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112 results for “Time trees”
Bayesian Analysis of Tree Distributions Across Space and Time in Eastern North America 2010-2011
The distributions of many organisms are spatially autocorrelated, but it is unclear whether including spatial terms in species distribution models (SDMs) improves projections of future species distributions. We provide the first comparative test of a purely spatial SDM, a purely non-spatial SDM, and an SDM that combines spatial and environmental information. Spatial SDMs provided better fits to the calibration data, more accurate predictions of a hold-out validation data set of modern trees, and lower false positive rates at all time periods than non-spatial SDMs. Hindcasted projection of spatial SDMs had higher variance than those of non-spatial SDMs. Overall predictive performance of non-spatial and spatial SDMs varied temporally and as a function of niche overlap. Ecological modelers should include spatial terms in SDMs used for projecting future distributions of species.
UAV time series and tree crowns
<p>This dataset contains:</p><p>-A UAV time series of mosaicked images of a woodland in Northeast UK. Complete detaisl are given in: "Elias Fernando Berra, Rachel Gaulton, Stuart Barr, Assessing spring phenology of a temperate woodland: A multiscale comparison of ground, unmanned aerial vehicle and Landsat satellite observations, Remote Sensing of Environment, Volume 223, 2019, Pages 229-242, ISSN 0034-4257, https://doi.org/10.1016/j.rse.2019.01.010." </p><p>-Manual (reference) and automatic delinetaed tree crowns for the area covered by the UAV time series data. Complete details in: Elias F. Berra. Individual tree crown detection and delineation across a woodland using leaf-on and leaf-off imagery from a UAV consumer-grade camera. Journal of Applied Remote Sensing, Vol. 14, Issue 3, 034501 (July 2020). https://doi.org/10.1117/1.JRS.14.034501</p>
Impact of Snowmelt Timing and Tree Proximity on Dutchman's Breeches Phenology and Performance in Mont Megantic National Park (Quebec, Canada; 2018-2019)
Data herein were collected in 2018 and 2019 in Mont Megantic National Park, Quebec, Canada, in a sugar maple-dominated temperate deciduous forest. Individuals of Dutchman's breeches (Dicentra cucullaria), a common understory spring ephemeral plant that is only active in the spring, were transplanted into a fully factorial experiment of snowmelt timing (early vs. late) and tree proximity (near vs. far) to determine the role of thaw circle formation in the local clustering of this species near canopy tree trunks. Plant phenology (emergence, senescence, and growing season length) and performance (stem abundance and leaf area) were tracked during two years of snow manipulation. Additionally, microclimate temperature data were collected in a subset of plots in 2018.
Dataset of pomegranate tree (Punica granatum L. 'Wonderful') image times series
<p>Dataset of pomegranate tree (Punica granatum L. ‘Wonderful’) image times series. The pictures were collected by means of Raspberry Pi cameras with OV5647 sensor (5 MP, f2.9). Sensors were installed on fixed platforms for continuous measurement with zenithal orientation at a distance of approximately 1 metre from the canopy. Images were captured daily at 9 a.m. (GMT+2) from July to mid-October in 2021 and 2022. The resolution of the images is 640x480 pixels.</p>
University of Kansas Field Station: Forest demography, 1980 – 2015. On ten study plots established on three management units all live trees with a dbh > 7.5 cm (3 in) were identified to species, measured, and tagged. Trees were initially measured in 1980/1981 and re-measured in three successive time periods: 1993/95; 2002/03; and 2014/15. Trees will be measured again in 2025/26.
In 1980 researchers at the University of Kansas initiated a long-term experiment monitoring the composition of oak-hickory forest communities at the University’s field station near Lawrence, Kansas. The purpose of the study was to determine how forest species composition varied temporally across distinct habitats that varied in topography, elevation, sun exposure, management history and successional stage. Ten permanent sites were sampled approximately each decade with data collection periods of 1980/81, 1993/95, 2002/03, and 2014/15. Trees with a minimum diameter at breast height (dbh) of ≥ 7.5 cm were tagged, identified to species and measured. Trees will be measured again in 2025/26.
White Spruce NPP: average NPP per tree by age cohort for 4 time periods between 1993 and 2008
This data set is derived from BNZ LTER inventory plots, where DBH of all trees is measured every 3 to 4 years, and increment changes in AG biomass are derived from allometric equations. Data included in this file were obtained from 1993, 1997, 2000, 2004 and 2008 inventories, generating 4 growth increments between 1997 and 2008. Data are reported by age cohort, and include NPP increments (averaged across all trees within each landscape and successional stage) for all trees of known age (determined from coring).
