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opencc-by-4.0Dec 2022View details →

Contribution of tree community structure to forest productivity across a thermal gradient in eastern Asia

These CSV and R script files are the dataset and codes used for the analysis in the following <a href="https://www.nature.com/articles/s41467-023-36671-1">journal paper</a>: Kohyama, T.I., Sheil, D., Sun, IF. et al. Contribution of tree community structure to forest productivity across a thermal gradient in eastern Asia. Nat Commun 14, 1113 (2023). https://doi.org/10.1038/s41467-023-36671-1   Contents <ul> <li>d0.csv — Individual tree-stem size data obtained by two censuses in 60 forest plots in eastern Asia <ul> <li><code>plot_id</code> — Plot ID</li> <li><code>species</code> — Scientific name</li> <li><code>t1</code> — Year of the first census</li> <li><code>t2</code> — Year of the second census</li> <li><code>dbh1</code> — Stem diameter (cm) at the first census*1</li> <li><code>dbh2</code> — Stem diameter (cm) at the second census*1</li> <li><code>w1</code> — Estimated above ground biomass (Mg C ha−1) at the first census</li> <li><code>w2</code> — Estimated above ground biomass (Mg C ha−1) at the first census</li> <li><code>wl1</code> — Estimated leaf biomass (Mg C ha−1) at the first census</li> <li><code>wl2</code> — Estimated leaf biomass (Mg C ha−1) at the second census</li> </ul> </li> </ul>   <ul> <li>d1.csv — Species-level biomass, productivity and other turnover rates in each of 60 forest plots in eastern Asia <ul> <li><code>plot_id</code> — Plot ID</li> <li><code>t1</code> — Year of the first census</li> <li><code>t2</code> — Year of the second census</li> <li><code>species</code> — Scientific name</li> <li><code>N</code> — Period mean number of stems (ha−1)</li> <li><code>B</code> — Period mean above ground biomass (Mg C ha−1)</li> <li><code>Bl</code> — Period mean leaf biomass (Mg C ha−1)</li> <li><code>p</code> — Relative above ground biomass productivity rate (year−1)</li> <li><code>l</code> — Relative above ground biomass loss rate (year−1)</li> <li><code>P</code> — Absolute above ground biomass productivity rate (Mg C ha−1 year−1)</li> <li><code>L</code> — Absolute above ground biomass loss rate (Mg C ha−1 year−1)</li> <li><code>pl</code> — Relative leaf biomass productivity rate (year−1)</li> <li><code>ll</code> — Relative leaf biomass loss rate (year−1)</li> <li><code>Pl</code> — Absolute leaf biomass productivity rate (Mg C ha−1 year−1)</li> <li><code>Ll</code> — Absolute leaf biomass loss rate (Mg C ha−1 year−1)</li> <li><code>w_max</code> — Period mean above ground biomass of the largest tree (Mg C ha−1)</li> <li><code>w_99</code> — The 99-th percentaile of tree above ground biomass (Mg C ha−1)</li> <li><code>rgr_max</code> — Relative growth rate of the largest tree (year−1)</li> </ul> </li> </ul>   <ul> <li>plot_metadata.csv — Metadata (e.g. location and climate variables) for 60 forest plots in eastern Asia <ul> <li><code>plot_id</code> — Plot ID</li> <li><code>latitude</code> — Latitude in decimal degrees (°)</li> <li><code>longitude</code> — Longitude in decimal degrees (°)</li> <li><code>elevation</code> — Elevation (m)</li> <li><code>area</code> — Plot area (ha)</li> <li><code>MAT</code> — Mean annual temperature (°C)*2</li> <li><code>AP</code> — Annual precipitation (mm year−1)*2</li> <li><code>PET</code> — Potential evapotranspiration (mm year−1)*2</li> </ul> </li> </ul>   <ul> <li>annual_litterfall.csv — Annual fine litterfall (i.e. canopy productivity) obtained by monthly litterfall records collected by litter traps during same census period in 22 forest plots <ul> <li><code>plot_id</code> — Plot ID</li> <li><code>Plitter</code> — Annual litterfall production (Mg C ha−1 year−1)</li> </ul> </li> </ul>   <ul> <li>max_tree_height.csv — Tallest tree height for 388 species in 11 forest plots <ul> <li><code>plot_id</code> — Plot ID</li> <li><code>species</code> — Scientific name</li> <li><code>H_max</code> — tallest tree height (m)</li> </ul> </li> </ul>   <ul> <li>productivity.r — R script for estimating forest-level aboveground net productivity</li> </ul>   *1 No-record diameters due to death in the second census and pre-recruitment in the first census were set to zero. *2 Climate data for the period 1981–2010 were obtained from CHELSA version 2.1 (Krager et al. 2021 EnviDat, https://doi.org/10.16904/envidat.228.v2.1)

