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907 results for “Pine”
Dataset for the Origin and Persistence of Lycopodium clavatum and Lycopodium annotinum (Lycopodiaceae) in Scots pine forests
<p>This dataset comprises observational data collected to study the club moss outgrowth origin and emergence in Lithuania, Vilnius and Varena Districts. Data was collected from 2013 to 2017 and include coordinates of <em>Lycopodium annotinum</em> L. and <em>Lycopodium clavatum</em> L. outgrowths, their parameters and surrounding vegetation releves, </p> <p>For clones in Veržuva and Nemenčinė, we additionally provide light spectrum values from hemispherical images and vegetative living and dead shoot cover evaluation and strobili counts.</p> <p>This study adopted an integrated approach to assess the probability of repetitive young sporophyte recruitment via sexual propagation in L. annotinum and L. clavatum. The size–age problem of these clonal spore bearing forest plants and their niche segregation were addressed. The canopy characteristics, insolation, small-scale disturbance, and genetic polymorphism were studied in temperate semi-natural Scots pine forests in Lithuania. Based on the size of the clones discovered, we hypothesize that initial sporophyte emergence occurred in 20-year-old pine stands, with subsequent sporophyte emergence continuing over time. The emergence was related to small-scale disturbances. </p> <p><strong>file metadata_la_lc.csv:</strong></p> <p>ID: LA - <em>Lycopodium annotinum</em>; LC - <em>Lycopodium clavatum</em>; NE - Nemenčinė; GV - Veržuva; MI - Sakiškės; JV - juvenile sporophytes, Varėna District.</p> <p>LIGHT, TEMPERATURE, MOISTURE, REACTION, NUTRIENTS, SALINITY - Ellenberg values for the outgrowths</p> <p>N, E - club moss outgrowth coordinates</p> <p>FOREST_AGE - acquired from Lithuanian Forest Cadastre</p> <p>WIDTH, LENGTH, AREA - club moss outgrowth parameters</p> <p>SECONDARY - shape of an outgrowth: primary - oval, secondary - shaped differently</p> <p><strong>file releves_la_lc.csv:</strong></p> <p>ID: LA - <em>Lycopodium annotinum</em>; LC - <em>Lycopodium clavatum</em>; NE - Nemenčinė; GV - Veržuva; MI - Sakiškės; JV - juvenile sporophytes, Varėna District.</p> <p>Species cover evaluated in a percentage scale</p> <p><strong>file cover_la_lc.csv:</strong></p> <p>ID: LA - <em>Lycopodium annotinum</em>; LC - <em>Lycopodium clavatum</em>; NE - Nemenčinė; GV - Veržuva;</p> <p>Reported: average vegetative shoot cover ( %/ m2); maximum vegetative shoot cover ( %/ clone size m2); average dead shoot cover ( %/ clone size m2); maximum dead shoot cover ( %/ clone size m2); average number of strobili; maximum number of strobili in 1 m2; total number of strobili; clone size; canopy closure (%) evaluated via hemispheric image analysis </p> <p><strong>file GenAlex_la_lc.csv:</strong></p> <p>LA - <em>Lycopodium annotinum</em>; LC - <em>Lycopodium clavatum</em>; NE - Nemenčinė; GV - Veržuva;</p> <p>Primers used: ISSR B; ISSR C; ISSR I-28; ISSR I-39a; ISSR I-50a' WARD 2; ARCADE 3.</p>
Quantifying pine processionary moth defoliation in a pine-oak mixed forest using unmanned aerial systems and multispectral imagery (dataset, paper published in PLOS ONE)
<p>Data processed to analyze pine processionary moth defoliation.</p> <p>Digital surface model and orthomosaics derived from UAS</p>
Distinguishing mutations and null alleles from genotyping errors using mother progeny comparisons in Brazilian pine (Araucaria angustifolia)
The use of microsatellite markers provides a window into the evolutionary processes of a given species. As such, these markers are widely used in scientific and applied research and are praised for their practicality and ease of use, however, the unavoidable incidence of genotyping deviations has been broadly neglected in the literature. Therefore, the present study aimed to estimate the rate of null alleles, mutations and genotyping errors in microsatellite loci, using Araucaria angustifolia, a threatened species, as a case study. We estimated the rates of the different types of genotyping deviations using mother-progeny genotype comparison from 50 seed-trees and their respective progeny (seeds). A total of 2336 A. angustifolia samples were genotyped, and we found that the rate of null alleles was 0.045. From the 1972 mother-progeny comparisons, the overall genotype deviation rate was 1.58%, consisting of 145 inconsistences (mutations), 339 null alleles and 210 genotyping errors. In terms of seed numbers, 128 (6.5%) showed inconsistencies in at least one locus, 118 (6.0%) null alleles, and 321 (16.3%) genotyping errors. This is the first study to describe the inconsistences (mutations) between mother-progeny genotypes for A. angustifolia, and the outcome makes it clear that an understanding of these genotyping deviations must be considered in assessing the accuracy of inferences made based on population genetics analyses.
