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2,052 results for “Species tree”
Effectiveness of the spectral area index created by three algorithms for tree species recognition
<p>This dataset is an experimental dataset used to extract PAIs and verify their effectiveness in tree species classification.</p>
Litter and root traits control soil microbial composition and enzyme activities in 28 common subtropical tree species
<p><span>1. </span><span>Plant trait-based approaches are frequently used to explore the linkages between aboveground plant communities and belowground ecosystem functions. However, the role of plant leaf litter and living root traits in driving soil microbial biomass, community composition, and enzyme activities has rarely been explored.</span></p> <p><span>2. </span><span>Here, we measured the soil microbial biomass, community composition and enzyme activities related to carbon (C), nitrogen (N), and phosphorus (P) acquisition under three-year-old monocultures of 28 common subtropical tree species in China.</span></p> <p><span>3. </span><span>We found that plant leaf litter and absorptive root traits, including leaf litter C content, litter water holding capacity, and root N content, were the three best predictors for soil microbial biomass and enzyme activities. In particular, resource-exploitative tree species with higher root N contents were associated with microbial communities with lower fungi to bacteria ratios and lower C- and P-acquisition enzyme activities. Tree species with higher leaf litter water holding capacity were associated with microbial resource acquisition strategies for C and P acquisition.</span></p> <p><span>4. </span><span>Synthesis: Our findings highlighted that plant leaf litter and root traits are important for mechanistically understanding the ecological linkage between the plant community and ecosystem functions.</span></p>
FIGURE 3. Maximum Likelihood tree inferred from a in A new species of Loxosceles Heineken & Lowe, 1832 (Araneae: Sicariidae) from Iranian caves
FIGURE 3. Maximum Likelihood tree inferred from a concatenated matrix of cox1 and rrnL mtDNA and H3 nuDNA gene fragments. Numbers next to nodes correspond to bootstrap support values. L. vonwredei, L. spinulosa, Loxosceles sp., L. speluncarum and L. variegata was used to root the tree. TR = Turkey; IP = Iberian Peninsula; SAR = Sardinia; PT = Portugal; GC = Gran Canaria.
FIGURES 13–18 in Nocturnal Velvet Ants (Hymenoptera: Mutillidae) of Joshua Tree National Park, Riverside County, California with the description of three new species
FIGURES 13–18. Odontophotopsis dalyi, sp. nov., genitalia, 13. ventral view, 14. dorsal view; Odontophotopsis odontoloxia, sp. nov., genitalia, 15. ventral view, 16. dorsal view; and Photomorphus schoenwerthi, sp. nov., genitalia, 17. ventral view, 18. dorsal view.
FIGURE 5. Maximum likelihood tree built with concatenated matrix using cytochrome oxidase sub-united I in New species of Trichomycterus (Siluriformes: Trichomycteridae) lacking pelvic fins from Paranapanema basin, southeastern Brazil
FIGURE 5. Maximum likelihood tree built with concatenated matrix using cytochrome oxidase sub-united I (COI) and 16S genes, showing the relationships of Trichomycterus pascuali within Trichomycterinae. Numbers on branches of tree denote bootstrap (B) values.
FIGURES 9–12 in Nocturnal Velvet Ants (Hymenoptera: Mutillidae) of Joshua Tree National Park, Riverside County, California with the description of three new species
FIGURES 9–12. Photomorphus schoenwerthi, sp. nov., 9. habitus; 10. head, frontal view; 11. mesosternum; and 12. pygidium.
FIGURES 5–8 in Nocturnal Velvet Ants (Hymenoptera: Mutillidae) of Joshua Tree National Park, Riverside County, California with the description of three new species
FIGURES 5–8. Odontophotopsis odontoloxia, sp. nov., 5. habitus; 6. head, frontal view; 7. mesosternum; and 8. pygidium.
FIGURES 1–4 in Nocturnal Velvet Ants (Hymenoptera: Mutillidae) of Joshua Tree National Park, Riverside County, California with the description of three new species
FIGURES 1–4. Odontophotopsis dalyi, sp. nov., 1. habitus; 2. head, frontal view; 3. mesosternum; and 4. pygidium.
Supplementary material 1 from: Pacheco da Silva VC, Kaydan MB, Germain J-F, Malausa T, Botton M (2016) Three new species of mealybug (Hemiptera, Coccomorpha, Pseudococcidae) on persimmon fruit trees (Diospyros kaki) in southern Brazil. ZooKeys 584: 61-82. https://doi.org/10.3897/zookeys.584.8065
COI DNA sequences obtained for Anisococcus granarae Pacheco da Silva & Kaydan, sp. n. and Ferrisia kaki Kaydan & Pacheco da Silva, sp. n. : Explanation note: This supplementary file contais the senquences of a fragment from the mitochondrial region of Cytochrome Oxidase Subunit I of two new species of mealybugs found on persimmon trees in Southern Brazil, Anisococcus granarae Pacheco da Silva & Kaydan, sp. n. and Ferrisia kaki Kaydan & Pacheco da Silva, sp. n.
