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Data for "Trait-based response of deadwood and tree-related microhabitats to decline in temperate lowland and montane forests"
<p><strong>Sampling design and case studies</strong></p> <p>The study was conducted in two French regions, the Loire valley and the French Pyrenees, and one German region, the Bavarian mountains. In the Loire valley, we studied two lowland sites in oak-dominated (both <em>Quercus petraea</em> (Matt.) Liebl. and <em>Quercus robur</em> L.) forests, one in the Orleans State Forest (107-174 m a.s.l.) and one in the Vierzon State Forest (120-190 m a.s.l.). The main secondary species in these forests were hornbeam (<em>Carpinus betulus</em> L.) and Scots pine (<em>Pinus sylvestris</em> L.). In 2020, we selected nine plots to represent a decline gradient in each of these forests. While the Orleans Forest was healthy overall, the Vierzon Forest had undergone several decline events due to successive droughts aggravated by edaphic factors. In the Pyrenees, we studied two sites in montane forests dominated by silver fir (<em>Abies alba</em> Mill.), whose decline is mainly the result of successive droughts occurring since the 1980’s, and with Norway spruce (<em>Picea abies</em> (L.) H. Karst) and European beech (<em>Fagus sylvatica</em> L.) as secondary species. In 2017, we selected 43 plots: (i) 21 plots in the Aure Valley (854-1570 m a.s.l.) and (ii) 22 plots on the Sault Plateau (705-1557 m a.s.l.). The severe summer drought of 2003 had significant effects on tree mortality in oak and fir forests (Cours and others, 2022). Finally, we studied 19 plots of montane forest in the Bavarian Forest National Park, dominated by Norway spruce (<em>Picea abies</em> (L.) H. Karst) with European beech and silver fir as the main secondary species (Bässler and others, 2009). The dieback results from several cycles of windstorms followed by bark beetle (<em>Ips typographus</em> (L.)) outbreaks (Müller and others, 2010), the dominant drivers of forest dynamics in Norway spruce forests in temperate Europe (Zemlerová and others, 2023). This dieback phenomenon was more severe than either of the aforementioned drought-induced declines, and resulted in greater tree mortality (Cours and others, 2021). In the fir and oak forests in France, our plots were set up in managed forests, and the surrounding forest was also predominantly managed. On the other hand, in the German spruce forest, our plots were set up both within the core area of the Bavarian Forest National Park, and in the surrounding zone (BIOKLIM project), with little or no human intervention (Müller and others, 2010).</p> <p><strong>Field measurements</strong></p> <p>Plots were set up with a Bitterlich relascope with an opening angle corresponding to counting factor n° 1 (ratio 1/50), and mean plot area was about 0.3 ha. For each tree within the plot, we recorded its status (i.e. dead, living, snag, log), tree-species and diameter at breast height (DBH; minimum DBH recorded = 17.5 cm for living trees and logs, 7.5 cm for snags, 67.5 cm for very large trees). We took the proportion of dead trees in basal area (i.e. the ratio of the cumulative basal area of standing and lying dead trees to the basal area of all the trees in the plot), hereinafter referred to as “mortality rate”, as a proxy for the level of local stand decline. Note that this “mortality rate” does not reflect true overall mortality rate in managed oak forests, as foresters removed most valuable declining trees. We visually inventoried TreMs on living trees, logs and snags, and included the 47 types described by Larrieu et al. (2018).</p> <p>For each deadwood item (length > 1 m) in the plot, we measured its decay stage (from 1 = hard dead wood fully covered with bark to 4 = soft wood without bark), length, diameter at mid-length for logs and snags < 4 m long, and DBH for dead trees and snags > 4 m. Deadwood was classified in the following categories: ground-lying (logs and uprooted dead trees) vs standing (snags and standing dead trees); small and mid-size (less than 40 cm in diameter) vs large and very large (more than 40 cm in diameter); and fresh (decay class 1 and 2) vs decayed (decay stage 3 and 4). We calculated the total number of items per hectare by allocating a coefficient N<sub>d</sub> related to diameter (d) to each item observed in the relascope sampling: (N<sub>d</sub> = π 10<sup>8</sup> [ArcTan(1/50)/(π d)]<sup>2</sup>). We estimated TreM diversity and the number of deadwood types per plot.</p> <p>We compiled a list of eco-morphological traits for woody elements (i.e., life status (living, dead) and vertical position (downed, standing), decay stage and diameter) and for TreMs detected in the field (TreM nature, association with deadwood (saproxylic, epixylic, mould), type of bearing substrate (i.e., living tree, dead tree or snag, and log), position in the tree (i.e. base, trunk, crown), degree of wetness, life span or ontogenesis).</p>
Model for: Characterizing long‐term population conditions of the elusive red tree vole with dynamic individual‐based modeling