opencc-by-4.0Jun 2023View details →

Fig. 4A-D in The impact of urban warfare on the structure of ant assemblages on trees (Hymenoptera: Formicidae)

Fig. 4A-D – Multivariate linear regression (1 independent, n dependent) for different parameters: A – between degree of damage and number of ants; B – between number of ants and tree diameter; C – between dendrobiont (nesting in trees) ants and degree of damage; D – between herpetobiont (nesting in soil) ants and degree of damage.

opencc-by-4.0Jun 2023View details →

Fig. 2A-F in The impact of urban warfare on the structure of ant assemblages on trees (Hymenoptera: Formicidae)

Fig. 2A-F – Degrees of damaged trees. A – undamaged trees, B – 1st degree of damage, C – 2nd degree, D – 3rd degree; E – 4th degree; F – 5th degree. Black arrows indicate superficial damage to the tree bark, red arrows indicate deep damage to conductive tissues, yellow arrows - destruction of the upper part of the tree trunk, blue arrows - irreparable damage to the tree (destruction of the trunk).

opencc-by-4.0Jun 2023View details →

Fig. 1A-B in The impact of urban warfare on the structure of ant assemblages on trees (Hymenoptera: Formicidae)

Fig. 1A-B – Investigated locations in the Kyiv region: A – Bucha; B – Irpin. Areas of cities affected by military operations are highlighted in red. Data by UN Satellite Center.

publicJan 2023View details →

Masting is shaped by tree-level attributes and stand structure, more than climate, in a Rocky Mountain conifer species

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publicApr 2025View details →

Data and code from: Evaluating genomic offset predictions in a forest tree with high population genetic structure

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publicJul 2024View details →

Data from: Effects of the control of an invasive tree on the structure of a plant-frugivore network

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publicDec 2022View details →

Sharing land via keystone structure: retaining naturally regenerated trees may efficiently benefit birds in plantations

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zenodo36/100

Input data for the analysis of changes in functional structures of Japanese tree species by species loss simulation

The dataset was used in Kusumoto, Shiono & Kubota (2020). It includes functional structure indices (community means, functional richness, and Rao's quadratic entropy) for 514 Japanese timber and non-timber tree species at 10-km grid cell level. The community means were based on specific leaf area and leaf nitrogen content, respectively. Functional richness and Rao's Q were based on wood density and tree height. There functional metrics were calculated for the observed species assemblages and simulated assemblages at 10-km grid cell level. The simulated assemblages were computed by removing species in each grid cell at 5 levels of species loss (10%, 20%, 30%, 40% and 50%) with two scenarios: random loss and ordered loss depending on species successional niche score (i.e. later successinal species are preferentially lost). See "README" sheet for detailed explanations of the contents. Kusumoto, Shiono & Kubota (2020)  Ethnobotany-informed trait ecology: measuring vulnerability of timber provisioning services across forest biomes in Japan. Biodiversity and Conservation. DOI: 10.1007/s10531-020-01974-y

opencc-by-4.0Apr 2020View details →

opencc-zeroAug 2020View details →

Data from: Multi-scale spatial genetic structure within and between populations of wild cherry trees in nuclear genotypes and chloroplast haplotypes

