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opencc-zeroDec 2018View details →

A standardized assessment of forest mammal communities reveals consistent functional composition and vulnerability across the tropics

Understanding global diversity patterns has benefitted from a focus on functional traits and how they relate to variation in environmental conditions among assemblages. Distant communities in similar environments often share characteristics, and for tropical forest mammals, this functional trait convergence has been demonstrated at coarse scales (110-200 km resolution), but less is known about how these patterns manifest at fine scales, where local processes (e.g., habitat features and anthropogenic activities) and biotic interactions occur. Here, we used standardized camera trapping data and a novel analytical method that accounts for imperfect detection to assess how the functional composition of terrestrial mammal communities for two traits – trophic guild and body mass – varies across 16 protected areas in tropical forests and three continents, in relation to the extent of protected habitat and anthropogenic pressures. We found that despite their taxonomic differences, communities generally have a consistent trophic guild composition, and respond similarly to these factors. Insectivores were found to be sensitive to the size of protected habitat and surrounding human population density. Body mass distribution varied little among communities both in terms of central tendency and spread, and interestingly, community average body mass declined with proximity to human settlements. Results indicate predicted trait convergence among assemblages at the coarse scale reflects consistent functional composition among communities at the local scale, suggesting that broadly similar habitats and selective pressures shaped communities with similar trophic strategies and responses to drivers of change. These similarities provide a foundation for assessing assemblages under anthropogenic threats and sharing conservation measures.Understanding global diversity patterns has benefitted from a focus on functional traits and how they relate to variation in environmental conditions among assemblages. Distant communities in similar environments often share characteristics, and for tropical forest mammals, this functional trait convergence has been demonstrated at coarse scales (110-200 km resolution), but less is known about how these patterns manifest at fine scales, where local processes (e.g., habitat features and anthropogenic activities) and biotic interactions occur. Here, we used standardized camera trapping data and a novel analytical method that accounts for imperfect detection to assess how the functional composition of terrestrial mammal communities for two traits – trophic guild and body mass – varies across 16 protected areas in tropical forests and three continents, in relation to the extent of protected habitat and anthropogenic pressures. We found that despite their taxonomic differences, communities generally have a consistent trophic guild composition, and respond similarly to these factors. Insectivores were found to be sensitive to the size of protected habitat and surrounding human population density. Body mass distribution varied little among communities both in terms of central tendency and spread, and interestingly, community average body mass declined with proximity to human settlements. Results indicate predicted trait convergence among assemblages at the coarse scale reflects consistent functional composition among communities at the local scale, suggesting that broadly similar habitats and selective pressures shaped communities with similar trophic strategies and responses to drivers of change. These similarities provide a foundation for assessing assemblages under anthropogenic threats and sharing conservation measures.

opencc-zeroDec 2017View details →

Data from: Diversity and composition of viral communities: coinfection of barley and cereal yellow dwarf viruses in California grasslands

Most species host multiple pathogens, yet field studies rarely examine the processes determining pathogen diversity within a single host or the effects of coinfection on pathogen dynamics in natural systems. Coinfection can affect pathogen transmission and virulence. In turn, coinfection can be regulated within hosts by interactions such as cross-protective immunity or at broader spatial scales via vector distributions. Using a general model, we demonstrate that coinfection by a group of vectored pathogens is highest with abundant generalist vectors and weak cross-protection and coinfection- induced mortality. Using these predictions, we investigate the distribution of five coexisting aphid-vectored, viral pathogens (barley and cereal yellow dwarf luteoviruses and poleroviruses) in a native perennial grass (Elymus glaucus) in both space (700 km) and time (4 years). Observed coinfection rates were much higher than expected at random, suggesting that within-host processes exerted weak effects on within-host pathogen diversity. Covariance among viruses in space and time was highest for viral species sharing a vector. Temporal correlation arose from the synchronous invasion of two viruses transmitted by a shared aphid species. On the basis of our modeling and empirical results, we expect that factors external to individual hosts may affect the coinfection dynamics in other communities hosting vectored pathogens.

