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Data from: Patterns of tree mortality in a temperate deciduous forest derived from a large forest dynamics plot
Tree mortality is one of the most influential drivers of forest dynamics, and characterizing patterns of tree mortality is critical to understanding forest dynamics and ecosystem function in the present era of global change. Here, we use a unique data set of mortality in a temperate deciduous forest to characterize rates and drivers of mortality. At the 25.6-ha Center for Tropical Forest Science—Forest Global Earth Observatory forest dynamics plot at the Smithsonian Conservation Biology Institute (Virginia, USA), we conducted two full tree censuses in 2008 and 2013 and then tracked mortality over the next 2 years (2014 and 2015). Overall, the mortality rate, m, of stems ≥10 cm diameter was 1.3–2.1%/yr. Biomass mortality, M, was 1.9–3.4 Mg·ha−1·yr−1 at the stand level (0.6–1.1%/yr of biomass), less than biomass gains from growth and recruitment, resulting in net live biomass accumulation. Small stems died at the highest rate; however, contributions to M increased toward larger size classes. Most species had m < 2%/yr and M < 0.25 Mg·ha−1·yr−1 (<3%/yr of biomass), whereas two to four species had anomalously high mortality rates during each census period, accounting for 15–24% of m (n = 2, Cercis canadensis, Ulmus species) and 39–75% of M (n = 4 Quercus species). Stems that died, whether or not in association with mechanical damage, tended to grow more slowly in preceding years than surviving stems and, for certain shade-intolerant species, tended to be in neighborhoods with higher basal area. These findings show how relatively fine-scale mortality processes contribute to stand-level compositional change and carbon cycling. The mortality patterns reported here will provide a valuable basis for understanding future disturbance events within eastern deciduous forests and for comparing across forest types.
Activation markers plotted against nutrient sensors in CD4+ and CD8+ T-cells.
<p>Activation markers (CD69, CD25, CD71, and CD38) plotted against nutrient sensors (GLUT1, GLUT4, HK1, HK2, and CD36) in CD4+ T-cells.</p>
FIGURE 2. Bivariate plot with 95 in Geographical variation and taxonomy of the snail-eating snake Dipsas albifrons (Sauvage, 1884), with comments on the systematic status of Dipsas albifrons cavalheiroi Hoge, 1950 (Serpentes: Colubridae: Dipsadinae)
FIGURE 2. Bivariate plot with 95% confidence regions for the first 2 axes derived from scores of PCA analysis of female (A) and male (B) populations of Dipsas albifrons. (C, D). Black dots = States of Paraná and Santa Catarina; black squares = Queimada Grande Island; and black triangles 3 = State of Espírito Santo.
FIG UR E 3 (a) Dated phylogeny of the genus Theodoxus constructed in BEAST based on COI, 16S and ATPα. Node labels denote divergence times in millions of years ago (Ma); node bars indicate the 95% credibility interval around these dates. Small squares at nodes indicate significant support of divergence events found with BEAST and other phylogenetic analyses (see Figures S2.1 and S2.2), as explained through the key. Where MOTUs (A–R) show conspecifics among a number of morphospecies, species names are given in order of their year of description. Morphospecies, incorporated from GenBank, where determination was potentially dubious are highlighted by an asterisk. Clades (C) and subclades (SC) are demarcated by dashed lines between MOTUs. (b) LTT plots indicating the build‐up of lineages in Theodoxus over geological time. Dashed lines surrounding the solid LTT lines indicate the 95% confidence intervals. Where intra‐ and interspecific diversity diverge, interspecific diversity is highlighted in blue and intraspecific diversity in red. Transitions in geological ages are highlighted by narrow grey lines, while the grey bar marks the period of pronounced glacial cycles (last 900 kyr) [Colour figure can be viewed at wileyonlinelibrary.com] in Contributions of biogeographical functions to species accumulation may change over time in refugial regions
