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Table 1 in Investigation on possible transmission of monkeys' Plasmodium to human in a populations living in the equatorial rainforest of the Democratic republic of Congo
<p><b>Table 1</b> Primers and probes sequences for the two RT-PCR.</p><table><tbody><tr><th>RT-PCR</th><th>Forward primer</th><th>Reverse primer</th><th>Probes</th></tr></tbody><tbody><tr><th><i>plasmodiums</i> <i>sp</i></th><td>5Į- GTTAAGGGAGTGAAGACGA TCAGA-3' (Plasmo1)</td><td>5Į- TTATGAGAAATCAAAGTCTTTGGGTT-3' (Plasmo2)</td><td>5Į- FAM-ACCGTCGTAA TCTTAACCAT AAACTATGCC GACTAG-TAMRA- 3' (plasprobe)</td></tr><tr><th><i>Pfal</i></th><td>5Į- CTAGGTGTTGGATG-3Į</td><td></td><td>5Į- FAM-AGCAATCTAAAAGTCACCTCGAAAGATGACT-DQ-3' (Falprobe)</td></tr><tr><th><i>Pova</i></th><td>5Į- CGACTAGGTTTTGGATG-3Į</td><td></td><td>5Į- VIC-CGAAAGGAATTTTCTTATT-DQ-3’ (Ovaprobe)</td></tr><tr><th><i>Pviv</i></th><td>5Į- GACTAGGCTTTGGATG-3Į</td><td></td><td>5Į- VIC-AGCAATCTAAGAATAAACTCCGAAGAGAAAATTCT-DQ-3' (Vivprobe)</td></tr><tr><th><i>Pmal</i></th><td>5Į- GACTAGGTGTTGGATG-3Į</td><td></td><td>5Į- FAM-CTATCTAAAAGAAACACTCAT-DQ-3’ (Malprobe)</td></tr></tbody></table>
Vertical profiles of leaf photosynthesis and leaf traits, and soil nutrients in two tropical rainforests in French Guiana before and after a three-year nitrogen and phosphorus addition experiment
<p>We provide a comprehensive dataset of vertical profiles of photosynthetic capacity and important leaf traits, including leaf N and P concentrations, from two three-year, large-scale fertilisation experiments conducted in two tropical rainforests in French Guiana. These data present a unique source of information to further improve model representations of the roles of N, P, and other leaf nutrients, in photosynthesis in tropical forests. To further facilitate the use of our data in syntheses and model studies, we provide an elaborate list of ancillary data, including important soil properties and nutrients, along with the leaf data. As environmental drivers are key to improve our understanding of carbon (C)-nutrient cycle interactions, this comprehensive dataset will aid to further enhance our understanding of how nutrient availability interacts with C uptake in tropical forests.</p>
Recent and local hyperdiversification of Central American rainforests
<p>Phylogenetic trees in nexus format to be visualised in e.g. FigTree</p> <p>Scripts and input data to reproduce the diversification analyses (LTT plots and GeoSSE) presented in this study</p>
The individual-based network structure of palm-seed dispersers is explained by a rainforest gradient
<p>How species interactions change in space and time is a major question in ecology. In tropical forests, plant individuals share mutualistic partners (pollinators or seed dispersers), yet we have little understanding of the factors affecting these individual interaction patterns. We used a seed dispersal individual-based network describing interactions between individuals of a palm species with bird species to investigate how intrinsic and extrinsic characteristics of individual plants influence the network structure. In our work we evaluated if average canopy height, number of fruits, distance to forest gap, and habitat type influence the role of palm individuals in the network. From 102 palms, 62 individuals had their seeds dispersed at least once: 17 individual palms in the restinga, 15 in the lowland and 30 in the pre-montane habitat. Twelve bird species were recorded dispersing <em>Euterpe edulis</em> seeds in our study area.</p>
Data from: Watershed classification predicts streamflow regime and organic carbon dynamics in the Northeast Pacific Coastal Temperate Rainforest
<p class="Abstract">Watershed classification has long been a key tool in the hydrological sciences, but few studies have been extended to biogeochemistry. We developed a combined hydro-biogeochemical classification for watersheds draining to the coastal margin of the Northeast Pacific coastal temperate rainforest (1,443,062<i> </i>km<sup>2</sup>), including 2,695 small coastal rivers (SCR) and 10 large continental watersheds. We used cluster analysis to group SCR watersheds into 12 types, based on watershed properties. The most important variables for distinguishing SCR watershed types were evapotranspiration, slope, snowfall, and total precipitation. We used both streamflow and dissolved organic carbon (DOC) measurements from rivers (<i>n</i> = 104 and 90 watersheds respectively) to validate the classification. Watershed types corresponded with broad differences in streamflow regime, mean annual