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112 results for “Time trees”
Supplementary material for: Impact of ghost introgression on coalescent-based species tree inference and estimation of divergence time
<p><span>The species studied in any evolutionary investigation generally constitute a small proportion of all the species currently existing or that have gone extinct. It is therefore likely that introgression, which is widespread across the tree of life, involves "ghosts," i.e., unsampled, unknown, or extinct lineages. However, the impact of ghost introgression on estimations of species trees has rarely been studied and is poorly understood. Here, we use mathematical analysis and simulations to examine the robustness of species tree methods based on the multispecies coalescent model to introgression from a ghost or extant lineage. We found that many results originally obtained for introgression between extant species can easily be extended to ghost introgression, such as the strongly interactive effects of incomplete lineage sorting (ILS) and introgression on the occurrence of anomalous gene trees (AGTs). The relative performance of the summary species tree method (ASTRAL) and the full-likelihood method (*BEAST) varies under different introgression scenarios, with the former being more robust to gene flow between non-sister species whereas the latter performing better under certain conditions of ghost introgression. When an outgroup ghost (defined as a lineage that diverged before the most basal species under investigation) acts as the donor of the introgressed genes, the time of root divergence among the investigated species generally was overestimated, whereas ingroup introgression, as commonly perceived, can only lead to underestimation. In many cases of ingroup introgression that may or may not involve ghost lineages, the stronger the ILS, the higher the accuracy achieved in estimating the time of root divergence, although the topology of the species tree is more prone to be biased by the effect of introgression.</span></p>
Genus level DNA sequence data for three genes (matK, rbcL, trnH-psbA) for the paper: A comprehensive, genus-level time-calibrated phylogeny of the tree flora of Mediterranean Europe and an assessment of its vulnerability
<p>This data file contains the consensus DNA sequences in fasta format, of 64 tree genera found in Mediterranean Europe, following the checklist of Médail et al. (2019). </p> <p>The data are used in a manuscript submitted for publication to Botany Letters and currently under revision. The manuscript is entitled: "<em>A comprehensive, genus-level time-calibrated phylogeny of the tree flora of Mediterranean Europe and an assessment of its vulnerability</em>". Its authors are: Marwan Cheikh Albassatneh, Marcial Escudero, Loic Ponge<sup>*</sup>, Anne-Christine Monnet, Juan Arroyo, Toni Nikolic, Gianluigi Bacchetta, Francesca Bagnoli, Panayotis Dimopoulos, Agathe Leriche, Frédéric Médail, Anne Roig, Ilaria Spanu, Giovanni Giuseppe Vendramin, Arndt Hampe, Bruno Fady.</p>
Influence of Altitudinal Gradient on the Voltinism and Generation Time of Cydia pomonella (Lepidoptera: Tortricidae) in walnut trees in northwestern Argentina
<p><span><span>11-<span> </span></span></span><em><span>Cydia pomonella L</span></em><span>. causes significant economic loss in the global fruit-growing industry. Its biology is influenced by environmental factors which have an impact on its voltinism in relation to its habitat.</span></p> <p><span>22- <span>The influence of the altitudinal gradient on the number and duration of <em>C. pomonella</em> populations on walnut trees grown at latitudes below 29° was determined. The relation between temperature and population curves was evaluated by an altitudinal gradient.</span></span></p> <p><span><span>33- </span></span><span><span><span> </span></span></span><span>A higher number of generations was quantitatively recorded in a shorter time on orchards located at lower altitudes. Walnut trees grown at higher altitudes, with lower temperatures, showed less pest pressure. The “Predictive Extension Timing Estimator”, used in several regions for the management of <em>C. pomonella</em>, does not accurately predict the length of the generation time in plantation crops at lower altitudes, requiring further studies in this area.</span></p> <p><span>44- </span><span>The results are relevant for designing of management strategies for walnut trees grown at latitudes below 29°, where environmental conditions differ considerably from other latitudes that were studied, impacting on the population dynamics of <em>C. pomonella</em>.</span></p> <p> </p>
Coordinated drought responses determine the time to hydraulic failure in five temperate tree species differing in their degree of isohydry
<p>This file contains variables of interest at tree level measured, calculated and presented in the study "Coordinated drought responses determine the time to hydraulic failure in five temperate tree species differing in their degree of isohydry". </p>
Attack time analysis in dynamic attack trees via integer linear programming
<p>Matlab code for the experiments of the paper "Attack time analysis in dynamic attack trees via integer linear programming" by Milan Lopuhaä-Zwakenberg & Mariëlle Stoelinga.</p> <p>The code can be accessed either via the virtual machine in Artifact_MILPforDATs_revised.zip, or through the code directly in Matlab_code.zip. The results are in Paper_results.zip.</p> <p>To run the code, installations of Matlab and Gurobi are required.</p>
Tree species abundance through time in tropical forest census plots, Panama
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Data from: Biomass production of tropical trees across space and time: The shifting roles of diameter growth and wood density
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Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification
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Data from: Vegetation growth responses to climate change: A cross-scale analysis of biological memory and time-lags using tree ring and satellite data
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Genomic vulnerability to rapid climate warming in a tree species with a long generation time
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Drought timing and species growth phenology determine intra-annual recovery of tree height and diameter growth
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Data from: Disturbance detection in Landsat time series is influenced by tree mortality agent and severity, not by prior disturbance
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Data from: Climate warming prolongs the time interval between leaf-out and flowering in temperate trees: effects of chilling, forcing and photoperiod
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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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Unapparent trees: escaping enemies in time by being discreet, unpredictable and inaccessible
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No apparent trade-off between the quality of nest grown feathers and time spent in the nest in an aerial insectivore, the tree swallow
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Restoration interventions mediate tropical tree recruitment dynamics over time
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Data from: Calibrating divergence times on species trees versus gene trees: implications for speciation history of Aphelocoma jays
Estimates of the timing of divergence are central to testing the underlying causes of speciation. Relaxed molecular clocks and fossil calibration have improved these estimates; however, these advances are implemented in the context of gene trees, which can overestimate divergence times. Here we couple recent innovations for dating speciation events with the analytical power of species trees, where multilocus data are considered in a coalescent context. Divergence times are estimated in the bird genus Aphelocoma to test whether speciation coincided with mountain uplift or glacial cycles. Gene trees and species trees show general agreement that diversification began in the Miocene amid mountain uplift. However, dates from the multilocus species tree are more recent, occurring predominately in the Pleistocene, consistent with theory that divergence times can be significantly overestimated with gene-tree based approaches that do not correct for genetic divergence that predates speciation. In addition to coalescent stochasticity, Haldane's Rule could account for differences in timing estimates between mitochondrial and nuclear genes. By incorporating a fossil calibration applied to the species tree, in addition to the process of gene lineage coalescence, the present approach provides a more biologically realistic framework for dating speciation events, and hence for testing the links between diversification and specific biogeographic and geologic events.
