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430 results for “Forest Structure”
Humid tropical vertebrates are at lower risk of extinction and population decline in forests with higher structural integrity
<p>The four Excel workbooks contain processed data in the form of humid tropical forest area under each of multiple values of the Structural Condition Index (SCI), Forest Structural Integrity Index (FSII), and Human Footprint (HFP) for Mammal, Bird, Reptile and Amphibian species. The associated README text file contains metadata to describe the data in the xlsx workbooks. Python code to replicate geospatial analyses and R code to replicate statistical analyses are provided in the respective scripts. ArcGIS Pro is required to be installed prior to running the Python script.</p>
The legacies of land-clearance and trophic downgrading accumulate to affect structure and function of kelp forests
<p>Aotearoa New Zealand is the last major landmass settled by people, and therefore provides a recent record of ecological legacy effects in the coastal zone. Large-scale land clearances of forests accelerated over the last century, affecting the concentration of suspended sediments, light environment and nutrient composition on rocky reefs, and consequently the distribution, abundance and composition of algal forests. Environmental effects were compounded in many places by overfishing and long-term declines of large predatory species, often leading to proliferation and extensive grazing by sea urchins. Here we examine these processes in three biogeographic regions that have been differentially affected by ecological legacy effects. The study was based on the depth-specific associations between sea urchins (<em>Evechinus chloroticus</em>) and the common kelp (<em>Ecklonia radiata</em>) from multiple sites within each region, some of which were sampled over two decades within no-take marine reserves and in actively fished areas. Satellite-derived estimates of water column properties were used as proxies for the relative effects of coastal sedimentation on kelp forest habitats. We then used an information-theoretic framework to assess the relative factor weightings of marine reserve effects on urchin density, total suspended solids and regional urchin density on the depth-specific density of <em>E. radiata</em>. Fishing effects were significant within and outside of reserves in the Northern and Central regions, but the effect-sizes were by far strongest in the Northern region. In the Central region characterised by extensive land clearance and forestry combined with high coastal retention of water, the concentration of total suspended solids had a major influence on the depth distribution of kelp, confining it to shallow water (<10m depth) in small patches where urchins did not overgraze. These patterns are in sharp contrast to the small marine reserve effects and deep distribution of <em>E. radiata</em> in the Southern region, which has intact native forested catchments, comparatively low fishing pressure and a large regional network of marine reserves. The results highlight important differences in how centuries-old legacies of land clearance and exploitation affect regional-scale dynamics of sea urchins and kelp, and define the appropriate spatial scale of ecosystem-based management of kelp forest habitats.</p>
Supplementary material 1 from: Hermes C, Döpper A, Schaefer MH, Segelbacher G (2016) Effects of forest fragmentation on the morphological and genetic structure of a dispersal-limited, endangered bird species. Nature Conservation 16: 39-58. https://doi.org/10.3897/natureconservation.16.10905
Development of species-specific microsatellite primers : Explanation note: The supplementary material contains a detailed description of the development of a set of 10 microsatellite primers for the Ecuadorian Tapaculo, including primer sequences and gene bank accession numbers.
Flying under the LiDAR: relating forest structure to bat activity and call diversity
<p>Bat call data collected at Ordway-Swisher Biological Station from June - September 2015.</p>
Data from: Climate interacts with the functional trait structure of tree communities to influence forest productivity
<p>Tree functional diversity can increase forest productivity by enhancing species interactions and providing greater growth stability. However, very few studies have examined the influence of tree community trait structure on survivor growth, recruitment, and mortality simultaneously, which are the main drivers of forest population dynamics. Here we explore the interactions among functional diversity, productivity, and climate to investigate the role of the trait structure of communities on forest productivity and to determine under what circumstances functional diversity should be promoted to ensure forest adaptive capacity under future climate. Using random-forest modeling and a network of permanent sample plots covering a broad gradient of climatic conditions, we isolated the effects of functional diversity—described as the distribution of trait values in a community—and climate variables on net forest productivity (NFP), survivor growth, recruitment, and mortality. Based on our findings, community-level trait structure affects forest productivity in different ways. NFP was influenced by three traits from three different plant strategy dimensions, whereas survivor growth and recruitment were strongly correlated with leaf and resource acquisition traits, and tree mortality with a mix of traits reflecting various plant strategies. We also observed climate interactions with the functional trait structure of tree communities. For instance, we observed an interaction between drought tolerance and mean annual temperature: at low temperatures, NFP biomass accumulation increased with the value of the drought tolerance trait; however, at higher temperatures, the opposite pattern was observed. However, we found contrasting patterns of population response to climate variability, depending on their functional diversity. Greater functional diversity does not necessarily increase biomass accumulation under different climatic conditions.</p> <p><em>Synthesis</em>. As all components of forest productivity contribute to NFP, studies on forest productivity should not only consider survivor growth but also recruitment and mortality. Each component responds differently in terms of biomass changes to climatic variation, according to the trait structure of tree communities. This study provides a framework to identify the trait structure that should be targeted under different climate scenarios to anticipate change and help strengthen forest response capacity to climate change.</p>
Data for: When do contemporary wildfires restore forest structures in the Sierra Nevada?