runoff, DOC seasonality, and mean DOC concentration. These links between watershed type and river conditions enabled the first region-wide empirical characterization of river hydro-biogeochemistry at the land-sea margin, spanning extensive ungauged and unsampled areas. We found very high annual runoff (mean > 3000 mm, <i>n</i> = 10) in three watershed types totaling 59,024 km<sup>2</sup> and ranging from heavily glacierized mountain watersheds with high flow in summer to a rain-fed mountain watershed type with high flow in fall-winter. DOC hotspots (mean > 4 mg L<sup>-1</sup>, <i>n</i> = 14) were found in three other watershed types (48,557 km<sup>2</sup>) with perhumid rainforest climates and less-mountainous topography. We described four patterns of DOC seasonality linked to watershed hydrology, with fall-flushing being widespread. Hydro-biogeochemical watershed classification may be useful for other complex regions with sparse observation networks.</p>
Haplocauda, a new genus of fireflies endemic to the Amazon Rainforest (Coleoptera: Lampyridae)
<p>Most firefly genera have poorly defined taxonomic boundaries, especially in the Neotropics, where they are more diverse and more difficult to identify. Recent advances that shed light on the diversity of fireflies in South America have focused mainly on Atlantic Rainforest taxa, whereas lampyrids in other biomes remained largely unstudied. We found three new firefly species endemic to the Amazon basin that share unique traits of the male abdomen where sternum VIII and the pygidium are modified and likely work as a copulation clamp. Here we test and confirm the hypothesis that these three species form a monophyletic lineage and propose Haplocauda gen. nov. to accommodate the three new species. Both Maximum Parsimony and probabilistic (Bayesian and Maximum Likelihood) phylogenetic analyses confirmed Haplocauda gen. nov. monophyly, and consistently recovered it as the sister group to Scissicauda, fireflies endemic to the Atlantic Rainforest that also feature a copulation clamp on abdominal segment VIII, although with a different configuration. We provide illustrations, diagnostic descriptions, and keys to species based on males and females. The three new species were sampled from different regions, and are likely allopatric, a common pattern among Amazonian taxa.</p>
Environmental variation and biotic interactions limit adaptation at ecological margins: lessons from rainforest Drosophila and European butterflies
<p>Models of local adaptation to spatially varying selection predict that maximum rates of evolution are determined by the interaction between increased adaptive potential owing to increased genetic variation, and the cost genetic variation brings by reducing population fitness. We discuss existing and new results from our laboratory assays and field transplants of rainforest Drosophila and UK butterflies along environmental gradients, which try to test these predictions in natural populations. Our data suggest that: (i) local adaptation along ecological gradients is not consistently observed in time and space, especially where biotic and abiotic interactions affect both gradient steepness and genetic variation in fitness; (ii) genetic variation in fitness observed in the laboratory is only sometimes visible to selection in the field, suggesting that demographic costs can remain high without increasing adaptive potential; and (iii) antagonistic interactions between species reduce local productivity, especially at ecological margins. Such antagonistic interactions steepen gradients and may increase the cost of adaptation by increasing its dimensionality. However, where biotic interactions do evolve, rapid range expansion can follow. Future research should test how the environmental sensitivity of genotypes determines their ecological exposure, and its effects on genetic variation in fitness, to predict the probability of evolutionary rescue at ecological margins. This article is part of the theme issue 'Species' ranges in the face of changing environments (Part II)'.</p>
Data from: Weak edge effects on trees in Bornean rainforest remnants bordering oil palm