<div class="abstract"> <p>Old growth forests are declining globally, threatening dependent wildlife. Many arboreal old‐growth obligates, such as the threatened red tree vole, are difficult to monitor for changes in habitat occupancy, and abundance. Yet, conservation planning relies on this information to prevent population declines. We integrated a range of species, habitat, and landscape change information to develop a dynamic habitat‐population model. The spatial individual‐based model simulated dynamic patterns of occupancy that responded to annual habitat maps, describing 36 years of observed change. We simulated population dynamics and local movement to characterize changes in occupancy and abundance, and the capacity of remaining habitat to support red tree voles. Red tree vole redistribution patterns strongly corresponded to wildfire footprints and timber extraction locations. Population strongholds are likely to exist in clumped pockets of old‐growth forest that were unaffected by wildfire and in protected old forest reserves. However, the exact number and locations of local clusters remain uncertain. Simulated population losses occurred at different paces in different places, underscoring the need for recurring evaluation of population changes with field occupancy surveys and modeled evaluations that can anticipate potential connectivity and extirpation thresholds. This modeling approach was effective at leveraging existing information for a data‐light species to assess how historical changes to the quantity, quality, and configuration of habitat likely influenced the potential landscape capacity, species abundance, and distribution. Dynamic individual‐based modeling can benefit conservation planning for red tree vole and other reclusive forest species by providing biologically nuanced assessments of abundance and distribution. Such models can also project the long‐term benefits and impacts of spatially explicit land management plans.</p> </div> <div class="abstract"></div>
Dataset used in the study "Urban microclimate simulations based on GIS data to mitigate thermal hot-spots: Tree design scenarios in an industrial area of Florence"
<p>This dataset repository includes input and output spatial data of urban microclimate simulations performed through QGIS and ENVI-met software used in the study "Urban microclimate simulations based on GIS data to mitigate thermal hot-spots: Tree design scenarios in an industrial area of Florence", published in the Building and Environment Journal, <a href="https://doi.org/10.1016/j.buildenv.2023.110854">https://doi.org/10.1016/j.buildenv.2023.110854</a>.</p>
Silicon-based anti-herbivore defense in tropical tree seedlings
<p>Silicon-based defenses effectively deter insect herbivores in many cultivated and wild grass species. Furthermore, in some of these species, silicon (Si) uptake and defense can be induced by herbivory. Tropical trees also take up Si and leaf Si concentrations vary greatly across and within species. As herbivory is a major driver of seedling mortality and niche differentiation of tropical tree species, understanding anti-herbivore defenses is pivotal. Yet, whether silicon is a constitutive and inducible herbivory defense in tropical forest tree species remains unknown.</p> <p>We grew seedlings of eight tropical tree species in a full factorial experiment, including two levels of plant-available soil Si concentrations (-Si/+Si) and a simulated herbivory treatment (-H/+H). The simulated herbivory treatment was a combination of clipping and application of methyl jasmonate. We then carried out multiple-choice feeding trials, separately for each tree species, in which leaves of each treatment combination were offered to a generalist caterpillar (<em>Spodoptera frugiperda</em>). Leaf damage was assessed.</p> <p>Three species showed a significant decrease in leaf damage under high compared to low Si conditions (by up to 72%), consistent with our expectation of Si-based defenses acting in tropical tree species. In one species, leaf damage was increased by increasing soil Si and in the remaining four species, no effect of soil Si on leaf damage was observed. Opposite to our expectation of Si uptake and defense being inducible by herbivory damage, simulated herbivory increased leaf damage in two species. Furthermore, simulated herbivory reduced Si concentrations in one species.</p> <p>Our results showed that tropical tree seedlings can be better defended when growing in Si-rich compared to Si-poor soils, and that the effects of Si on plant defense vary strongly across species. Furthermore, Si-based defenses may not be inducible in tropical tree species. Overall, constitutive Si-based defense should be considered part of the vast array of anti-herbivore defenses of tropical tree species. Our finding that Si-based defenses are highly species-specific combined with the fact that herbivory is a major driver of mortality in tropical tree seedling, suggests that variation in soil Si concentrations may have pervasive consequences for regeneration and performance across tropical tree species.</p>
Dating the bacterial tree of life based on ancient symbiosis
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Data from: Combining allele frequency and tree-based approaches improves phylogeographic inference from natural history collections
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Files associated with: Migration-based simulations for Canadian trees show limited tracking of suitable climate under climate change
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A new tree-based methodological framework to infer the evolutionary history of Mesopolyploid lineages: An application to the Brassiceae tribe (Brassicaceae)
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Data from: ASTRAL: genome-scale coalescent-based species tree estimation
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Silicon-based anti-herbivore defense in tropical tree seedlings
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Supplementary material for: Impact of ghost introgression on coalescent-based species tree inference and estimation of divergence time
