Find research datasets worth reusing

opencc-zeroJan 2023View details →

Data for: Improving estimates of land protection costs in a tropical biodiversity hotspot

Accurate estimates of the cost of land protection are useful for understanding where biodiversity conservation goals can be achieved at the lowest cost to society. However, because good cost maps are rare in tropical countries, conservation planning studies often ignore cost or rely on untested proxies, such as agricultural rent or land use intensity. Here, we show how analysts can estimate land protection costs using original data of public land acquisitions, global predictor datasets, and simple machine-learning models. For the Colombian Andes, a global biodiversity hotspot, we find that the principal driver of land protection cost is urban proximity, not agricultural rent. We derive cost estimates that predict public land protection costs more accurately than available cost proxies and identify new protection priorities for 143 threatened bird species. A more systematic collection of cost records of land protection will help inform public decisions on national and global biodiversity protection priorities.

opencc-zeroJan 2023View details →

Spatial genetic differentiation correlates with species assemblage turnover across tropical reef fish lineages

Aim: Evaluating the similarity of diversity patterns across micro- to macroevolutionary scales in natural communities, such as species-genetic diversity correlations (SGDC), may inform on processes shaping community assembly. However, whether SGDCs not only hold across communities but also across lineages has never been explored so far. Here we investigated SGDCs across co-distributed taxa for different spatial components (α, β, γ), and formally tested the influence of dispersal traits on β SGDCs. Location: Western Indian Ocean Time period: 2016–2017 Major taxa studied: Tropical reef fish species with contrasting dispersal traits Methods: Using ddRADseq single nucleotide polymorphism (SNP) data for 20 tropical reef fishes and distribution data of 2,446 species belonging to 12 families, we analysed the correlations between within-species genetic diversity and within-family species diversity (i.e., lineage diversity) for the three spatial components (α, β, γ SGDCs). We then related the strength of β-SGDCs per species to proxies of larval dispersal abilities. Results: We detected positive and significant lineage-based SGDC only for the β component, i.e., the families showing the greatest level of species turnover among sites contains the species with the greatest levels of genetic differentiation. We showed that the Monsoon drift mainly explained the β diversity patterns at both intraspecific and interspecific levels. Higher β-SGDCs were found for species with short pelagic larval duration and weak larval swimming capacity. Main conclusions: Our study reveals a strong correlation between genetic and species β diversity, a result explained by the presence of a 'soft' barrier and mediated by larval dispersal processes. This suggests that vicariance and dispersal limitation are major processes shaping β-diversity patterns from microevolutionary to macroevolutionary scales in tropical reef fishes.

opencc-zeroFeb 2023View details →

Changing patterns of nest predation and predator communities along a tropical elevation gradient

Tropical montane communities host the world's highest beta diversity of birds, a phenomenon usually attributed to community turnover caused by changes in biotic and abiotic factors along elevation gradients. Yet, empirical data on most biotic factors are lacking. Nest predation is thought to be especially important because it appears to be common and can change selective pressures underlying life history traits, which can alter competitive interactions. We monitored 2,538 nests, 338 of which had known nest predators, to evaluate if nest predation changes along a tropical elevational gradient. We found that nest predation decreased with elevation, reflecting the loss of lowland predators that do not tolerate colder climates. We found different "super" nest predators at each elevation that accounted for a high percentage of events, suggesting that selection pressures exerted by nest predator communities may be less diffuse than has been hypothesized, at least for birds nesting in the understory.

opencc-zeroFeb 2023View details →

Effects of warming on structure of aquatic communities in tropical bromeliad microecosystems