White Spruce NPP: average NPP per tree by diameter sizeclass for 4 time periods between 1993 and 2008
This data set is derived from BNZ LTER inventory plots, where DBH of all trees is measured every 3 to 4 years, and increment changes in AG biomass are derived from allometric equations. Data included in this file were obtained from 1993, 1997, 2000, 2004 and 2008 inventories, generating 4 growth increments between 1997 and 2008. Data are reported by diameter sizeclass (10 cm increments), and include NPP increments (averaged across all trees within each landscape and successional stage) for which adequate numbers of trees (typically >5) were present to obtain useful measurements (see N in data file).
Aspen NPP: average NPP per tree by diameter sizeclass for 4 time periods between 1993 and 2008
This data set is derived from BNZ LTER inventory plots, where DBH of all trees is measured every 3 to 4 years, and increment changes in AG biomass are derived from allometric equations. Data included in this file were obtained from 1993, 1997, 2000, 2004 and 2008 inventories, generating 4 growth increments between 1997 and 2008. Data are reported by diameter sizeclass (10 cm increments), and include NPP increments (averaged across all trees within each landscape and successional stage) for which adequate numbers of trees (typically >5) were present to obtain useful measurements (see N in data file).
Birch NPP: average NPP per tree by diameter sizeclass for 4 time periods between 1993 and 2008
This data set is derived from BNZ LTER inventory plots, where DBH of all trees is measured every 3 to 4 years, and increment changes in AG biomass are derived from allometric equations. Data included in this file were obtained from 1993, 1997, 2000, 2004 and 2008 inventories, generating 4 growth increments between 1997 and 2008. Data are reported by diameter sizeclass (10 cm increments), and include NPP increments (averaged across all trees within each landscape and successional stage) for which adequate numbers of trees (typically >5) were present to obtain useful measurements (see N in data file).
Balsam Poplar NPP: average NPP per tree by diameter sizeclass for 4 time periods between 1993 and 2008
This data set is derived from BNZ LTER inventory plots, where DBH of all trees is measured every 3 to 4 years, and increment changes in AG biomass are derived from allometric equations. Data included in this file were obtained from 1993, 1997, 2000, 2004 and 2008 inventories, generating 4 growth increments between 1997 and 2008. Data are reported by diameter sizeclass (10 cm increments), and include NPP increments (averaged across all trees within each landscape and successional stage) for which adequate numbers of trees (typically >5) were present to obtain useful measurements (see N in data file).
Figure 2 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time
Figure 2. Cicada timetree built by BEAST v1.X, applying 1,534 bp COI sequence. OUTs with isolate number: our own analyzed specimens shown in Table 1, and others: from GenBank/DDJB. In outgroup Hemiptera; #: analyzed family by Johnson et al. (2018); % analyzed family by Misof et al. (2014). Inserted figure: Base substitution rate (= rate median shown at each node; substitutions per site per million year; s/s/myr) vs age (= posterior age shown at each node) diagram. Red approximate curve with its formula was drawn by Excel function, with the intersection for the curve = 0.0128 s/s/myr, the rate median shown on Tracer.
Figure 4 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time
Figure 4. Number of base changes of transition and tansversion vs corrected pairwide distance diagram for whole mitochondrial gene.
Figure 1 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time
Figure 1. Simplified cicada timetree built by BEAST v1.X, applying a 1,534 bp in maximum COI sequence. Inserted figure: Base substitution rate (= ratemedian shown at each node; substitutions per siteper millionyear; s/s/ myr) vsage (= posterior age shown at each node) diagram. Red approximate curve with its formula was drawn by an Excel function, with the intersection for the curve = 0.0128 s/s/myr, the rate median shown on Tracer.
Figure 3 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time
Figure 3. Cicada timetree built by BEAST v1.X, applying 1,534 bp COI and 874 bp 18S rRNA sequences. OUTswith isolate number: our own analyzed specimens shown in Table 1, and others: from GenBank/DDJB. In outgroup Hemiptera; #: analyzed family by Johnson et al. (2018); % analyzed family by Misof et al. (2014). Inserted figure: Base substitution rate (= rate median shown at each node; substitutions per site per million year; s/s/myr) vs age (= posterior age shown at each node) diagram. Red approximatecurve with its formulawas drawn by Excel function, with the intersection for the curve = 0.0114 s/s/myr, the rate median shown on Tracer. Note that this rate is a little slower than thatsolely of COI in Figures 1 and 2, reflecting slowerrate of 18S rRNAthan COI (see Osozawa et al. 2017a).