opencc-zeroJun 2021View details →

Source pool diversity and proximity shape the compositional uniqueness of insular mammal assemblages worldwide

Islands have been the test bed of several theories in community ecology, biogeography, and evolutionary biology. Progress within these disciplines has given a more comprehensive and mechanistic understanding of the processes governing variation in species richness among islands. However, it remains unclear whether these same processes also explain variation in species and phylogenetic composition among islands. Integrating theory from ecology and biogeography, we infer the roles of dispersal, selection, and stochasticity on the composition of insular assemblages within archipelagos. We further assess the influence of source pool diversity and connectivity on the compositional uniqueness of insular assemblages. Island systems worldwide. We compiled data on species composition of non-volant mammals on ∼200 islands in nine archipelagos distributed worldwide from the literature. We used variation partitioning to quantify the relative influence of the environment (selection) and geographic distance (dispersal) relative to a null model (stochasticity, randomness) on taxonomic and phylogenetic compositional turnover within archipelagos. We then used a linear mixed model to gain further insight into the underlying mechanisms shaping variation in assemblage composition among islands at a global scale. Specifically, we assessed the influence of source pool diversity, isolation from the source pool, and island characteristics on compositional uniqueness. Our results suggest that within-archipelago variation in the composition of insular mammal assemblages is associated with stochastic or unmeasured processes rather than abiotic selection or dispersal limitation. The diversity and proximity of the source pool, as well as some island characteristics, explained variation in phylogenetic, but not taxonomic, compositional uniqueness globally. Within archipelagos, the largely unexplained variation in compositional turnover points to the overwhelming influence of extinction mediated by ecological drift or other stochastic processes, which obscures or overrides the signature of selection and/or dispersal. Globally, isolated islands associated with highly diverse source pools exhibit high phylogenetic uniqueness whereas well-connected islands associated with small source pools show the opposite trend. Phylogenetically unique assemblages also tend to occur on islands with a small elevational span and low annual temperature variation. Taken together, our results suggest that source pool diversity, along with the potential for colonization from those pools, plays an important role in shaping the composition of insular mammal assemblages worldwide.

opencc-zeroJun 2021View details →

Composite landscape predictors improve distribution models of ecosystem types

Aim: Distribution modelling is a useful approach to obtain knowledge about the spatial distribution of biodiversity, required for e.g., red list assessments. While distribution modelling methods have been applied mostly to single species, modelling of communities and ecosystems (EDM; ecosystem-level distribution modelling) produces results that are more directly relevant for management and decision-making. Although the choice of predictors is a pivotal part of the modelling process, few studies have compared the suitability of different sets of predictors for EDM. In this study, we compare the performance of 50 single environmental variables with that of 11 composite landscape gradients (CLGs) for prediction of ecosystem types. The CLGs represent gradients in landscape element composition derived from multivariate analyses, e.g., 'inner-outer coast' and 'land use intensity'. Location: Norway. Methods: We used data from field-based ecosystem type mapping of nine ecosystem types, and environmental variables with a resolution of 100×100 m. We built nine models for each ecosystem type with variables from different predictor sets. Logistic regression with forward selection of variables was used for EDM. Models were evaluated with independently collected data. Results: Most ecosystem types could be predicted reliably, although model performance differed among ecosystem types. We identified significant differences in predictive power and model parsimony across models built from different predictor sets. Climatic variables alone performed poorly, indicating that the current climate alone is not sufficient to predict the current distribution of ecosystems. Used alone, the CLGs resulted in parsimonious models with relatively high predictive power. Used together with other variables, they consistently improved the models. Main conclusions: We argue that the use of composite variables as proxies for complex environmental gradients has the potential to improve predictions from EDMs and thus to inform conservation planning as well as improve the precision and credibility of red lists and global change assessments.

opencc-zeroJun 2021View details →

Data reported in: Effects of ozone isotopologue formation on the clumped-isotope composition of atmospheric O2

