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40 results for “Tree distance”
Data from: Seed and pollen dispersal distances in two African legume timber trees and their reproductive potential under selective logging
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Data from: Short distance pollen dispersal and low genetic diversity in a subcanopy tropical rainforest tree, Fontainea picrosperma (Euphorbiaceae)
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Critical seed transfer distances for selected tree species in eastern North America
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Supplementary figures for: Of traits and trees: probabilistic distances under continuous trait models for dissecting the interplay among phylogeny, model, and data
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Data from: Probabilistic species tree distances: implementing the multispecies coalescent to compare species trees within the same model-based framework used to estimate them
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Data from: Biogeographic variation of distance-dependent effects in an invasive tree species
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Bioclimatic, soil, terrain, distance to Native American settlement, and historical tree taxon relative abundance data at 8-km resolution for the northeastern United States
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Which enemies mediate distance- and density-dependent mortality of tree seeds and seedlings? A meta-analysis of fungicide, insecticide, and exclosure studies
<p>Conspecific negative distance- and density-dependence is believed to be one of the most important mechanisms controlling forest community assembly and species diversity globally. SoilPlant pathogens, and insect and mammalian herbivores, are the most common natural enemy types that have been implicated in this phenomenon, but their relative importancegeneral effects at different plant life stages isare still unclear. Here, we conduct a meta-analysis of studies that involved robust manipulative experiments, using fungicides, insecticides, and exclosures, to assess the contributions of different natural enemy types to distance- and density-dependent effects at seed and seedling stages. We found that natural enemies cause stronger distance- and density-dependent mortality caused by natural enemies was most likely at the seedling stage than the seed stage. Fungicide treatments can change significantand was greater at higher mean annual temperatures. Seedling mortality was significantly weakened when fungi were removed. By contrast, negative distance- and density-dependent mortality to non-significance at the seedling stage. Negative conspecific distance- and density-dependence is not a general pattern at the seed stage. High seed mass reduced distance- and density-dependent mortality. Seed studies excluding only large mammals found significant negative conspecific distance-dependent mortality, but exclusion of all mammals resulted in a non-significant mortality.effect of conspecifics. Our study suggests that soilplant pathogens are a major cause of distance- and density-dependent mortality at the seedling stage, althoughwhile the impacts of herbivores on seedlings have been understudied. At the seed stage, large and small mammals respectively weaken and enhance negative conspecific distance-dependent mortality. Future research should identify specific agents of mortality, investigate the interactions among different enemy types, and assess how global change drivers may affect the dynamics of natural enemies and thus influence the strength of conspecific distance- and density-dependence.</p>
Data from: Minimizing the average distance to a closest leaf in a phylogenetic tree
When performing an analysis on a collection of molecular sequences, it can be convenient to reduce the number of sequences under consideration while maintaining some characteristic of a larger collection of sequences. For example, one may wish to select a subset of high-quality sequences that represent the diversity of a larger collection of sequences. One may also wish to specialize a large database of characterized "reference sequences" to a smaller subset that is as close as possible on average to a collection of "query sequences" of interest. Such a representative subset can be useful whenever one wishes to find a set of reference sequences that is appropriate to use for comparative analysis of environmentally-derived sequences, such as for selecting "reference tree" sequences for phylogenetic placement of metagenomic reads. In this paper we formalize these problems in terms of the minimization of the Average Distance to the Closest Leaf (ADCL) and investigate algorithms to perform the relevant minimization. We show that the greedy algorithm is not effective, show that a variant of the Partitioning Among Medoids (PAM) heuristic gets stuck in local minima, and develop an exact dynamic programming approach. Using this exact program we note that the performance of PAM appears to be good for simulated trees, and is faster than the exact algorithm for small trees. On the other hand, the exact program gives solutions for all numbers of leaves less than or equal to the given desired number of leaves, while PAM only gives a solution for the pre-specified number of leaves. Via application to real data, we show that the ADCL criterion chooses chimeric sequences less often than random subsets, while the maximization of phylogenetic diversity chooses them more often than random. These algorithms have been implemented in publicly available software.
