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907 results for “Pine”
Flat-bed scanner images and daily growth of Scots pine (Pinus sylvestris L.) roots data in SMEAR II Hyytiälä
<p>This zip-file contains</p> <p>(1) the daily root scanner images of three flat-bed scanners during the growing season of 2018 in SMEAR II, Hyytiälä. </p> <p>The images were brightness adjusted by the Authors. The images were taken between 25.04.2018-01.10.2018. The missing images for scanner 2 due to connection errors: 27.05-28.05.2018 and 04.08.2018. Missing dates for scanner 3: 29.08-02.09.2018 and 14.10.2018.</p> <p>(2) daily_root_growth<br> We used 'Winrhizotron 2015a' software to analyze the daily root elongation data, divided by pioneer and fibrous roots, including daily active root number, and average daily elongation rate</p> <p>(3) CASSIA_root<br> We estimated the growth phenology of aboveground tree organs, such as shoots, needles, buds and secondary xylem using the ‘Carbon Allocation Sink Source Interaction’ (CASSIA) model (Schiestl-Aalto et al. 2015). Simulated aboveground organs' data and our root data were combined in the same dataset.</p> <p>(4) surface_area<br> Root surface area increase rate ( analyzed by 'Winrhizotron 2015a' software), divided by pioneer and fibrous roots</p> <p> </p>
Additional code and data for running the simulations presented in the article "Using observations of surface fracture to address ill-posed ice softness estimation over Pine Island Glacier"
<p>The data required to run the inverse problems described in the article "Using observations of surface fracture to address ill-posed ice softness estimation over Pine Island Glacier" along with code specific to the modified inverse problem described therein, additional to that downloadable from BISICLES is downloadable from https://commons.lbl.gov/display/bisicles/BISICLES.</p> <p>These data are restricted to those involved in reviewing the aforementioned article.</p>
Graph neural network emulator for modeling of ice dynamics and calving in the Pine Island Glacier, Antarctica
<p>These files include the following codes and datasets for developing graph neural network (GNN) emulators for the Ice-sheet and Sea-level System Model (ISSM) for modeling ice sheet dynamics and calving in the Pine Island Glacier, Antarctica</p> <ul> <li>ISSM_DGL_PIG2.py: Python file for training GNN models (*single.py: code for single GPU environment)</li> <li>ISSM_CNN_PIG.py: Python file for training convolutional neural network (CNN) models</li> <li>*.mat: Datasets of the ISSM transient simulation results (graphs for GNNs)</li> <li>*.pkl: Datasets of the ISSM transient simulation results (grids for CNNs)</li> </ul>
Data from: Demography and speciation history of the homoploid hybrid pine Pinus densata on the Tibetan Plateau
Pinus densata is an ecologically successful homoploid hybrid that inhabits vast areas of heterogeneous terrain on the southeastern Tibetan Plateau as a result of multiple waves of colonization. Its region of origin, route of colonization onto the plateau and the directions of introgression with its parental species have previously been defined, but little is known about the isolation and divergence history of its populations. In this study, we surveyed nucleotide polymorphism over eight nuclear loci in 19 representative populations of P. densata and its parental species. Using this information and coalescence simulations, we assessed the historical changes in its population size, gene flow, and divergence in time and space. The results indicate a late Miocene origin for P. densata associated with the recent uplift of southeastern Tibet. The subsequent differentiation between geographical regions of this species began in the late Pliocene and was induced by regional topographic changes and Pleistocene glaciations. The ancestral P. densata population had a large effective population size but the central and western populations were established by limited founders, suggesting that there were severe bottlenecks during the westward migration out of the ancestral hybrid zone. After separating from their ancestral populations, population expansion occurred in all geographic regions especially in the western range. Gene flow in P. densata was restricted to geographically neighboring populations, resulting in significant differentiation between regional groups. The new information on the divergence and demographic history of P. densata reported herein enhances our understanding of its speciation process on the Tibetan Plateau.
