf-chewing herbivory on plant functional groups

Nutrient demands of leaf-chewing invertebrate herbivores change with temperature, which causes shifts in herbivores' diets. Temperature may act differently on herbivore species, so that factors shaping herbivore species richness may modulate temperature effects on invertebrate herbivory among plant functional groups with different nutrient composition (C:N ratio low to high: legumes, non-leguminous forbs, grasses). Global warming urges a deeper understanding of temperature effects on herbivory among plant functional groups in different habitats and landscapes. This study obtained measures on proportional leaf area loss to leaf-chewing invertebrate herbivores ('herbivory') on three plant functional groups on 80 plots of open herbaceous vegetation adjacent to different habitat types (forest, grassland, arable field, settlement) along climate and land-use gradients in Bavaria, Germany. Herbivory was analysed with regard to habitat characteristics (habitat type, plant richness at species and family level, local mean temperature), landscape characteristics (proportion of grassland, landscape diversity; 0.2–3.0-km), climate (multi-annual mean temperature, 'MAT') and interactive effects of plant functional group, temperature and habitat or landscape characteristics. Herbivory on plant functional groups changed differently in response to plant richness (family level only) and habitat type, but not to differences in landscape characteristics and temperature – only on grassland plots, multi-annual mean temperature differentially affected herbivory among plant functional groups. Thus, abiotic and biotic factors can differently affect leaf-chewing herbivory on plant functional groups. Under current conditions, plant richness and habitat type more strongly affected herbivory among legumes, forbs and grasses than temperature and landscape-scale land use.

Functional assembly of tropical montane tree islands in the Atlantic Forest is shaped by stress-tolerance, bamboo-presence and facilitation

Aims: Amidst the Campos de Altitude (Highland Grasslands) in the Brazilian Atlantic Forest, woody communities grow either clustered in tree islands or interspersed within the herbaceous matrix. The functional ecology, diversity and biotic processes shaping these plant communities are largely unstudied. We characterised the functional assembly and diversity of these tropical montane woody communities and investigated how they fit within Grime's CSR (C – competitor, S – stress-tolerant, R – ruderal) scheme, what functional trade-offs they exhibit and how traits and functional diversity vary in response to bamboo presence/absence. Methods: To characterize the functional composition of the community, we sampled five leaf traits and wood density along transects covering the woody communities both inside tree islands and outside (i.e. isolated woody plants in the grasslands community) . Then, we used Mann Whitney test, t-test and variation partitioning to determine the effects of inside vs outside tree island and bamboo presence on community weighted means, woody species diversity and functional diversity. Results: We found a general SC/S strategy with drought-related functional trade-offs. Woody plants in tree islands had more acquisitive traits than those within the grasslands. Trait variation was mostly taxonomically than spatially driven, and species composition varied between inside and outside tree islands. Leaf thickness, wood density and foliar water uptake were unrelated to CSR-strategies, suggesting independent trait dimensions and multiple drought-coping strategies within the predominant S-strategy. Islands with bamboo presence showed lower Simpson diversity, lower functional dispersion, lower foliar water uptake and greater leaf thickness than in tree islands without bamboo. Conclusions: The observed functional assembly hints towards large-scale environmental abiotic filtering shaping stress-tolerant community strategy, and small-scale biotic interactions driving small-scale trait variation. We recommend experimental studies with fire, facilitation treatments, eco-physiological and recruitment traits to elucidate on tree island expansion and communities response to climate change.

opencc-zeroJul 2022View details →

Data from: Out of the tropics: Macroevolutionary size trends in an old insect order are shaped by temperature and predators

Global body size distributions are shaped by selection pressures arising from biotic and abiotic factors such as temperature, predation and parasitism. Here, we investigated the ecological and evolutionary drivers of global latitudinal size gradients in an old insect order (Odonata; dragonflies and damselflies). Phylogenetic comparative analyses revealed that global size variation of extant taxa is negatively influenced by both regional avian diversity and temperature. Interestingly, fossil data show that the relationship between wing size and latitude has shifted: latitudinal size trends had initially negative slopes but became shallower or positive following the emergence of birds 150 MYA. These changing size-latitude trends over geological time were likely driven by bird predation and high dispersal ability of large dragonflies. Our results therefore suggest that latitudinal size gradients were shaped by temperature but also by predators driving the dispersal of large-sized clades out of the tropics and in to the temperate zone.

