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Supporting data: The biogeographic origin of a radiation of trees in Madagascar: Implications for the assembly of a tropical forest biome
<p>This directory contains xml files (which in turn contain concatenated alignments), newick, and phylip formatted tree files. Code and scripts used for generating figures, phylogenies and biogeographic models is available on request.</p> <p>~/trees/ contains tree files and maximum clade credibility trees from the three phylogenetic inferences: 1) Canarieae with a fossil tip; 2) Canarieae with fossil nodes; and 3) Canarieae with fossil nodes, but without the Canarieae fossil node calibration. See the paper and supplemental text for more information.</p> <p>~/trees/RAxML/ contains the RAXML starter trees used </p> <p>~/xml_files/ contains the xml files used for Bayesian phylogenetic inference in BEAST for all three phylogenetic inferences (see above). Concatenated alignments of molecular data can be found within the xml files.</p>
Molecular investigation of bacterial communities on two frequently used surfaces in the São Paulo institute of tropical medicine
<p>In this study, we aimed to investigate the overall bacterial population on two frequently used surfaces in the São Paulo institute of tropical medicine (ITM) using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. The massive parallel sequencing data presented here were derived from the surface samples collected from restroom surfaces and the fingerprint door clock system (FDLS) in our ITM in São Paulo.</p>
FIGURE 7 in A new genus and six new species of the tropical Camptotypus genusgroup (Hymenoptera: Ichneumonidae; Pimplinae) from northern South America
FIGURE 7. Amazopimpla farallonensis Palacio, sp. n. The tip of the ovipositor (Holotype female).
FIGURES 2 – 3. Pachamama speciosa, wings. 2 in Pachamama, an uncommon and distinctive new genus of Trichogrammatidae (Hymenoptera: Chalcidoidea) from tropical America
FIGURES 2 – 3. Pachamama speciosa, wings. 2, Forewing (arrow to preretinacular lobe). 3, hind wing.
FIGURE 1 in Pachamama, an uncommon and distinctive new genus of Trichogrammatidae (Hymenoptera: Chalcidoidea) from tropical America
FIGURE 1. Pachamama speciosa, habitus (Ψ from Ecuador: Napo: Reserva Etnica Waorani).
FIGURE 5 in New records of sabellids and serpulids (Polychaeta: Sabellidae, Serpulidae) from the Tropical Eastern Pacific
FIGURE 5. Distribution of Hydroides glandifera, H. humilis, H. inermis and H. ochotereana
FIGURE 6 in New records of sabellids and serpulids (Polychaeta: Sabellidae, Serpulidae) from the Tropical Eastern Pacific
FIGURE 6. Distribution of Hydroides panamensis, H. sanctaecrucis, H. similis and H. trompi.
FIGURE 4 in New records of sabellids and serpulids (Polychaeta: Sabellidae, Serpulidae) from the Tropical Eastern Pacific
FIGURE 4. Distribution of Hydroides deleoni, H. dirampha, H. elegans and H. gairacensis..
FIGURE 5. Cyt b in New molecular phylogeny of Lucinidae: increased taxon base with focus on tropical Western Atlantic species (Mollusca: Bivalvia)
FIGURE 5. Cyt b tree for Monitilorinae and Lucininae, expanded from Figure 4.
FIGURE 3. Combined gene tree for Lucininae, expanded from Figure 1 in New molecular phylogeny of Lucinidae: increased taxon base with focus on tropical Western Atlantic species (Mollusca: Bivalvia)
FIGURE 3. Combined gene tree for Lucininae, expanded from Figure 1.
FIGURE 2. Combined gene tree for Codakiinae, expanded from Figure 1 in New molecular phylogeny of Lucinidae: increased taxon base with focus on tropical Western Atlantic species (Mollusca: Bivalvia)
FIGURE 2. Combined gene tree for Codakiinae, expanded from Figure 1.