<p>Many tropical forests are dominated by edge habitat, with consequences for forest structure, carbon stocks and biodiversity. However, edge effects are highly variable and context-dependent, and are poorly quantified in oil palm landscapes. We studied edge effects in 10 lowland rainforest remnants bordering mature oil palm plantations on Borneo, by surveying 0.2 ha plots along transects running perpendicular to the forest edge (ten 1.6 km transects, 5-6 plots per transect; 57 plots in total). We examined how edge proximity affected plot-level forest structure (canopy cover, number and size of stems ⩾10 cm diameter), aboveground carbon stocks, microclimate (air temperature and light intensity), and tree community composition and richness. The largest trees were significantly smaller (up to 21% reduced diameter) in plots near edges, and plot-level carbon was up to 30% lower (model-fitted average = 64.7 Mg ha−1 at 50m from the edge, versus 92.3 Mg ha−1 at 1600 m), with the strongest effects within 300m of edges. However, these significant effects of edge proximity were relatively small in the context of existing variation, with distance-from-edge explaining <13% of the total variability in maximum tree size or carbon. Additionally, there were generally no effects of edge proximity on any other component of forest structure, composition or diversity, and only a weak effect on microclimate. We conclude that limited edge effects in this system may reflect low structural contrast between forest and mature oil palm, and limited invasion of pioneer trees from plantations, which diminished edge influence in highly heterogeneous forest remnants.</p>
Laying low: Rugged lowland rainforest preferred by feral cats in the Australian wet tropics
<p>Invasive mesopredators are responsible for the decline of many species of native mammals worldwide. Feral cats have been causally linked to multiple extinctions of Australian mammals since European colonisation. While feral cats are found throughout Australia, most research has been undertaken in arid habitats, thus there is a limited understanding of feral cat distribution, abundance, and ecology in Australian tropical rainforests. We carried out camera-trapping surveys at 108 locations across seven study sites, spanning 200 km in the Australian Wet Tropics. Single-species occupancy analysis was implemented to investigate how environmental factors influence feral cat distribution. Feral cats were detected at a rate of 5.09 photographs/100 days, 11 times higher than previously recorded in the Australian Wet Tropics. The main environmental factors influencing feral cat occupancy were a positive association with terrain ruggedness, a negative association with elevation, and a higher affinity for rainforest than eucalypt forest. These findings were consistent with other studies on feral cat ecology but differed from similar surveys in Australia. Increasingly harsh and consistently wet weather conditions at higher elevations, and improved shelter in topographically complex habitats may drive cat preference for lowland rainforest. Feral cats were positively associated with roads, supporting the theory that roads facilitate access and colonisation of feral cats within more remote parts of the rainforest. Higher elevation rainforests with no roads could act as refugia for native prey species within the critical weight range. Regular monitoring of existing roads should be implemented to monitor feral cats, and new linear infrastructure should be limited to prevent encroachment into these areas. This is pertinent as climate change modelling suggests that habitats at higher elevations will become similar to lower elevations, potentially making the environment more suitable for feral cat populations.</p>
Data from: Effects of climate change on plant resource allocation and herbivore interactions in a Neotropical rainforest shrub
<p>Data from "Effects of climate change on plant resource allocation and herbivore interactions in a Neotropical rainforest shrub" published in <em>Ecology and Evolution. </em>doi.org/10.1002/ece3.9198</p>
Figure 5 in A three-year Herpetofauna survey from one of the largest remnants of the Atlantic Rainforest Biome (Reserva Natural Vale)
Figure 5. Some of the reptile species we recorded in the Vale Natural Reserve, municipality of Linhares, Espírito Santo, southeastern Brazil: (a) Acanthochelys radiolata, (b) Chelonoidis carbonaria, (c) Chelonoidis denticulatus, (d) Rhinoclemmys punctularia, (e) Brasiliscincus agilis, (f) Psychosaura macrorhyncha, (g) Norops ortonii, (h) Polychrus marmoratus, (i) Strobilurus torquatus, (j) Tropidurus torquatus, (k) Ameivula nativo, (l) Salvator merianae.
Figure 4 in A three-year Herpetofauna survey from one of the largest remnants of the Atlantic Rainforest Biome (Reserva Natural Vale)
Figure 4. Accumulation (black line) and rarefaction curves (gray line) of the amphibian species recorded during the 23 sampling campaigns from 2015 to 2018 in the Vale Natural Reserve, municipality of Linhares, Espírito Santo, southeastern Brazil.
