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FIGURE 7 in New records of sabellids and serpulids (Polychaeta: Sabellidae, Serpulidae) from the Tropical Eastern Pacific
FIGURE 7. Distribution of and Pomatostegus kroyeri, Protula balboensis, Pseudovermilia occidentalis and Pyrgopolon ctenactis.
FIGURE 9 in New records of sabellids and serpulids (Polychaeta: Sabellidae, Serpulidae) from the Tropical Eastern Pacific
FIGURE 9. Gross scheme of the likely routes followed by introduced sabellids and serpulids: 1) Branchiomma bairdi, Crucigera websteri, Hydroides elegans, H. gairacensis, H. salazarvallejoi, H. sanctaecrucis, Pseudovermilia multispinosa and Pyrgopolon ctenactis; 2) Protula balboensis and Spirobranchus minutus; 3) Parasabella pallida, H. dirampha and H. elegans; 4) Ficopomatus miamiensis; 5) H. crucigera; 6) Pseudobranchiomma punctata; 7) F. miamiensis; 8) B. bairdi, H. elegans (?), H. gairacensis and H. sanctaecrucis; 9) Ficopomatus uschakovi.
FIGURE 3 in New records of sabellids and serpulids (Polychaeta: Sabellidae, Serpulidae) from the Tropical Eastern Pacific
FIGURE 3. Distribution of Ficopomatus uschakovi, Crucigera websteri, Hydroides cf. amri, H. brachyacantha and H. crucigera.
FIGURE 2 in New records of sabellids and serpulids (Polychaeta: Sabellidae, Serpulidae) from the Tropical Eastern Pacific
FIGURE 2. Distribution of the sabellids Branchiomma bairdi, Megalomma carunculata, Parasabella pallida and Pseudobranchiomma punctata in the Tropical Eastern Pacific, Southern California and Hawaii.
FIGURE 10 in New records of sabellids and serpulids (Polychaeta: Sabellidae, Serpulidae) from the Tropical Eastern Pacific
FIGURE 10. Sabellids and serpulids in the Mexican Pacific. A. Branchiomma bairdi, anterior part; B – C. Megalomma carunculata, anterior part and caruncle; D. Parasabella pallida, anterior part; E – F. Pseudobranchiomma punctata, body and detail of abdominal section; G. Ficopomatus uschakovi, anterior part; H – I. Crucigera websteri, opercula, lateral and aboral side (colors in life and preserved).
FIGURE 1 in New records of sabellids and serpulids (Polychaeta: Sabellidae, Serpulidae) from the Tropical Eastern Pacific
FIGURE 1. Study area. The Tropical Eastern Pacific, Southern California and Hawaii, with main geographical names mentioned in text.
FIGURE 4 in New molecular phylogeny of Lucinidae: increased taxon base with focus on tropical Western Atlantic species (Mollusca: Bivalvia)
FIGURE 4. Single gene tree for Lucinidae based on cyt b sequences, using Bayesian inference as implemented by MrBayes. Support values are posterior probabilities (PP); branches with PP <50 % were collapsed. Western Atlantic species in red. See Table 1 for sample details. Monitilorinae and Lucininae expanded in Fig. 5.
FIGURE 1 in New molecular phylogeny of Lucinidae: increased taxon base with focus on tropical Western Atlantic species (Mollusca: Bivalvia)
FIGURE 1. Combined gene tree for Lucinidae based on sequences from three genes (18 S rRNA, 28 S rRNA and cyt b), using Bayesian inference as implemented by MrBayes. Support values are posterior probabilities (PP). Codakiinae and Lucininae expanded in Figs 2 and 3. See Table 1 for sample details. Western Atlantic species in red. Scale is number of substitutions per site. Locality codes used on trees. ABD—Abu Dhabi; ANG—Angola; BD—Bermuda; BOC—Bocas, Panama; BR—Broome, Australia; CAL—California; CB – Chesterfield Bank; COSRIC West Costa Rica; CR—Croatia; DMP—Dampier, Australia; DEV—Devon, UK; FK—Florida Keys; FR—France; GD—Guadeloupe; HK—Hong Kong; JPN – Japan; KK—Kungkraben Bay, Thailand; LH—Lord Howe Island; LI – Lizard Island, Australia; MAD—Madagascar; MADANG—Madang, Papua New Guinea; MAUR – Mauritius; MB—Moreton Bay, Australia; MEX—West Mexico; NC—New Caledonia; NIG—Nigeria; OK— Okinawa; PAN – Panglao, Philippines; PNG – Papua New Guinea; ROD—Rodrigues; RUK—Ryukyus, Japan; SAF—Safaga, Red Sea; SGP—Singapore; SOL—Solomon Sea; SYD—Sydney, Australia; TCB—Tin Can Bay, Australia; TIM—East Timor; TJ—Tjärnö, Sweden; TUN—Djerba, Tunisia; VAN—Vanuatu; VEN—Venezuela; UK—England.