Freshwaters are among the most vulnerable ecosystems to climate warming, with projected temperature increases over the coming decades leading to significant losses of aquatic biodiversity. Experimental studies that directly warm entire natural ecosystems in the tropics are needed, for understanding the disturbances in aquatic communities. Therefore, we conducted an experiment to test the impacts of predicted future warming on density, alpha diversity, and beta diversity of freshwater aquatic communities, inhabiting natural microecosystems – Neotropical tank bromeliads. Aquatic communities within the tank bromeliads were experimentally exposed to warming, temperatures ranging from 23.58 to 31.72°C. Linear regression analysis was used to test the impacts of warming. Next, distance-based redundancy analysis was performed to assess how warming might alter total beta diversity and its components. This experiment was conducted across a gradient of habitat size (bromeliad water volume) and availability of detrital basal resources. A combination of the highest detritus biomass and higher experimental temperatures resulted in the greatest density of flagellates. However, the density of flagellates declined in bromeliads with higher water volume and lower detritus biomass. Moreover, the combination of the highest water volume and high temperature reduced density of copepods. Finally, warming changed microfauna species composition, mostly through species substitution (βrepl component of total beta-diversity). These findings indicate that warming strongly structures freshwater communities by reducing or increasing densities of different aquatic community groups. It also enhances beta-diversity, and many of these effects are modulated by habitat size or detrital resources.

opencc-by-4.0Feb 2023View details →

Data for "Convective Organization and Dry Tropical Cyclones in Direct Numerical Simulations of Idealized Fluid Setups"

Supporting data and analysis scripts for work contained in the manuscript Velez-Pardo, Martin & Cronin, Timothy W. (2023) Convective Organization and Dry Tropical Cyclones in Direct Numerical Simulations of Idealized Fluid Setups. README and scripts for running simulations and for data post-processing are found in README_and_scripts.zip. Data obtained using supercomputer Cheyenne (doi:10.5065/D6RX99HX) provided by NCAR's Computational and Information Systems Laboratory (CISL), sponsored by the National Science Foundation.

Contrasting Responses of Surface Heat Fluxes to Tropical Deforestation

2D_GSWP3*.nc are the CLM simulation outputs with GSWP3 as input forcings. 2D_*_piControl.nc and 2D_*_deforest-globe.nc are the CMIP6 model outputs. Offline.m and LUMIP.m are matlab code files to reproduce figures in the article. nc_*.py are python code files to generate netCDF files for producing figures.

opencc-zeroDec 2022View details →

Data for: Butterfly foraging is remarkably synchronous in an experimental tropical macrocosm

Diel patterns in foraging activity are dictated by a combination of abiotic, biotic, and endogenous limits. Understanding these limits is important for insects because ectotherm taxa will respond more pronouncedly to ongoing climatic change, potentially affecting crucial ecosystem services. We leverage an experimental macrocosm, the Montreal Insectarium Grand Vivarium, to test the importance of endogenous mechanisms in determining temporal patterns in foraging activity of butterflies. Specifically, we assessed the degree of temporal niche partitioning among 24 butterfly species originating from the Earth's tropics within controlled environmental conditions. We found strong niche overlap, with the frequency of foraging events peaking around solar noon for 96% of the species assessed. Our models suggest that this result was not due to the extent of cloud cover, which affects radiational heating and thus limits body temperature in butterflies. Together, these findings suggest that an endogenous mechanism evolved to regulate the timing of butterfly foraging activity within suitable environmental conditions. Understanding similar mechanisms will be crucial to forecast the effects of climate change on insects, and thus on the many ecosystem services they provide.

opencc-zeroFeb 2023View details →

Symbiotic nitrogen fixation does not stimulate soil phosphatase activity under temperate and tropical trees

Symbiotic nitrogen (N)-fixing plants can enrich ecosystems with N, which can alter the cycling and demand for other nutrients. Researchers have hypothesized that fixed N could be used by plants and soil microbes to produce extracellular phosphatase enzymes, which release P from organic matter. Consistent with this speculation, the presence of N-fixing plants is often associated with high phosphatase activity, either in the soil or on root surfaces, although other studies have not found this association, and the connection between phosphatase and rates of N fixation—the mechanistic part of the argument—is tenuous. Here, we measured soil phosphatase activity under N-fixing trees and non-fixing trees transplanted and grown in tropical and temperate sites in the USA: two sites in Hawaii, and one each in New York and Oregon. This provides a rare example of phosphatase activity measured in a multi-site field experiment with rigorously quantified rates of N fixation. We found no difference in soil phosphatase activity under N-fixing vs. non-fixing trees nor across rates of N fixation, though we note that no sites were P limited and only one was N limited. Our results add to the literature showing no connection between N fixation rates and phosphatase activity.

opencc-by-4.0Feb 2023View details →

Canopy height, rather than neighborhood effects, shapes leaf herbivory in a tropical rainforest

These files contain the datasets and R codes used in the data analyses in the paper " Canopy height, rather than neighborhood effects, shapes leaf herbivory in a tropical rainforest " that will be published in Ecology.