opencc-by-4.0Aug 2022View details →

Host developmental stages shape the evolution of a plant RNA virus

Datasets used in the generation of figures 1 and 2 of: Melero, I., González, R., Elena, S.F. 2022. Host developmental stages shape the evolution of a plant RNA Virus. Philos. Trans. R. Soc. B doi: 10.1098/rtsb.2022.0005

opencc-by-4.0Aug 2022View details →

e-shape P5.6 EO based phytoplankton biomass for WFD reporting - samples of Chl-a and WFD classes maps of lakes Lauwersmeer and Saadjärv

The current data set is a sample of the data generated within the e-shape pilot 5.6 called "EO based phytoplankton biomass for WFD reporting" and consists of maps based on earth observation (EO) data from the Sentinel 2 satellite. There is a set of chlorophyll-a (Chl-a) maps, and a set maps of WFD ecological status of phytoplankton biomass, derived from the Chl-a maps by applying local WFD phytoplankton biomass thresholds. These maps can complement the monitoring for the Water Framework Directive (WFD). The lakes within this sample set are lakes Saadjärv (Estonia) and Lauwersmeer (the Netherlands). For more info please see the readme files which are provided with the data files.

opencc-zeroAug 2022View details →

The shape of phylogenies under phase-type distributed times to speciation and extinction

Phylogenetic trees describe relationships between extant species, but beyond that their shape and their relative branch lengths can provide information on broader evolutionary processes of speciation and extinction. However, currently, many of the most widely used macro-evolutionary models make predictions about the shapes of phylogenetic trees that differ considerably from what is observed in empirical phylogenies. Here, we propose a flexible and biologically plausible macroevolutionary model for phylogenetic trees where times to speciation or extinction events are drawn from a Coxian phase-type (PH) distribution. First, we show that different choices of parameters in our model lead to a range of tree balances as measured by Aldous' $\beta$ statistic. In particular, we demonstrate that it is possible to find parameters that correspond well to empirical tree balance. Next, we provide a natural extension of the $\beta$ statistic to sets of trees. This extension produces less biased estimates of $\beta$ compared to using the median $\beta$ values from individual trees. Furthermore, we derive a likelihood expression for the probability of observing an edge-weighted tree under a model with speciation but no extinction. Finally, we illustrate the application of our model by performing both absolute and relative goodness-of-fit tests for two large empirical phylogenies (squamates and angiosperms) that compare models with Coxian PH distributed times to speciation with models that assume exponential or Weibull distributed waiting times. In our numerical analysis, we found that, in most cases, models assuming a Coxian PH distribution provided the best fit.

opencc-by-4.0Sep 2022View details →

Gut microbiota inter-species interactions shape the response of Clostridioides difficile to clinically relevant antibiotics

In the human gut, the growth of Clostridioides difficile is impacted by a complex web of inter-species interactions with members of human gut microbiota. We investigate the contribution of inter-species interactions on the antibiotic response of C. difficile to clinically relevant antibiotics using bottom-up assembly of human gut communities. We discover two classes of microbial interactions that alter C. difficile’s antibiotic susceptibility: infrequent increases in tolerance at high antibiotic concentrations and frequent growth enhancements at low antibiotic concentrations. Based on genome-wide transcriptional profiling data, we demonstrate that metal sequestration due to hydrogen sulfide production by the prevalent gut species Desulfovibrio piger increases metronidazole tolerance of C. difficile. Competition with species that display higher sensitivity to the antibiotic than C. difficile leads to enhanced growth of C. difficile at low antibiotic concentrations. A dynamic computational model identifies the ecological design principles driving this effect. Our results provide a deeper understanding of ecological and molecular principles shaping C. difficile’s response to antibiotics, which could inform therapeutic interventions.

opencc-zeroAug 2022View details →

Exceptions to the rule: Relative roles of time, diversification rates and regional energy in shaping the inverse latitudinal diversity gradient