Distinguishing mutations and null alleles from genotyping errors using mother progeny comparisons in Brazilian pine (Araucaria angustifolia)
the rate of null alleles, mutations and genotyping errors in microsatellite loci, using Araucaria angustifolia, a threatened species, as a case study. We estimated the rates of the different types of genotyping deviations using mother-progeny genotype comparison from 50 seed-trees and their respective progeny (seeds). A total of 2336 A. angustifolia samples were genotyped, and we found that the rate of null alleles was 0.045. From the 1972 mother-progeny comparisons, the overall genotype deviation rate was 1.58%, consisting of 145 inconsistences (mutations), 339 null alleles and 210 genotyping errors. In terms of seed numbers, 128 (6.5%) showed inconsistencies in at least one locus, 118 (6.0%) null alleles, and 321 (16.3%) genotyping errors. This is the first study to describe the inconsistences (mutations) between mother-progeny genotypes for A. angustifolia, and the outcome makes it clear that an understanding of these genotyping deviations must be considered in assessing the accuracy of inferences made based on population genetics analyses.
Figure 2 in To what extent do pine and oak clear-cut stumps support mite (Acari: Mesostigmata) communities in temperate forests?
Figure 2. Unique species in CWD, ecotone, and adjacent litter in Scots pine and sessile oak forest.
Fig. 1 in Vulnerability of Northern Pine Snakes (Pituophis melanoleucus Daudin, 1803) during fall den ingress in New Jersey, USA
Fig. 1. Schematic of deployment of the Tracker device at the entrance of a hibernaculum.
Data from: Hyperspectral imaging reveals differential carotenoid and chlorophyll temporal dynamics and spatial patterns in Scots pine under water stress
<p>Data and codes associated with the manuscript '<span>Hyperspectral imaging reveals differential carotenoid and chlorophyll temporal dynamics and spatial patterns in Scots pine under water stress</span>'. </p>
The δ13C series of different components from Masson pine
<p>The idea of this study is to analyze the effects of climatic drivers on the radial growth (total ring width, earlywood width, and latewood width) and the <span>δ<sup>13</sup>C</span> series of different wood components (whole wood, α-cellulose, and holocelluose) from Masson pine in subtropical China. Pairwise correlation is significant between three ring width parameters. Earlywood and latewood width<span> did not reveal much stronger climatic sensitivity rather than total ring width</span>. This indicates that the use of intra-annual ring width maybe have little benefit in extracting more climate information. The mean δ<sup>13</sup>C series of the three components of the total ring had the strongest climatic response to the July–September relative humidity (r= -0.792 (whole wood, WW), -0.758 (holocellulose, HC) and -0.769 (α-cellulose, AC)). These results suggest that whole wood from Masson pine is sufficient to enhance the climate signal without cellulose isolation.</p> <p>Through both stationary temporal and spatial-statistical perspectives, the moisture drivers (summer/autumn) had a significant impact on three ring width parameters and three components of Masson pine. Overall, the tree ring width parameters and the <span>δ<sup>13</sup>C</span> series from the total ring showed a different response to the same climate drivers during the same period. The <span>δ<sup>13</sup>C</span> series may be a more representative climate proxy than tree-ring width parameters for the dendroclimatology in subtropical China.</p>
Weak spatial-genetic structure in a native invasive, the southern pine beetle (Dendroctonus frontalis), across the eastern United States
<p>The southern pine beetle<i>, Dendroctonus frontalis</i>, is a native pest of pine trees that has recently expanded its range into the northeastern United States. Understanding its colonization, dispersal, and connectivity will be critical for mitigating negative economic and ecological impacts in the newly invaded areas. Characterization of spatial-genetic structure can contribute to this; however, previous studies have reached different conclusions about regional population genetic structure, with one study reporting a weak east-west pattern, and the most recent reporting absence of structure. Here we systematically assessed several explanations for the absence of spatial-genetic structure. To do this, we developed nine new microsatellite markers and combined them with an existing 24-locus data matrix for the same individuals. We then reanalyzed this full dataset alongside datasets in which certain loci were omitted with the goal of creating more favorable signal to noise ratios. We also partitioned the data based on the sex of <i>D. frontalis</i> individuals, and then employed a broad suite of genotypic clustering and isolation-by-distance (IBD) analyses. We found that neither inadequate information content in the molecular