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FIGURE 3 in Relationship between fish assemblage structure and predictors related to estuarine productivity in shallow habitats of a Neotropical estuary
FIGURE 3 | Monthly variation in the mean historical rainfall data (monthly average between 1975 and 2015) and mean water temperature sampled from May 2000 to April 2001 at eight sites along the estuarine gradient of shallow areas of the northsouth axis of the PEC. For temperature, the values were averaged by month and bars represent standard deviation. Months were ordered according to the sequence of the sampling surveys.
FIGURE 5 in Relationship between fish assemblage structure and predictors related to estuarine productivity in shallow habitats of a Neotropical estuary
FIGURE 5 | Richness (S) relationship with the environmental variables that formed the most parsimonious GLM. Line represents the modeled values, and a gray area corresponds to the standard deviation. Temp = temperature; Transp = transparency; Sal = salinity; Time = succession of days from beginning to end of the sampling surveys (see Material and Methods section for details).
Data from: Active restoration accelerates recovery of tropical forest bird assemblages over two decades
<p>Choosing effective methods to restore habitat for the diverse faunal assemblages of tropical forests is hampered by lack of long-term data comparing multiple restoration treatments. We conducted area counts of bird assemblages over 12 years (~5-17 years since restoration) in a blocked experiment with two active planted treatments (tree plantations and applied nucleation) and a passive restoration treatment (natural regeneration) replicated at 11 sites in Costa Rica. We also surveyed six pastures and five remnant forest sites to assess recovery of avian species richness, composition, forest specialists, and range-restricted species in restoration plots relative to degraded and reference systems. Restoration treatments showed increased resemblance of avian assemblages to remnant forest over time. Applied nucleation proved equally effective as plantation, despite a reduced planted area, whereas natural regeneration recovered more slowly. Assemblage-level trends in avian species richness and compositional similarity to reference forest are underpinned by reductions in use by pasture birds and by gradual increases in richness of forest-affiliated species. Because forest-affiliated species tend to have narrower distributions than the open-country species they replace, forest restoration can reduce biotic homogenization at the local scale. Restoration practitioners should consider applied nucleation as an alternative to standard plantations if seeking rapid recovery of bird assemblages. However, the ecological return on investment from natural regeneration increases over a couple of decades. Managers should monitor trends in forest-affiliated and range-restricted species to track the recovery of the full avian assemblages, since coarse metrics like species richness and overall compositional similarity may plateau relatively quickly.</p>
Mesophotic coral ecosystems of French Polynesia are hotspots of alpha and beta generic diversity for scleractinian assemblages
<p>Revealing how diversity varies across the depth gradient is key to understanding the role of mesophotic coral ecosystems in the functioning of coral reefs. We examined how alpha and beta generic diversity of scleractinian coral assemblages vary across a wide depth gradient for coral reefs. We studied generic diversity patterns of scleractinian corals at sixteen sites in eight islands of three archipelagos in French Polynesia, as derived from the analysis of photo-quadrats, across the seafloor from shallow to lower mesophotic depths (6 to 120 m) and on a wide geographic scale. Our sampling considered quantitative coral cover to explore the patterns of alpha and beta components of diversity across depth and horizontal space. We show that in French Polynesia, mesophotic coral ecosystems host higher alpha and beta generic diversity than shallow reefs despite decreasing coral cover with depth. The variation of coral genus richness across the depth gradient is mainly driven by a mid-domain effect with a peak at 40 m depth. At the same time, we found that the turnover of coral genera across islands (i.e., spatial beta diversity) increased steadily along the depth gradient. Our findings report the first quantitative results of coral cover and diversity from mesophotic coral ecosystems in French Polynesia and also present one of the few existing studies to examine the broad breadth of the mesophotic depth gradient. We demonstrate that mesophotic depths can host unexpectedly high generic richness of scleractinian coral assemblages. At the same time, we showed that increasing depth increases the differences in generic diversity composition across islands, whereas shallow reefs are similar in between. While a single island could conserve shallow regional biodiversity, mesophotic depths containing the richest diversity require site-specific measures, suggesting that considering these mesophotic depths in conservation is necessary to maintain regional diversity.</p>
Fig. 5 in Epidemiological surveillance and amphibian assemblage status at the Estación Experimental de San Lorenzo, Sierra Nevada de Santa Marta, Colombia
Fig. 5. Healthy skin and fibropapilloma in Pristimantis megalops (A). Cross section of the healthy skin of Pristimantis megalops (B): The epidermis is thin, can be seen pigmented layer and layers of collagen in the dermis. Cross section of Fibropapilloma (C). Detail of fibroblasts forming fibropapilloma (D): the tissue is highly vascularized. Detail of the epidermis and collagen layers covering fibropapilloma (E–F). Histochemical staining in Fibropapilloma (F): The layers of collagen in the dermis can be seen in magenta color. fb: fibroblasts; col: layers of collagen; de: dermis; ep: epidermis; gla: dermal glands; hs: healthy skin; lp: pigmented layer; sm: striated muscle tissue; tu: tumor or fibropapilloma; vt: vascular tissue. Photographs by Edgar Javier Rincón Barón.
