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Detailed point cloud data on stem size and shape of Scots pine trees
<p>This data set is comprised of three packed zip files and they include text files of 3D information from terrestrial laser scanning (TLS) and aerial imagery from unmanned aerial vehicle (UAV) from individual Scots pine trees within 27 sample plots from three test sites located in southern Finland.</p> <p>TLS data acquisition was carried out with Trimble TX5 3D laser scanner (Trible Navigation Limited, USA) for all three study sites between September and October 2018. Eight scans were placed to each sample plot and scan resolution of point distance approximately 6.3 mm at 10-m distance was used. Artificial constant sized spheres (i.e. diameter of 198 mm) were placed around sample plots and used as reference objects for registering the eight scans onto a single, aligned coordinate system. The registration was carried out with FARO Scene software (version 2018). Aerial images were obtained by using an UAV with Gryphon Dynamics quadcopter frame. Two Sony A7R II digital cameras were mounted on the UAV in +15° and -15° angles. Images were acquired in every two seconds and image locations were recorded for each image. The flights were carried out on October 2, 2018. For each study site, eight ground control points (GCPs) were placed and measured. Flying height of 140 m and a flying speed of 5 m/s was selected for all the flights, resulting in 1.6 cm ground sampling distance. Total of 639, 614 and 663 images were captured for study site 1, 2, and 3, respectively, resulting in 93% and 75% forward and side overlaps, respectively. Photogrammetric processing of aerial images was carried out following the workflow as presented in Viljanen et al. (2018). The processing produced photogrammetric point clouds for each study site with point density of 804 points/m<sup>2</sup>, 976 points/m<sup>2</sup>, and 1030 points/m<sup>2</sup> for study site 1, 2, and 3, respectively.</p> <p>The sample plots within the three test sites have been managed with different thinning treatments in either 2005 or 2006. The experimental design of the sample plots includes two levels of thinning intensity and three thinning types resulting in six different thinning treatments, namely i) moderate thinning from below, ii) moderate thinning from above, iii) moderate systematic thinning, iv) intensive thinning from below, v) intensive thinning from above, and vi) intensive systematic thinning, as well as a control plot where no thinning has been carried out since the establishment. More information about the study sites and samples plots as well as the thinning treatments can be found in Saarinen et al. (2020a).</p> <p>The data set includes stem points of individual Scot pine trees extracted from the point clouds. More about the method of extraction can be found in Saarinen et al. (2020a, 2020b) and Yrttimaa et al. (2020). The title of the zip file refers to the study sites 1, 2, and 3. The title of the text files includes the information on the test site, the plot within the test site, and the tree within the plot. The text files contain stem points extracted from the TLS point clouds. The columns “x” and “y” contain x- and y-coordinates in a local coordinate system (in meters), in column “h” is the height of each point in meters above ground, and treeID is the tree identification number. The columns are separated by space.</p> <p>Based on the study site and plot number, files from different thinning treatments can be identified by using the information in Table 1 in Saarinen et al. (2020b).