Vanellus chilensis dataset accompanying PLOS ONE paper "Automated Sound Recognition Provides Insights into the Behavioral Ecology of a Tropical Bird"
<p>Southern Lapwing <em>Vanellus chilensis</em> dataset accompanying the PLOS ONE article</p> <p>O. Jahn, T. Ganchev, M.I. Marinez and K.L. Schuchmann: Automated Sound Recognition Provides Insights into the Behavioral Ecology of a Tropical Bird. DOI:10.1371/journal.pone.0169041</p> <p>---<br> BL01:<br> Background Library 01 consists of</p> <p>BL01 >> BL_CHVACH_free_final:<br> 54 hand-cleaned (<em>Vanellus chilensis</em>-free) background files and</p> <p>BL01 >> PSC008_forest:<br> 36 original soundscapes recorded inside forest, which may contain a few target signals from overflying lapwings.</p> <p>---<br> PONE_VACH_AnnualCycle_Statistics:<br> Contains the Excel files<br> - 2013CHVACH_BreedingCycle_Statistics_PONE: statistics on <em>V. chilensis</em> activity patterns, Apr. 2013 to Sep. 2013.<br> - 2013CHVACH_FalseNegatives_PONE: determination of the false negative rate based on an expert-annotated sample of 26 soundcsape recordings<br> - 2013CHVACH_FalsePositives_PONE: determination of the false positive rate based on an expert-annotated random sample of 1250 automated <em>V. chilensis</em> detections.</p> <p>---<br> TL01_BIAVCHCHVACH_20130813v2_HandCleaned:<br> Training library for the development of the <em>V. chilensis</em> recognizer, consisting of 90 hand-filtered recordings of the target species.</p> <p>---<br> VACH_Detector_results >> VACHdetectorOutput_PONE.zip:<br> TXT detector output files, listing timestamps of potential <em>V. chilensis</em> sound events.</p> <p>---<br> VACH_FNrate_20160706:<br> Validation library used to determine the false negative rate. The library consists of 26 expert-annotated sound files. Annotations were made in Adobe Audion v3.0.</p> <p>---<br> VL01_VACH_MonoB<br> and<br> VL01_VACH_MonoB:<br> Validation library used for the fine-tuning of the recognizer settings.</p> <p>---<br> Important notes on the annotation of the VACH_FNrate_20160706 library:</p> <p>1) In general, we used the procedure described in Ganchev et al. 2015 for the annotation of VACH validation libraries (see next section).</p> <p>2) However, the detector-generated timestamps were not changed! For the following reasons, it is not possible to use the VACH_FN_rate library as a validation library for the development of improved recognizer versions:</p> <p>(a) The VACH detector overlooked many of the weaker signals within a VACH call series. Therfore the detector-generated annotations are incomplete.<br> (b) For the same reason some automatically-generated detections may refer to a single VACH call event (double hits).</p> <p>Details on the method used for the annotation of the VACH validation libraries are described in Ganchev et al. 2015, pp.6100f: 2.1.3.3.Vanellus chilensis validation dataset.</p>
Figure 12. - APlacotrochidescylindrica, holotype, Museum of Tropical Queensland G55627, off Queensland BPlacotrochidesfrustum, holotype, USNM 36451, Lesser Antilles; paratype, NMC, Hudson 4B, Lesser Antilles C Placotrochuslaevis, USNM 81994, Great Barrier Reef, Australia D Falcatoflabellumraoulensis, upper image, holotype, Museum of New Zealand, CO 258, Kermadec Ridge; lower images, paratype, USNM 94313, Kermadec Ridge. Scale bars: 1mm (A); 2 mm (B); 10 mm (C), except for basal scar, which is 5 mm; 1 mm (D), except latera view, which is 5 mm.
Figure 12. - APlacotrochidescylindrica, holotype, Museum of Tropical Queensland G55627, off Queensland BPlacotrochidesfrustum, holotype, USNM 36451, Lesser Antilles; paratype, NMC, Hudson 4B, Lesser Antilles C Placotrochuslaevis, USNM 81994, Great Barrier Reef, Australia D Falcatoflabellumraoulensis, upper image, holotype, Museum of New Zealand, CO 258, Kermadec Ridge; lower images, paratype, USNM 94313, Kermadec Ridge. Scale bars: 1mm (A); 2 mm (B); 10 mm (C), except for basal scar, which is 5 mm; 1 mm (D), except latera view, which is 5 mm.
Whale shark tracking data from the eastern tropical Pacific
<p>These two data files contain Argos position data and subsurface time-at-temperature data from whale sharks tagged at Darwin's Arch, Galapagos during 2011 - 2012.</p>
Data and code for: "Large reductions in tropical bird abundance attributable to heat extreme intensification "
<p>Data and code necessary to reproduce results of paper:</p> <p>Large reductions in tropical bird abundance attributable to heat extreme intensification</p> <p>By Maximilan Kotz, Tatsuya Amanon and James Watson.</p> <p>Please contact maximilian.kotz@bsc.es / maxkotz@pik-potsdam.de for questions.</p> <p> </p>
Data sets used in "Is there a tropical response to recent observed Southern Ocean cooling?"