<p>This dataset contains GeoTIFF raster layers derived from the analyses described in Chamberlain et al. (2024) ("When do contemporary wildfires restore overstore structures in Sierra Nevada forests"). Each layer represents classified predictions of the probability (using a 0.5 threshold) of restorative fire effects for the year 2020 under a mild (burning index = 53) and moderate (burning index = 71) fire weather scenario. The three layers include predicted probabilities for cover restoration, partial restoraiton, and full restoration. Cover restoration suggests that only canopy cover is likely to be restored in subsequent first-entry wildfires, partial restoration indicates that canopy cover and ladder fuel densities are likely to be restored, and full restoration indicates that canopy cover, ladder fuel density, and clump complexity are all likely to be restored. Please refer to the text in Chamberlain et al. (2024) for complete descriptions of each forest structure metric and how the restoration indices were defined. </p> <p>The codes in each raster layer are as follows:<br>NoData = outside study area<br>0 = restoration unlikely (probability < 0.5) under mild or moderate fire weather conditions<br>1 = restoration likely (probability > 0.5) under mild fire weather conditions<br>2 = restoration likely (probability > 0.5) under moderate fire weather conditions</p> <p>Terms of use: These data are solely for the purpose of general public information; the user should not rely upon the contents of this data for any specific purpose without making independent investigation. The authors assume no responsibility for any risk, loss, or liability that may result from the use of the data. Please contact Caden Chamberlain at cc274@uw.edu if there are any questions or concerns. </p>
FIGURE 4. Phallus aureolatus. A. Pseudoparenchymatous structure from the indusium. B in Phallus aureolatus (Phallaceae, Agaricomycetes), a new species from the Brazilian Atlantic Forest
FIGURE 4. Phallus aureolatus. A. Pseudoparenchymatous structure from the indusium. B. Basidiospores. Scale bars = 10 μm.
Figure 2. Phylogenetic structure within Petrodromus. Colour coding indicates the main phylogenetic lineages found. A in Four-toed sengi (Petrodromus tetradactylus, Afrotheria, Mammalia) museomics reveals a crucial role of East African forests in macroscelidean diversification
Figure 2. Phylogenetic structure within Petrodromus. Colour coding indicates the main phylogenetic lineages found. A, Bayesian phylogenetic tree from mitochondrial (less) and nuclear DNA (right) with major genetic lineages highlighted. Numbers indicate posterior probability of deeper nodes. B, Collecting locations of samples assigned to lineages, with squares representing the P.t.s.s. lineages and dots all other lineages. C, Haplotype network of the nuclear gene IRBP (top) and mitochondrial gene 16S rRNA (boưom).
Changes in structure and composition of protected forest habitats after 10 years: Analyzes from different Natura 2000 sites in Saxony-Anhalt, Germany
<p>The data utilized in the paper "Wild et al. (2024)," submitted in Ecology and Evolution, are provided herein. The study examines the alterations in forest structure and species composition in Natura 2000 sites over a period of approximately ten years in the Harz and Harz foreland regions of Saxony-Anhalt, Germany.</p> <p>The data were collected as part of the research project "Possibilities and Methods for the Promotion of Tree Species and Habitats of Native Forests as a Building Block for Adaptation to Climate Change and for Coping with Forest Damage Using the Example of Selected Natura 2000 Areas in Saxony-Anhalt" (10/2020 – 06/2023) (project no. 407.1.10-60128/630120000006) funded by the European Agricultural Fund for Rural Development and the State Administration Office of Saxony-Anhalt. </p> <p>The surveys were conducted between the months of July and September in the years 2021 and 2022. </p>
Assessing the effects of elephant foraging on the structure and diversity of an Afrotropical forest
<p>African forest elephants (<i>Loxodonta cyclotis</i>) are ecosystem engineers that browse and damage large quantities of vegetation during their foraging and movement. Though elephant trail networks and clearings are conspicuous features of many African forests, the consequences of elephant foraging for forest structure and diversity are poorly documented. In this study in northeastern Gabon, we compare stem size, stem density, proportional damage, species diversity, and species relative abundance of seedlings and saplings in the vicinity of seven tree species that produce elephant-preferred fruits ("elephant trees") relative to control trees that do not. Across 34 survey trees, with a combined census area of 2.04 ha, we recorded data on 26,128 woody stems in three sizes