Data from: Changing light conditions in pine rockland habitats affect the intensity and outcome of ant–plant interactions
Extrafloral nectar (EFN) mediates food-for-protection mutualisms between plants and ants. Such mutualisms exist within a complex web of biotic interactions, and in a framework provided by the abiotic environment. Both biotic and abiotic factors, therefore, affect the outcome of ant–plant interactions. We conducted an experiment to determine the effects of ant activity, and light intensity, on herbivory rates, growth, and reproductive fitness in Senna mexicana var. chapmanii, a perennial legume native to pine rockland habitats of south Florida. Forty plants were divided among four treatments in a factorial experimental design with two independent variables: ant activity and light intensity. Plants were divided equally between sunny and shady habitats, and ants were excluded from half of the plants in each habitat type. The presence of ants significantly reduced herbivory rates in S. chapmanii. In shaded habitats, the presence of ants had no effect on plant reproductive fitness, however, in sunny habitats plants with ants produced significantly more seeds over the duration of the 1-yr study. Ants represent an important biotic defense against herbivores in S. chapmanii; however, their effects on plant fitness are dependent on light conditions. Pine rockland habitats in south Florida have been widely destroyed or mismanaged. In fragments that remain, suppression of fire has led to increased canopy closure and shading of the understory. These changes will likely negatively impact plants that rely on ants for defense. We highlight the importance of conservation efforts to preserve the pine rocklands and the fire regimes on which they rely.
Data from: Declines in pinyon pine cone production associated with regional warming
Global climate change is expected to produce large shifts in vegetation distribution and has already increased tree mortality, altering forest structure. However, long-term shifts will be partly dependent on the ability of species to reproduce under a novel climate. Few studies have examined the impact of climate change on the reproductive output of long-lived 'masting' species, or species characterized by episodic reproductive events. Here, we show that seed cone production among pinyon pine (Pinus edulis), a masting species, declined by 40% from the 1974 decade (1969–1978) to the 2008 decade (2003–2012) in revisited stands throughout New Mexico and northwestern Oklahoma. Seed cone production was highly correlated with late summer temperatures at the time of cone initiation. Further, declines in seed cone production were greatest among populations that experienced the greatest increases in growing season temperatures, which were the populations located at the cooler, upper elevations. As growing season temperatures are predicted to increase across this region over the next century, these findings suggest seed cone production may be an increasingly important bottleneck for future pinyon pine regeneration, especially in areas with greater increases in temperature. Declines in seed cone production may not only affect pinyon pine population dynamics but also the various wildlife species that rely on pinyon pine seeds. Because pinyon pine has similar reproductive strategies as other semi-arid pine species, increasing temperature may negatively influence reproductive output of other conifers. Further investigation into the full geographic and taxonomic extent of these seed declines is warranted.
Data from: Naturalized distributions show that climatic disequilibrium is structured by niche size in pines (Pinus L.)
Aim: The assumption that species' native distributions are in equilibrium with climate has been shown to be frequently violated, despite its centrality to many niche model applications. We currently lack a framework that predicts these violations. Here we examine whether variation in climatic disequilibrium is structured by properties of species' native distributions and climatic niches. Location: Global Methods: We built climatic niche models for 106 pine (Pinus L.) species, including 25 that have naturalized outside their native range. We measured the extent of climate space occupied exclusively by naturalized populations and considered what fraction of this space was available within the native continent and near the native range. We examined the consequences of disequilibrium for estimates of potential range filling and sister-species niche conservatism. Results: Most species (23 of 25) have naturalized in climate conditions outside of the native niche, leading to increases in the total known suitable climate space. Increases in niche size were negatively related to native niche size. Increases were often large – one species expanded its niche by almost 10% of the global climate space. These increases were associated primarily with cooler, wetter, and less seasonal climates. Increases in known niche size lowered potential range filling estimates within species' native continent and ecoregion. Naturalized data did not strengthen support for niche conservatism among sister species. Main Conclusions: Among pines, climatic disequilibrium is the norm and not the exception. The magnitude of this disequilibrium can be vast, such that the native range greatly underrepresents the true climatic tolerances of some species. Fortunately, this disequilibrium can largely be predicted by the size of a species' native niche. Accounting for this disequilibrium can improve our ability to characterize ecological phenomena, including potential range filling. This is an essential step toward improving the conservation value of ecological niche models.