The dataset contains processed data for the GRL publication (to be submitted) "Is there a tropical response to recent observed Southern Ocean cooling?" The dataset includes global maps of linear trends of various fields presented in the figures, as well as pattern correlation coefficients for the three experiment ensembles using CESM1: Large Ensemble, Tropical Pacific Pacemaker Experiment, and Southern Ocean Pacemaker Experiment.
Dataset from paper: "Mind the Gap: Reconciling tropical forest carbon flux estimates from Earth Observation and National Reporting requires transparency"
<p>This repository contains the processed data used in the publication of Heinrich et al., 2023 (Mind the Gap: Reconciling tropical forest carbon flux estimates from Earth Observation and National Reporting requires transparency). Carbon Balance and Management: https://cbmjournal.biomedcentral.com/articles/10.1186/s13021-023-00240-2 </p><p>When using this data, full reference to the raw data publications and the publication Heinrich et al., 2023 must be made.</p><p>The raw datasets used in this study are all available from their original sources.</p><p> </p>
Data from: Both the selection and complementarity effects underpin the effect of structural diversity on aboveground biomass in tropical forests
<p><strong>Aim:</strong> Despite mounting empirical evidence regarding the positive effects of forest structural diversity (STR<sub>DIV</sub>) on forest functioning, the underlying biotic mechanisms and controlling abiotic factors remain poorly understood. This study provides the first assessment of the interactive effects of STR<sub>DIV</sub> and diversity in species and functional traits on aboveground biomass (AGB) in natural forests in West and East Africa.</p> <p><strong>Location: </strong>West and East Africa</p> <p><strong>Time period: </strong>2014-2020</p> <p><strong>Major taxa studied:</strong> Woody plants</p> <p><strong>Methods:</strong> Using data from 276 plots and 7993 trees of 207 species distributed across various types of natural forests and major climatic zones of Africa, linear mixed-effects and structural equation models, we have evaluated how alternative causal relationships between STR<sub>DIV</sub> and taxonomic and functional diversity attributes influence AGB, while accounting for the effects of environmental covariates. We also assessed the consistency of these relationships across floristically and environmentally homogenous forest types.</p> <p><strong>Results:</strong> We found that the positive effects of STRDIV on AGB were underpinned by both the community-weighted mean (CWM) of trait values (selection effects) and species richness (niche complementarity), but the relative importance of these effects varied depending on forest types. Across the forest types, STR<sub>DIV </sub>primarily mediated the effects of CWM of traits and species richness on AGB. We also found that STR<sub>DIV</sub>–AGB relationships were constrained by resource (water and nutrient) availability.</p> <p><strong>Main conclusions:</strong> Our findings provide novel insights into the role of functional traits as key determinants of the effects of STR<sub>DIV</sub> on AGB in tropical forests. We suggest that forest management and climate change mitigation strategies aimed at conserving biodiversity and fostering biomass storage through increased STR<sub>DIV </sub>should focus on maintaining high levels of functionally dominant species while also increasing tree species diversity.</p>
Characterization of leaf transcriptome in a tropical tree species, Shorea curtisii, over a flowering season
<p><span>General flowering (GF) is a synchronous flowering event in the Southeast Asian tropical rainforests that occurs at irregular intervals of multiple years. The unpredictable intervals of GF raise conservation concerns for these under-researched forests with rich economically and ecologically important species. In this study, the leaf transcriptome of a GF species, <em>Shorea</em> <em>curtisii</em> obtained from three time points – before and after floral initiation, and post flowering stage – was sequenced. We assembled 243,759,478 sequencing reads into 39,943 non-redundant unigenes including 677 putative homologs of <em>Arabidopsis</em> <em>thaliana</em> flowering-related genes. Differential expression analysis conducted on pairwise comparisons of the time points identified 930 differentially expressed unigenes, which includes 17 flowering-related homologs. The differential expression of unigenes with significant enrichments of functions related to drought corroborated the involvement of drought as an environmental cue for GF. The outcomes of this study offer an insight into the conservation of floral regulatory genes and pathways in Shorea and could be used as a model to better understand the floral initiation cues and regulation of GF trees.</span></p>
- Wings with dark patterns, yellowish to black (a, b); tropical Africa ………………………………4 in A review of the Afrotropical Rhyssinae (Hymenoptera: Ichneumonidae) with the descriptions of five new species
- Wings with dark patterns, yellowish to black (a, b); tropical Africa ………………………………4
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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.