Figure 1 in A three-year Herpetofauna survey from one of the largest remnants of the Atlantic Rainforest Biome (Reserva Natural Vale)
Figure 1. Location of the Vale Natural Reserve, municipality of Linhares, Espírito Santo, southeastern Brazil, showing the location of the plots and the vegetation types present in the reserve: (a) Coastal plain forest, (b) Permanent swamp, (c) Sandy soil forest, (d) Natural grassland.
Figure 7 in A three-year Herpetofauna survey from one of the largest remnants of the Atlantic Rainforest Biome (Reserva Natural Vale)
Figure 7. Accumulation (black line) and rarefaction curves (gray line) of the reptile species recorded during the 23 sampling campaigns from 2015 to 2018 in the Vale Natural Reserve, municipality of Linhares, Espírito Santo, southeastern Brazil.
Figure 3 in A three-year Herpetofauna survey from one of the largest remnants of the Atlantic Rainforest Biome (Reserva Natural Vale)
Figure 3. Some of the anuran species we recorded in the Vale Natural Reserve, municipality of Linhares, Espírito Santo, southeastern Brazil: (a) Trachycephalus mesophaeus, (b) Leptodactylus fuscus, (c) Leptodactylus latrans, (d) Leptodactylus mystacinus, (e) Physalaemus aguirrei, (f) Physalaemus gr. signifer, (g) Chiasmocleis capixaba, (h) Chiasmocleis schubarti, (i) Dasypops schirchi, (j) Stereocyclops incrassatus, (k) Proceratophrys laticeps, (l) Phyllomedusa burmeisteri.
Figure 6 in A three-year Herpetofauna survey from one of the largest remnants of the Atlantic Rainforest Biome (Reserva Natural Vale)
Figure 6. Some of the reptile species we recorded in theVale Natural Reserve,municipality of Linhares, Espírito Santo, southeastern Brazil:(a) Amerotyphlops brongersmianus, (b) Corallus hortulanus, (c) Chironius foveatus, (d) Chironius fuscus, (e) Leptophis ahaetulla, (f) Oxybelis aeneus, (g) Spilotes sulphureus, (h) Erythrolamprus miliaris, (i) Siphlophis compressus, (j) Thamnodynastes hypoconia, (k) Micrurus corallinus preying on A. brongersmianus, (l) Bothrops jararaca.
Figure 2 in A three-year Herpetofauna survey from one of the largest remnants of the Atlantic Rainforest Biome (Reserva Natural Vale)
Figure 2. Some of the anuran species we recorded in the Vale Natural Reserve, municipality of Linhares, Espírito Santo, southeastern Brazil: (a) Rhinella crucifer, (b) Rhinella diptycha, (c) Haddadus binotatus, (d) Aparasphenodon brunoi, (e) Boana semilineata, (f) Dendropsophus elegans, (g) Dendropsophus seniculus, (h) Ololygon agilis, (i) Phyllodytes luteolus, (j) Scinax eurydice, (k) Scinax sp., (l) Sphaenorhynchus planicola.
Figure 5 in The rediscovery of Pimelodella longipinnis (Borodin, 1927), an enigmatic Atlantic Rainforest catfish species from Southeastern Brazil (Siluriformes: Heptapteridae)
Figure 5. Distribution of Pimelodella longipinnis in Southeastern coastal Mata Atlântica streams of São Paulo State. In green is demarked part of the Parque Estadual da Serra do Mar extension.The collection sites are indicated by a black dot.The dot may correspond to more than one collection site. The center of Santos municipality is indicated by a black square.
Figure 4 in The rediscovery of Pimelodella longipinnis (Borodin, 1927), an enigmatic Atlantic Rainforest catfish species from Southeastern Brazil (Siluriformes: Heptapteridae)
Figure 4. Live specimens of P. longipinnis, showing the coloration in life (preserved in MZUSP 116324).
Figure 3 in The rediscovery of Pimelodella longipinnis (Borodin, 1927), an enigmatic Atlantic Rainforest catfish species from Southeastern Brazil (Siluriformes: Heptapteridae)
Figure 3. Left lateral view of an ethanol-preserved, recently collected specimen of P. longipinnis, MZUSP 116324, 57.6 mm SL.
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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.