Collins Pine and FIA Comparison
<p>The overwhelming majority of information on historical forest conditions in the western North America comes from public lands, which may provide an incomplete description of historical landscapes. Historical data from privately-owned lands could help inform large-scale forest restoration efforts across ownerships. In this study we made use of an archive containing extensive timber survey data collected in the early 1920's from privately owned forestland. We then used contemporary FIA data to compare changes in tree density, basal area, and pine dominance with historical conditions. With this dataset provided, we subset FIA data from plots within the region of our historical timber inventory that showed similar biophysical environments as our historical dataset. The climatic and topographic data provided here were extracted from those FIA plots and from the locations of the historical timber survey. We subsequently used those extractions in random forest modeling and regression tree analysis to produce our final results reported in our manuscrip. Our specific objectives with this study were (1) describe the range of historical forest conditions across the survey area and compare that to contemporary forest conditions, (2) investigate the influence of biophysical factors on observed variability in historical and contemporary forest conditions and (3) predict historical forest conditions across a large spatial domain using modeled relationships with biophysical variables.</p>
Data from: Mediation of seed provisioning in the transmission of environmental maternal effects in Maritime pine (Pinus pinaster Aiton)
Although maternal environmental effects are increasingly recognized as an important source of phenotypic variation with relevant impacts in evolutionary processes, their relevance in long-lived plants such as pine trees is largely unknown. Here, we used a powerful sample size and a strong quantitative genetic approach to analyse the sources of variation of early seedling performance and to identify seed mass (SM)-dependent and -independent maternal environmental effects in Maritime pine. We measured SM of 8924 individual seeds collected from 10 genotypes clonally replicated in two environments of contrasting quality (favourable and stressful), and we measured seedling growth rate and biomass allocation to roots and shoots. SM was extremely variable (up to 14-fold) and strongly determined by the maternal environment and the genotype of the mother tree. The favourable maternal environment led to larger cones, larger seeds and reduced SM variability. The maternal environment also determined the offspring phenotype, with seedlings coming from the favourable environment being 35% larger and with greater root/shoot ratio. Transgenerational plasticity appears, thus, to be a relevant source of phenotypic variation in the early performance of this pine species. Seed provisioning explained most of the effect of the maternal environment on seedling total biomass. Environmental maternal effects on seedling biomass allocation were, however, determined through SM-independent mechanisms, suggesting that other epigenetic regulation channels may be involved.
Figure 2 in The role of hatching asynchrony in brood size reduction of the great tit Parus major in a Mediterranean pine forest
Figure 2. Distribution of estimated age at time of death of nestlings in synchronous (asynchrony of 0 or 1 days, white bars) and asynchronous (asynchrony of 2 or more days, black bars) broods.
Figure 1 in The role of hatching asynchrony in brood size reduction of the great tit Parus major in a Mediterranean pine forest
Figure 1. Mean hatching asynchrony by five-day periods against laying date (vertical lines indicate range of values).
Fig. 1 in Diversity and Notes on the Reproductive Biology of Cerambycidae (Coleoptera) onHydrangea arborescensL. andDaucus carotaL. at LaRue-Pine Hills Research Natural Area in Southern Illinois, U.S.A.
Fig. 1. Map of LaRue-Pine Hills Natural Research Area (shaded area) in Union Co., Illinois showing the cerambycid collection sites on Daucus carota (A) and Hydrangea arborescens (B). Courtesy of the United States Forest Service.
Fig. 1 in Emergence of Buprestidae, Cerambycidae, and Scolytinae (Coleoptera) from Mountain Pine Beetle-Killed and Fire-Killed Ponderosa Pines in the Black Hills, South Dakota, USA
Fig. 1. Box plot showing the number of wood borers collected from bolts of one-year-old mountain pine beetle (MPB)-killed trees (n = 4), two-year- old MPB-killed trees (n = 6), one-year-old fire-killed trees (n = 5), and two-year-old fire-killed trees (n = 5). Letters above the bars represent means which if followed by the same letter are not significantly different (p ≤ 0.05, Tukey- Kramer multiple comparisons test). The solid and dashed lines within the box represent the median and the mean, respectively. Box ends represent the first and third quartiles. The lower and upper horizontal lines above and below the box are at the last points less than 1.5 times the interquartile range from the first and third quartiles. Points represent the actual data, and the circle for the 1-yr fire indicates that the point next to it is an outlier.