Data and analysis scripts for Zizka et al., Finding needles in the haystack: Where to look for rare species in the American tropics
<p>The analysis scripts and data from: Zizka A, ter Steege H, Pessoa MDC, Antonelli A (2017) Finding needles in the haystack: Where to look for rare species in the American tropics. Ecography.</p>
Air pollution in a tropical city: the relationship between wind direction and lichen bio-indicators in San José, Costa Rica
<p>Lichens are good bio-indicators of air pollution, but in most tropical countries there are few studies on the subject; however, in the city of San José, Costa Rica, the relationship between air pollution and lichens has been studied for decades. In this article we evaluate the hypothesis that air pollution is lower where the wind enters the urban area (Northeast) and higher where it exits San José (Southwest). We identified the urban parks with a minimum area of approximately 5 000m² and randomly selected a sample of 40 parks located along the passage of wind through the city. To measure lichen coverage, we applied a previously validated 10 x 20cm template with 50 random points to five trees per park (1.5m above ground, to the side with most lichens). Our results (years 2008 and 2009) fully agree with the generally accepted view that lichens reflect air pollution carried by circulating air masses. The practical implication is that the air enters the city relatively clean by the semi-rural and economically middle class area of Coronado, and leaves through the developed neighborhoods of Escazú and Santa Ana with a significant amount of pollutants. In the dry season, the live lichen coverage of this tropical city was lower than in the May to December rainy season, a pattern that contrasts with temperate habitats; but regardless of the season, pollution follows the pattern of wind movement through the city</p>
Air pollution in a tropical city: the relationship between wind direction and lichen bioindicators in San Jose, Costa Rica
<p>Lichens are good bio-indicators of air pollution, but in most tropical countries there are few studies on the subject; however, in the city of San José, Costa Rica, the relationship between air pollution and lichens has been studied for decades. In this article we evaluate the hypothesis that air pollution is lower where the wind enters the urban area (Northeast) and higher where it exits San José (Southwest). We identified the urban parks with a minimum area of approximately 5 000m² and randomly selected a sample of 40 parks located along the passage of wind through the city. To measure lichen coverage, we applied a previously validated 10 x 20cm template with 50 random points to five trees per park (1.5m above ground, to the side with most lichens). Our results (years 2008 and 2009) fully agree with the generally accepted view that lichens reflect air pollution carried by circulating air masses. The practical implication is that the air enters the city relatively clean by the semi-rural and economically middle class area of Coronado, and leaves through the developed neighborhoods of Escazú and Santa Ana with a significant amount of pollutants. In the dry season, the live lichen coverage of this tropical city was lower than in the May to December rainy season, a pattern that contrasts with temperate habitats; but regardless of the season, pollution follows the pattern of wind movement through the city</p>
Air pollution in a tropical city: the relationship between wind direction and lichen bio-indicators in San José, Costa Rica
<p>Lichens are good bio-indicators of air pollution, but in most tropical countries there are few studies on the subject; however, in the city of San José, Costa Rica, the relationship between air pollution and lichens has been studied for decades. In this article we evaluate the hypothesis that air pollution is lower where the wind enters the urban area (Northeast) and higher where it exits San José (Southwest). We identified the urban parks with a minimum area of approximately 5 000m² and randomly selected a sample of 40 parks located along the passage of wind through the city. To measure lichen coverage, we applied a previously validated 10 x 20cm template with 50 random points to five trees per park (1.5m above ground, to the side with most lichens). Our results (years 2008 and 2009) fully agree with the generally accepted view that lichens reflect air pollution carried by circulating air masses. The practical implication is that the air enters the city relatively clean by the semi-rural and economically middle class area of Coronado, and leaves through the developed neighborhoods of Escazú and Santa Ana with a significant amount of pollutants. In the dry season, the live lichen coverage of this tropical city was lower than in the May to December rainy season, a pattern that contrasts with temperate habitats; but regardless of the season, pollution follows the pattern of wind movement through the city</p>
Supporting data for "Mammalian species abundance across a gradient of tropical land-use intensity: A hierarchical multi-species modelling approach"
<p>Combined camera trap and live trap dataset underlying the analyses in a Biological Conservation paper (https://doi.org/10.1016/j.biocon.2017.05.007), provided in .csv format. This spatially- and temporally-replicated dataset is suitable for occupancy modelling.</p> <p>The first 3 columns in the dataset are:</p> <p>1) Trap location name – old-growth forest, logged forest and oil palm plantation locations have the prefixes "Old", "Log" and "Palm", respectively</p> <p>2) Sampling occasion number – camera trap and live trap occasions have the prefixes “Lvtrap” and “Ctrap”, respectively, and are defined in the paper</p> <p>3) Calendar year in which sampling took place (most locations were sampled in > 1 calendar years)</p> <p>Following these 3 columns, there are 66 columns for each of the mammal species detected during the study (species common names are used). The values for each species represent the number of independent captures, as defined in the paper. This can be reduced to detection/non-detection data (zeroes and ones), if needed, for occupancy modelling.</p>
Turbulence in Simulated Tropical Instability Wave
This dataset consists of fields output from a 1/20° regional simulation of the Tropical Pacific ocean. The data are hourly averaged and cover the time period of a single Tropical Instability Wave. Data are extracted at a central longitude of 110°W and one grid point to the east and west of that longitude. The fields describe the modulation of ocean mixing by the Tropical Instability Wave.