classes. Compared to control trees, the area around elephant trees had: a) a significantly greater proportion of damaged seedlings and a marginally greater proportion of damaged saplings (with 82% and 24% greater odds of damage, respectively); b) no significant difference in stem density or species diversity; and c) a significantly greater relative abundance of seedlings of elephant tree species. Increasing distance away from focal elephant trees was associated with significantly reduced sapling stem damage, significantly increased sapling stem density, and significantly increased sapling species diversity. Considered in sum, our results suggest that elephants can affect the structure and diversity of Afrotropical forests through their foraging activities, with some variation based on location and plant size class. Developing a more complete understanding of elephants' ecological effects will require continued research, ideally with manipulative experiments.</p>
Data from: Connectivity explains local ant community structure in a Neotropical forest canopy: a large-scale experimental approach
Understanding how habitat structure and resource availability affect local species distributions is a key goal of community ecology. Where habitats occur as a mosaic, variation in connectivity among patches influences both local species richness and composition, and connectivity is a key conservation concern in fragmented landscapes. Similarly, availability of limiting resources frequently determines species co-existence or exclusion. For primarily cursorial arthropods like ants, gaps between neighboring trees are a significant barrier to movement through the forest canopy. Competition for limited resources such as nest sites also promotes antagonistic interactions. Lianas (woody vines) connect normally isolated neighboring tree crowns and often have hollow stems inhabited by ants. We used two large-scale liana removal experiments to determine how connectivity and nest site availability provided by lianas affect arboreal ant species richness, species composition, and β-diversity in a lowland tropical forest in Panama. Removing lianas from a tree crown reduced ant species richness up to 35%, and disproportionately affected species that require large foraging areas. Adding artificial connectivity to trees mitigated the effects of liana removal. Ant colonization of artificial nests was higher (73% occupied) in trees without lianas vs. trees with lianas (28% occupied). However, artificial nests typically were colonized by existing polydomous, resident ant species. As a result, nest addition did not affect ant community structure. Collectively, these results indicate that lianas are important to the maintenance of arboreal ant diversity specifically by providing connectivity among neighboring tree crowns. Anticipated increases in liana abundance in this forest could increase the local (tree-level) species richness of arboreal ants, with a compositional bias toward elevating the density of broad-ranging specialist predators.
Data from: Population structure of the invasive forest pathogen Hymenoscyphus pseudoalbidus
Understanding the genetic diversity and structure of invasive pathogens in source and introduced areas is crucial to reveal hidden biological aspects of an organism, to reconstruct the course of invasions and to establish effective control measures. Hymenoscyphus pseudoalbidus (anamorph: Chalara fraxinea) is an invasive and highly destructive fungal pathogen on common ash Fraxinus excelsior in Europe and occurs natively in east Asia. To get insights into the dispersal mechanism and the history of invasion, we used microsatellite markers and characterized the genetic structure and diversity of H. pseudoalbidus populations at three spatial levels: (i) in Europe; (ii) at the epidemic front and (iii) between Europe and Japan. The 1208 European strains form one large population as no evident structure was detected using Bayesian and multivariate clustering analysis. Only the distribution of genetic diversity in space, pairwise population differentiation (GST) and the spatial analysis of principal components revealed a faint geographic pattern around Europe. A significant allele deficiency in most European populations pointed to a recent genetic bottleneck whereas no pattern of isolation by distance was found. Populations from Japan harbored a higher genetic diversity and were genetically differentiated from European ones. Nevertheless, phylogenetic and network analysis clearly demonstrated that individuals from both regions are conspecific. Our data suggest that H. pseudoalbidus was introduced only once by a minimum of two individuals. The potential source region of H. pseudoalbidus is huge and further investigations are required for a more accurate localization of the source population.