marker set, nor unfavorable signal-to-noise ratio, nor insensitivity of the analytical approaches could explain the absence of structure. Regardless of dataset composition, there was little evidence for clusters (i.e., distinct geo-genetic groups) or clines (i.e., gradients of increasing allele frequency differences over larger geographic distances), with one exception: significant IBD was repeatedly detected using an individual-based measure of relatedness whenever datasets included males (but not for female-only datasets). This is strongly indicative of broad-scale female-biased dispersal, which has not previously been reported for <i>D. frontalis</i>, in part owing to logistical limitations of direct approaches (e.g., capture-mark-recapture). Weak spatial-genetic structure suggests long-distance connectivity and that gene flow is high, but additional research is needed to understand range expansion dynamics in this species using alternate approaches.</p>
Data from: Insectivorous birds can see and smell systemically herbivore‐induced pines
<p>Several studies have shown that insectivorous birds are attracted to herbivore-damaged trees even when they cannot see or smell the actual herbivores or their faeces. However, it often remained an open question whether birds are attracted by herbivore-induced changes in leaf odour or in leaf light reflectance or by both types of changes. Our study addressed this question by investigating the response of great tits (<em>Parus major</em>) and blue tits (<em>Cyanistes caeruleus</em>) to Scots pine (<em>Pinus sylvestris</em>) damaged by pine sawfly larvae (<em>Diprion pini</em>). We released the birds individually to a study booth, where they were simultaneously offered a systemically herbivore-induced and a non-infested control pine branch. In the first experiment, the birds could see the branches, but not smell them, because each branch was kept inside a transparent, air-tight cylinder. In the second experiment, the birds could smell the branches, but not see them, because each branch was placed inside a non-transparent cylinder with a mesh lid. The results show that the birds were more attracted to the herbivore-induced branch in both experiments. Hence, either type of the tested cues, the herbivore-induced visual plant cue alone as well as the olfactory cues <em>per se</em>, is attractive to the birds.</p>
Annotated datasets of Scots pine cross-sectional images for root rot detection and resin detection
<p>These are the annotated datasets used in the publication available at</p> <p><a href="https://doi.org/10.1080/14942119.2024.2327247">https://doi.org/10.1080/14942119.2024.2327247</a></p> <p>The first dataset is for root rot detection, the other dataset is for resin detection. Please see the publication for details.</p>
Phenotypic plasticity versus ecotypic differentiation under recurrent summer drought in two drought-tolerant pine species
<p>1. Despite worldwide reports of high tree mortality, growing evidence indicates that many tree species are well adapted to survive repeated dry spells. The drought resilience of trees is related to their phenotypic plasticity and ecotypic differentiation. Whether these two mechanisms act at the same organisational level of a tree and involve similar plant traits is still unknown.</p> <p>2. We assessed phenotypic plasticity and ecotypic differentiation across four populations of Pinus sylvestris and Pinus nigra seedlings grown for three years under a recurrent summer drought treatment or well-watered control conditions in a common garden. We measured the response to the summer drought treatment of a total of 26 traits including shoot and needle morphology, needle anatomy, and foliar macronutrients, and related the traits to the growing season water deficit (GSWD) at the location of the seed origin.</p> <p>3. Foliar phenotypic plasticity in response to recurrent summer drought was surprisingly low, with the needle length and the fraction of mesophyll and phloem tissue adjusting to some extent. In comparison, shoot morphological traits were much more plastic in both species with predominant responses to the summer drought stress including shorter and less numerous apical and lateral shoots. These three traits were also correlated with GSWD at the seed origin, indicating local adaptation. In contrast, between-population variation of foliar morphological and anatomical traits, and macronutrients were mostly unrelated to the GSWD at the seed origin.</p> <p>4. Consequently, phenotypic plasticity and ecotypic differentiation occurred at the same level of organisation and in the same plant traits, i.e. shoot morphology. This combination of plasticity and ecotypic differentiation allowed P. sylvestris and P. nigra seedlings to rapidly acclimate to recurrent and long-lasting dry-spells.</p> <p>5. Synthesis: P. sylvestris and P. nigra seedlings showed considerable ecotypic differentiation and phenotypic plasticity of shoot morphological traits, and not foliar traits. Acclimation to recurrent severe summer drought was achieved by reducing shoot growth.</p>