Tropospheric 18O18O is an emerging proxy for past tropospheric ozone and free-tropospheric temperatures. The basis of these applications is the idea that isotope-exchange reactions in the atmosphere drive 18O18O abundances toward isotopic equilibrium. However, previous work used an offline box-model framework to explain the 18O18O budget, approximating the interplay of atmospheric chemistry and transport. This approach, while convenient, has poorly characterized uncertainties. To investigate these uncertainties, and to broaden the applicability of the 18O18O proxy, we developed a scheme to simulate atmospheric 18O18O abundances (quantified as ∆36 values) online within the GEOS-Chem chemical transport model. These results are compared to both new and previously published atmospheric observations from the surface to 33 km. Simulations using a simplified O2 isotopic equilibration scheme within GEOS-Chem show quantitative agreement with measurements only in the middle stratosphere; modeled ∆36 values are too high elsewhere. Investigations using a comprehensive model of the O-O2-O3 isotopic photochemical system and proof-of-principle experiments suggest that the simple equilibration scheme omits an important pressure dependence to ∆36 values: the anomalously efficient titration of 18O18O to form ozone. Incorporating these effects into the online ∆36 calculation scheme in GEOS-Chem yields quantitative agreement for all available observations. While this previously unidentified bias affects the atmospheric budget of 18O18O in O2, the modeled change in the mean tropospheric ∆36 value since 1850 C.E. is only slightly altered; it is still quantitatively consistent with the ice-core ∆36 record, implying that the tropospheric ozone burden increased less than ~40% over the twentieth century.

opencc-by-4.0Dec 2020View details →

Sedimentation, sediment grain size, vegetation composition and vegetation characteristics on a salt marsh in nature reserve the Slufter (Wadden island Texel, the Netherlands)

Data on sedimentation, sediment grain size, vegetation composition and vegetation characteristics of a field experiment on a salt marsh in nature reserve the Slufter (Wadden island Texel, the Netherlands). The data is described in the following publication: Baaij, B.M., Kooijman, J., Limpens, J., Marijnissen, R.J.C., van Loon-Steensma, J.M. Monitoring Impact of Salt-Marsh Vegetation Characteristics on Sedimentation: an Outlook for Nature-Based Flood Protection. Wetlands 41, 76 (2021). https://doi.org/10.1007/s13157-021-01467-w A short description of the aim, study design, measurements and data files is given in README.txt.

opencc-by-4.0Jul 2021View details →

Datasets from tensile testing of unidirectional carbon fiber composites using different specimen types

The raw tensile data behind figure 8 in the reference: Rajnish Kumar, Lars P Mikkelsen, Hans Lilholt and Bo Madsen, Experimental Method for Tensile Testing of Unidirectional Carbon Fibre Composites Using Improved Specimen Type and Data Analysis, Materials, 14, 3939, https://doi.org/10.3390/ma14143939, 2021. to where a reference should be given.

opencc-by-4.0Dec 2020View details →

Acorn worm ossicle ultrastructure and composition and the origin of the Echinoderm skeleton

The excel.data file with ossicle size measurement used to get the mean sizes and supplementary Fig. 2. Raw Raman spectra and R code used to determinate the polymorph of enteropneusts calcium carbonate ossicles, and make Fig. 3

opencc-zeroJul 2021View details →

Uncovering the vertebrate scavenger guild composition and functioning in the Cerrado biodiversity hotspot

Scavenging is widespread among vertebrates, being very important for maintaining certain ecosystem functions. Despite this, the scavenger communities remain poorly known in some biomes, especially in the Neotropics. Our main objective was to describe for the first time the scavenger community and identify the factors affecting scavenging efficiency in the Brazilian Cerrado. We analyzed the effects of vegetation cover, time of carcass placement and carcass weight, on scavenger species richness, individual abundances, carcass detection and consumption times, and carcass consumption rate. We monitored 11 large and 45 small carcasses using automatic cameras. We documented a total of 19 vertebrate scavenging species, four species of vultures and 15 facultative scavengers. We found that carcass size was the most important factor affecting the scavenger assemblage and consumption patterns. Large carcasses were dominated by vultures, whereas small carcasses were consumed mainly by facultative scavengers. We also found differences between large and small carcasses in all carcass consumption variables except for detection time. However, we did not find an effect of vegetation cover or time of carcass placement on scavenging patterns. The negligible role of mammals and non-raptor birds in large carcasses is also noteworthy, probably due to the consumption and foraging efficiency of the vultures, and the more frugivorous habits of the mesocarnivores. Our results show a highly diverse and efficient scavenging vertebrate community in the Brazilian Cerrado, and the need to preserve them in the face of the significant habitat transformations suffered by this biodiversity hotspot.