Data from: Impact of habitat fragmentation on the spatial structure of the Eastern Arc Forests in East Africa: implications for biodiversity conservation
The Eastern Arc Mountains in Tanzania and Kenya are one of 35 global biodiversity hotspots. The Eastern Arc forests are, as are many other tropical biodiversity hotspots, highly fragmented. Understanding the impact of habitat fragmentation (i.e., habitat loss and subdivision) on the spatial structure of the Eastern Arc forests is important because forest spatial structure highly influences species richness, persistence, and extinction debt. Here we examine the impact of habitat fragmentation on the spatial structure of the Eastern Arc forests at a patch scale using very high resolution aerial imagery having a spatial resolution of 0.5–1.5 m. Forest area across the 13 Eastern Arc Mountains is 405,852 ha and is distributed into 311 fragments ≥ 10 ha in size with a median fragment size of 84 ha. The 18 largest forest fragments in the Eastern Arc Mountains contain greater than three-quarters of total forest area. Average fragment isolation, as assessed by median distance to nearest fragment and median distance to the nearest larger fragment, is 867 and 1533 m, respectively. Of total forest area, 14% is < 100 m from the forest edge and 33% is < 300 m from the forest edge. Establishing forested linkages among the largest and closest forest fragments through forest regeneration and protection of secondary regenerating forest as well as providing protected area status to the remaining non-protected forest including unprotected smaller forest fragments are important to enhancing the long-term persistence of many plant and animal species here.
Data from: Quantifying floristic and structural forest maturity: an attribute-based method for wet eucalypt forests
1. Maintaining developmental heterogeneity of ecological communities within landscapes is crucial for sustainable native forest management. Consequently, methods to assess forest maturity (i.e. the degree to which the forest contains attributes and supports processes characteristic of late-successional forests) are valuable for making management decisions. However, no consistent, pragmatic method to quantify maturity that incorporates multiple ecosystem elements is available for many forest systems, including Australian wet eucalypt forests. 2. We draw upon forest community dynamics theory to develop a method to quantify maturity based on forest attributes, and use this method to create two metrics of wet eucalypt forest floristic and structural maturity. We then test the ability of remotely-sensed and field-collected variables to predict these metrics. 3. Both the floristic and structural maturity metrics performed well at capturing underlying trends of forest maturation. Remotely-sensed LiDAR (Light Detection and Ranging) and photo-interpretation data provided estimates of moderate accuracy for both floristic and structural maturity (R2 = 0.57-0.77). Field variables that are relatively efficient and accurate to measure provided greater model accuracy (R2 = 0.73-0.85). Including more complex field variables increased model accuracy to high levels (R2 = 0.93). Therefore, while maturity predicted from remote-sensing data enables a useful and accessible large-scale maturity measure, field indices would provide a more accurate means of assessing maturity at the local stand level. 4. Synthesis and applications: The metrics developed in this study provide a powerful tool for undertaking consistent assessments of wet eucalypt forest maturity. This assessment tool could improve forest management by providing information to optimise practices such as prioritising stands for retention or harvesting, determining the effectiveness of restoration or management practices, and monitoring changes in maturity over time. The method could be adapted to any forest system that undergoes well-defined directional development.
Data from: Rodent-avoidance, topography and forest structure shape territory selection of a forest bird
Background - Understanding the factors underlying habitat selection is important in ecological and evolutionary contexts, and crucial for developing targeted conservation action in threatened species. However, the key factors associated to habitat selection often remain poorly known. We evaluated hypotheses related to abiotic and biotic factors thought to affect territory selection of the wood warbler Phylloscopus sibilatrix, a passerine living in an unpredictable environment owing to irregular rodent outbreaks and showing long-term declines particularly in Western Europe. Results - Comparing breeding territories to unoccupied areas located close-by revealed that territory occupancy in north-western Switzerland was positively related to slope steepness (topographic hypothesis supported) as well as to numbers of tussocks and trees, respectively, while it showed a unimodal relationship to cover of herb layer (forest structure hypothesis supported). Furthermore, a strong negative correlation between breeding territory occupancy and rodent numbers was found, suggesting that wood warblers avoid areas with high rodent densities (rodent-avoidance hypothesis supported). Comparing breeding territories to abandoned territories showed that breeding territories were located on steeper slopes (topography hypothesis supported), at larger distance from the forest edge (anthropogenic disturbance hypothesis supported) and harboured more trees (forest structure hypothesis supported) than abandoned territories. Conclusions - Aside from structural and topographic features of the habitat, wood warblers are affected by rodent numbers when settling, making habitat selection unpredictable from year to year. Forestry practices promoting relatively high tree densities, few bushes and an intermediate low-growing ground vegetation cover would enhance habitat quality for this declining passerine. In contrast, forestry practices aiming at increasing light in forests (selective thinning, group-felling) or keeping forest stands permanently covered with shrubs, bushes and trees of various sizes (continuous cover forestry) do not benefit the wood warbler.
