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Fig. 7 in Taxonomic review of the tree snail genus Amphidromus Albers, 1850 (Pulmonata: Camaenidae) in Laos, with the description of two new species
Fig. 7. SEM images of the radula. A–C. Amphidromus roseolabiatus Fulton, 1896 from Ban Phavong, Khammouan, Laos (CUMZ 7012). D–F. Amphidromus syndromoideus sp. nov., holotype (CUMZ 7019). G–I. Amphidromus areolatus (Pfeiffer, 1861) from Thad Fek, Attapue, Laos (CUMZ 7023). A, D, G = central tooth with the first to fifth to eighth lateral teeth; B, E, H = lateral teeth with the tricuspid marginal teeth transition; C, F, I = outermost marginal teeth. Numbers indicate the order of the lateral and marginal teeth. Central tooth indicated by 'C'.
Fig. 5 in Taxonomic review of the tree snail genus Amphidromus Albers, 1850 (Pulmonata: Camaenidae) in Laos, with the description of two new species
Fig. 5. Shells of Amphidromus pervariabilis Bavay & Dautzenberg, 1909. A–B. Syntype of the nominotypical form (MNHM-IM-2000-2049). C. Var. "bifasciata" Bavay & Dautzenberg, 1909, syntype (MNHM-IM-2000-2059). D. Var. "goniostoma" Bavay & Dautzenberg, 1909, syntype (MNHM- IM-2000-2058). E. Var. "lilacina" Bavay & Dautzenberg, 1909, syntype (MNHM-IM-2000-2052). F. Var. "minor" Bavay & Dautzenberg, 1909, syntype (MNHM-IM-2000-2050). G. Var. "monozonalis" Bavay & Dautzenberg, 1909, syntype (MNHM-IM-2000-2057). H. Var. "obesa" Bavay & Dautzenberg, 1909, syntype (MNHM-IM-2000-2053). I. Var. "protracta" Bavay & Dautzenberg, 1909, syntype (MNHM-IM-2000-2051). J. Var. "tricolor" Bavay & Dautzenberg, 1909, syntype (MNHM- IM-2000-2054). K–L. Specimens from Khua District, Phongsaly, Laos (CUMZ 7014).
Fig. 1 in TreePics: visualizing trees with pictures
Fig. 1. Screenshot of the page with tree visualizations and associated images, showing the phylogenetic trees and the associated thumbnails. The selected thumbnails (red squares) also appear in the list below the tree.
Fig. 1. Bayesian majority rule consensus tree reconstructed for 90 in Phylogenetic analysis and systematic position of two new species of the ant genus Crematogaster (Hymenoptera, Formicidae) from Southeast Asia
Fig. 1. Bayesian majority rule consensus tree reconstructed for 90 taxa using five genes (ArgK, CAD, LWRh, Top1, Wg) in a MrBayes analysis. Above node numbers indicate posterior probability. Data were partitioned by PartitionFinder v.1.1.1 and analyzed using a best fit model for each gene and codon position, with 10 million generations and a burn-in of 25 %. Area enclosed by dashed lines is enlarged on Fig. 2.
Fig. 2. Phylogenetic tree constructed with 57 in A review of Bennelongia De Deckker & McKenzie, 1981 (Crustacea, Ostracoda) species from eastern Australia with the description of three new species
Fig. 2. Phylogenetic tree constructed with 57 novel COI sequences of Bennelongia, 26 published Bennelongia sequences and one Heterocypris spec. as outgroup (sequence names are given in brackets at the end of species names). This tree represents two trees of identical topology inferred by ML and BI. Bootstrap values (for 1000 bootstrap replicates) from ML analyses and Bayesian posterior probabilities (ranging from 0 to 1) are shown for each node (in the format: 'Bootstrap Support/Posterior Probability'). Branch lengths are proportional to the genetic distance scale at the bottom left. Clades with published sequences have been collapsed; the number of sequences in these clades is included in brackets after the species name. Nodes with less than 50% bootstrap support and a posterior probability of less than 0.5 have been collapsed. The tree shows six strongly supported clades that correspond to the species presented in this study.
Neighbor-joining phylogenetic tree based on 16S rRNA sequences.
<p><strong>Supplementary Figure (S1):</strong> Bayesian 50% majority rule phylogram of 16S ribosomal RNA region showing the phylogenetic relationships among the bacterial isolates in our study. The newly generated sequences are preceded by red circle. The GenBank sequences are preceded by blue squares. The GenBank accession number appears after the species name. Numbers above the branches represent Bayesian posterior probabilities (≥ 0.90), and the maximum parsimony bootstrap support values are given below the branches (≥70%). The out group used for tree construction preceded by empty circle.</p>
Data for "Age effect on tree structure and biomass allocation in Scots pine (Pinus sylvestris L.) and Norway spruce (Picea abies [L.] Karst.)"