Tropical range extending herbivorous fishes gain foraging benefits by shoaling with native temperate species
<p>Data1.csv contains the data to analyze the abundance of fish herbivore individuals as a function of the species and the type of shoal. </p> <p>Data2.xlsx contains the data to analyze the foraging activity of the herbivorous fish found in our study. We explored the relationship between bite rates per fish min-1 and the species, shoal type and shoal size. </p> <p>Data3.xlslx contains the data to analyze the shoaling configurations based on species origin. </p> <p>Minguito-Frutos_etal.R contains the R reproducible code to run all the analyses carried out in this study. </p> <p>Species_coocurrence_based_associations.R contains the reproducible R code to run the analyses to explore the strength of mixed-species associations between herbivorous fish. </p> <p>-------------------------------------------------------------------------------------------------------------------------------------------</p> <p>Data1.csv, Data2.xlsx, Data3.xlslx, and Minguito-Frutos_etal.R contains the data and code used before submitting this work. </p> <p>-------------------------------------------------------------------------------------------------------------------------------------------<br><br>Minguito_Frutos_etal2025_SR_Rscript, Data_Rev_SR, and Data2_Rev_SR contain the data and code derived from the last submission to Scientific Reports. In this latest version, we modified our analyses of fish foraging activity that now evaluate: (i) the frequency and size of mixed-species shoals based on the origin of the species examined (using data in Data2_Rev_SR), (ii) the strength of pair-wise associations between native and range-expanding species (using Species_coocurrence_based_associations.R), and (iii) how the foraging activity of native and range-extending fishes was shaped by the composition and size of the shoals (using data in Data_Rev_SR). </p>
Dataset on light measuments in the understory of a Tropical forest restoration submitted to four thinning intensities through chemical management
<p>The lack of information on the management of light in tropical forests causes a technical constraint for timber production in restoration sites, especially given the light restrictions for timber production. This issue could be amended with the development of methods to easily manage and estimate light availability, targeting practices that balance restoration success and productivity. We conducted the study that gathered this data in an area within the Atlantic Forest, Brazil, where we tested the efficiency of chemical thinning fast-growing species to increase light availability in the understory of a five-year-old restoration planting. Our goal was to increase the growth rates of desirable timber species in the understory of the restoration site. <br>Moreover, we tested the viability of using hemispherical photography taken with a smartphone to assess light incidence and assist restoration management practices. We calculated the percentage of photosynthetically active radiation (PAR) using a ceptometer in four different thinning intensities and compared them to the smartphone measures using correlation analysis and generalized mixed models. Chemical thinning increased light incidence in the understory Light management through PAR and canopy opening were highly correlated overall, especially after three months of management and above 60% of the basal area thinned. Data demonstrates the potential of chemical thinning as a management practice to enhance light availability in the understory of tropical forest restoration sites and highlights the value of using smartphones and fisheye clips for the indirect assessment of light conditions. </p>
Processed ERA5, IMERG and TRMM PR/GPM DPR precipitation data for Nicolas & Boos - "Understanding the spatiotemporal variability of tropical orographic rainfall using convective plume buoyancy."