</p> <p> </p> <p><strong>References</strong></p> <p>Saarinen, N., Kankare, V., Yrttimaa, T., Viljanen, N., Honkavaara, E., Holopainen, M., Hyyppä, J., Huuskonen, S., Hynynen, J., Vastaranta, M. 2020a. Assessing the effects of stand dynamics on stem growth allocation of individual Scots pines. bioRxiv 2020.03.02.972521. <a href="https://doi.org/10.1101/2020.03.02.972521">https://doi.org/10.1101/2020.03.02.972521</a></p> <p>Saarinen, N., Kankare, V., Yrttimaa, T., Viljanen, N., Honkavaara, E., Holopainen, M., Hyyppä, J., Huuskonen, S., Hynynen, J., Vastaranta, M. 2020b. Detailed point cloud data on stem size and shape of Scots pine trees. bioRxiv 2020.03.09.983973. <a href="https://doi.org/10.1101/2020.03.09.983973">https://doi.org/10.1101/2020.03.09.983973</a></p> <p>Viljanen, N., Honkavaara, E., Näsi, R., Hakala, T., Niemeläinen, O., Kaivosoja, J. 2018. A Novel Machine Learning Method for Estimating Biomass of Grass Swards Using a Photogrammetric Canopy Height Model, Images and Vegetation Indices Captured by a Drone. Agriculture 8: 70. <a href="https://doi.org/10.3390/agriculture8050070">https://doi.org/10.3390/agriculture8050070</a></p> <p>Yrttimaa, T., Saarinen, N., Kankare, V., Hynynen, J., Huuskonen, S., Holopainen, M., Hyyppä, J., Vastaranta, M. 2020. Performance of terrestrial laser scanning to characterize managed Scots pine (<em>Pinus sylvestris</em> L.) stands is dependent on forest structural variation. EarthArXiv. March 5. <a href="https://doi.org/10.31223/osf.io/ybs7c">https://doi.org/10.31223/osf.io/ybs7c</a></p>
Tree species, size class, and DBH in the University of Michigan Biological Station (UMBS) Burn Chronosequence established in 1957 and remeasured in 1979 and 1998
A complete survey of overstory vegetation and saplings in the Bob Farmer plots within the UM Biological Station clearut and burn chronosequence. Surveys were completed in 1979 and 1998 to measure the change in biomass and forest composition in the burn plots with forest succession.
Tree size, microhabitat diversity and landscape structure determine the value of isolated trees for bats in farmland
<p>Isolated trees are increasingly recognised as playing a vital role in supporting biodiversity in agricultural landscapes, yet their occurrence has declined substantially in recent decades. Most bats in Europe are tree-dependent species that rely on woody elements in order to persist in farmlands. However, isolated trees are rarely considered in conservation programs and landscape planning. Further investigations are therefore urgently required to identify which trees – based on both their intrinsic characteristics and their location in the landscape – are particularly important for bats. We acoustically surveyed 57 isolated trees for bats to determine the relative and interactive effects of size, tree-related microhabitat (TreM) diversity and surrounding landscape context on bat activity. Tall trees with large diameter at breast height and crown area positively influenced the activity of <em>Pipistrellus pipistrellus</em> and small Myotis bats (<em>Myotis</em> spp.) while smaller and thinner trees favoured <em>M. myotis</em> activity. The diversity of TreMs that can be used as roosts had a positive effect on (i) <em>Barbastella barbastellus</em> activity only when trees were relatively close (10% within 100 radius scale). The potential benefits of isolated trees for bats result from ecological mechanisms operating at both tree and landscape scales, underlining the crucial need for implementing a multi-scale approach in conservation programs. Maintaining the largest and most TreM-diversified trees located in the most heterogeneous agricultural landscapes will provide the greatest benefits.</p>
Text-fig. 13. Macrophotographs of the fossil stems from Mhengere. a: large (90 cm diameter) palm tree trunk in situ; b: external view of the outer roots at the base of the trunk; average diameter of single root is 7 mm; c, d: cross-sections of a fragment of trunk showing the random distribution of equal-sized fibre vascular bundles throughout the trunk, the so-called Coccos-type. in Stratigraphy, Chronology And Palaeontology Of The Tertiary Rocks Of The Cheringoma Plateau, Mozambique
Text-fig. 13. Macrophotographs of the fossil stems from Mhengere. a: large (90 cm diameter) palm tree trunk in situ; b: external view of the outer roots at the base of the trunk; average diameter of single root is 7 mm; c, d: cross-sections of a fragment of trunk showing the random distribution of equal-sized fibre vascular bundles throughout the trunk, the so-called Coccos-type.