Data from: Phylogenetic relationships within the lizard clade Xantusiidae: using trees and divergence times to address evolutionary questions at multiple levels
Xantusiidae (night lizards) is a clade of small-bodied, cryptic lizards endemic to the New World. The clade is characterized by several features that would benefit from interpretation in a phylogenetic context, including: (1) monophyletic status of extant taxa Cricosaura, Lepidophyma, and Xantusia; (2) a species endemic to Cuba (Cricosaura typica) of disputed age; (3) origins of the parthenogenetic species of Lepidophyma; (4) pronounced micro-habitat differences accompanied by distinct morphologies in both Xantusia and Lepidophyma; and (5) placement of Xantusia riversiana, the only vertebrate species endemic to the California Channel Islands, which is highly divergent from its mainland relatives. This study incorporates extensive new character data from multiple gene regions to investigate the phylogeny of Xantusiidae using the most comprehensive taxonomic sampling available to date. Parsimony and partitioned Bayesian analyses of more than 7 kb of mitochondrial and nuclear sequence data from 11 loci all confirm that Xantusiidae is monophyletic, and comprises three well-supported clades: Cricosaura, Xantusia, and Lepidophyma. The Cuban endemic Cricosaura typica is well supported as the sister to all other xantusiids. Estimates of divergence time indicate that Cricosaura diverged from the (Lepidophyma + Xantusia) clade ∼81 million years ago (Ma), a time frame consistent with the separation of the Antilles from North America. Our results also confirm and extend an earlier study suggesting that parthenogenesis has arisen at least twice within Lepidophyma without hybridization, that rock-crevice ecomorphs evolved numerous times (>9) within Xantusia and Lepidophyma, and that the large-bodied Channel Island endemic X. riversiana is a distinct, early lineage that may form the sister group to the small-bodied congeners of the mainland.
Data from: From the individual to the landscape and back: Time-varying effects of climate and herbivory on tree sapling growth at distribution limits
1. As herbivory can modulate climate-induced shifts in species distribution, disentangling the relative importance of herbivory and climate on plant growth can help to predict and manage future changes in vegetation, such as those occurring at treeline areas. 2. An individual-based hierarchical Bayesian time-series model (Individual-Based Model; IBM) was developed to estimate the time-varying impact of climate and herbivory on individual pine-sapling height growth in woodland and treeline ecosystems of Southern Europe during a 16-year period. The performance of the IBM was compared to a Linear Mixed-Effects (LME) model to test for potential inferential effects when individual variability is marginalized. Time-varying models were also compared to constant parameter approaches. 3. Model fitting and posterior predictive checking suggests a better statistical performance of individual-scale, time-varying inference. LME modeling overestimated herbivory effects and underestimated environmental stochastic effects, and model validation indeed suggested severe overfitting in the LME model relative to the IBM strategy. These results reveal a potential failure of common aggregation strategies to correctly resolve the effects of climate and herbivory variability at the individual scale. Moreover, ignoring the time-varying nature of the effects may preclude the correct estimation of the temporal scale of climate and herbivory impacts. 4. In general, we found stronger individual- and time-averaged effects of summer precipitation relative to the effects of herbivory, particularly at the treelines. Also, individual pines responses showed effects of the same sign more consistently in the case of precipitation. This suggests that precipitation is more pervasive at the population level, while herbivory act as a spatially aggregating force through individual-level damage. 5. Synthesis. Our results suggest that accounting for individual and temporal variability in ecological inference greatly improve the assessment of the relative importance of climate and herbivory on species distribution shifts. Strong effects of precipitation at the treeline could allow tree upward expansion, although increasing ungulate populations and associated browsing damages might limit positive climatic responses of pine-saplings in the near future. In this context, the spatially heterogeneous effect exerted by herbivory could result in diverse vegetation structures in ecotones, adding a new dimension to the predictions on climate-driven vegetation shifts.
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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.