Fig. 1 in Epidemiological surveillance and amphibian assemblage status at the Estación Experimental de San Lorenzo, Sierra Nevada de Santa Marta, Colombia
Fig. 1. Map of the Serrania de San Lorenzo, Sierra Nevada de Santa Marta, Colombia. Red square area highlights the Estación Experimental de San Lorenzo to 2,200 meters.
Fig. 3 in Epidemiological surveillance and amphibian assemblage status at the Estación Experimental de San Lorenzo, Sierra Nevada de Santa Marta, Colombia
Fig. 3. Healthy individuals of Atelopus laetissimus (A) (Bufonidae); Atelopus nahumae (B) (Bufonidae); Pristimantis megalops (C) (Craugastoridae); and Ikakogi tayrona (D) (Centrolenidae). Photographs by Luis Alberto Rueda Solano.
Fig. 4 in Epidemiological surveillance and amphibian assemblage status at the Estación Experimental de San Lorenzo, Sierra Nevada de Santa Marta, Colombia
Fig. 4. Sick individuals of Ikakogi tayrona (A, B same individual); Pristimantis megalops (C, D), and malformation in Atelopus nahumae (E) and Atelopus laetissimus (F) found in epidemiological surveillance 2008–2014 in La Estación Experimental de San Lorenzo (2,200 meters), Sierra Nevada de Santa Marta, North of Colombia. Photographs by Luis Alberto Rueda Solano (A, B, D), Cesar Molina (C); Andres Rocha Usuga (E, F).
Fig. 6 in Epidemiological surveillance and amphibian assemblage status at the Estación Experimental de San Lorenzo, Sierra Nevada de Santa Marta, Colombia
Fig. 6. Monitoring of Atelopus laetissimus through the years in the Quebrada San Lorenzo Serrania de San Lorenzo, SNSM. Circle = average number obtained from individuals in each year (n = 2 samples for the years 2008, 2013 and 2014) (n = 1 sample for 2009); Error Bars = maximum and minimum individual in each year. Dotted line = trend in the number of individuals over time.
Fig. 2 in Epidemiological surveillance and amphibian assemblage status at the Estación Experimental de San Lorenzo, Sierra Nevada de Santa Marta, Colombia
Fig. 2. Serrania de San Lorenzo (B) Querbrada San Lorenzo (A) Sierra Nevada de Santa Marta, Colombia. Photographs by Luis Alberto Rueda Solano.
Bumble bee responses to climate and landscapes: Investigating habitat associations and species assemblages across geographic regions in the United States of America
<p><span>Bumble bees are integral pollinators of native and cultivated plant communities, but species are undergoing significant changes in range and abundance on a global scale. Climate change and land cover alteration are key drivers in pollinator declines; however, limited research has evaluated the cumulative effects of these factors on bumble bee<em> </em>assemblages. This study tests bumble bee assemblage (calculated as richness and abundance) responses to climate and land use by <span>modeling </span>species-specific habitat requirements, and assemblage-level responses across geographic regions. <span>We integrated species richness, abundance, and distribution data for 18 bumble bee species with site-specific bioclimatic, landscape composition, and landscape configuration data to evaluate</span> the effects of multiple environmental stressors <span>on bumble bee assemblages throughout</span> 433 agricultural fields in<span> Florida, Indiana, Kansas, Kentucky, Maryland, South Carolina, Utah, Virginia, and West Virginia from 2018 to 2020. Distinct east vs. west groupings emerged when evaluating species-specific habitat associations, prompting a detailed evaluation of bumble bee assemblages by geographic region. Maximum temperature of warmest month and precipitation of driest month had a positive impact on bumble bee assemblages in the Corn Belt/Appalachian/northeast, southeast, and northern plains regions, but a negative impact in the mountain region. Further, </span>forest land cover surrounding agricultural fields was highlighted as supporting more rich and abundant bumble bee assemblages<span>. Overall, climate and land use combine to drive bumble bee assemblages, but how those processes operate is idiosyncratic and spatially contingent across regions. From these findings, we suggested regionally specific management practices to best support rich and abundant bumble bee assemblages in agroecosystems. </span>Results from this study contribute to a better understanding of climate and landscape factors affecting bumble bees and their habitats throughout the USA. </span></p>
Impact of the 2011 Tohoku earthquake on the species diversity of rocky intertidal sessile assemblages