The trait-mediated trade-off between growth and survival depends on tree sizes and environmental conditions
<p><span>Interspecific relationships between growth and survival are critical determinants of tree species diversity maintenance in forests. The trade-offs between growth and survival in co-occurring tree species are believed to arise along a continuum of life-history strategies. For example, co-occurring species range from those that grow slowly and survive well in resource-poor environments to those that grow quickly but have low survival rates in resource-rich environments. However, uncertainties remain regarding how growth-survival trade-offs are related to species traits, tree sizes, or environmental conditions.</span></p> <p><span>We examined how the relationships between species traits and growth–survival relationships shift in response to changes in stem sizes and across census periods with different climate conditions (frequency of strong winds, drought intensity) across 45 co-occurring tree species based on 23 years of growth and survival records in a warm temperate rain forest on Yakushima Island, Japan. We developed hierarchical Bayesian models of relative growth and survival rates, including leaf traits, wood density, and 95-percentile maximum stem diameter as explanatory variables. We tested the relationships between estimated trait-mediated growth–survival relationships and the intensities of climate events during five census periods.</span></p> <p><span>Each trait's effects on growth–survival relationships differed across the five census periods in response to climate conditions. Interspecific growth–survival relationships affected by a single trait axis for leaves or wood tended to be negative. In contrast, those affected by the maximum stem diameter tended to be positive. Such trends </span><span>increased with more frequent </span><span>strong winds or more intense droughts. The single-trait effects on growth–survival relationships were stronger for smaller sizes than for larger sizes. For all traits combined, we found a significant growth–survival trade-off only for small-sized stems in three of five census periods.</span></p> <p><span>Synthesis: Our results indicate that the effect of species traits on the growth–survival relationships depended on tree sizes, the census periods, or both in response to the frequency or intensity of climate events. We argue the importance of incorporating spatial and temporal variations in environmental conditions into long-term data from tree census to predict forest dynamics.</span></p>
Data from: Shade tolerance controls the spectrum of crown sizes and its response to local competition across European and North American tree species: Implications for light interception strategies
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The trait-mediated trade-off between growth and survival depends on tree sizes and environmental conditions
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Size and composition of all live and dead trees and large shrubs across a compositional gradient of intermediate-aged and mature forest stands within Interior Alaska collected 2008-2011.
This dataset includes snag biomass data for intermediate-aged (20-59 yr old) and mature (60+ yr old) boreal forest stands across interior Alaska. Data from intermediate-aged stands was published in Alexander et al. 2012.
Far northeastern Siberia boreal forest data: Larch tree snag (dead tree) size distribution across a density gradient
This dataset includes basal diameter (bd) or diameter at breast height (DBH) of dead larch trees (snags) within four stands near Cherskii, Siberia. Data have not been published.
Far northeastern Siberia boreal forest data: Larch tree size distribution across a density gradient
This dataset includes basal diameter (bd) or diameter at breast height (DBH) of larch trees within four stands near Cherskii, Siberia. Data have not been published.
Forest cover and fruit crop size differentially influence frugivory of select rainforest tree species in Western Ghats, India (Part II)
<p><span><span><span><span><span><span><span><span><span><span><span>Forest fragmentation and habitat loss are major disruptors of plant–frugivore interactions, affecting seed dispersal and altering recruitment patterns of tree species dependent on vertebrate dispersers. In a heterogeneous production landscape (primarily tea and coffee plantations) in the southern Western Ghats, India, we <span><span>examined effects of surrounding forest cover and fruit crop size on frugivory of four rainforest bird-dispersed tree species</span></span> (<i>N</i> = 131 trees, ≥ 30 trees per species, observed for 623 h). Frugivore composition differed among the four tree species with the large-seeded <i>Canarium strictum </i>and<i> Myristica dactyloides</i> exclusively dependent on large-bodied avian frugivores, whereas, medium-seeded <i>Persea macrantha</i> and <i>Heynea trijuga </i>were predominantlyvisited by small-bodied and large-bodied avian frugivores, respectively. Using the seed-dispersal-effectiveness