Species composition and functional trait data for wet pine savannas
<p>Trait differences among plant species can favor species coexistence. The role that such differences play in the assembly of diverse plant communities maintained by frequent fires remains unresolved. This lack of resolution results in part from the possibility that species with similar traits may coexist because none has a significant fitness advantage and in part from the difficulty of experimental manipulation of highly diverse assemblages dominated by perennial species.</p> <p>We examined a 65-year chronosequence of losses of herbaceous species following fire suppression (and subsequent encroachment by <i>Pinus elliottii</i>) in three wet longleaf pine savannas. We used cluster analysis, similarity profile permutation tests and k-R cluster analysis to identify statistically significant functional groups. We then used randomization tests to determine if the absence of functional groups near pines was greater (or less) than expected by chance. We also tested whether tolerant and sensitive species were less (or more) likely to co-occur by chance in areas in savannas away from pines in accordance with predictions of modern coexistence theory.</p> <p>Functional group richness near pines was lower than expected from random species extirpations. Wetland perennials with thick rhizomes and high leaf water content, spring-flowering wetland forbs (including <i>Drosera tracyi</i>), orchids, <i>Polygala</i> spp., and club mosses were more likely to be absent near pines than expected by chance. C3 grasses and sedges with seed banks and tall, fall-flowering C4 grasses were less likely to be absent near pines than expected by chance. Species sensitive to pine encroachment were more likely to co-occur with other such species away from pines at two of the three sites.</p> <p>Results suggest that herb species diversity in frequently-burned wet savannas is maintained in part by a weak fitness (e.g., competitive) hierarchy among herbs, and not as a result of trait differences among co-occurring species.</p>
FIGURE 3 in A novel Mariannaea species isolated from decayed pine needles in Japan
FIGURE 3. Morphology of Mariannaea imbricata sp. nov. A‒H. Culture characteristics on potato dextrose agar (PDA) and malt extract agar (MEA). The upper and lower rows of plates show colonial growth after 7 (A, B, E, F) and 14 days (C, D, G, H), respectively. From left to right, the upper and basal surfaces of colonies grown on PDA (A‒D) and MEA (E‒H) are placed in sequential order. I. A scanning electron micrograph of the surface of conidia. J‒N. Microstructure after 7 days of incubation on PDA under a differential interference contrast microscope. J, conidia. K, imbricate conidial chains. L, phialides, and M and N, intercalary or terminal chlamydospores. Scale bars indicate 10 µm.
Data for: Mechanisms of fire-maintained plant species diversity in species-rich wet pine savannas
<p><span>Temperate savannas and grasslands maintained by frequent, low-intensity disturbances such as fire contain among the most species-rich plant communities in the world. Precisely how these disturbances maintain such high fine-scale diversity is poorly understood. This study examined the effects of the frequency of simulated fire (clipping combined with litter removal) and the relative importance of recruitment and survival on species diversity and trait and species composition at each of two pine savannas in southeastern Mississippi (USA) that had not been recently burned. Ten 2 </span><span>×</span><span> 2 m plots at each site were clipped/cleared annually from 2014 to 2019 and again in spring 2021 (annual frequency). The other 10 clipping plots were not clipped from 2018 to 2020 (reduced frequency). Vegetation in small subplots in annual frequency and reduced frequency plots was compared in August 2021 to test the effects of a short period without clipping on diversity and composition. To test the relative importance of recruitment and survival on diversity and composition, four 0.25 </span><span>×</span><span> 0.25 m quarter plots were established within each of 10 annual-frequency plots per site following a clipping treatment in fall 2019 and assigned a 2 </span><span>×</span><span> 2 factorial arrangement of transplantation of sods from long-unburned areas and herbicide application. Reducing the frequency of clipping reduced plant diversity and altered composition at both sites. A comparison of diversity and trait composition responses to transplant and herbicide treatments revealed how recruitment and survival combined to affect species diversity. Partial or complete recovery of diversity following clipping and litter removal at both sites was driven by rapid increases in short-lived, resilient species that show fire-stimulated emergence from a seed bank and the persistence of long-lived species capable of surviving the prolonged period without fire or clipping. Species with reduced resilience and persistence were more likely to be lost in the reduced frequency treatment. Results are consistent with a model of short-term coexistence of maximum species diversity maintained by the most frequent fire regimes fuels will permit.</span></p>