BISICLES Pine Island Glacier simulations with linear friction
<p>Model simulations of the ice sheet model BISICLES for 100 years on a set of topographies, sampled form a GP (plus BM2 and BedMachine) with linear Weertman friction law.</p> <p>See chapter 5 of <a href="https://doi.org/10.21954/ou.ro.0001223d">https://doi.org/10.21954/ou.ro.0001223d</a> for more information</p>
BISICLES Pine Island Glacier simulations with nonlinear friction
<p>Model simulations of the ice sheet model BISICLES for 100 years on a set of topographies, sampled form a GP (plus BM2 and BedMachine) with m=1/3 Weertman friction law exponent.</p> <p>See chapter 5 of DOI: <a href="https://doi.org/10.21954/ou.ro.0001223d">https://doi.org/10.21954/ou.ro.0001223d</a> for more information</p>
Faster‐haplodiploid evolution under divergence‐with‐gene‐flow: Simulations and empirical data from pine‐feeding hymenopterans
<p>Although haplodiploidy is widespread in nature, the evolutionary consequences of this mode of reproduction are not well characterized. Here, we examine how genome-wide hemizygosity and a lack of recombination in haploid males affects genomic differentiation in populations that diverge via natural selection while experiencing gene flow. First, we simulated diploid and haplodiploid "genomes" (500-kb loci) evolving under an isolation-with-migration model with mutation, drift, selection, migration, and recombination; and examined differentiation at neutral sites both tightly and loosely linked to a divergently selected site. So long as there is divergent selection and migration, sex-limited hemizygosity and recombination cause elevated differentiation (i.e., produce a "faster-haplodiploid effect") in haplodiploid populations relative to otherwise equivalent diploid populations, for both recessive and codominant mutations. Second, we used genome-wide SNP data to model divergence history and describe patterns of genomic differentiation between sympatric populations of <em>Neodiprion lecontei </em>and <em>N. pinetum</em>, a pair of pine sawfly species (order: Hymenoptera; family: Diprionidae) that are specialized on different pine hosts. These analyses support a history of continuous gene exchange throughout divergence and reveal a pattern of heterogeneous genomic differentiation that is consistent with divergent selection on many unlinked loci. Third, using simulations of haplodiploid and diploid populations evolving according to the estimated divergence history of <em>N. lecontei </em>and <em>N. pinetum</em>, we found that divergent selection would lead to higher differentiation in haplodiploids. Based on these results, we hypothesize that haplodiploids undergo divergence-with-gene-flow and sympatric speciation more readily than diploids.</p>
Scots pine log end face images for developing identity matching methods for tree logs
<p>For developing log identification methods, i.e., "face recognition" methods for log individuals, a total of 493 unique Scots pine logs were photographed to create this data set of 4930 log end face images.</p> <p>The photography was completed in two sessions, each lasting one working day. In the first session, each log was photographed from five different perspectives: directly head-on, plus four other imaging angles. In the second session, which took place five days later, the same photography procedure was repeated for each log.</p> <p>The data is structured into directories as <log number>/<imaging day>/<angle index>.jpg, where <log number> is the uniquely identifying number for each individual log, imaging day is either 01 (meaning the first imaging session) or 02 (meaning the second imaging session), and angle index is an integer from 0 (the direct head-shot image) to 4, where indeces from 1 to 4 signify the other imaging angles besides the direct head-on perspective.</p> <p>Please see the publication at <a href="https://doi.org/10.1016/j.atech.2023.100201">https://doi.org/10.1016/j.atech.2023.100201</a> for more details.</p>
Body mass and triglycerides predict departure of free-living nomadic pine siskins
<p>1. Facultative migrations are observed across vertebrate taxa, include irruptive and nomadic movements, and occur in response to ephemeral and unpredictably variable resources. While the physiology underlying seasonal, obligate migrations is thoroughly studied, much less is known about the physiological mechanisms of facultative movements. We test two hypotheses in a free-living, nomadic bird, the pine siskin (Spinus pinus).</p> <p>2. The Prepare Hypothesis predicts that, like obligate migrants, siskins increase fuel stores to prepare for migratory movements and elevations of baseline corticosterone (CORT) support departure. The Escape Hypothesis predicts that siskins do not prepare for departure, body condition declines as food availability declines, and stress-related levels of CORT induce escape from resource-poor areas.