framework, we identified effective frugivores and examined their response to forest cover and fruit crop size. Results were idiosyncratic and governed by plant and frugivore traits. Visitations to medium-seeded <i>Persea </i>had a positive relationship with forest cover but the relationship was negative for the large-seeded <i>Myristica</i>. In addition, two of the three effective frugivores for <i>Persea </i>responded to the interactive effect of forest cover and fruit crop size<i>. </i>Frugivore visitations to <i>Hyenea</i> were not related to forest cover or fruit crop and<i> </i>there were too few visitations to <i>Canarium </i>to discern any trends<i>. </i>These results highlight the context-specific response of plant-frugivore interactions to forest cover and fruit crop size influenced by the plant and frugivore traits.</span></span></span></span></span></span></span></span></span></span></span></p>
Forest cover and fruit crop size differentially influence frugivory of select rainforest tree species in Western Ghats, India (Part I)
<p>Forest fragmentation and habitat loss are major disruptors of plant–frugivore interactions, affecting seed dispersal and altering recruitment patterns of tree species dependent on vertebrate dispersers. In a heterogeneous production landscape (primarily tea and coffee plantations) in the southern Western Ghats, India, we <span>examined effects of surrounding forest cover and fruit crop size on frugivory of four rainforest bird-dispersed tree species</span> (<i>N</i> = 131 trees, ≥ 30 trees per species, observed for 623 h). Frugivore composition differed among the four tree species with the large-seeded <i>Canarium strictum </i>and<i> Myristica dactyloides</i> exclusively dependent on large-bodied avian frugivores, whereas, medium-seeded <i>Persea macrantha</i> and <i>Heynea trijuga </i>were predominantly visited by small-bodied and large-bodied avian frugivores, respectively. Using the seed-dispersal-effectiveness framework, we identified effective frugivores and examined their response to forest cover and fruit crop size. Results were idiosyncratic and governed by plant and frugivore traits. Visitations to medium-seeded <i>Persea </i>had a positive relationship with forest cover but the relationship was negativefor the large-seeded <i>Myristica</i>. In addition, two of the three effective frugivores for <i>Persea </i>responded to the interactive effect of forest cover and fruit crop size<i>. </i>Frugivore visitations to <i>Hyenea</i> were not related to forest cover or fruit crop and<i> </i>there were too few visitations to <i>Canarium </i>to discern any trends<i>. </i>These results highlight the context-specific response of plant-frugivore interactions to forest cover and fruit crop size influenced by the plant and frugivore traits.</p>
Macroevolutionary patterns of sexual size dimorphism among African tree frogs (Family: Hyperoliidae)
<p>Sexual size dimorphism (SSD) is shaped by multiple selective forces that drive the evolution of sex-specific body size, resulting in male or female-biased SSD. Stronger selection on one sex can result in an allometric body-size scaling relationship consistent with Rensch's rule or its converse. Anurans (frogs and toads) generally display female-biased SSD, but there is variation across clades and the mechanisms driving the evolution of SSD remain poorly understood. We investigated these topics in a diverse family of African treefrogs (Hyperoliidae). Hyperoliids display traits considered rare among amphibians, including sexual dichromatism and protogynous sex change. Using phylogenetic comparative methods, we tested if adult ecology, sexual dichromatism, and sex change were predictors of body size or SSD. We also tested whether hyperoliids displayed allometric interspecific body-size-scaling relationships. We found a majority of hyperoliid taxa display female-biased SSD, but that adult ecology and sexual dichromatism are poor predictors of sex-specific body size and SSD. Regardless of the groupings analyzed (partitioned by clades or traits), we found support for isometric body-size scaling. However, we found that sex change is a significant predictor of SSD variation. Species in the <i>Hyperolius viridiflavus </i>complex, which putatively display this trait, show a significant reduction in SSD and tend to be sexually monomorphic in size. Although protogynous sex change needs to be validated for several of these species, we tentatively propose this trait is a novel mechanism influencing anuran body size evolution. Beyond this association, additional factors that shape the evolution of anuran body size and SSD remain elusive.</p>
Data from: Evolutionary constraints on tree size and aboveground biomass in tropical dry forests