<p>VAPU dataset for tree biomass was collected from southern Finland in 1988-1990 by the Finnish Forest Research Institute (Metla, now Natural Resources Institute Finland, Luke) (VAPU data set).</p> <p>Those sample trees (162 Scots pine and 163 Norway spruce) are originated from the whole VAPU data set. The sheet 'Pine' and 'Spruce' data have been matched between 'sample branch measurements' and the 'biomass' information (by cluster X, Y, and plot, tree number).</p> <p>Biomass estimation for foliage and branches has been described here: https://doi.org/10.1016/j.ecolmodel.2004.04.024 and https://doi.org/10.1093/treephys/25.7.803<br> </p>
Data from: Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics
1. The amount and patterns of phylodiversity in a community are often used to draw inferences about the local and historical factors affecting community assembly and can be used to prioritize communities and locations for conservation. Because measures of phylodiversity are based on the topology and branch lengths of phylogenetic trees, which are affected by the number and diversity of taxa in the tree, these analyses may be sensitive to changes in taxon sampling and tree reconstruction methods. 2. To investigate the effects of taxon sampling and tree reconstruction methods on measures of phylodiversity, we investigated the community phylogenetics of the Ordway-Swisher Biological Station (Florida), which is home to over 600 species of vascular plants. We studied the effects of 1) the number of taxa included in the regional phylogeny; 2) random vs. targeted sampling of species to assemble the regional species pool; 3) including only species from specific clades rather than broad sampling; 4) using trees reconstructed directly for the taxa under study compared to trees pruned from a larger reconstructed tree; and 5) using phylograms compared to chronograms. 3. We found that including more taxa in a study increases the likelihood of observing significantly non-random phylogenetic patterns. However, there were no consistent trends in the phylodiversity patterns based on random taxon sampling compared to targeted sampling, or within individual clades compared to the complete dataset. Using pruned and reconstructed phylogenies resulted in similar patterns of phylodiversity, while chronograms in some cases led to significantly different results from phylograms. 4. The methods commonly used in community phylogenetic studies can significantly impact the results, potentially influencing both inferences of community assembly and conservation decisions. We highlight the need for both careful selection of methods in community phylogenetic studies and appropriate interpretation of results, depending on the specific questions to be addressed.
Figure 1. Bayesian phylogenetic tree inferred from the 640 in Two new Geoplaninae species (Platyhelminthes: Continenticola) from Southern Brazil based on an integrative taxonomic approach
Figure 1. Bayesian phylogenetic tree inferred from the 640-bp of cytochrome c oxidase subunit I gene under GTR + I + G model of sequence evolution. The two new species are highlighted in light grey (Cratera ochra sp. nov.) and dark grey (Obama maculipunctata sp. nov.). Values indicate support for each node according to the maximum posterior probabilities>70% and bootstrap support values> 70%, respectively.
Data of Cerrado´s Tree Crown Networks
<p>Information about the architecture of the woody crown obtained through representations in the form of a network (graphs). The essential components of these networks are nodes and connectors. Decomposition, topology, and properties calculated for analyzing the strategies of crown airspace acquisition in any environment. The networks represented in a two-dimensional space follow the general laws of network theory, but with specific meanings for the crown architecture. Thus, a dataset generated and included information about five individuals from fifteen tree species growing under the natural conditions of the Cerrado vegetation. We presented the types and the total number of nodes. Initial node (IN) was the node that starts the network, regular node (RN) was the vast majority of nodes with three connectors. Emission node (EN) showed four connectors, and the final node (FN) was the last in leafy axes. There are data about the distances between the initial and final nodes (IN-IF), and initial and emission nodes (IN-IE). Decomposition and topological combinations permitted to disclose the properties (navigability, vulnerability, symmetry, and complexity). The data presented can be used by researchers from all over the world in works that investigate the behavior of networks in biological systems, in addition to the specific applications of studies of functional ecology and plant ecophysiology. We obtained the data directly from a skeletonized representation of the woody crown in a two-dimensional space in the form of a drawing. Subsequently, the nodes counted, and their proportions (decomposition), the distances between the different types of nodes (topology), and the values of network properties (the combination of decomposition and topology) obtained.</p>
Figure 7 in Additions to the British list of Megaselia Rondani (Diptera: Phoridae), including two new species, from the crowns of ancient pollarded trees
Figure 7. Megaselia russellsmithi male, hypopygium. (A) Left face; (B) right face (minus penis complex). Scale bar: 0.1 mm.
Figure 22 in Additions to the British list of Megaselia Rondani (Diptera: Phoridae), including two new species, from the crowns of ancient pollarded trees
Figure 22. Megaselia veluitinicavus male. (A) Left face of hypopygium; (B) tips of right paraphysis and posteroventral region of epandrium; (C) anterior face of hind basitarsus; (D) the internal hairy cavity of the hind basitarsus (anterior focal plane). Scale bars: 0.1 mm.