Soil nutrient dissimilarity and litter nutrient limitation as major drivers of home field advantage in riparian tropical forests

Decomposition is a key process driving carbon and nutrient cycling in ecosystems worldwide. The home field advantage effect (HFA) has been found to accelerate decomposition rates when litter originates from "home" when compared to other ("away") sites. It is still poorly known how HFA plays out in tropical, riparian forests, particularly in forests under restoration. We carried out three independent reciprocal litter transplant experiments to test how litter quality, soil nutrient concentrations and successional stage (age) influenced HFA in tropical riparian forests. These experimental areas formed a wide gradient of soil and litter nutrients, which we used to evaluate the more general hypothesis that HFA varies with dissimilarity in soil nutrients and litter quality. We found that HFA increased with soil nutrient dissimilarity, suggesting that litter translocation uncouples relationships between decomposers and litter characteristics; and with litter N:P, indicating P limitation in this system. We also found negative HFA effects at a site under restoration that presented low decomposer ability, suggesting that forest restoration does not necessarily recover decomposer communities and nutrient cycling. Within each of the independent experiments, the occurrence of HFA effects was limited and their magnitude was not related to forest age, nor soil and litter quality. Our results imply that HFA effects in tropical ecosystems are influenced by litter nutrient limitation and soil nutrient dissimilarity between home and away sites, but to further disentangle major HFA drivers in tropical areas, a gradient of dissimilarity between litter and soil properties must be implemented in future experimental designs.

MOM5 FAFMIP datasets for the study of Tropical Pacific Ocean Heat Budget in Control, FAF-STRESS and FAF-HEAT experiments

Data sets for reproducing results in "Tropical Pacific Ocean Heat Budget and the Role of Shallow and Deep Circulations" by Navarro-Labastida and Farneti, including all time-mean temperature tendencies and Meridional Overturning mass transports in density space for both Control and perturbation experiments.

Data from: Effects of tree functional traits on soil respiration in tropical forest plantations

The study covers four plantations stands of Acacia auriculiformis (A), Eucalyptus urophylla (E), Hopea odorata (H), and X. xylocarpa (X) through a sample plot (50 m x 50 m) in each stand from July 2015 until June 2016. Physical and chemical soil properties were collected at two depths (0-15 cm, 15-30 cm) at the beginning of the study (soil_properties_initial.csv). Additional samplings of topsoil pH, bulk density (BD, g cm-3), organic matter (OM, %), total carbon (TC, %), and nitrogen (TN, %) were conducted monthly (mo_yr) at five random locations (soil_properties_month.csv). Soil respiration (SR) was measured at the beginning of each month (mo_yr) at 12 locations (Point) within each species sample plot (Species) for ten hours (h_time) simultaneously with soil temperature (ST, C), air temperature (AT, C), relative humidity (RH), and soil moisture (SM, %) (soil_respiration.csv). The location of each soil respiration measurement point within the sample plots is provided as well (soil_respiration_location.csv). All trees within each sample plot were mapped (X, Y) and their stem basal area (BA_cm2) and height (H) were measured (stand_inventories.csv).

Data from: Biotic pressures and environmental heterogeneity shape beta-diversity of seedling communities in tropical montane forests

Many theories have been proposed to explain the high diversity of plants in the tropics. However, we lack an understanding of the processes that drive plant diversity and community assembly at different spatial scales. Here, we applied beta-diversity partitioning to test how biotic and abiotic factors are associated with seedling beta-diversity in a tropical montane forest in Southern Ecuador. We recorded seedling communities on 81 subplots at nine plots located at three elevations along a 2000-m elevational gradient. We measured biotic pressures (i.e. herbivory and fungal pathogen attacks) and environmental conditions (i.e. soil moisture and canopy closure) at all subplots and related them to species turnover and richness differences in seedling communities within and between elevations. We found that species turnover increased with differences in biotic dissimilarity within elevations, while differences in species richness within elevations increased with increasing environmental dissimilarity. Between elevations, species turnover increased with increasing environmental dissimilarity. Our findings show that species turnover and changes in species richness are related differently to abiotic and biotic factors, and that the importance of these factors for shaping seedling diversity is scale-dependent. Our study contributes to better understand the processes driving seedling beta-diversity and the assembly of plant communities in highly diverse tropical montane forests.

