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151 results for “population tree”
Data from: Harvesting has variable effects on demographic rates and population growth across three dry forest tree species
<p>Understanding how anthropogenic activities, such as harvesting, influence plant populations is important to quantify sustainable practices that conserve species of socioeconomic importance. There is limited knowledge on how harvesting of branches and non-timber forest products affect populations of trees in the dry tropics. We measure demographic vital rates of three dry tropical tree species in the presence and absence of harvesting and apply integral projection models to quantify population growth rates, which represent the mean fitness across the life cycle. Our results show that the three species vary in their demographic rates and life history. Harvesting significantly decreases the growth of two species. Current levels of harvesting only significantly decreased the population growth rate of one species that experienced both branch and main stem harvesting. Life table response experiments reveal that the negative effect of harvesting on the population growth rate of this species is primarily due to individuals being forced to re-sprout from their base. Few individuals were observed recruiting from seed, and this might be due to the presence of other threats, such as fire, soil erosion, and grazing. Our results provide knowledge on the demography and the effects of harvesting on endemic tree species of the Eastern Ghats, a region for which few demographic studies are available. These results are relevant to conserving forest biodiversity for the benefits of people and can contribute to quantitative threat assessment for IUCN red listing.</p>
FIGURE 1 in Combining morphology and population genetic analysis uncover species delimitation in the widespread African tree genus Santiria (Burseraceae)
FIGURE 1. Genetic clusters (GC) detected in Santiria samples from western Central Africa. Bayesian clustering analyses were performed on 479 individuals genotyped at 10 microsatellites loci. A. Variation in means of Ln (likelihood) of the data as a function of the number of hypothetical genetic clusters (K), showing a plateau at K=3. B. Histogram of genetic assignment of the 481 individuals at K = 3. C. Distribution of the three genetic clusters in western Central Africa, and delimitation of the distribution of each genetic cluster (dotted line: GC1, solid line: GC2, dashed line: GC3). We extended the distribution ranges of GC2 and GC3 because morphotypes of both genetic clusters were observed in the south of the Republic of the Congo. Note: Interm. GCx and GCy = intermediate individuals between GCx and GCy.
FIGURE 2 in Combining morphology and population genetic analysis uncover species delimitation in the widespread African tree genus Santiria (Burseraceae)
FIGURE 2. Extended Principal Component Analysis (the Hill-Smith ordination) of quantitative and qualitative traits assessed in 103 Santiria herbarium samples assigned to GC1 (N = 46, open circles), GC2 (N = 21, stars) and GC3 (N = 36, open triangles). Note: NL = number of leaflets per leaf; LL = length of leaves; LP = length of petiole; WP = width of petiole; LP/WP = ratio between LP and WP; TPeL = terminal petiolule length; TLL = terminal leaflet length; TLW = terminal leaflet width; TLL/TLW = ratio between TLL and TLW; TLWe = terminal leaflet weight dry portion; AL = apex length; GD = glandular dots; Le = lenticels.
Tree germination sensitivity to increasing temperatures: a global meta-analysis across biomes, species and populations.
<p>The dataset contains the files used for the meta-analysis on the role of temperature increases on the germination of tree species from different biomes around the world.</p> <p>This meta-analysis is accepted for publication in Global Ecology and Biography (MS reference number: GEB-2024-0273.R1 ; Article DOI: 10.1111/geb.13921).</p> <p>Files S6 and S7 gather data of germination percentage and time, respectively, at population scale. File S5 is a summary of the publications used as data sources for the meta-analysis. The whole dataset comprises 50 papers addressing 63 species and 250 populations, it covers boreal, temperate, Mediterranean and tropical-subtropical biomes, and a time period between 1996 and 2024.</p>
Data and code for "Assessing the spatial scale of synchrony in forest tree population dynamics"
<p>The data sets and code provided here facilitate reproduction of our results from this paper on synchrony of forest tree population dynamics. </p> <h3>Description of the data and file structure</h3> <p>The analyses in the paper were conducted at three scales, and each involves its own data files:</p> <ul> <li>Local scale: The relevant data files are named, e.g., "BCI1-7,L=250m,dbh=100mm.Rdata", where "BCI1-7" indicates the ForestGEO site name ("BCI") and census intervals (1 to 7 for BCI), "L=250m" indicates the quadrat size, and "dbh=100mm" indicates the diameter-at-breast height (DBH) threshold used. There are 12 such files (two ForestGEO plots--BCI and Pasoh--times three quadrat sizes times two DBH thresholds). Each file contains a single list "N_all", whose length is equal to the number of quadrats at the given grain. Each element in the list is a data frame containing mean census times (in days), tree species' population sizes and number of survivors across the two censuses for the corresponding quadrat.</li> <li>Regional scale: The relevant data files are "Marena_data,dbh=100mm,spp_anonymised.Rdata" and "Marena_data,dbh=100mm,spp_anonymised.Rdata". Each file contains three objects: "dists" is a matrix giving the distances between all pairs of sites; "N_all1" is a list with one element for each plot, and each element being a data frame with (anonymised) species ids in the first column and abundances in the remaining columns (column names give mean census dates in days); "S_all1" has a similar structure to "N_all1" except that the data give numbers of survivors from any given census to any subsequent census (column headings indicate the two census numbers).</li> <li>Global scale: The relevant data files are "global_data,dbh=10mm,spp_anonymised.Rdata" and "global_data,dbh=100mm,spp_anonymised.Rdata". The data in the files have the same structure as in the regional-scale files.</li> </ul>
Data from: Population genetic structure of the tree-hole tick Ixodes arboricola (Acari: Ixodidae) at different spatial scales
The endophilic tick Ixodes arboricola infests cavity-nesting birds, and its dispersal strongly depends on the movements of its host. Population genetic structure of I. arboricola was studied with seven polymorphic microsatellite markers. We collected 268 ticks from 76 nest boxes in four woodlots near Antwerp, Belgium. These nest boxes are mainly used by the principal hosts of I. arboricola, the great tit Parus major and the blue tit Cyanistes caeruleus. As these birds typically return to the same cavity for roosting or breeding, ticks within nest boxes were expected to be highly related, and tick populations were expected to be spatially structured among woodlots and among nest boxes within woodlots. In line with the expectations, genetic population structure was found among woodlots and among nest boxes within woodlots. Surprisingly, there was considerable genetic variation among ticks within nest boxes. This could be explained by continuous gene flow from ticks from nearby tree holes, yet this remains to be tested. A pairwise relatedness analysis conducted for all pairs of ticks within nest boxes showed that relatedness among larvae was much higher than among later instars, which suggests that larvae are the most important instar for tick dispersal. Overall, tick populations at the studied spatial scale are not as differentiated as predicted, which may influence the scale at which host–parasite evolution occurs.
Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the Chocolate Tree
<p>Genomic structural variants (SVs) can play important roles in adaptation and speciation. Yet, the overall fitness effects of SVs are poorly understood, partly because accurate population-level identification of SVs requires multiple high-quality genome assemblies. Here, we use 31 chromosome-scale, haplotype-resolved genome assemblies of Theobroma cacao – an outcrossing, long-lived tree species that is the source of chocolate – to investigate the fitness consequences of SVs in natural populations. Among the 31 accessions, we find over 160 thousand SVs, which together cover eight times more of the genome than SNPs and short indels (125 Mb vs. 15 Mb). Our results indicate that a vast majority of these SVs are deleterious: they segregate at low frequencies and are depleted from functional regions of the genome. We show that SVs influence gene expression, which likely impairs gene function and contributes to the detrimental effects of SVs. We also provide empirical support for a theoretical prediction that SVs, particularly inversions, increase genetic load through the accumulation of deleterious nucleotide variants as a result of suppressed recombination.<br> Despite the overall detrimental effects, we identify individual SVs bearing signatures of local adaptation, several of which are associated with genes differentially expressed between populations. Genes involved in pathogen resistance are strongly enriched among these candidates, highlighting the contribution of SVs on this important local adaptation trait. Beyond revealing new empirical evidence for the evolutionary importance of SVs, these 31 de novo assemblies provide a valuable resource for genetic and breeding studies in T. cacao. </p>
Fig. 4. Fifty percent majority rule trees using Maximum Likelihood. A in Weak Genetic Differentiation among Populations of the Andean Ground Beetle Pelmatellus columbianus (Reiche, 1843) (Coleoptera: Carabidae)
Fig. 4. Fifty percent majority rule trees using Maximum Likelihood. A) COI, B) CAD. Bootstrap support shown above the branches.
Figure 2. A, maximum likelihood tree inferred from 18S in Morphological, ontogenetic, and molecular investigations of freshwater hypotrich ciliates from China revealed a new genus Heterodeviata gen. nov. (Protista: Ciliophora), and a novel limnetic population of Deviata multilineae
Figure 2. A, maximum likelihood tree inferred from 18S rRNA gene sequences, showing the phylogenetic positions of the two newly sequenced species. Numbers near the nodes represent the ML bootstrap support and BI posterior probability values. Fully supported (100%/1.00) branches are marked with solid circles. 'Asterisks' indicate disagreement between the ML and BI trees. Sequences newly obtained are in pink. The scale bar corresponds to one substitution per 100 nucleotide positions. B, the tree is made referring to the ML tree in a radiation view, showing the likely systematic relationship of Heterodeviata with related genera. C, topology of species within Deviatidae in Bayesian inference (BI) tree. '**' indicates the sequence Perisincirra sp. (KY855575) is probably misidentified, which should be conspecific with Deviata brasiliensis.
Data from: Spatial variation in bird pollination and its mitigating effects on the genetic diversity of pollen pools accepted by Camellia japonica trees within a population at a landscape level
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Data from: Reliability of macrofossils in woodrat (Neotoma) middens for detecting low-density tree populations
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Contrasting effects of host tree isolation on population connectedness in two tropical epiphytic bromeliads
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Data from: Scatterhoarders drive long- and short-term population dynamics of a nut-producing tree, while pre-dispersal seed predators and herbivores have little effect
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Data from: Extending glacial refugia for a European tree: genetic markers show that Iberian populations of white elm are native relicts and not introductions
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Data from: The effects of inference method, population sampling and gene sampling on species tree inferences: an empirical study in slender salamanders (Plethodontidae: Batrachoseps)
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Data from: Small but not isolated: a population genetic survey of the tropical tree Cariniana estrellensis (Lecythidaceae) in a highly fragmented habitat
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Data from: Woody climbers show greater population genetic differentiation than trees: insights into the link between ecological traits and diversification
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Data from: Genetic diversity and population divergences of an indigenous tree (Coffea mauritiana) in Reunion Island: role of climatic and geographical factors
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Data from: Will natural resistance result in populations of ash trees remaining in British woodlands after a century of ash dieback disease?
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Data from: Linking innate immunogenetic variation with phenotypic traits in a wild population of tree swallows, Tachycineta bicolor
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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.