Find research datasets worth reusing

opencc-zeroFeb 2023View details →

Data for: Carbon-concentrating mechanisms are a key trait in lichen ecology and distribution

Carbon-concentrating mechanisms (CCMs) are a widespread phenomenon in photosynthetic organisms. In vascular plants, the evolution of CCMs (C4 and CAM) is associated with significant shifts, most often to hot, dry and bright or aquatic environments. If and how CCMs drive distributions of other terrestrial photosynthetic organisms, remains little studied. Lichens are ecologically important obligate symbioses between fungi and photosynthetic organisms. The primary photosynthetic partner in these symbioses can include CCM-presenting cyanobacteria (as carboxysomes), CCM-presenting green algae (as pyrenoids) or green algae lacking any CCM. We use an extensive dataset of lichen communities from eastern North America, spanning a wide climatic range, to test the importance of CCMs as predictors of lichen ecology and distribution. We show that presence or absence of CCMs leads to opposite responses to temperature and precipitation in green algal lichens, and with different responses in cyanobacterial lichens. These responses contrast with our understanding of lichen physiology, whereby CCMs mitigate carbon limitation by water saturation at the cost of efficient use of vapor hydration. This study demonstrates that CCM-status is a key functional trait in obligate lichen symbioses, equivalent in importance to its role in vascular plants, and central for studying present and future climate responses.

opencc-by-4.0Jun 2022View details →

Saul Flores data for manuscript in ECOLOGY: Extreme drought disrupts plant phenology: insights from 35 years of cloud forest data in Venezuela

Venezuela cloud forest phenology data for tree flowers and fruits.

opencc-by-4.0Mar 2023View details →

Supplementary data to the article "The first larva of the cucujiform superfamily Cleroidea from the Mesozoic and its ecological implications (Coleoptera)"

The supplementery data to the article "The first larva of the cucujiform superfamily Cleroidea from the Mesozoic and its ecological implications (Coleoptera)" contain the 8 bit TIFF image stack obtained at the Imaging Beamline P05 (IBL) operated by the Helmholtz-Zentrum Hereon at the storage ring PETRA III (Deutsches Elektronen Synchrotron-DESY, Hamburg, Germany) using synchrotron radiation based micro-computed tomography (SRμCT). The scan of the holotype specimen of Cretorhadalus constantini Kolibáč & Prokop, 2023 was used for the segmentation and volume renders.

opencc-zeroMar 2023View details →

Data for: Capturing complex interactions in disease ecology with simplicial sets

Here we provide archived code for: Code for Capturing Complex Interactions in Disease Ecology with Simplicial Sets. Ecology Letters. The code provided can be used to generate the figures used in the manuscript as well as to generate appendix 3 in the supplementary materials. In the paper, we describe how higher-order network approaches can be applied in disease ecology research. We explain what simplicial sets are; why their use would be beneficial in different subject areas; where these areas are: social, transmission, movement/spatial and ecological networks; and when using them would help most in each context. To demonstrate their application, we develop a novel approach to identify how pathogens persist within a host population (see code for Appendix 3 in this repository). We also provide an overview of how to use simplicial sets, highlighting specific metrics, generative models and software. Finally, we synthesize key research questions simplicial sets will help us answer and highlight the methodological developments required.

openother-openApr 2023View details →

Data from: Chilean bee diversity: Contrasting patterns of species and phylogenetic turnover along a large-scale ecological gradient