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Data from: A trait-based root acquisition-defence-decomposition framework in angiosperm tree species
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Plastid introgression and evolution of African miombo woodlands: new insights from the plastome-based phylogeny of Brachystegia trees
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Model for: Characterizing long‐term population conditions of the elusive red tree vole with dynamic individual‐based modeling
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Online tree-based planning for active spacecraft fault estimation and collision avoidance
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ASTRAL-Pro: Quartet-based species-tree inference despite paralogy
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Data for: Weighting by gene tree uncertainty improves accuracy of quartet-based species trees
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FIGURE5. Maximum likelihood tree based on the Kimura 2-parameter model of the COI sequences from the Siphamia species with P. kauderni as the outgroup. Tree shown here has the highest log likelihood following 10 000 replications. The percentage of trees in which the associated taxa clustered together is shown next to the branches, branch lengths are measured in the number of substitutions per site and all positions containing gaps and missing data have been eliminated. in Redescription and distributional range extension of the Speckled Siphonfish, Siphamia guttulata (Pisces: Apogonidae)
FIGURE5. Maximum likelihood tree based on the Kimura 2-parameter model of the COI sequences from the Siphamia species with P. kauderni as the outgroup. Tree shown here has the highest log likelihood following 10 000 replications. The percentage of trees in which the associated taxa clustered together is shown next to the branches, branch lengths are measured in the number of substitutions per site and all positions containing gaps and missing data have been eliminated.
Negative trait-based association between abundance of nitrogen fixing trees and long-term tropical forest biomass accumulation
<p>1. Plant functional traits are thought to drive biomass production and biogeochemical cycling in tropical forests, but it remains unclear how nitrogen (N)-fixing legumes influence the functional traits of neighboring trees and forest-wide biomass dynamics. Further, the degree to which effects of N-fixers are density-dependent and may depend on stem size and spatial scale remain largely unknown.</p> <p>2. Here, we examine 30-years of stem demography data for ~20,000 trees in a lowland tropical forest in Trinidad that span a wide range of functional traits thought to drive aboveground biomass (AGB) dynamics.</p> <p>3. These forests show positive but decreasing long-term net AGB accumulation resulting from constant average productivity but increasing mortality of non-fixing trees over time. We find that high abundance of N-fixing trees is associated with compositional shifts in non-fixer functional traits that confer lower competitive performance and biomass accumulation. Across tree size classes, most interactions between N-fixers and non-fixers were negative, density dependent, and strongest at smaller spatial scales.</p> <p>4. Synthesis. Overall, our findings suggest that local trait-based interactions between N-fixing and non-fixing trees can influence long-term carbon accumulation in tropical forests.</p>
Supplementary figures for SpeciesTopoTestR: likelihood-based tests of species trees
<p class="MsoBodyText"><span><span><span><span><span><span><span><span><span><span><span>Likelihood-based tests of phylogenetic trees are a foundation of modern systematics, and examples of such tests are among the most widely-referenced scientific literature of all time. Over the past decade, an enormous wealth and diversity of model-based approaches have been developed for phylogenetic inference of both gene trees and species trees. However, while many techniques exist for conducting formal likelihood-based tests of gene trees, such frameworks are comparatively underdeveloped and underutilized for testing species-level hypotheses. To date, widely-used tests of tree topology are designed to assess the fit of classical models of molecular sequence data and individual gene trees, and thus, are not readily applicable to the problem of species tree inference. We derive several analogous likelihood-based approaches for testing species-level topologies using modern species tree models and algorithms for maximum likelihood estimation under the multispecies coalescent. For the purpose of comparing support for species-level relationships, these tests leverage the statistical procedures of their original gene tree-based counterparts that have a long history for testing phylogenetic hypotheses at single loci. We discuss and demonstrate a number of applications, limitations, and important considerations of these tests using simulated and empirical phylogenomic datasets that include both bifurcating topologies and reticulate network models of species relationships. Finally, we introduce the open-source R package <i>SpeciesTopoTestR </i>(<u>Species</u> <u>Topo</u>logy <u>Test</u>s in <u>R</u>) that includes a suite of functions for conducting formal likelihood-based tests of species topologies. </span></span></span></span></span></span></span></span></span></span></span></p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.