Time trees and Clock genes: a Systematic Review and Comparative Analysis of Contemporary Avian Migration Genetics (Dataset)
<p>Complete dataset of <em>Clock</em> and <em>Adcyap1</em> alleles, distance matrices, and migration data used in the review and meta-analysis "<strong>Time trees and Clock genes: a Systematic Review and Comparative Analysis of Contemporary Avian Migration Genetics".</strong> </p>
Supplementary Data for: A time-calibrated 'Tree of Life' of aquatic insects for knitting historical patterns of evolution and measuring extant phylogenetic biodiversity across the world
<p>This compendium of files includes the dated phylogenetic tree in Newick format (<strong>Data S1</strong>), the list of statistical routines used for the three empirical case studies (<strong>Data S2</strong>), and the high-resolution version of the figures in the supplementary materials and main text (<strong>Data S3</strong>) for the <em>Earth-Science Reviews</em> paper "A time-calibrated ‘Tree of Life’ of aquatic insects for knitting historical patterns of evolution and measuring extant phylogenetic biodiversity across the world", which is under consideration. The best-scoring molecular tree (<strong>Data S1</strong>) can be opened using freely available programs like R (R Development Core Team, 2021), Dendroscope (Huson and Scornavacca, 2012), and FigTree (Rambaut, 2018).</p> <p>Please, feel free to send an email to the maintainer Dr. Jorge García Girón (jogarg@unileon.es OR Jorge.Garcia-Giron@oulu.fi) if you face any trouble downloading, opening, or using these files.</p> <ul> <li>Huson, D. H., & Scornavacca, C. (2012). Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks. <em>Systematic Biology</em>, <em>61(6)</em>, 1061–1067.</li> <li>R Development Core Team (2021). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/</li> <li>Rambaut, A. (2018). FigTree. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK. http://tree.bio.ed.ac.uk/software/figtree/</li> </ul>
Mapping Tree Species Fractions in Temperate Mixed Forests Using Sentinel-2 Time Series and Synthetically Mixed Training Data
<p>This dataset contains the latest version of a selection of result data of the paper "Mapping Tree Species Fractions in Temperate Mixed Forests Using Sentinel-2 Time Series and Synthetically Mixed Training Data" (DOI: https://doi.org/10.1016/j.rse.2025.114740 )</p> <p>The dataset contains:</p> <ol> <li>A geopackage of training points of pure tree species</li> <li>The resulting 12-band tree species fraction map of Rhineland-Palatinate</li> <li>HSV-colored map of dominant tree species. For information which tree species are represented by the different colors, refer to the Supplemental in the original paper.</li> <li>CSV-table of predicted and reference propotion of the tree species in the validation polygon (the original polygon data can not be published due to data privacy regulations) </li> </ol> <p> </p>
The implications of incongruence between gene tree and species tree topologies for divergence time estimation
<p>Phylogenetic analyses are increasingly being performed with datasets that incorporate hundreds of loci. Due to incomplete lineage sorting, hybridization, and horizontal gene transfer, the gene trees for these loci may often have topologies that differ from each other and from the species tree. The effect of these topological incongruences on divergence time estimation has not been fully investigated. Using a series of simulation experiments and empirical analyses, we demonstrate that when topological incongruence between gene trees and the species tree is not accounted for, the temporal duration of branches in regions of the species tree that are affected by incongruence is underestimated, whilst the duration of other branches is considerably overestimated. This effect becomes more pronounced with higher levels of topological incongruence. We show that this pattern results from erroneous estimation of the number of substitutions along branches in the species tree, although the effect is modulated by the assumptions inherent to divergence time estimation, such as those relating to the fossil record or among-branch-substitution-rate variation. By only analysing loci with gene trees that are topologically congruent with the species tree, or only taking into account the branches from each gene tree that are topologically congruent with species tree, we demonstrate that the effects of topological incongruence can be ameliorated. Nonetheless, even when topologically congruent gene trees or topologically congruent branches are selected, error in divergence time estimates remains. This stems from temporal incongruences between divergence times in species trees and divergence times in gene trees, and more importantly, the difficulty of incorporating necessary assumptions for divergence time estimation.</p>
Fig 6. A Bayesian time-tree generated from mitochondrial 16S in A New Species of Microhyla (Anurα: Microhylidαe) from Nilphαmαri, Bαnglαdesh
Fig 6. A Bayesian time-tree generated from mitochondrial 16S gene fragment for all known species in the genus Microhyla. Calibration points are indicated with arrows. Numbers are in million years, and the light blue colored bars indicate 95% confidence intervals for divergence time estimates. doi:10.1371/journal.pone.0119825.g006
Fig. 1. The modified time calibrated Bayesian tree and a in Fig. 3 in Fig. 4 in Fig. 4 in Responses of Phyllostomid Bats to Traditional Agriculture in Neotropical Montane Forests of Southern Mexico.
Fig. 1. The modified time calibrated Bayesian tree and a plot of four major avian developmental modes (Prum et al. 2015). The complete tree is divided into parts A and B. Scale in the Y-axis: millions of years ago.
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Allen Brain Atlas
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OpenNeuro
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