Title of dataset Data from: Chilean bee diversity: Contrasting patterns of species and phylogenetic turnover along a large-scale ecological gradient Authors of dataset Leon Marshall1,2, John S. Ascher3, Cristian Villagra4, Amaury Beaugendre1, Valentina Herrera4, Patricia Henríquez-Piskulich4, Alejandro Vera5, Nicolas J. Vereecken1 <ol> <li>Agroecology Lab, Université libre de Bruxelles (ULB), Boulevard du Triomphe CP 264/2, B 1050 Brussels, Belgium</li> <li>Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands</li> <li>Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore</li> <li>Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Región Metropolitana, Chile</li> <li>Departamento de Biología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Región Metropolitana, Chile</li> </ol> Abstract Chile's isolation and varied climates have driven the evolution of a unique biodiversity with a high degree of endemism. As a result, Chile encompasses diverse environments, including the Mediterranean-type ecosystem, a global biodiversity hotspot. These environments are currently threatened by anthropogenic land use change impacting the integrity of local biomes and associated species. This area is the most intensively sampled of the country with high endemicity of native bee species. Characterising habitat requirements of bees is a pressing priority to safeguard these insects and the ecosystem services they provide. We investigated broad-scale patterns of bee (Hymenoptera: Apoidea: Anthophila) diversity using newly accessible expert-validated datasets comprising digitized specimen records from Chilean and US collections, and novel expert-validated type specimen data for the bees of Chile. We used a generalised dissimilarity modelling (GDM) approach to explore both compositional and phylogenetic β-diversity patterns across latitudinal, altitudinal, climate and habitat gradients in well-sampled bee assemblages in Central Chile. Using the GDM measures of increasing compositional and environmental dissimilarity we categorised and compared the most important drivers of these patterns and used them to classify 'wild bee ecoregions' (WBE) representing unique assemblages. Turnover of bee assemblages was explained primarily by latitudinal variation (proxy for climate) from south to north in Chile. However, temperature variations, precipitation and the presence of bare soil also significantly explained turnover in bee assemblages. In comparison, we observed less turnover in phylogenetic biodiversity corresponding to spatial gradients. We identified six de novo ecoregions (WBE), all with distinct taxa, endemic lineages, and representative species. The WBE represent distinct spatial classifications but have similarities to existing biogeographical classifications, ecosystems and bioclimatic zones. This approach establishes the baseline needed to prioritise bee species conservation efforts across this global biodiversity hotspot. We discuss the novelty of this classification considering previous biogeographical characterisations and their relevance in assessing conservation priorities for bee conservation. We argue that Chile's WBE highlight areas in need of funding for bee species surveys and description, distribution mapping and strengthening of conservation policies. Usage notes The dataset contains species occurrence data of chilean bees aggregated to a 5 x 5 km grid shapefile. The shapefile of the grid and the raster mask of the Central Chilean study area are also included. Finally, a database of type specimen data used to supplement the dataset is included here.  The code for the analysis can be found at: <a href="https://github.com/lmar116/ChileanBeeDiversity">https://github.com/lmar116/ChileanBeeDiversity</a>. Shapefiles, rasters, CSV files and code were all loaded and analyzed using R statistics software.  Four files are included: <ol> <li>Marshall-et-al-2023_Ecosphere_DataTable_bee_grid: contains all species occurrence data used in GDM analysis, Grid column refers to cl.5km.shp.</li> <li>cl.5km.shp (and associated files): 5 x 5 km grid shapefile of the Central Chilean study area</li> <li>chile.mask.tif: raster outline of the Central Chilean study area</li> <li>Marshall-et-al-2023_Ecosphere_CentralChileTypeSpecimens.xlsx: contains type specimen data used to supplement species occurrence dataset.</li> </ol>

Data for: Vegetation and soil ecology of threatened Himalayan Trillium habitats in Kashmir, Himalaya