The vegetation composition, structure and regeneration status of Gole Natural Forest, West Arsi Zone, Oromia Regional State, Ethiopia
<p>This study was conducted in Gole natural forest (Dodola) West Arsi Zone of Oromia Regional State, Ethiopia. The study was intended to investigate the vegetation composition, structure, community types and the regeneration status. To collect the vegetation data, systematically 62 plots 20 m × 20 m (400 m<sup>2</sup>) were established at 100 m interval, starting from the top of the mountain. Tree and shrub species were counted and their cover abundance value was estimated. The data for herbaceous species were collected from five 2 m × 2 m sub-plots laid at the four corners each and one at the centre of the main plot. Height and diameter at breast height (DBH) of all woody species taller than 1.5 m and thicker than 2 cm were measured. R package was applied for cluster analysis. Indicator species analysis was performed in R Interpolated species accumulation curves. Estimate S 8.2 Software and Microsoft Excel were used to analyze the data. Rarefaction was applied to compare the species richness of the plant communities in the study area. Sorensen's similarity coefficient was used to detect similarities and dissimilarities among communities.</p> <p>A total of 114 plant species belonging to 57 families and 94 genera were identified. The most dominant families were Asteraceae, followed by Acanthaceae and Lamiaceaae. Out of 114 species 17 were endemic to Ethiopia. The study showed that high density was seen at lower height and DBH classes. Five plant community types were identified. The rarefaction revealed that there is difference in species richness among communities. The Sorensen's similarity index showed that, there was a difference in the distribution of plant species composition among the five plant communities.</p>
Data from: Tropical forests structure and diversity: a comparison of methodological choices
<p>1. Large-scale data compilation is increasing steadily in tropical forest research, but the lack of standardized methods for data collection limits drawing inference from large datasets and cross-biome analyses. Different inclusion methods and minimum tree diameter threshold are among these varying factors. To tackle this issue, we evaluated how different approaches for tree sampling affects our understanding of diversity and functioning in different tropical vegetation types.</p> <p>2. We used a unique dataset of 44 inventory plots (43.54 ha) encompassing an aridity gradient: evergreen moist forests, semideciduous and deciduous tropical forests. Data were collected using the by-tree inclusion method, in which, all stems are measured if the equivalent diameter of the tree reaches the minimum threshold. We simulated the impact of adopting different inclusion methods (by-stem and by-tree) and different minimum diameter thresholds on the estimation of number of trees and stems, biomass and species richness. We used linear mixed models to investigate the effect of minimum diameter threshold and inclusion method on our different response variables. We also evaluated species chance to be sampled under different minimum inclusion criteria.</p> <p>3. Inclusion method and minimum diameter threshold mainly affect the estimation of number of trees and stems and species richness, especially in deciduous and semideciduous forests, where resprouting is a prevalent strategy. In these forests, many trees that have several stems do not reach the minimum size individually when adopting the by-stem method, yet they do reach the minimum size threshold when all stems are considered together. For these environments under water stress, our analysis showed that using large minimum sizes, such as the 10 cm typically used in rainforests, implies large sampling losses, especially when used jointly with the by-stem inclusion method.</p> <p>4. The by-tree inclusion method represents an alternative approach that offers a more reliable sampling in different vegetation types, particularly in those habitats where resprouting is a widely encountered strategy along all age classes. We demonstrate the infeasibility of adopting broad and standard minimum thresholds for different tropical vegetation types, particularly considering their widely different ecological strategies.</p>
Data from: BIOVERA-Tree: tree diversity, community composition, forest structure and functional traits along gradients of forest-use intensity and elevation in Veracruz, Mexico
<p>Here, we describe BIOVERA-Tree, a database on tree diversity, community composition, forest structure, and functional traits collected in 120 forest plots distributed along an extensive elevational gradient in Veracruz State, Mexico. BIOVERA-Tree includes information on forest structure from three levels of forest-use intensity, namely old-growth, degraded, and secondary forest, replicated across eight elevations from sea-level to near the tree line at 3500 m and on size and location of 4549 tree individuals with a diameter at breast height ≥ 5 cm belonging to 216 species, 154 genera, and 80 families. We also report measurements of eight functional traits, namely wood density for 143 species, maximum height for 216 species and leaf traits including: specific leaf area, lamina density, leaf thickness, chlorophyll content, and leaf area for 148 species and leaf dry matter content for 145 species.</p>
Figure 1 in Structure of insect community in the fungus Inonotus radiatus in riparian boreal forests
Figure 1. Map showing the five lakes (black dots) from which Inonotus radiatus basidiomes were sampled in Uppland, Sweden.
Figure 2 in Structure of insect community in the fungus Inonotus radiatus in riparian boreal forests
Figure 2. Accumulation curves for species richness (and 95% confidence intervals) for species that use Inonotus radiatus as breeding habitat. Solid lines represent northern and dotted lines southern shores.
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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)
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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.