opencc-zeroDec 2022View details →

Data from: Seasonality in the equatorial tropics: Flower, fruit and leaf phenology of montane trees in the highlands of southwest Uganda

Phenology influences many forest functions and can inform forest conservation and management, yet representative phenological data for most common tropical forest tree species remain sparse or absent. Between June 2011 and December 2013, we investigated flowering, fruiting and leafing patterns in the Bwindi Impenetrable National Park, a montane forest located near the equator in Uganda, drawing on 16,410 observations of 530 trees of 54 species located between 2,066 and 2,527 m in elevation. The park's climate is equatorial with two wet and dry seasons each year. Flowering and fruiting were strongly seasonal while patterns in leafing were less pronounced. Flower occurrence peaked at the beginning of the short dry season followed by a pronounced trough during the beginning and the middle of the short wet season. Fruit occurrence had a pronounced peak during high rainfall months in March through April with most fruits ripening during drier months in May through July. Fruit scarcity was observed for a 4-month period spanning September to December and most flushing of leaves noted at the end of the wet season in November and December. Our binomial generalised linear mixed models (GLMM) indicated that flowering and fruiting were negatively associated with temperature and that leafing activity was positively associated with rainfall and temperature. These findings are consistent with the insolation- and water-limitation hypotheses suggesting that the seasonally varying availability of resources such as light, water and nutrients determines these phenological patterns. Ideally, prolonged, multi-year community-level studies would be supported so as to better characterise the influence of climate and of climate variability.

Sunda-Sahul floristic exchange and pathways into the Southwest Pacific: New insights from wet tropical forest trees

Aim Recent investigations on the floristic exchange between Southeast Asia and Australia have shown a clear dispersal directionality bias (West to East) of wet-adapted plant taxa. However, dispersal routes and directions of wet forest taxa into the South Pacific remain insufficiently known. We here aimed to establish the most likely routes and directions of plant dispersal into the Southwest Pacific islands. Location Southeast Asia, East Asia, Australia, Southwest Pacific. Taxon Dysoxylum s.l. (Meliaceae). This includes Dysoxylum s.s., Didymocheton, Epicharis, Goniocheton, Pseudocarapa and Prasoxylon. Method We sampled 75% of the species diversity in Dysoxylum s.l., covering the entire distribution range, all genera and major lineages. Phylogenetic relationships of 149 accessions were reconstructed using Bayesian Evolutionary Analysis and two internal constraints. The dispersal–extinction–cladogenesis variant, founder-event speciation (DEC+J), was used for reconstructing the biogeographic history, and 100 BSMs were simulated. Results Dysoxylum s.l. originated and firstly diversified in the western part of its current distribution range (incl. Indochina) during the Miocene to Pliocene, followed by an overall eastern range expansion towards Malesia, Australia and the Southwest Pacific in the Pliocene. Main conclusions The south-eastward expansion of lineages into Wallacea and Australia is in temporal agreement with the convergence of the Asian and Australian tectonic plates since the Miocene. Long-distance dispersal is the main mechanism that led to the current distribution. Two dispersal pathways into the Southwest Pacific are identified, (1) through New Guinea and the Solomon Islands to Fiji, and (2) from New Zealand to Fiji. For both routes, Fiji was an important secondary source area for dispersal into the Southwest Pacific.

Wind gust during tropical cyclone Ida, with and without deep convection parametrization from 1.4km global simulation with ECMWF IFS

Animations of wind gust during tropical cyclone Ida, from global TCo7999L137 (1.4km horizontal grid-spacing) simulation with hydrostatic IFS from INCITE2022 project.  One animation shows simulation with deep convection parametrization on and the other with off.