Understanding the vegetation and soil ecology of natural habitats harbouring threatened species is critical in conservation planning and restoration. The present study investigated the vegetation composition and soil physico-chemical attributes of natural habitats of Trillium govanianum – a threatened Himalayan endemic species. We laid 120 quadrats across eight randomly selected sites where the species was growing in the Kashmir Himalaya. We collected the soil samples from these sites and determined soil physico-chemical attributes using standard methods. Across all the sites, we found a total of 57 plant species with dominance of Rosaceae and Ranunculaceae. The IVI results revealed that Fragaria nubicola, Corydalis diphylla, Galium aparine, and Leucanthemum vulgare, were the dominant species in T. govanianum communities. The density, abundance and IVI of 3-leaf vegetative plants was higher than 1-leaf vegetative and 3-leaf reproductive plants across all the study sites. We found that T. govanianum alone forms 23.5 % positive, 0 negative, 76.4% random co-occurrences with other associated species in its community. Our results reveal that the variations in vegetation composition among the sites was influenced by differences in soil properties. Principal component analysis revealed that several soil parameters such as organic carbon, nitrogen, potassium, and sulphur were concentrated in five sites, namely Dara, Drung, Bangus, Gulmarg, and Doodhpathri, which also showed the highest density, frequency, and abundance of T. govanianum. Overall, our study contributes quantitative information on the vegetation and soil ecology of T. govanianum-assemblages, which in turn can help in developing conservation strategies for this threatened species, and its sustainable management and habitat restoration.

Data from: Integrating ecological niche and hydrological connectivity models to assess the impacts of hydropower plants on an endemic and imperiled freshwater turtle

We built this dataset to assess the impacts of hydropower plants on the distribution of an endemic and imperiled freshwater turtle with very unique ecological requirements, the Williams' side-necked turtle (Phrynops williamsi). To prevent and mitigate impacts, we prioritized sites for species conservation by classifying planned HPP locations according to their predicted adverse effects on species distribution. The dataset has two files: i) species occurrence records and ii) hydropower plant data. The first dataset was fully built by the authors and the second was modified from the Brazilian Electricity Regulatory Agency (ANEEL) georeferenced data system.

Data from: Drought-induced relocation of ant colonies and its consequences for the long-term spatial ecology of a population under stress

<ol> <li>Maintaining a central refuge such as a nest or burrow can offer protection against environmental stressors but comes at the expense of the capacity to disperse to new locations. This trade-off with mobility can be detrimental when environmental conditions become adverse for extended periods, necessitating animals to relocate in order to track shifting niche envelopes.</li> <li>Long-lived ant colonies that invest in the construction of large nests are especially susceptible to changing environmental conditions. The Australian meat ant, Iridomyrmex purpureus, build large terrestrial nests at sites that balance shade and solar exposure.</li> <li>Long-term study of a population of meat ants showed low nest turnover and a stable spatial distribution of nests across typical rainfall years. With the onset of drought, a dramatic surge in the production of new nests occurred through a process of budding that far exceeded historic trends. This appears to have allowed colonies to relocate nests into areas with more favourable microclimate conditions in a strategy reminiscent of the production of runners in stressed plants. The consequence has also been the packing of nests into a narrow habitable zone that has resulted in an apparent increase in competition among large rival colonies. Following the break in drought and the thinning of some nests through abandonment, competition has progressively eased in later years.</li> <li>The surge in nest budding triggered by acute environmental stress in this population offers a possible strategy for long-lived colonies to effectively migrate across the landscape. With changes in environmental conditions becoming more frequent and severe with the climate crisis, any strategy available to central place foragers to track windows of preferred conditions are likely to become increasingly important.</li> </ol>

Supporting data for: Physical controls and ecological implications of the timing of the spring phytoplankton bloom on the Newfoundland and Labrador shelf

The Newfoundland and Labrador (NL) shelf and the Grand Banks of Newfoundland have been known as iconic fishing areas for centuries. In such areas with seasonal sea ice coverage, the timing of the spring bloom has been linked to sea ice melting, which stratifies the water column and promotes favorable conditions for phytoplankton to grow and accumulate. With sea ice gradually disappearing, we revisited the physical drivers controlling the initiation of the spring bloom in the region. We found that the timing of the phytoplankton bloom on the Grand Banks corresponds to the timing of ocean re-stratification following winter mixing. We also found that large-scale climate indicators are good proxies for the timing of the bloom and the abundance of Calanus finmarchicus, a key zooplankton species for the ecosystem. By revealing links between physical and biological processes, this work paves the way for an improved ecosystem approach to fisheries management.