Data from: Phylogenetic tree estimation with and without alignment: new distance methods and benchmarking
Phylogenetic tree inference is a critical component of many systematic and evolutionary studies. The majority of these studies are based on the two-step process of multiple sequence alignment followed by tree inference, despite persistent evidence that the alignment step can lead to biased results. Here we present a two-part study that first presents PaHMM-Tree, a novel neighbour joining-based method that estimates pairwise distances without assuming a single alignment. We then use simulations to benchmark its performance against a wide-range of other phylogenetic tree inference methods, including the first comparison of alignment-free distance-based methods against more conventional tree estimation methods. Our new method for calculating pairwise distances based on statistical alignment provides distance estimates that are as accurate as those obtained using standard methods based on the true alignment. Pairwise distance estimates based on the two-step process tend to be substantially less accurate. This improved performance carries through to tree inference, where PaHMM-Tree provides more accurate tree estimates than all of the pairwise distance methods assessed. For close to moderately divergent sequence data we find that the two-step methods using statistical inference, where information from all sequences is included in the estimation procedure, tend to perform better than PaHMM-Tree, particularly full statistical alignment, which simultaneously estimates both the tree and the alignment. For deep divergences we find the alignment step becomes so prone to error that our distance-based PaHMM-Tree outperforms all other methods of tree inference. Finally, we find that the accuracy of alignment-free methods tends to decline faster than standard two-step methods in the presence of alignment uncertainty, and identify no conditions where alignment-free methods are equal to or more accurate than standard phylogenetic methods even in the presence of substantial alignment error.
Data from: The founding of Mauritian endemic coffee trees by a synchronous long-distance dispersal event
The stochastic process of long-distance dispersal is the exclusive means by which plants colonize oceanic islands. Baker's rule posits that self-incompatible plant lineages are unlikely to successfully colonize oceanic islands because they must achieve a coordinated long-distance dispersal of sufficiently numerous individuals to establish an outcrossing founder population. Here, we show for the first time that Mauritian Coffea species are self-incompatible and thus represent an exception to Baker's rule. The genus Coffea (Rubiaceae) is composed of approximately 124 species with a paleotropical distribution. Phylogenetic evidence strongly supports a single colonization of the oceanic island of Mauritius from either Madagascar or Africa. We employ Bayesian divergence time analyses to show that the colonization of Mauritius was not a recent event. We genotype S-RNase alleles from Mauritian endemic Coffea, and using S-allele gene genealogies, we show that the Mauritian allelic diversity is confined to just seven deeply divergent Coffea S-RNase allelic lineages. Based on these data, we developed an individual-based model and performed a simulation study to estimate the most likely number of founding individuals involved in the colonization of Mauritius. Our simulations show that to explain the observed S-RNase allelic diversity, the founding population was likely composed of fewer than 31 seeds that were likely synchronously dispersed from an ancestral mainland species.
Data from: Probabilistic distances between trees
Most existing measures of distance between phylogenetic trees are based on the geometry or topology of the trees. Instead, we consider distance measures which are based on the underlying probability distributions on genetic sequence data induced by trees. Monte Carlo schemes are necessary to calculate these distances approximately, and we describe efficient sampling procedures. Key features of the distances are the ability to include substitution model parameters and to handle trees with different taxon sets in a principled way. We demonstrate some of the properties of these new distance measures and compare them to existing distances, in particular by applying multidimensional scaling to data sets previously reported as containing phylogenetic islands.
Which enemies mediate distance- and density-dependent mortality of tree seeds and seedlings? A meta-analysis of fungicide, insecticide, and exclosure studies
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Data from: Probabilistic distances between trees
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Data from: The founding of Mauritian endemic coffee trees by a synchronous long-distance dispersal event
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Supplementary material for: Building alternative consensus trees and supertrees using k-means and Robinson and Foulds distance
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Data from: Minimizing the average distance to a closest leaf in a phylogenetic tree
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Data from: Phylogenetic tree estimation with and without alignment: new distance methods and benchmarking
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Data from: Insect herbivory on seedlings of rainforest trees: effects of density and distance of conspecific and heterospecific neighbours
1. Natural enemies of plants such as insect herbivores can contribute to structuring and maintaining plant diversity in tropical forests. Most research in this area has focused on the role of specialised enemies and the extent to which herbivory on individual plant species is density-dependent. 2. Relatively few insect herbivores specialise on a single host plant species. Insect herbivores that feed on more than one plant species may link the regeneration dynamics of their host species through 'apparent competition' or 'apparent mutualism'. 3. We investigated herbivory and survival of seedlings of two tropical tree species (Cordia alliodora and Cordia bicolor) in the forests of Barro Colorado Island (Panama). We used experiments and observations to assess seedling fate in relation to the presence of conspecifics and heterospecifics across a range of spatial scales. 4. Herbivory significantly increased seedling mortality and was highest at high local densities of C. alliodora seedlings. There was also evidence that high local densities of C. alliodora increased herbivory on co-occurring C. bicolor seedlings. 5. Synthesis. The elevated rates of seedling herbivory at high densities of conspecifics documented in our study are consistent with the predictions of the Janzen-Connell hypothesis, which explains how so many plant species can coexist in tropical forests. Our data also highlight the possibility that herbivore-mediated density-dependence, facilitated by herbivores that feed on multiple plant species, can also occur across plant species. Enemy-mediated indirect effects of this sort have the potential to structure plant communities.
Data from: Insect herbivory on seedlings of rainforest trees: effects of density and distance of conspecific and heterospecific neighbours
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.