FIG UR E 3 (a) Dated phylogeny of the genus Theodoxus constructed in BEAST based on COI, 16S and ATPα. Node labels denote divergence times in millions of years ago (Ma); node bars indicate the 95% credibility interval around these dates. Small squares at nodes indicate significant support of divergence events found with BEAST and other phylogenetic analyses (see Figures S2.1 and S2.2), as explained through the key. Where MOTUs (A–R) show conspecifics among a number of morphospecies, species names are given in order of their year of description. Morphospecies, incorporated from GenBank, where determination was potentially dubious are highlighted by an asterisk. Clades (C) and subclades (SC) are demarcated by dashed lines between MOTUs. (b) LTT plots indicating the build‐up of lineages in Theodoxus over geological time. Dashed lines surrounding the solid LTT lines indicate the 95% confidence intervals. Where intra‐ and interspecific diversity diverge, interspecific diversity is highlighted in blue and intraspecific diversity in red. Transitions in geological ages are highlighted by narrow grey lines, while the grey bar marks the period of pronounced glacial cycles (last 900 kyr) [Colour figure can be viewed at wileyonlinelibrary.com]
FIGURE 3. Bivariate probability density plot for the variables bracteole length and bracteole width. The isolines are 0.2 in Morphometric characterization of Eryngium viviparum (Umbelliferae): description of a new subspecies from the Iberian Peninsula
FIGURE 3. Bivariate probability density plot for the variables bracteole length and bracteole width. The isolines are 0.2 probability units apart, and those with a thicker line are the 1.0 and 2.0 levels. Note that although the three modes are clearly distinguishable, there is a large overlap between the Galician and French subpopulations.
Tree abundance in eight 1-ha tropical forest plots in northeastern Costa Rica from 1997-2017
<p>In 1997, four 1-ha plots were established in secondary forests (12-25 yr since establishment on former pasture) in northeastern Costa Rica, in and around La Selva Research Station. In 2005, four additional plots were established, two in 10-yr old sites and two in old growth sites. The dataset contains information for 155,378 trees. Each year, from 1997-2017 all stems with a diameter of breast height ≥ 5 cm were censused in each site within 100 subplots of 10m x 10m. All but a few individuals were identified to species with confirmed identifications by local experts and vouchers. Life form for each species was also recorded as tree (reaching canopy), midtree (midstory tree), treelet (understory tree), shrub, liana, palm, or understory palm. The specimen-based data set contains data for all trees that were alive (not completely dead) and standing in each annual census, including notes on new recruits or damaged trees. Each tree individual is identified by a unique stem identifiation code and each entry has a unique specimen code. Each tree had a unique numbered tag, nailed into the stem. Locations of diameter measurements were painted on each tree to minimize annual variation and field technians had data from the prior year to confirm information for each tree. These were generally taken at 1.3 m height. In cases where a buttress or stilt root caused a stem irregularity, the measurement point was moved upwards beyond any stem irregularity. The diameter measurement for each specimen reflects each year's measurement point.</p>
Figure 2. Bubble plot showing diamondback terrapin clutch sizes recorded 1998–2012 in Long-term increases in clutch size in common snapping turtles (Chelydra serpentina) and diamondback terrapins (Malaclemys terrapin)
Figure 2. Bubble plot showing diamondback terrapin clutch sizes recorded 1998–2012. Bubble size indicates the number of clutches of the same size.
Figure 1. Bubble plot showing snapping turtle clutch sizes recorded 2004–2015 in Long-term increases in clutch size in common snapping turtles (Chelydra serpentina) and diamondback terrapins (Malaclemys terrapin)
Figure 1. Bubble plot showing snapping turtle clutch sizes recorded 2004–2015. Bubble size indicates the number of clutches of the same size.
Figure 1. Sheared principal component analysis plot depicting morphometric variation among Cambarus aff. dubius, C. pauleyi, C in Cambarus loughmani, a new species of crayfish (Decapoda: Cambaridae) endemic to the pre-glacial Teays River Valley in West Virginia, USA
Figure 1. Sheared principal component analysis plot depicting morphometric variation among Cambarus aff. dubius, C. pauleyi, C. loughmani, and nominate C. dubius.