Data from: Ecological genetics of local adaptation in Arabidopsis: an 8-year field experiment

There is considerable evidence for local adaptation in nature, yet important questions remain regarding its genetic basis. How many loci are involved? What are their effect sizes? What is the relative importance of conditional neutrality vs. genetic trade-offs? Here we address these questions in the self-pollinating, annual plant Arabidopsis thaliana. We used 400 recombinant inbred lines (RIL) derived from two locally adapted populations in Italy and Sweden, grew the RILs and parents at the parental locations, and mapped quantitative trait loci (QTL) for mean fitness (fruits/seedling planted). We previously published results from the first three years of the study, and here add five additional years, providing a unique opportunity to assess how temporal variation in selection might affect QTL detection and classification. We found ten adaptive and one maladaptive QTL in Italy, and six adaptive and four maladaptive QTL in Sweden. The discovery of maladaptive QTL at both sites suggests that even locally adapted populations are not always at their genotypic optimum. Mean effect sizes for adaptive QTL, 0.97 and 0.55 fruits in Italy and Sweden respectively, were large relative to the mean fitness of the RILs (approximately 8 fruits/seedling planted at both sites). Both genetic trade-offs (four cases) and conditional neutrality (seven cases) contribute to local adaptation in this system. The eight-year dataset provided greater power to detect QTL and to estimate their locations compared to our previous three-year study, identifying one new genetic trade-off and reclassifying one QTL from genetic trade-off to conditionally neutral.

Data from: Experimentally simulating the evolution-to-ecology connection: Divergent predator morphologies alter natural food webs

The idea that changing environmental conditions drive adaptive evolution is a pillar of evolutionary ecology. But, the opposite—that adaptive evolution alters ecological processes—has received far less attention yet is critical for eco-evolutionary dynamics. We assessed the ecological impact of divergent values in a key adaptive trait using 16 populations of the brown anole lizard (Anolis sagrei). Mirroring natural variation, we established islands with short- or long-limbed lizards at both low and high densities. We then monitored changes in lower trophic levels, finding that on islands with short-limbed lizards at high-density, web spiders decreased and plants grew more via an indirect positive effect, likely through an herbivore-mediated trophic cascade. Our experiment provides strong support for evolution-to-ecology connections in nature, likely closing an otherwise well-characterized eco-evolutionary feedback loop.

openother-openJun 2023View details →

Harvey-Lab-UW/Buonanduci_etal_2023_EcolLett: Release of data and code for Buonanduci et al. 2023 Ecology Letters

This is the latest release of data for reproducing the analyses in the manuscript 'Consistent spatial scaling of high-severity wildfire can inform expected future patterns of burn severity' by Buonanduci, Donato, Halofsky, Kennedy, and Harvey, accepted for publication in Ecology Letters. See the main text of the manuscript for complete descriptions of how data were processed and analyzed. This information is licensed under a <a href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>. Any user of these data ("User" hereafter) is required to cite it appropriately in any publication that results from its use. These data may be actively used by others for ongoing research, so coordination may be necessary to prevent duplicate publication. The User is urged to contact the authors of these data for questions about methodology or results. The User is encouraged to consider collaboration or co-authorship with authors where appropriate. Misinterpretation of data may occur if used out of context of the original study. Substantial efforts are made to ensure accuracy of the data and documentation, however complete accuracy of data sets cannot be guaranteed. All data are made available as is. Data may be updated periodically and it is the responsibility of the User to check for new versions of the data. The authors and the repository where these data were obtained shall not be liable for damages resulting from any use or misinterpretation of the data.