Spatial genetic structure (SGS) of plants mainly depends on the effective population size and gene dispersal. Maternally inherited loci are expected to have higher genetic differentiation between populations and more intensive SGS within populations than biparentally inherited loci because of smaller effective population sizes and fewer opportunities of gene dispersal in the maternally inherited loci. We investigated biparentally inherited nuclear genotypes and maternally inherited chloroplast haplotypes of microsatellites in 17 tree populations of three wild cherry species under different conditions of tree distribution and seed dispersal. As expected, inter-population genetic differentiation was 6–9 times higher in chloroplast haplotypes than in nuclear genotypes. This difference indicated that pollen flow 4–7 times exceeded seed flow between populations. However, no difference between nuclear and chloroplast loci was detected in within-population SGS intensity due to their substantial variation among the populations. The SGS intensity tended to increase as trees became more aggregated, suggesting that tree aggregation biased pollen and seed dispersal distances toward shorter. The loss of effective seed dispersers, Asian black bears, did not affect the SGS intensity probably because of mitigation of the bear loss by other vertebrate dispersers and too few tree generations after the bear loss to alter SGS. The findings suggest that SGS is more variable in smaller spatial scales due to various ecological factors in local populations.

zenodo36/100

Dataset of trees, insects and forest structure of forests disturbed and undisturbed by elephants on Mount Cameroon

Datasets for Maicher et al. Effects of disturbances by forest elephants on diversity of trees and insects in tropical rainforests on Mount Cameroon. Scientific Reports doi: 10.1038/s41598-020-78659-7 All related information can be found in the cited paper. When using the dataset for anything, cite the Maicher et al. Scientific Reports paper. For additional information, refer the paper or write to robert.tropek@gmail.com and vincent.maicher@hotmail.fr

opencc-by-4.0Nov 2020View details →

opencc-zeroOct 2019View details →

Data from: Environmental filtering structures fungal endophyte communities in tree bark

The factors that control the assembly and composition of endophyte communities across plant hosts remains poorly understood. This is especially true for endophyte communities inhabiting inner tree bark, one of the least studied components of the plant microbiome. Here, we test the hypothesis that bark of different tree species acts as an environmental filter structuring endophyte communities, as well as the alternative hypothesis, that bark acts as a passive reservoir that accumulates a diverse assemblage of spores and latent fungal life stages. We develop a means of extracting high‐quality DNA from surface sterilized tree bark to compile the first culture‐independent study of inner bark fungal communities. We sampled a total of 120 trees, spanning five dominant overstorey species across multiple sites in a mixed temperate hardwood forest. We find that each of the five tree species harbour unique assemblages of inner bark fungi and that angiosperm and gymnosperm hosts harbour significantly different fungal communities. Chemical components of tree bark (pH, total phenolic content) structure some of the differences detected among fungal communities residing in particular tree species. Inner bark fungal communities were highly diverse (mean of 117–171 operational taxonomic units per tree) and dominated by a range of Ascomycete fungi living asymptomatically as putative endophytes. Together, our evidence supports the hypothesis that tree bark acts as an environmental filter structuring inner bark fungal communities. The role of these potentially ubiquitous and plant‐specific fungal communities remains uncertain and merits further study.

opencc-zeroDec 2012View details →

Data from: Variation in population structure and dynamics of montane forest tree species in Ethiopia guide priorities for conservation and research

The greatest extent of Afromontane environments in the world is found in Ethiopia. These areas support exceptional biodiversity, but forest cover and ecological integrity have declined sharply in recent decades. Conservation and management efforts are hampered in part by an inadequate understanding of the basic ecology of major tree species. We investigated population structure and inferred population dynamics from size frequency distributions of 22 forest tree species encountered in montane forests of Ethiopia. We collected new empirical data from four sites in the Bale Mountains, where some of the country's most extensive and least disturbed forests remain, and conducted a systematic review and analysis of all such studies that reported population structure for one or more of these species in Ethiopia. Thirteen widespread montane tree species showed a reverse-J size distribution, indicating a relatively stable population structure. Six other species had size-frequency distributions that indicate episodic recruitment and/or removal of certain size classes. Specific causes of these patterns are uncertain: they may involve timber harvesting, herbivory, fire, or natural disturbances, but patterns were inconsistent and locality dependent. For three other tree species, existing data are inadequate for any interpretation of population structure and dynamics. A species of particular conservation concern that emerged from this analysis was Hagenia abyssinica, which was found in all areas to consist only of larger individuals with no recent recruitment. For management and conservation purposes, the species in most urgent need of new research are those with inadequate or inconsistent data, and H. abyssinica..

opencc-zeroJan 2024View details →

Patterns in the genetic structure of 49 lowland rain forest tree species co-distributed on opposite sides of the Northern Andes