<p>The dataset contains processed data from large datasets that are freely available online. <br>All data cover the period 01/2001 - 12/2020. The file names describe the months & region that each file contains. Variable codes for ERA5 data (all files starting in e5.) are:</p><p> - 228_246_100u : 100m u-wind<br> - 228_247_100v : 100m v-wind<br> - qL : 900-600hPa averaged specific humidity<br> - thetaeb : surface - 900hPa averaged equivalent potential temperature<br> - thetaeL : 900-600hPa averaged equivalent potential temperature<br> - thetaeLstar : 900-600hPa averaged saturation equivalent potential temperature<br> - tL : 900-600hPa averaged temperature<br> - uBL : surface - 900hPa averaged u wind<br> - vBL : surface - 900hPa averaged v wind<br> - 128_034_sstk : sea surface temperature<br> - 162_071_viwve : eastward component of vertically integrated water vapor transport<br> - 162_072_viwvn : northward component of vertically integrated water vapor transport</p><p> </p>
Growth traits of a tropical timber species at Southeast Asia, Shorea macrophylla, and scripts for genome wide association study and genomic prediction
<p><em><span>Shorea macrophylla</span></em><span> is a commercially important tropical tree species grown for timber and oil. It is amenable to plantation forestry due to its fast initial growth. Genomic selection (GS) has been used in tree breeding studies to shorten long breeding cycles but has not previously been applied to <em>S. macrophylla</em>. To build genomic prediction models for GS, leaves and growth trait data were collected from a half-sib progeny population of <em>S. macrophylla</em> in Sari Bumi Kusuma forest concession, central Kalimantan, Indonesia. 18037 SNP markers were identified in two ddRAD-seq libraries. Genomic prediction models based on these SNPs were then generated for breast height and total height in the 7th year from planting (D7 and H7). These traits were chosen because of their relatively high narrow-sense genomic heritability and because seven years was considered long enough to assess initial growth. Genomic prediction models were built using 12 methods with the full set of identified SNPs and subsets of 48, 96, and 192 SNPs selected based on the results of a genome-wide association study (GWAS). The GBLUP and RKHS methods gave the highest predictive ability (PA) for D7 and H7 and showed that D7 has an additive genetic architecture while H7 has an epistatic genetic architecture. LightGBM and CNN1D also achieved high PA for D7 with 48 and 96 selected SNPs, and for H7 with 96 and 192 selected SNPs, showing that gradient boosting decision trees and deep learning can be useful in genomic prediction. For almost all methods and both traits, PA was higher when SNPs were selected based on their GWAS P-values than when using the full set of SNPs. These results suggest that GS with GWAS-based SNP selection could be used in <em>S. macrophylla </em>breeding to improve initial growth and reduce genotyping costs for next generation seedlings.</span></p>
- Tergite 2 smooth to superficially punctate laterally (a), if ambiguous (some E. tombeaodiba) then tergite 1 stouter, less than 1.5x longer than apically wide; general coloration bright yellow (b); tropical Africa ………………………………………………………………………………………10 in A review of the Afrotropical Rhyssinae (Hymenoptera: Ichneumonidae) with the descriptions of five new species
- Tergite 2 smooth to superficially punctate laterally (a), if ambiguous (some E. tombeaodiba) then tergite 1 stouter, less than 1.5x longer than apically wide; general coloration bright yellow (b); tropical Africa ………………………………………………………………………………………10
Low-frequency somatic mutations are heritable in tropical trees Dicorynia guianensis and Sextonia rubra
<p>Somatic mutations potentially play a role in plant evolution, but common expectations pertaining to plant somatic mutation remain insufficiently tested. Unlike in most animals, the plant germline is assumed to be set aside late in development, leading to the expectation that plants accumulate somatic mutations along growth. Therefore, several predictions were made on the fate of somatic mutations: mutations have generally low frequency in plant tissues; mutations at high frequency have a higher chance of intergenerational transmission; branching topology of the tree dictates mutation distribution; and, exposure to UV radiation increases mutagenesis. To provide new insights into mutation accumulation and transmission in plants, we produced two high-quality reference genomes and a unique dataset of 60 high-coverage whole-genome sequences of two tropical tree species, <i>Dicorynia guianensis</i> (Fabaceae) and <i>Sextonia rubra </i>(Lauraceae). We identified 15,066 <i>de novo</i> somatic mutations in <i>D. guianensis</i> and 3,208 in <i>S. rubra</i>, surprisingly almost all found at low frequency. We demonstrate that: 1) low-frequency mutations can be transmitted to the next generation; 2) mutation phylogenies deviate from the branching topology of the tree; and 3) mutation rates and mutation spectra are not demonstrably affected by differences in UV exposure. Altogether, our results suggest far more complex links between plant growth, ageing, UV exposure, and mutation rates than commonly thought.</p>
ScienceDex guides
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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.