<p>The impacts of large-scale disturbance events on the species diversity of rocky intertidal sessile assemblages across multiple spatial scales are not well understood. To evaluate the influence of the 2011 Tohoku Earthquake on alpha and beta diversities of rocky intertidal sessile assemblages, we censused sessile assemblages in the mid-shore zone from 2011 to 2019. The census was conducted across 22 study sites on five rocky shores along 30 km of the Sanriku Coast of Japan, which is located 150–160 km north–northwest of the earthquake epicenter. Alpha diversity was measured with three Hill numbers (<em>H</em><sub>0</sub>, <em>H</em><sub>1</sub>, and<em> H</em><sub>2</sub>), which represent the number of equally common species that would exist in a community with the same diversity as the sampled community, with higher values of the subscript indicating more weight placed on abundant species. Beta diversity was measured with two metrics (<em>BD</em><sub>total</sub> at two spatial scales). Values were compared between the years 2011–2019 and the pre-earthquake period (2003–2010). The results show that the Tohoku Earthquake significantly altered the species diversity of intertidal sessile assemblages across multiple spatial scales. All diversity metrics obtained at multiple spatial scales (i.e., alpha diversities: <em>H</em><sub>0</sub>, <em>H</em><sub>1,</sub> and <em>H</em><sub>2</sub>; beta diversities: <em>BD<sub>t</sub></em><sub>otal</sub> at the shore and regional scales) decreased immediately after the earthquake and then increased in subsequent years. Two years after the earthquake, <em>H</em><sub>0</sub> recovered to within the range of pre-earthquake values and <em>H</em><sub>1</sub> and <em>H</em><sub>2</sub> became significantly higher than pre-earthquake values. Most metrics of alpha and beta diversities recovered to pre-earthquake levels after several years, but regional <em>BD</em><sub>total</sub> remained low for a longer period.</p>
Fig. 1 in Extensive testing of a multi-locus sequence typing scheme for Giardia dUodenaliS assemblage A confirms its good discriminatory power
Fig. 1 DCC outbreak in Sweden, described by Ankarklev et al. [13]; GVB outbreak in Italy, described by Resi et al. [14]; and several longitudinal samples of different patients showing similar genotypes, described by Woschke et al. [15]
Fig. 4 in Benthic hydrozoan assemblages as potential indicators of environmental health in a mediterranean marine protected area Abstract
Fig. 4: Two-dimensional nMDS representation of the similarity (Bray-Curtis) of hydrozoan assemblages among samples in the winter campaign. Samples displayed according to stations (numbers) and sampling depth (a), anthropogenic impact (b) and substrate type (c).
Fig. 2 in Benthic hydrozoan assemblages as potential indicators of environmental health in a mediterranean marine protected area Abstract
Fig. 2: Species numbers according to depth strata and total depth integrated species numbers in the study area.
Fig. 5 in Fish assemblages along the coasts of Tunisia: a baseline study to assess the effectiveness of future Marine Protected Areas
Fig. 5: Size-class (S: small, M: medium and L: large) frequency distribution (%) of relevant target fishes in Unprotected (UP) and Future Protected (FP) zones at the three studied locations (KU: Kuriat Islands, CNCS: Cap Negro-Cap Serrat, TA: Tabarka), (Number of individuals used to calculate percentages is given in Supp. Mat. 2).
Fig. 3 in Fish assemblages along the coasts of Tunisia: a baseline study to assess the effectiveness of future Marine Protected Areas
Fig. 3: Mean density (±standard error) per trophic category at the sampling locations (KU: Kuriat Islands, CNCS: Cap Negro-Cap Serrat, TA: Tabarka) and per protection level (UP: Unprotected, FP: Future Protected).
Fig. 1 in Fish assemblages along the coasts of Tunisia: a baseline study to assess the effectiveness of future Marine Protected Areas
Fig. 1: Locations where MPAs will be established along the Tunisian coast. Location of future protected sites (FP) and those outside (that will remain unprotected) (UP) (separated with dotted lines indicating borders of future MPAs as they are proposed in management plans).
Fig. 4 in Fish assemblages along the coasts of Tunisia: a baseline study to assess the effectiveness of future Marine Protected Areas
Fig. 4: Mean biomass (±standard error) per trophic category at the sampling locations (KU: Kuriat Islands, CNCS: Cap Negro-Cap Serrat, TA: Tabarka) and per protection level (UP: Unprotected, FP: Future Protected).
Fig. 2 in Fish assemblages along the coasts of Tunisia: a baseline study to assess the effectiveness of future Marine Protected Areas
Fig. 2: Mean species richness (a), mean density (b) and mean biomass (c) (±standard error) per location (KU: Kuriat islands, CNCS: Cap Negro-Cap Serrat, TA: Tabarka) and protection level (UP: Unprotected, FP: Future Protected).
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.