FIGURE 1. Bayesian time-tree for 32 in A review of all Recent species in the genus Novocrania (Craniata, Brachiopoda)
FIGURE 1. Bayesian time-tree for 32 craniids, specimen details and clade names as in Cohen, Kaulfuss et al. (2014), based on the alignment shown in Supplementary file 1. The root node height (relative age) is defined as 1.0 and other mean node heights (relative ages) are shown in proportion to the root node. The gray bars across nodes show the 95% highest posterior density ranges, roughly equivalent to 95% confidence intervals. Note that other analyses may place the root node elsewhere in the craniid radiation.
FIGURE 3. Majority-rule consensus tree for 20002 in Recognition of a new species of Carmenta from New Mexico supported by morphology and mitochondrial cytochrome oxidase I data (Lepidoptera: Sesiidae: Sesiinae: Synanthedonini)
FIGURE 3. Majority-rule consensus tree for 20002 trees kept from the Bayesian analysis of 1 million generations using the morphological and DNA data. Posterior probabilities greater then 75% are shown.
FIGURE 7. Maximum-likelihood tree for 11 in Scolionema sanshin sp. n., a new species (Hydrozoa, Limnomedusae, Olindiidae) from the Ryukyu Archipelago, southern Japan
FIGURE 7. Maximum-likelihood tree for 11 limnomedusan taxa based on the nuclear 18S rDNA data set. Scale bars indicate branch length in substitutions per site. Nodal support values are presented as the ML bootstrap value; only values>50% are shoWn.
FIGURE 1. Condensed Bayesian tree inferred from cyt b in Capoeta anamisensis, a new species from the Minab and Hasan Langhi River drainages in Iran (Teleostei: Cyprinidae)
FIGURE 1. Condensed Bayesian tree inferred from cyt b. Numbers right of the slash, indicate the posterior probabilities of the Bayesian analysis, using MrBayes, while numbers left of the slash are the bootstrap support for 10,000 replicates in the Maximum Likelihood tree, using RaxML. Asterisks (*) indicate less than 50% Maximum Likelihood support for the node.
FIGURE 10. Unrooted maximum likelihood phylogenetic tree reconstructed from a 481 in A new species of nurse-frog (Aromobatidae, Allobates) from the Madeira River basin with a small geographic range
FIGURE 10. Unrooted maximum likelihood phylogenetic tree reconstructed from a 481 bp fragment of the mitochondrial 16S rDNA sampled from six Allobates bacurau paratypes and other cryptically colored species of Allobates distributed in Brazil and across cis-Andean South America. Clade labels indicate bootstrap support values estimated from 5000 bootstrap replicates (only support values>80% are shown). Basal clades with low bootstrap support should not be considered to reflect the true evolutionary history between taxa. Locations described in parentheses indicate sequence samples obtained from voucher specimens that did not proceed from the species type locality.
FIGURE 7. Comparison concatenated tree ITS2 – 28S rDNA D2 in Description of two new species closely related to Doryctobracon areolatus (Szépligeti, 1911) (Hymenoptera, Braconidae), based on morphometric and molecular analyses
FIGURE 7. Comparison concatenated tree ITS2 – 28S rDNA D2 (UPGMA) produced from the nucleotide sequences (A), cluster analysis of the Mahalanobis distance (UPGMA) calculated from the shape of the wings components (B). (DAAP = Doryctobracon areolatus from Amapá, DAGO = D. areolatus from Goiás, DATO = D. areolatus from Tocantins, DASP = D. areolatus from São Paulo, YSAP = Doryctobracon whartoni sp. nov. (yellow stigma) from Amapá; BSAP = Doryctobracon adaimei sp. nov. (brown stigma) from Amapá, BSGO = D. adaimei sp. nov. from Goiás, BSTO = D. adaimei sp. nov. from Tocantins.
FIGURE 1. Maximum likelihood tree inferred from 3221 in A new species of direct-developing frog of the genus Pristimantis (Anura: Terrarana: Craugastoridae) from Cordillera del Cóndor, Ecuador, with comments on threats to the anuran fauna of the region
FIGURE 1. Maximum likelihood tree inferred from 3221 aligned positions of the 16S (2589 aligned bp) and RAG-1 (632 aligned bp) genes depicting the relationships of Pristimantis yantzaza sp. nov.. Bootstrap values are shown above the branches and Bayesian posterior probabilities are shown below except when they are below 50 (bootstrap) or 0.5 (posterior probability). The tree was rooted with Pristimantis versicolor. Museum catalog numbers and locality of origin for vouchers are listed in Table 1.