<p>1. The extent (or lack) of phylogenetic signal for key ecological traits reveals the role of evolutionary processes on present-day ecosystem function and hints on future ecological trends under climate change scenarios. This approach has been applied to South American tropical moist forests, but not to the highly threatened seasonally dry tropical forests (SDTF), despite acknowledgement of their unique evolutionary history. To fill this knowledge gap, we investigated the legacy of evolutionary processes on vital ecological characteristics among SDTF trees: regional dominance, tree size and soil preference.</p> <p>2. We used tree community data on 313 plots of SDTF (12.52 hectares) and locally collected soil data in central-eastern Brazil. For each assessed trait (three for regional dominance, three for tree size and nine for soil preference), we investigated the legacy of evolution using two different approaches: calculating the extent of phylogenetic signal and comparing the fit of four different models of evolution.</p> <p>3. Aboveground woody biomass and tree size showed strong phylogenetic signal. Most of the SDTF biomass stock was concentrated in a few large-sized and closely related tree genera. Among the soil preference variables, only phosphorus displayed significant, albeit weak, phylogenetic signal.</p> <p>4. Synthesis. Our study is the first to show that evolutionary constraints related to tree size significantly determine regional biomass stocks of SDTF in a few closely related tree lineages. This suggests that even isolated SDTF fragments with low taxonomic and phylogenetic diversity can play an important role in the global carbon cycle, storing disproportionally large amounts of carbon in trees that belong to high-biomass lineages. Whether these lineages also share climate change-induced mortality risk deserves future investigation, as they are largely responsible for the maintenance of regional SDTF biomass stocks.</p>
Data from: Localized neighborhood species mingling is correlated with individual tree size inequality in natural forests in South China
<p>Context: Numerous hypotheses such as Janzen–Connell and herd immunity effects have been proposed to explain the coexistence of diverse species in plant communities. However, these mechanisms for maintaining diversity have been studied primarily through the lens of species diversity, whereas tree size diversity or relationships between size and species diversity resulting from local interactions have rarely been investigated.</p> <p>Aims: We aimed to identify relationships between spatial species mingling and tree size inequality using extensive plot data from species-rich forest ecosystems.</p> <p>Methods: We applied neighborhood-based methods and explored relationships between spatial species mingling and size inequality indices in 22 large forest plots (30 ha in total) in subtropical and tropical China.</p> <p>Results: Forest communities with low species mingling, or segregation of heterospecific trees, exhibited increased segregation of trees with dissimilar sizes. In most plots, large trees (e.g. dbh > 30 cm) were extensively associated with high species mingling, and individual-tree neighborhood species and size diversity were closely correlated.</p> <p>Conclusion: Our findings suggest that both the spatial patterns of conspecific dispersal and neighborhood interactions play an important role in determining the spatial patterns of tree size and species diversity and eventually in shaping the structure of forest communities.</p>
Is tree age or tree size reducing height increment in Abies alba Mill. at its southernmost distribution limit?
<p>Many factors limit height increment of trees when age and size increase in large-statured tree species. Height-diameter allometric relationships are commonly used measures of tree growth.</p> <p>The data were collected in a silver fir forest located in Southern Italy, at the southernmost distribution limit for this species. Through a stratified random sampling, 100 trees were selected. All the selected trees were then felled and the total tree height, height increments (internode distances), diameter at breast height, and diameter increments (ring widths) were measured.</p> <p>Conventional methods for estimating the current annual increment of stand volume are based on the uncertain assumption that height increment decreases with tree age. Conversely, size, rather than age, should be accounted for the observed senescence-related declines in relative growth rate and, consequently, implemented in silvicultural manuals. Results stem from a study on Abies alba Mill. at its southern limit of distribution.</p>
Application of leaf size and leafing intensity scaling across subtropical trees