Aim: Inverse latitudinal diversity gradients (i-LDG), whereby regional richness peaks outside the tropics, have rarely been investigated and their causes remain unclear. Here, we investigate three prominent explanations, postulating that species-rich regions have had (1) longer time to accumulate species, (2) faster diversification, and (3) more energy to support more diverse communities. These mechanisms have been shown to explain the tropical megadiversity, and we examine whether they can also explain i-LDG. Location: Global Time period: Contemporary Major taxa studied: Amphibians, birds, mammals Methods: We estimated the time for species accumulation, regional diversification rates, and regional energy for six tetrapod taxa (≈ 800 species). Then, we quantified the relative effects and interactions among these three classes of variables, using variance partitioning, and confirmed the results across alternative metrics for time (community phylometrics and BioGeoBEARS), diversification rates (BAMM and DR), and regional energy (past and current temperature, productivity). Results: While regional richness across each of the six taxa peaked in the temperate region, it varied markedly across hemispheres and continents. The effects of time, diversification rates, and regional energy varied greatly from one taxon to another, but high diversification rates generally emerged as the best predictor of high regional richness. The effects of time and regional energy were limited, with the exception of salamanders and cetaceans. Main conclusions: Together, our results indicate that the causes of i-LDG are highly taxon-specific. Consequently, large-scale richness gradients might not have a universal explanation and different causal pathways might converge on similar gradients. Moreover, regional diversification rates might vary dramatically between similar environments and, depending on the taxon, regional richness might or might not depend on the time for species accumulation. Together, these results underscore the complexity behind the formation of richness gradients, which might involve a symphony of variations on the interplay of time, diversification rates, and regional energy.

opencc-by-4.0Sep 2022View details →

Gut microbiota inter-species interactions shape the response of Clostridioides difficile to clinically relevant antibiotics

opencc-zeroSep 2022View details →

Near-shore island lizard fauna shaped by a combination of human-mediated and natural dispersal

Aim: Island biotas provide opportunities to study colonization and adaptation to novel environments. Islands, especially near-shore islands, may have a long record of human habitation such that some lineages result from human-assisted introductions. Here, we combine phylogenetic analyses with fossil data and historical specimen records to reconstruct colonization histories, characterize among-island divergence, and assess the role of humans in shaping the evolutionary history of lizards inhabiting a near-shore island archipelago. Location: Channel Islands and adjacent mainland of California, USA. Taxa: Western fence lizard ( Sceloporus occidentalis), southern alligator lizard (Elgaria multicarinata), common side-blotched lizard (Uta stansburiana). Methods: We sequenced mitochondrial DNA (ND1, cyt-b) from each of three lizard species, covering their entire island distributions plus the adjacent mainland. For each, we estimated diversity within and among each island, obtained maximum likelihood bootstrapped phylogenies, constructed haplotype networks, and tested for population expansion. We used museum specimen records and microfossil evidence to infer colonization scenarios. Results: Sceloporus occidentalis is characterized by a single island-colonization event, and exhibits the deepest divergences from mainland relatives and the highest among-island divergence. Elgaria multicarinata and Uta stansburiana each have at least three distinct colonization events, with fossil and historical data indicating that some of these occurred after humans arrived to the islands. Main Conclusions: The evolution of Channel Island lineages for two lizard taxa has been mediated by ancient and contemporary anthropogenic activity, while the evolution of the third is shaped by natural dispersal and vicariance caused by sea-level rise. Genetic divergence corroborates the treatment of S. occidentalis as an endemic island species, S. becki. The unique histories of these three taxa are synthesized with other Channel Island lineages highlighting that taxa inhabiting islands with long histories of human activity should be carefully studied to assess the role of people in facilitating colonization and subsequent gene flow.

opencc-zeroSep 2022View details →

Temperature-dependent evolutionary speed shapes the evolution of biodiversity patterns across tetrapod radiations

Biodiversity varies predictably with environmental energy around the globe, but the underlying mechanisms remain incompletely understood. The evolutionary speed hypothesis predicts that environmental energy shapes variation in speciation rates through temperature- or life history-dependent rates of evolution. To test whether variation in evolutionary speed can explain the relationship between energy and biodiversity in birds, mammals, amphibians, and reptiles, we simulated diversification over 65 million years of geological and climatic change with a spatially explicit eco-evolutionary simulation model. We modeled four distinct evolutionary scenarios in which speciation-completion rates were dependent on temperature (M1), life history (M2), temperature and life history (M3), or were independent of temperature and life-history (M0). To assess the agreement between simulated and empirical data, we performed model selection by fitting supervised machine learning models to multidimensional biodiversity patterns. We show that a model with temperature-dependent rates of speciation (M1) consistently had the strongest support. In contrast to statistical inferences, which showed no general relationships between temperature and speciation rates in tetrapods, we demonstrate how process-based modeling can disentangle the causes behind empirical biodiversity patterns. Our study highlights how environmental energy has played a fundamental role in the evolution of biodiversity over deep time.

opencc-by-sa-4.0Sep 2022View details →

Blowing_and_shaping

This is a part of Bontemps carafe making process (from the Mingei project).