Tree species recognition with quantitative structure models
<p>A quantitative structure model (QSM) contains the geometric and topological structure of a reconstructed tree. As such, QSMs enable computation of detailed tree properties that have been laborious or impossible to measure before. The computed tree properties can be used as classification features for tree species recognition.</p> <p>The first half of this video illustrates how we define the 15 classification features our research group has used for a species recognition study. An example QSM is used to visualize the relevant tree parts and key steps in the feature computations.</p> <p>The second half shows how the feature values of over a thousand Finnish trees of three different species, Silver birch, Scots pine and Norway Spruce, are distributed, and how well the species separate in the defined feature dimensions. One example QSM of each tree species shown on the right-hand-side with the only the tree parts visible that are related to the current feature.</p> <p>Table of contents:<br> 0:01 Feature illustration<br> 3:46 Viewer guide on screen elements<br> 5:20 Feature value distributions<br> 9:07 Credits</p> <p>The contents of this video link directly to the paper titled "Automatic tree species recognition with quantitative structure models" published in Remote Sensing of Environment (http://dx.doi.org/10.1016/j.rse.2016.12.002).</p> <p>For more information about QSMs, please visit the groups homepage, or watch the other videos on the topic: "3D Forest Information" (https://www.youtube.com/watch?v=wANRdliE1zQ) and "Cylinder reconstruction" (https://www.youtube.com/watch?v=j0Emjwp-fmU).</p> <p>This animation was produced by the Inverse Problems research group in the Department of Mathematics at Tampere University of Technology (http://math.tut.fi/inversegroup).</p> <p>Animation created using Blender 2.77a (http://www.blender.org).</p> <p>Music:<br> "Life of Riley"<br> "Thinking of you"<br> "Jarvic 8"<br> by Kevin MacLeod (http://incompetech.com)<br> Licensed under Creative Commons: By Attribution 3.0<br> http://creativecommons.org/licenses/by/3.0/</p>
FIGURE 2. Paraputo blackmani Joshi sp. n., collection site and life stages. A. Butea monosperma (Lam.) Taub. tree with infested part indicated by arrows; B. A furrow left by a broken branch, with exposed cambium tissue infested by mealybugs; C. Mealybug nymphs, indicated by arrows; D. Adult females; E.Ants, Nylanderia sp. (Hymenoptera: Formicidae), attending the mealybugs; F. Spalgis epius (Westwood) larva (Lepidoptera: Lycaenidae) preying on the mealybugs. in --A--new--species--of--Paraputo--Laing--1929--(Hemiptera:--Coccomorpha:-- Pseudococcidae)--from--India
FIGURE 2. Paraputo blackmani Joshi sp. n., collection site and life stages. A. Butea monosperma (Lam.) Taub. tree with infested part indicated by arrows; B. A furrow left by a broken branch, with exposed cambium tissue infested by mealybugs; C. Mealybug nymphs, indicated by arrows; D. Adult females; E.Ants, Nylanderia sp. (Hymenoptera: Formicidae), attending the mealybugs; F. Spalgis epius (Westwood) larva (Lepidoptera: Lycaenidae) preying on the mealybugs.
Data for: Sun, Ogushi, Tseng -Lepidoptera species richness and community composition in urban street trees
<p>The triple threats of climate change, habitat loss, and environmental pollution have stimulated discussion on how urban areas can be modified to both mitigate heat increases and provide habitat for wildlife such as insects. The strategy of using trees to reduce temperatures has been adopted by numerous cities. However, the majority of street trees planted around the world are non-native. Studies conducted in non-urban areas have demonstrated in comparison to native plants, non-native plants are less likely to support native insect diversity. Here we use a database approach to quantify the number of native Lepidoptera species associated with 76 of the most common street tree species planted in Vancouver, Canada. We tested the prediction that compared to non-native trees, native street trees will support a higher diversity and unique community of native Lepidoptera. As predicted, native street trees were associated with five times as many native Lepidoptera species, and the Lepidoptera communities supported by native vs. non-native street trees were distinct. There was no difference in native Lepidoptera associations between broadleaf vs. coniferous street trees. These results are consistent with studies that have used active sampling techniques to investigate insect richness on a smaller subset of native and non-native tree species. Collectively, these data provide good evidence that the planting native instead of non-native trees will help stem the loss of insect diversity in urban areas.</p>
Figure 3. Multilocus tree for the Corypha africana–C. sharpii–C. hypermetra–C. somalica–C in Integrative taxonomy reveals unrecognised species diversity in African Corypha larks (Aves: Alaudidae)
Figure 3. Multilocus tree for the Corypha africana–C. sharpii–C. hypermetra–C. somalica–C. ashi complex based on Bayesian analysis (BEAST) of concatenated mitochondrial and nuclear loci (5,285 bp). Posterior probabilities (PPs) are indicated at the nodes, with an asterisk indicating a PP of 1.00. Clades that are discussed in the text are labelled I–VIII and with the name of the taxon that has priority in the respective clade. The names of C. africana s.l. are in black font; the other species are in other colours (the six outgroup species are all in pale blue). The three taxa that are not present in any other analyses are indicated by a red '§'. Topological incongruence compared with other phylogenetic trees is indicated by a red '#'. The blue lines indicate the divergence times of two of the outgroup species pairs.
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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.