Figure 8. Correspondence analysis plots. M1–M4 in The foraging activity of Mesobuthus gibbosus (Scorpiones: Buthidae) in central and south Aegean archipelago
Figure 8. Correspondence analysis plots. M1–M4: moon phase classes from minimum (M1) to maximum (M4); Al1–Al4: moon altitude classes; Az1–Az4: moon azimuth classes; sw, sitand-wait; dk, doorkeeping; C, Crete; K, Koufonisi.
Figure 7. Correspondence analysis plots. A1–A4 in The foraging activity of Mesobuthus gibbosus (Scorpiones: Buthidae) in central and south Aegean archipelago
Figure 7. Correspondence analysis plots. A1–A4: air temperature classes from minimum (A1) to maximum (A4); H1–H4: air relative humidity classes; S1–S4: soil temperature classes; W1– W4: wind speed classes; M1–M4: moon phase classes; sw, sit-and-wait; dk, doorkeeping; C, Crete; K, Koufonisi.
Replication package for: Geography and Agricultural Productivity: Cross-Country Evidence from Micro Plot-Level Data
<p>The package contains all the data and code necessary to reproduce the results in Adamopoulos and Restuccia (forthcoming). "Geography and Agricultural Productivity: Cross-Country Evidence from Micro Plot-Level Data." <em>Review of Economic Studies</em>. Detailed instructions on how to use the files are provided in a README file.</p>
FIGURE 19. Ordination plots from a in Revision of the fish family Kyphosidae (Teleostei: Perciformes)
FIGURE 19. Ordination plots from a principal component analysis for comparison of multiple morphometric and meristic characters for: A) Kyphosus vaigiensis (open triangles/blue area), K. analogus (open circles/purple area) and K. incisor (open diamonds/grey area), type specimens of K. incisor (closed diamonds), specimen of K. incisor with molecular identity confirmed (closed square), 'Ligas et al. 2011' marks the specimen examined by Ligas et al. (2011), type specimens of K. vaigiensis (closed triangles), specimen of K. vaigiensis with molecular identity confirmed (open downpointing triangle), B) grey specimens of K. sectatrix (open circles/blue area), xanthic specimens of K. sectatrix collected at other remote islands than the Revillagigedo Islands (squares), xanthic specimens of K. sectatrix collected at the Revillagigedo Islands (open triangles/ yellow area), type specimens of K. sectatrix (open diamonds), specimens of grey K. sectatrix with molecular identity confirmed (closed circles), specimens of xanthic K. sectatrix with molecular identity confirmed (closed squares). Type specimens are noted with catalog numbers, see text for further details on morphometric and meristic characters used in combination.
Plots source data for the Communications Earth & Environment research article titled: Diurnal expansion and contraction of englacial fracture networks revealed by seismic shear wave splitting
<p>The source data for plotting figures presented in the main text of article titled: Diurnal expansion and contraction of englacial fracture networks revealed by seismic shear wave splitting.</p>
FIGURE 12. Bivariate plots with 95 in Taxonomic revision of the Brazilian Atlantic Forest Atractus (Reptilia: Serpentes: Dipsadidae) 2364
FIGURE 12. Bivariate plots with 95% confidence regions for the first two axes derived from scores of DFA analyses for male (A) and female (B) colour patterns of Atractus paraguayensis.