Divergent growth-differentiation balance strategies and resource competition shape mortality patterns in ponderosa pine
<p><span>Dynamic resource availability leads to trade-offs among functions in plants. The growth-differentiation balance hypothesis (GDBH) predicts greater allocation of carbon to defense than growth when resources are scarce; with optimum defense production occurring at a point between the minimum and maximum growth rates. While the GDBH has been widely tested, consideration of phenotypic variation in rates for which defense is traded for growth and what this variation means for plant resistance remains rare. For defense, pines produce and store oleoresin in "resin ducts." Retrospective comparisons of resin ducts in pines have revealed that trees with greater numbers, sizes, or areas of xylem resin ducts are more likely to avoid or survive insect attacks. We used tree ring chronologies to quantify phenotypic variation in growth and resin duct defenses in pairs of living and bark beetle-killed <em>Pinus ponderosa</em> trees in southern New Mexico, USA, and to test the utility of the GDBH for explaining tree mortality. We also assessed the sensitivity of annual growth to climate and competitor density in years preceding mortality in each pair. Survivors had greater growth rates and total cross-sectional areas of resin ducts than trees killed by bark beetles. We did not observe a difference in climate-growth relationships among the groups, however, trees killed by bark beetles suffered negative effects of competition while survivors did not. Growth-defense trade-offs conformed to the GDBH's prediction of a quadratic relationship, however, the two groups significantly differed in the rate at which defense was traded for increasing levels of annual growth.<em> </em> Our results demonstrate that phenotypic variation in the trade-off between growth and defense could be used to characterize trees that were killed by or survived recent natural enemy epidemics. We hypothesize that the GDBH could be integrated with the characterization of phenotypic variation in growth-differentiation strategies—along with parsing of gene versus environment influences on phenotypes—at both local and landscape scales to increase our understanding of patterns of natural enemy impacts in plant populations.</span></p>
FIGURE 2 in Type designation of the Maritime pine Pinus pinaster (Pinaceae)
FIGURE 2. Specimen of Pinus pinaster Aiton, BM (barcode BM001066259). Specimen from Chelsea Physic Garden sent to the Royal Society. Image reproduced with permission of the herbarium BM.
FIGURE 1 in Type designation of the Maritime pine Pinus pinaster (Pinaceae)
FIGURE 1. Lectotype of Pinus pinaster Aiton, illustration "Pinus maritima altera" in Duhamel du Monceau (1755: t. 29).
Craniodental divergence associated with bite force between hybridizing pine squirrels (Tamiasciurus)
<p>Bite force can be a limiting factor in foraging and can significantly affect the competitive ability and lifetime fitness of mammals. <em>Tamiasciurus</em> squirrels feed primarily on conifer seeds and have a strong bite force to mechanically extract seeds from conifer cones with their mouths. In the North Cascades region, Douglas squirrels (<em>Tamiasciurus</em> <em>douglasii</em>) and red squirrels (<em>T</em>. <em>hudsonicus</em>) occupy ecologically different forests with different hardnesses in conifer cones. The ranges of these species overlap in a narrow hybrid zone where these forests meet near the crest of the North Cascades. We examined interspecific divergence in dietary ecomorphology in allopatry, in sympatry within the hybrid zone, and between hybrids and each parental species. We focused on three craniodental traits, including the incisor-strength index as a proxy measure for maximal bite force, cranial-suture complexity, and mandible shape. We find that these sister squirrel species differ in bite force and suture complexity in allopatry and sympatry and that mandible shape changes with the expected hardness of accessed food items, but is not significantly different between species. Furthermore, we find that hybrids display morphologies that overlap with hybrid zone red squirrels but not with hybrid zone Douglas squirrels. This work shows how important ecological processes at shallow evolutionary timescales can impact the divergence of morphological traits in taxa with extreme conservation of craniomandibular shape.</p>
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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.