opencc-by-4.0Jul 2021View details →

Data of individual aerosol particle compositions using STEM-EDS

Data set of aerosol particle compositions measured using scanning transmission electron microscopy with energy-dispersive X-ray spectroscopy (STEM-EDS) used in a paper by Adachi et al. TEM samples were collected during the Fire Influence on Regional to Global Environments and Air Quality (FIREX-AQ), the Biomass Burning Observation Project (BBOP), and the Megacity Initiative: Local and Global Research Observations (MILAGRO) campaigns. Here I show all EDS data and the sample average data measured using STEM-EDS.

opencc-by-4.0Aug 2021View details →

Dataset for manuscript entitled "The effects of a synthetic and biological surfactant on the community composition and metabolic activity of a freshwater biofilm"

The following datasets were used for the 16s rRNA analysis in the manuscript entitled " The effects of a synthetic and biological surfactant on the community composition and metabolic activity of a freshwater biofilm". BZ2 files were obtained from next generation sequencing with the Illumina Mi-Seq. Mothur was used to analyze the BZ2 files, creating the listed excel documents.

opencc-zeroAug 2021View details →

Beyond species richness and community composition: Using plant functional diversity to measure restoration success in jarrah forest

Aim: The importance of restoring ecosystem functions to native systems that have been degraded, damaged or destroyed is increasingly recognised. Yet few studies have measured the effect of restoration efforts on ecosystem functioning or the functional diversity (FD) that underpins it. Here we assessed change in FD of restored assemblages one to 25 years after the onset of post-mine restoration. Location: Northern Jarrah (Eucalyptus marginata Donn ex Sm.) Forest bioregion of south-western Australia. Methods: Functional richness, evenness, divergence and dispersion were derived from five plant functional traits relevant to community reassembly. Effects of three explanatory variables (i.e., age, year restoration was initiated, and time since fire) on six response variables (i.e., four FD indices, species richness, and compositional similarity to nearby reference forest) were analysed using linear mixed models for a dataset with repeated measures of plots through time (n= 810 plots), and linear models for a sub-set of one-time measures of different aged assemblages (i.e., space-for-time approach; n= 490 plots). Results: Functional evenness and functional dispersion increased with age, while functional divergence and functional richness decreased with age. Functional dispersion increased with time since fire, while functional richness decreased with time since fire. Species richness decreased with age, but at 25-years, species richness was comparable to that observed in reference forest. In contrast, similarity showed no relationship with age of restored forest, and at 25-years, similarity of restored forest to reference was low compared with similarity of reference forest to itself. Three of four FD indices had not reached those of reference jarrah forest 25-years after restoration had been initiated. Conclusions: Reassembly of FD suggests importance of environmental filtering and high functional redundancy. A longer time frame may be needed to assess FD of restored assemblages, and in the meantime, species richness is not an adequate surrogate of FD.

opencc-by-4.0Aug 2021View details →

The analysis of composition and abundance of the raft proteome of microglia using a tandem mass tag (TMT)-based quantitative proteomic analysis.

To determine the proteins in the membrane raft, we used the TMT-labeling and nano-liquid chromatography mass spectrometry (nano-LC-MS/MS) analysis by Creative Proteomics (NY, USA; https://www.creative-proteomics.com/). Rat primary microglia were treated with IL-6 (25 ng/ml) for 15 min. Membrane rafts were obtained by flotation assay. Samples were prepared from three independent experiments. Proteins in equal volumes of raft fractions were digested with trypsin, desalted, and labeled with a TMT reagent (Thermo Fisher Science). The TMT-labeled peptides were fractionated and analyzed by nano-LC-MS/MS. The resulting MS/MS data were analyzed and searched against the rat protein database using Proteome Discoverer 2.1.