Figure 3. Gaussian Markov random field skyride plots for 11 in Phylogeography of the Poecilimon luschani species group (Orthoptera, Tettigoniidae): a radiation strictly correlated with climatic transitions in the Pleistocene
Figure 3. Gaussian Markov random field skyride plots for 11 populations of the Poecilimon luschani species group. The median estimates are shown as a thick solid line, and the 95% highest posterior density limits are shown by the grey area. The background grey graphs show fluctuations in temperature during the respective periods of the Pleistocene. The upper and lower margins show the time in kiloyears (Kyr), the left margin shows the log of the effective population size (Nef), and the right margin the departure in temperature (ΔT in °C). Names of the glacial periods are indicated in the boxes at the bottom of the graphs. The background graph shows the temperature reconstruction of Vostok; modified from http://agwobserver.wordpress.com. A, İzmir (P. ledereri); B, Aydın (P. tuncayi); C, Kütahya (P. egrigozi); D, Balıkesir (P. helleri); E- Es¸en2 (P. l. chobanovi); F, Es¸en3 (P. l. chobanovi); G, Demre (P. l. luschani); H, Kalkan (P. l. luschani); I, Patara (P. l. luschani); J, Olympos (P. l. birandi); K, Bakırlıdag (P. l. birandi).
Figure 4. Bar charts plotting mean p in Operational criteria for cryptic species delimitation when evidence is limited, as exemplified by North American Entomobrya (Collembola: Entomobryidae)
Figure 4. Bar charts plotting mean p-distances (uncorrected) of cytochrome c oxidase I (COI; complete gene, 1539 bp). A, mean intrapopulation, interpopulation, and interspecific distances for all Entomobrya species comparisons. Mean intrapopulation distances and mean distances for comparisons between allopatric populations of the same colour form, different colour forms (i.e. a−b represents mean distance of all comparisons between colour forms a and b), and morphologically differentiated sister species, are graphed for each test species; B, Entomobrya assuta; C, Entomobrya clitellaria; D, Entomobrya ligata; and E, Entomobrya quadrilineata. The line representing the lowest reported interspecific COI distance for Collembola (8%) is highlighted in bold. The number of comparisons (n) for each mean distance is listed. Error bars indicate the SD. See Table S4 for actual mean p-distance values.
FIGURE 17. Bivariate plot with 95 in Taxonomic revision of the Brazilian Atlantic Forest Atractus (Reptilia: Serpentes: Dipsadidae) 2364
FIGURE 17. Bivariate plot with 95% confidence regions for the first two axes derived from scores of DFA analyses for females of Atractus francoi sp. nov., A. serranus, and A. trihedrurus.
Figure 11. Residual plots from the regression analyses for the four measurements that had low r in Phylogenetic implications of the morphology of the braincase of caecilian amphibians (Gymnophiona)
Figure 11. Residual plots from the regression analyses for the four measurements that had low r-squared values in their respective regression plots. Species circled represent those that deviate from the expected value of each measurement predicted by the regression plot. Data point labels correspond to the first letter of the genus followed by the first three letters of the species. A, residuals from the regression plot of dorsomedial process length against skull length, for which Typhlonectes natans (T.natans), Chthonerpeton indistinctum (C.indistinctum), and Crotaphatrema lamottei (C.lamottei) possess a process that is shorter than predicted; B, residuals from the regression plot of nasal septum length against skull length, for which T. natans and Ch. indistinctum possess a septum that is shorter than predicted; C, residuals of the regression plot of lateral wall length against skull length, for which Scolecomorphus kirkii (S.kirkii), Scolecomorphus vittatus, and Cr. lamottei possess walls that are longer than predicted; and D, residuals of the regression plot of occipital condyle protrusion against skull length, for which Epicrionops bicolor (E.bicolor), Rhinatrema bivittatum (R.bivittatum), Ichthyophis beddomei (I.beddomei), Ichthyophis kohtaoensis, Caudacaecilia asplenia (C.asplenia), and Scolecomorphus vittatus (S.vittatus) possess less protruded condyles than predicted.
FIGURE 3 in Checklist of Kilimanjaro grasses shows that both plot and herbarium methods are necessary to record diversity
FIGURE 3. Species (a) and genera (b) of Mount Kilimanjaro grasses ranked by the number of times they are recorded in our database, including both herbarium and plot records. The red line marks 50% of the total number of specimen records.
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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.