Figure 8 in Additions to the British list of Megaselia Rondani (Diptera: Phoridae), including two new species, from the crowns of ancient pollarded trees
Figure 8. Megaselia russellsmithi female, details of abdomen. (A) Tergites 5–7; (B) sternite 7 and lobes at rear of sternum 8; (C) right cercus. Scale bars: 0.1 mm.
Figure 4 in Additions to the British list of Megaselia Rondani (Diptera: Phoridae), including two new species, from the crowns of ancient pollarded trees
Figure 4. Megaselia henrydisneyi male, hypopygium. (A) Left face; (B) right face. Scale bar: 0.1 mm.
Figure 1 in Additions to the British list of Megaselia Rondani (Diptera: Phoridae), including two new species, from the crowns of ancient pollarded trees
Figure 1. Megaselia crassipes male. (A) Posterior face of front tarsus; (B) left face of hypopytgium. Scale bar: 0.1 mm.
Variations in tree growth provide limited evidence of species mixture effects in Interior West U.S.A. mixed-conifer forests
<p>1. In mixed stands, species complementarity (e.g., facilitation and competition reduction) may enhance forest tree productivity. Although positive mixture effects have been identified in forests worldwide, the majority of studies have focused on two-species interactions in managed systems with high functional diversity. We extended this line of research to examine mixture effects on tree productivity across landscape-scale compositional and environmental gradients in the low functional diversity, fire-suppressed, mixed-conifer forests of the U.S. Interior West.</p> <p>2. We investigated mixture effects on the productivity of <i>Pinus ponderosa</i>, <i>Pseudotsuga menziesii</i>, and <i>Abies concolor</i>. Using region-wide forest inventory data, we created individual-tree generalized linear mixed models and examined the growth of these species across community gradients. We compared the relative influences of stand structure, age, competition, and environmental stress on mixture effects using multi-model inference. We analyzed growth of neighboring tree species to infer whether a mixture effect in a single species translated to the stand-level.</p> <p>3. We found support for a positive mixture effect in <i>P. menziesii</i>, although our results were equivocal in light of a weaker but still plausible alternative model. Growth of <i>P. menziesii</i> neighboring species in mixed stands declined or held constant depending on aridity, suggesting that a positive mixture effect in <i>P. menziesii</i> does not necessarily extend to the stand level. We found no evidence for mixture effects in <i>P. ponderosa</i>, <i>A. concolor</i> or their neighboring species.</p> <p>4. Complementarity appears to have a limited influence on tree growth in the mixed-conifer systems of the U.S. Interior West, reflecting limited functional diversity. Historical changes in stand structure following fire exclusion, particularly high stand densities, may limit the potential for positive species mixture effects. The limited species pool of Interior West forests increases the risk that, without careful management, what functional diversity exists could be lost to compositional changes resulting from stand dynamics or disturbance.</p>
Figure 3. Consensus tree for the cytochrome b in Four New Bat Species (Rhinolophus hildebrandtii Complex) Reflect Plio-Pleistocene Divergence of Dwarfs and Giants across an Afromontane Archipelago
Figure 3. Consensus tree for the cytochrome b dataset for representative genotyped specimens of the Rhinolophus hildebrandtii complex. The topology represents the consensus topology from a 20 million MCMC run implemented in BEAST. Estimates of divergence times (million years ago; Mya) are indicated adjacent to nodes or above branches and grey bars indicate 95% HPD values. The split between the Hipposideridae and Rhinolophidae was used as the calibration point. Taxa names include museum/field numbers which correspond to Appendix S1 or GenBank accession numbers and abbreviations are: RcfH - R. cf. hildebrandtiiı RD - R. darlingiı RE - R. eloquensı RF - R. fumigatusı RH - R. hildebrandtii s.l.ı RL - R. landeri and RR - R. ruwenzorii. Localitiesı where availableı are providedı abbreviations include SA - South Africaı MZ - Mozambiqueı and ZW - Zimbabweı and the numbers in parentheses correspond with place names in Table S1 and Fig. 2 for Clade 1 and 2 individuals. doi:10.1371/journal.pone.0041744.g003
Level and spatial pattern of overstory retention impose tradeoffs for regenerating and retained trees