</p> <p>3. Under the controlled lab conditions of previous studies, food restriction induces declines in body condition and increases in CORT and locomotor activity, supporting the Escape Hypothesis. This study evaluates the ecological relevance of these captive findings by testing the Prepare and Escape Hypotheses in the field for the first time.</p> <p>4. During two fall field seasons, we radio-tagged siskins and tracked their local movements using handheld and automated telemetry. We assess how body condition and CORT relate to feeding behavior (estimated via plasma triglycerides (TRIG)), space use, and departure.</p> <p>5. We do not find support for either the Prepare or Escape Hypothesis, but rather observe an intermediate pattern. Birds with higher TRIG, and therefore greater food intake, are more likely to depart. Birds in poor condition stay longer near the field site; however, above a threshold body mass, body condition does not predict departure.</p> <p>6. These findings suggest moderate energy stores are necessary for departure but movement decisions depend on other factors among birds with sufficient fuel. Siskin movements are physiologically distinct from both obligate and fugitive movements, and we discuss how food availability and body condition interact to drive different types of movement.</p>
Exome sequencing of a hybrid pine species complex on the Qinghai-Tibetan Plateau
<p>This study investigates the evolutionary history of <em>Pinus</em> <em>densata</em> on the Qinghai-Tibetan Plateau (QTP) and genomic heterogeneity across a zone of species transition to understand contemporary dynamics of selection and evolution of species barriers. We analyzed the genetic diversity in a range-wide collection of <em>P. densata</em> and representative populations of its progenitors <em>P. tabuliformis</em> and <em>P. yunnanensis</em> using 40,000 exome probe capture sequencing.</p>
A range-wide postglacial history of Swiss stone pine based on molecular markers and palaeoecological evidence
<p><strong><span>Aim: </span></strong><span>Knowing a species' response to historical climate shifts helps understanding its perspectives under global warming.<strong> </strong>We infer the hitherto unresolved postglacial history of <em>Pinus cembra.</em> Using independent evidence from genetic structure and demographic inference of extant populations, and from palaeoecological findings, we derive putative refugia and re-colonisation routes.</span></p> <p><strong><span>Location: </span></strong><span>European Alps and Carpathians.</span></p> <p><strong><span>Taxa: </span></strong><em><span>Pinus cembra.</span></em></p> <p><strong><span>Methods: </span></strong><span>We genotyped nuclear and chloroplast microsatellite markers in nearly 3,000 individuals from 147 locations across the entire natural range of <em>P. cembra</em>. Spatial genetic structure (Bayesian modelling) and demographic history (Approximate Bayesian Computation) were combined with palaeobotanical records (pollen, macrofossils) to infer putative refugial areas during the Last Glacial Maximum (LGM) and re-colonisation of the current range.</span></p> <p><strong><span>Results: </span></strong><span>We found distinct spatial genetic structure, despite low genetic differentiation even between the two disjunct mountain ranges. Nuclear markers revealed five genetic clusters aligned East–West across the range, while chloroplast haplotype distribution suggested nine clusters. Spatially congruent separation at both marker types highlighted two main genetic lineages in the East and West of the range. Demographic inference supported early separation of these lineages dating back to a previous interstadial or interglacial <em>c.</em> 210,000 years ago. Differentiation into five biologically meaningful genetic clusters likely established during post-glacial re-colonisation.</span></p> <p><strong><span>Main conclusions: </span></strong><span>Combining genetic and palaeoecological evidence suggests that <em>P. cembra</em> primarily survived the LGM in "cold period" refugia south of the Central European Alps and near the Carpathians, from where it expanded during the Late Glacial into its current Holocene "warm period" refugia. This colonisation history has led to the distinct East–West structure of five genetic clusters. The two main genetic lineages likely derived from ancient divergence during an interglacial or interstadial. The respective contact zone (Brenner line) matches a main biogeographic break in the European Alps also found in herbaceous alpine plant species.</span></p>
Intra-annual-tree-ring-stable-carbon-and-oxygen-isotope-of-Chinese-pine-in-Helan-Mountains
<p>The data are intra-annual series of tree-ring stable carbon (δ<sup>13</sup>Ccor) and oxygen (δ<sup>18</sup>O) isotopes from Chinese pine (<em>Pinus tabuliformis</em>) in Helan Mountains</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.