Data from: Interplay between rainfall and hillslope hydrology determines drought resistance of tropical vegetation

Droughts are predicted to increase in both frequency and intensity by the end of the 21st century, but ecosystem response is not expected to be uniform. At the landscape scale, ecosystem response to drought is highly heterogeneous. Here we assess the importance of the hill-to-valley hydrologic gradient in shaping vegetation hydraulic properties related to drought resistance for three locations across a rainfall seasonality gradient in South America. For this, we use hydraulic traits related to xylem resistance to embolism and compare the functional composition and diversity of tree communities. We show that the hydrologic gradient systematically selects for community assemblages that are more vulnerable to embolism in valleys, regardless of rainfall. Under the same rainfall regime, diversity in resistance to embolism is higher on hills than valleys, suggesting that strategies to cope with drought are more important on hills. With increasing seasonality, diversity in embolism resistance increases on hills and decreases in valleys. Our results show that differential groundwater access from hilltops to valleys select for distinctive hydraulic properties, potentially explaining species turnover along topographical gradients. Incorporating this relationship might improve the representation of vegetation in climate models and the prediction of how different communities will respond to extreme droughts.

opencc-zeroApr 2023View details →

Input data and model implementation from: How do terrestrial wildlife communities respond to small-scale Acacia plantations embedded in harvested tropical forest?

To offset the declining timber supply from shifting towards more sustainable forestry practices, industrial tree plantations are expanding in tropical production forests. The conversion of natural forest to tree plantation is generally associated with loss of biodiversity and shifts toward more generalist and disturbance tolerant communities; but effects of mixed-landuse landscapes integrating natural and plantation forest remain little understood. Using camera traps, we surveyed the medium-to-large bodied terrestrial wildlife community across two mixed-land-use forest management areas in Sarawak, Malaysia Borneo which include areas dedicated for logging of natural forest and adjacent planted Acacia forests. We analysed data from a 25-wildlife species community using a Bayesian community occupancy model to assess species richness and species-specific occurrence responses to Acacia plantations at a broad scale, and to remote-sensed local habitat conditions within the different forest land-use types. All species were estimated to occur in both land-use types, but species-level percent area occupied and predicted average local species richness were slightly higher in the natural forest management areas compared to licensed planted forest. Similarly, occupancy-based species diversity profiles and defaunation indices for both a full community and only threatened and endemic species suggested the diversity and occurrence were slightly higher in the natural forest management areas. At the local scale, forest quality was the most prominent predictor of species occurrence. These associations with forest quality varied among species but were predominantly positive. Our results highlight the ability of a mixed-land-use landscape with small-scale Acacia plantations embedded in natural forest to retain terrestrial wildlife communities while providing an alternate source of timber. Nonetheless, there was a tendency towards reduced biodiversity in planted forests, which would likely be more pronounced in plantations that are larger or embedded in a less natural matrix.

opencc-zeroApr 2023View details →

Data and analysis code for Norton and DuVal - Causes and consequences of nest site fidelity in a tropical lekking bird: win-stay-lose-shift tactics are unrelated to subsequent success, but site-faithful females nest earlier

Nest site selection influences the survival of care-giving parents and their offspring, but search costs and site availability may limit site choices. Returning to previous nest sites may reduce costs and allow parents to better avoid local predators or access familiar resources. We investigated nest site fidelity in the Lance-tailed Manakin (Chiroxiphia lanceolata), in which long-lived females raise offspring without male assistance, and found that site choices are responsive to past success but do not predict future outcomes. We compared georeferenced nest locations for the same females detected in consecutive years (245 comparisons for 138 females) and females nesting repeatedly within a year (137 comparisons for 97 females). Females were faithful to nesting sites in 13.9% of comparisons across years and 10.2% within years, and were more likely to nest again in the same site if their offspring fledged. When switching sites, females moved farther if their previous nest failed. Nest-site fidelity was unrelated to mate fidelity or female age. We then assessed whether site choice related to subsequent female survival, nest timing, or nest survival. Contrary to the hypothesis that win-stay-lose-shift tactics improve subsequent nesting outcomes, we found females were no more likely to fledge chicks or survive to a later year after they reused nest-sites. However, across years, site-faithful females nested earlier on average than females that switched sites. Early nests were more likely to fledge chicks, and early-nesting females were more likely to renest when their first nesting effort was complete. Win-stay-lose-shift tactics may allow females to avoid areas where predation is likely, but new nest sites are not safer. Females that reuse nest sites benefit from early nest initiation, which both correlates with immediate success and creates potential for longer-term benefits of fidelity through increased opportunities to renest throughout the breeding season.