<p>Understanding the scaling between leaf size and leafing intensity (leaf number per stem size) is crucial for comprehending theories about the leaf costs and benefits in the leaf size–twig size spectrum. However, the scaling scope of leaf size vs. leafing intensity changes along the twig leaf size variation in different leaf habit species remains elusive. Here, we hypothesize that the numerical value of scaling exponent for leaf mass versus leafing intensity in twig is governed by the minimum leaf mass versus maximum leaf mass (<i>M</i><sub>min</sub> vs. <i>M</i><sub>max</sub>) and constrained to be ≤ -1.0.</p> <p>We tested this hypothesis by analyzing the twigs of 123 species datasets complied in the subtropical mountain forest. The standardized major axis regression (SMA) analyses showed the <i>M</i><sub>min</sub> scaled as the 1.19 power of <i>M</i><sub>m</sub><sub>ax</sub> and the -a (-1.19) was not statistically different from the exponents of <i>M</i><sub>min</sub><i> </i>vs. leafing intensity in whole data. Across leaf habit groups, the <i>M</i><sub>max</sub> scaled negatively and isometrically with respect to leafing intensity. The pooled data's scaling exponents ranged from -1.14 to -0.96 for <i>M</i><sub>min</sub> and <i>M</i><sub>max</sub> vs. the leafing intensity based on stem volume (LIV). In the case of <i>M</i><sub>min</sub> and <i>M</i><sub>max</sub> vs. the leafing intensity based on stem mass (LIM), the scaling exponents ranged from -1.24 to -1.04.</p> <p>Our hypothesis successfully predicts that the scaling relationship between leaf mass and leafing intensity is constrained to be ≤ -1.0. More importantly, the lower limit to scaling of leaf mass and leafing intensity maybe closely correlate with <i>M</i><sub>min</sub> vs. <i>M</i><sub>max</sub>. Besides, constrained by the maximum leaf mass expand, the broad scope range between leaf size and number may be insensitive to leaf habit groups in subtropical mountain forest.</p>
Data for: Tree species size class patterns portend compositional shifts and low resilience in managed northern hardwood forests
<p><span>Declining biodiversity is a global challenge to sustainability and resilience of ecosystems facing multiple novel stressors, including climate change and invasive pests-pathogens. Northern hardwood forests (NHF) of the Great Lakes region have experienced declines in canopy tree diversity since European colonization, with current tree regeneration patterns in some areas suggesting perpetuation of this trend. However, regional (10<sup>6</sup> ha) patterns and possible causes are underexplored. To address this information gap, we used data from 141 managed NHF stands, Michigan, USA to examine diversity indices across tree size classes (seedling, sapling, and canopy); stand-level drivers of regeneration (seedling and sapling) diversity and individual species density; and patterns among species in relative abundances across size classes. Diversity was similar across size classes (mean asymptotic species richness of 6 – 7 species and <3 effective common species); however, some species contributing to sapling diversity are unlikely to contribute to future canopy diversity (<em>Fraxinus americana </em>and<em> Fagus grandifolia</em>, insect/pathogen limited; <em>Ostrya virginiana, </em>small maximum size). For the 11 most common species, conspecific canopy density (+, significant for 11 seedlings, 11 species) and stand basal area (-, saplings, 3 species) were the most consistent drivers of density, with less consistent effects for deer use, site quality, and substrate. Patterns of relative density by size class among the 18 species present on > 10 % of sites were consistent with theories of establishment or recruitment limitations due to deer browsing, deep shade, or limited suitable substrate. For seven species (including e.g., <em>Tsuga canadensis</em><span>, </span><em>Betula alleghaniensis, Populus grandidentata, Tilia americana</em><span>)</span>, relative abundance was lowest in the seedling layer and increased in larger size classes, <span>suggesting seedling establishment substrate and/or early shade mortality limitations. For two species (<em>Acer saccharum, Quercus rubra.</em>), patterns of reduced sapling relative abundance compared to seedling or canopy strata suggests a sapling recruitment bottleneck from deer browsing/shade, whereas six species (e.g., <em>F</em></span><em>agu<span>s grandifolia, Ostrya virginiana, Pinus strobus</span></em><span>) had highest relative density for saplings suggesting sapling to canopy recruitment limitations. Lastly, seedlings were relatively most abundant for </span><em>Acer rubrum </em><span>and </span><em>Prunus </em><span>spp., indicating disproportionally high seedling establishment, if not sapling or canopy recruitment, and for F. Americana, consistent with recent pest-related canopy mortality. Our results</span> suggest sustained low diversity and shifting composition are being driven by limited local seed availability, deep shading, limited seedling establishment substrate, and abundant deer. Management aimed at overcoming these specific limitations may be necessary to promote future NHF resilience.</span></p>
Forest cover and fruit crop size differentially influence frugivory of select rainforest tree species in Western Ghats, India (Part I)
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Data for: Tree species size class patterns portend compositional shifts and low resilience in managed northern hardwood forests
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Allen Brain Atlas
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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.
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