The Andes are a major dispersal barrier for lowland rain forest plants and animals, yet hundreds of lowland tree species are distributed on both sides of the Northern Andes, raising questions about how the Andes influenced their biogeographic histories and population genetic structure. To explore these questions, we generated standardized datasets of thousands of SNPs from paired populations of 49 tree species co-distributed in rain forest tree communities located in Panama and Amazonian Ecuador and calculated genetic diversity (π) and absolute genetic divergence (dXY) within and between populations, respectively. We predicted (1) higher genetic diversity in the ancestral source region (east or west of the Andes) for each taxon, and (2) correlation of genetic statistics with species attributes, including elevational range and life-history strategy. We found that genetic diversity was higher in putative ancestral source regions, possibly reflecting founder events during colonization. We found little support for a relationship between genetic divergence and species attributes except that species with higher elevational range limits exhibited higher dXY, implying older divergence times. One possible explanation for this pattern is that dispersal through mountain passes declined in importance relative to dispersal via alternative lowland routes as the Andes experienced uplift. We found no difference in mean genetic diversity between populations in Central America and the Amazon. Overall, our results suggest that dispersal across the Andes has left enduring signatures in the genetic structure of widespread rain forest trees. We outline additional hypotheses to be tested with species-specific case studies.

opencc-zeroMar 2024View details →

Data from: Genomic diversity and structure of a Neotropical microendemic fig tree

Genetic diversity is a key component of evolution and unraveling factors that promote genetic differentiation in space and time is a central question in evolutionary biology. One of the most diverse and ecologically important tree genera in tropical forests worldwide is Ficus (Moraceae). It has been suggested that, given the great dispersal capacity of pollinating fig wasps (Chalcidoidea; Agaonidae), the spatial genetic structure, particularly in monoecious fig species, should be weak. However, no studies have addressed the factors that determine the genetic structure of Ficus species in regions of high geological, geographic, and climatic complexity, such as the Mexican Transition Zone. Using nuclear single nucleotide polymorphisms (5,311 SNPs) derived from low-coverage whole genomes and 17 populations, we analyzed the population genomics of Ficus pringlei to characterize neutral and adaptive genetic variation and structure and its association with geographic barriers such as the Trans-Mexican Volcanic Belt, environmental heterogeneity, and wind connectivity. From genomic data of 71 individuals, high genetic diversity, and the identification of three genomic lineages were recorded (North, South, and Churumuco). The results suggest that genetic variation is primarily determined by climatic heterogeneity. Ficus pringlei populations from the north and south of the Trans-Mexican Volcanic Belt also exhibited minimal genetic differentiation (FST= 0.021), indicating that this mountain range may not act as an insurmountable barrier to gene flow. Wind connectivity is also highlighted in structuring putative adaptive genetic variation, underscoring the intricate complexity of the various factors influencing genetic variation in the species. This study provides information on the possible mechanisms underlying the genetic variation of endemic species of the tropical dry forest of Western Mexico, such as F. pringlei.

opencc-zeroApr 2024View details →

Pigeons use tree structures as the leadership structure for flocking

Collective behaviors leading to various fascinating movement patterns are believed to be the product of complex interplay among individuals. Previous studies have identified two types of leadership structures in pigeon flocks, i.e., hierarchical networks and reciprocal relationships. However, both of these leadership structures are predicated based on data analysis and lack substantial empirical evidence. Additionally, it is difficult to delineate a direct correspondence between leadership structures and trajectory data for pigeon flocks because birds cannot report their leadership structure. Herein, we demonstrated that pigeons adopt leadership relationships that can be characterized as tree structures. In a tree structure, each follower follows its only leader during collective flights, and the single top leader determines the entire flock's flight direction. In the present study, we performed experiments using student volunteers who could report leadership relationships. We identified a one-to-one correspondence between leadership structures and data characteristics and proposed a method for determining the leadership structure based on trajectory data. This strategy was used to analyze flight trajectory data from a pigeon flock and elucidate the pigeons' leadership relationships. The developed approach could effectively model the collective behavior of pigeon flocks, thus accurately replicating findings from previous experimental studies. The results of this study provide insights regarding the leadership structure in pigeon flocks and have implications for artificial collective systems, e.g., autonomous formation control of multiple unmanned aerial vehicles or unmanned surface vehicles.