opencc-zeroAug 2021View details →

Afrotropical secondary forests exhibit fast diversity and functional recovery, but slow compositional and carbon recovery after shifting cultivation

Question: Human disturbance is increasingly affecting forest dynamics across the tropics. Forests can recover via natural secondary succession to pre-disturbance levels of biodiversity, species composition, and ecosystem carbon stocks. Central Africa will be subject to increasingly high shifting cultivation pressure in the next decades, but succession trajectories of these ecosystem properties are still poorly known for the Congo basin. We addressed two questions: (1) how does taxonomic and functional composition and diversity shift? (2) How fast do aboveground carbon stocks recover during secondary succession in tropical forests? Location: Central Congo basin Methods: We conducted an inventory of trees (DBH ≥10 cm diameter), measured species traits and soil texture and carbon content in 18 plots, located along six secondary succession stages (i.e. from agricultural to old growth forest sites). We measured tree diameter, height for 20% of trees distributed across diameter classes, wood traits from all species, and leaf traits from species that contributed to 85% of the plot basal area. Results: We showed that secondary forests recover relatively fast in terms of tree species diversity, alpha functional diversity, and fine root carbon, with near-old-growth forest values after six decades past disturbance, while floristic composition exhibited slower recovery. Secondary forests only partially shifted from acquisitive to a conservative life-history, with shifts in leaf traits being largely decoupled from wood traits. Only 43% of above-ground carbon recovered after 60 years of forest regrowth, potentially through a slow recovery of the large-sized tree stems that dominate carbon stocks of old-growth forests. Conclusions: Our findings underline the capacity of Afrotropical forests to recover species and alpha functional diversity after clear-cutting through shifting cultivation. Simultaneously, old-growth forests harbors a particular floristic community and store a large quantity of carbon with much longer recovery trajectories, stressing the need for conservation of these forests in the Congo Basin.

Figure 4 in The Herpetofauna from Ilha Grande (Angra dos Reis, Rio de Janeiro, Brazil): updating species composition, richness, distribution and endemisms

Figure 4. Specimen of Corallus hortulanus (not collected) found in Vila do Aventureiro village, Ilha Grande (Photo by F.B.S. Telles).

Figure 3 in The Herpetofauna from Ilha Grande (Angra dos Reis, Rio de Janeiro, Brazil): updating species composition, richness, distribution and endemisms

Figure 3. New records of snakes for Ilha Grande. (A) Dipsas indica (Photo by D. Cunha-Passos); (B) Echinantera cephalostriata (Photo by P. Fatorelli).

Figure 1 in The Herpetofauna from Ilha Grande (Angra dos Reis, Rio de Janeiro, Brazil): updating species composition, richness, distribution and endemisms

Figure 1. Image of Ilha Grande with the localities where the species were recorded, and their respective density points of species. CAX = Caxadaço trail; CDM = Costão do Demo, RBEPS; EAD = Abraão-Dois Rios road; FPS = Forest of Praia do Sul; JAR = Jararaca trail, Dois Rios; LPM = Lopes Mendes; PAP = Pico do Papagaio; PRN = Parnaioca trail; RPS = Restinga of Praia do Sul; VAB = Vila do Abraão; VAV = Vila do Aventureiro; VDR = Vila Dois Rios.

Figure 2 in The Herpetofauna from Ilha Grande (Angra dos Reis, Rio de Janeiro, Brazil): updating species composition, richness, distribution and endemisms

Figure 2. New records of amphibians for Ilha Grande. (A) Ischnocnema bolbodactyla; (B) Leptodactylus latrans; (C) Leptodactylus flavopictus (Photos by F.B.S. Telles).

opencc-by-nc-4.0Aug 2019View details →

Figure 4 in Medium- and large-sized mammal composition in the Chapada dos Veadeiros National Park and adjacent areas, state of Goiás, Brazil

Figure 4. Non-Metric Multidimensional Scaling (NMDS) with Bray-Curtis distance matrix between the frequencies of mammalian registered in each camera trap located in the Chapada dos Veadeiros National Park, state of Goiás, central Brazil.