<p>Variable retention (VR) has been adopted globally as an alternative to more intensive forms of regeneration harvest. By retaining live trees within harvest units, VR seeks balance among the commodity, ecological, and aesthetic values of managed forests. Achieving these multiple, often competing objectives requires an understanding of how level and spatial pattern of retention shape the abundance, growth, and mortality of regenerating and retained trees. Using long-term (18-19 yr) data from a regional-scale VR experiment, we explore the individual and interactive effects of retention level (15% vs. 40% of initial basal area) and pattern (dispersed vs. aggregated) on the post-harvest dynamics of forests of differing structure and seral composition.</p> <p>Level and pattern of retention imposed tradeoffs for the density and growth of regenerating trees (>0.1 m tall, <5 cm dbh) and ingrowth (trees attaining 5 cm during the study). Greater retention led to greater density of late-seral regeneration, but lower density of early-seral ingrowth, and slower growth of late-seral ingrowth. Dispersed retention enhanced the density of early- and late-seral regeneration (compared to aggregated treatments), but reduced the growth of early-seral ingrowth. We also observed tradeoffs for retained trees. Lower retention enhanced the growth of smaller trees (<25 cm dbh)—particularly in dispersed settings—but reduced the survival of larger trees, which were more susceptible to windthrow. Greater retention reduced the growth, but enhanced the survival of smaller trees. Pattern imposed similar tradeoffs, with dispersed retention enhancing growth, but reducing survival of small trees. Finally, level and pattern resulted in tradeoffs for productivity of regenerating vs. retained-tree cohorts. Ingrowth productivity was greater at lower retention and in aggregated treatments; retained-tree productivity was greater at higher retention and in dispersed treatments.</p> <p>Our results provide a unique, long-term perspective on the sensitivity of tree regeneration, growth, and mortality to key structural elements of VR systems. Strong responses to level and pattern of retention produce tradeoffs for different ecological or resource objectives. Balancing these objectives may require the combined use of aggregates, dispersed retention, and clearings, to mimic the spatial heterogeneity of habitats, physical structures, and resource conditions that are produced by natural disturbances.</p>
Conversion of measurements of tree ring gains: Canada, Africa, Mexico, South America from RWL- files to JSON format.
<p>The International Tree Rings Data Bank (ITRDB) is the most comprehensive tree growth database (https://www1.ncdc.noaa.gov/pub/data/paleo/treering).</p> <p>Shoudong Zhao, et al. (2019, 2018) analyzes the representativity of dendrochronological data (ITRDB) and proposes a corrected database with error indications. One of the bottlenecks of data use (ITRDB) is that the data is loaded as a collection of separate files in the Tucson positional format.</p> <p>The purpose of our data presentation is to change the Tucson data format to JSON format and combine the separate files into one.</p> <p>We convert the initial data for the <strong>Canada</strong>, <strong>Africa</strong>, <strong>Mexico</strong> and <strong>Southamerica</strong> rwl-files into Json format of data on tree growth in four files: <strong>canada.json</strong>, <strong>africa.json</strong>, <strong>mexico.json</strong> and <strong>southamerica.json</strong>. The data was converted using the R programming language and the dplR program library Bunn, A. (2008)</p> <p>The experience of developing the structure of dendroclimatic data in JSON format is described in the works of Kachaev A. (2016, 2017, 2020).</p> <p>Description of the structure of JSON data format is attached in the files ReadMe.pdf</p> <p> </p> <p>References</p> <p>Bunn, A. G. (2008). A dendrochronology program library in R (dplR). Dendrochronologia, 26, 115-124. https://doi.org/10.1016/j.dendro.2008.01.002</p> <p>Kachaev, Alexander (2020), "Compact dataset of dendrochronological data of pri-mary metric characteristics of tree rings of Asia.", Mendeley Data, V1, doi: 10.17632 / p9zhpmzgtk.1</p> <p>Kachaev A. V. (2017) Model for describing the structure of dendroclimatic data In the collection: Regional problems of remote sensing of the Earth Materials of the IV international scientific conference. Siberian Federal University, Institute of Space and Information Technologies. p. 120-122. (Russia)</p> <p>Kachaev A. V. (2016) NOSQL Approach for Development of Dendroclimatic Data Bank. In the collection: Regional problems of remote sensing of the Earth. Materials of the III International Scientific Conference. p. 89-91. (Russia)</p> <p>Shoudong Zhao, et al. (2019). The International Tree-Ring Data Bank (ITRDB) revisited: Data availability and global ecological representativity. Journal of Biogeography, 46 (2), 355-368. doi: 10.1111 / jbi.13488</p> <p>Zhao, Shoudong et al. (2018), Data from: The International Tree-Ring Data Bank (ITRDB) revisited: data availability and global ecological representativity, Dryad, Dataset, https://doi.org/10.5061/dryad.kh0qh06</p>
FIG. 5. — Strict consensus tree from eight most parsimonious trees recovered for Molossus E. Geoffroy, 1805 in Diversity, morphological phylogeny, and distribution of bats of the genus Molossus E. Geoffroy, 1805 (Chiroptera, Molossidae) in Brazil
FIG. 5. — Strict consensus tree from eight most parsimonious trees recovered for Molossus E. Geoffroy, 1805. Numbers above the branches indicate Bootstrap values and bottom numbers indicate Bremer support values.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.