opencc-zeroFeb 2023View details →

Influence of tree hollow characteristics and forest structure on saproxylic beetle diversity in tree hollows in managed forests in a regional comparison

Tree hollows are among the rarest habitats in today's Central European managed forests but are considered key structures for high biodiversity in forests. To analyze and compare the effects of tree hollow characteristics and forest structure on diversity of saproxylic beetles in tree hollows in differently structured managed forests, we examined between 41 and 50 tree hollows in beech trees in each of three state forest management districts in Germany. During the two-year study, we collected 283 saproxylic beetle species (5880 individuals; 22% threatened species), using emergence traps. At small spatial scales, size of hollow entrance and number of surrounding microhabitat structures positively influenced beetle diversity, while stage of wood mould decomposition had a negative influence, across all three forest districts. We utilized forest inventory data to analyze the effects of forest structure in radii of 50 to 500 m around tree hollows on saproxylic beetle diversity in the hollows. At these larger spatial scales, the three forest management districts differed remarkably regarding the parameters that influenced saproxylic beetle diversity in tree hollows. In Ebrach, characterized by mostly deciduous trees, the amount of dead wood positively influenced beetle diversity. In the mostly coniferous Fichtelberg forest district, with highly isolated tree hollows, in contrast, only the proportion of beech trees around the focal tree hollows showed a positive influence on beetle diversity. In Kelheim, characterized by mixed forest stands, there were no significant relationships between forest structure and beetle diversity in tree hollows. In this study, the same local tree hollow parameters influenced saproxylic beetle diversity in all three study regions, while parameters of forest structure at larger spatial scales differed in their importance, depending on tree-species composition.

opencc-zeroMar 2022View details →

Data from: Trait hierarchies are stronger than trait dissimilarities in structuring spatial co-occurrence patterns of common tree species in a subtropical forest

1. The dissimilarity and hierarchy of trait values that characterize niche and fitness differences, respectively, have been increasingly applied to infer mechanisms driving community assembly and to explain species co-occurrence patterns. Here, we predict that limiting similarity should result in the spatial segregation of functionally similar species, while functionally similar species will be more likely to co-occur either due to environmental filtering or competitive exclusion of inferior competitors (hereafter hierarchical competition). 2. We used a fully mapped 50-ha subtropical forest plot in southern China to explore how pairwise spatial associations between saplings and between adult trees were influenced by trait dissimilarity and hierarchy in order to gain insight into assembly mechanisms. We assessed pairwise spatial associations using two summary statistics of spatial point patterns at different spatial scales and compared the effects of trait dissimilarity and trait hierarchy of different functional traits on the interspecific spatial associations. These comparisons allow us to disentangle the effects of limiting similarity, environmental filtering and hierarchical competition on species co-occurrence. 3. We found that trait dissimilarity was generally negatively related with interspecific spatial associations for both saplings and adult trees across spatial scales, meaning that species with similar trait values were more likely to co-occur and thus supporting environmental filtering or hierarchical competition. We further found that trait hierarchy outweighed trait dissimilarity in structuring pairwise spatial associations, suggesting that hierarchical competition played a more important role in structuring our forest community than environmental filtering across life stages. 4. This study employed a novel method, by offering the integration of pairwise spatial association and trait dissimilarity as well as trait hierarchy, to disentangle the relative importance of multiple assembly mechanisms in structuring co-occurrence patterns, especially the mechanisms of environmental filtering and hierarchical competition, which lead to indistinguishable co-occurrence patterns. This study also reinforced the importance of trait hierarchy rather than trait dissimilarity in driving neighborhood competition.

zenodo36/100

Gene flow between wild trees and cultivated varieties shapes the genetic structure of sweet chestnut (Castanea sativa Mill.) populations

The sweet chestnut orchards (Castanea sativa Mill.) are traditionally planted in the northern Adriatic region. This study investigates their population structure, as well as the genetic background of three toponymous clonal varieties. Six genomic simple sequence repeat (gSSR) and nine EST-derived SSR (EST-SSR) loci were utilized in this study. We have identified five closely related clones, which represent a singular, polyclonal marron variety, found in all three cultivation areas, acompanied by many hybrids, resulting from the breeding between cultivated and wild chestnuts.

opencc-by-4.0Apr 2022View details →