Data from: Form function relationships support fast ecological shift in a lizard

Macroevolutionary changes such as variation in habitat use or diet are often associated with convergent, adaptive changes in morphology. However, it is still unclear how small-scale morphological variation at the population level can drive shifts in ecology as observed at a macroevolutionary scale. Here, we address this question by investigating how variation in cranial form and feeding mechanics relate to rapid changes in diet in an insular lizard (Podarcis siculus) after experimental introduction into a new environment. We first quantified differences in the skull and jaw muscle architecture between the source and introduced population using 3D geometric morphometrics and dissections. Next, we tested the impact of the observed variation in morphology on the mechanical performance of the masticatory system using computer-based biomechanical simulation techniques. Our results show that the small differences in shape, combined with variation in muscle architecture, can result in significant differences in performance allowing access to novel trophic resources. The confrontation of these data with the already described macroevolutionary relationships between cranial form and function in these insular lizards provides insights into how selection can, over relatively short time scales, drive major changes in ecology through its impact on mechanical performance.

Biophysical data for: Dispersive currents explain patterns of population connectivity in an ecologically and economically important fish

How to identify the drivers of population connectivity remains a fundamental question in ecology and evolution. Answering this question can be challenging in aquatic environments where dynamic lake and ocean currents coupled with high levels of dispersal and gene flow can decrease the utility of modern population genetic tools. To address this challenge, we used RAD-Seq to genotype 959 yellow perch (Perca flavescens), a species with an ~40-day pelagic larval duration (PLD), collected from 20 sites circumscribing Lake Michigan. We also developed a novel, integrative approach that couples detailed biophysical models with eco-genetic agent-based models to generate 'predictive' values of genetic differentiation. By comparing predictive and empirical values of genetic differentiation, we estimated the relative contributions for known drivers of population connectivity (e.g., currents, behavior, PLD). For the main basin populations (i.e., the largest contiguous portion of the lake), we found that high gene flow led to low overall levels of genetic differentiation among populations (FST = 0.003). By far the best predictors of genetic differentiation were connectivity matrices that were derived from periods of time when there were strong and highly dispersive currents. Thus, these highly dispersive currents are driving the patterns of population connectivity in the main basin. We also found that populations from the northern and southern main basin are slightly divergent from one another, while those from Green Bay and the main basin are highly divergent (FST = 0.11). By integrating biophysical and eco-genetic models with genome-wide data, we illustrate that the drivers of population connectivity can be identified in high gene flow systems.

opencc-zeroJul 2023View details →

Data from: Human activities modulate reciprocal effects of a subterranean ecological engineer rodent, Tachyoryctes macrocephalus, on Afroalpine vegetation cover

Human activities, directly and indirectly, impact ecological engineering activities of subterranean rodents. As engineering activities of burrowing rodents are affected by, and reciprocally affect vegetation cover via feeding, burrowing and mound building, human influence such as settlements and livestock grazing, could have cascading effects on biodiversity and ecosystem processes such as bioturbation. However, there is limited understanding of the relationship between human activities and burrowing rodents. The aim of this study was therefore to understand how human activities influence the ecological engineering activity of the giant root-rat (Tachyoryctes macrocephalus), a subterranean rodent species endemic to the Afroalpine ecosystem of the Bale Mountains of Ethiopia. We collected data on human impact, burrowing activity and vegetation during February and March of 2021. Using path analysis, we tested (1) direct effects of human settlement on the patterns of livestock grazing intensity, (2) direct and indirect impacts of humans and livestock grazing intensity on the root-rat burrow density, and (3) whether human settlement and livestock grazing influence the effects of giant root-rat burrow density on vegetation and vice versa. We found lower levels of livestock grazing intensity further from human settlement than in its proximity. We also found a significantly increased giant root-rat burrow density with increasing livestock grazing intensity. Seasonal settlement and livestock grazing intensity had an indirect negative and positive effect on giant root-rat burrow density, respectively, both via vegetation cover. Analysing the reciprocal effects of giant root-rat on vegetation, we found a significantly decreased vegetation cover with increasing density of giant root-rat burrows, and indirectly with increasing livestock grazing intensity via giant root-rat burrow density. Our results demonstrate that giant root-rats play a synanthropic engineering role that affects vegetation structure and ecosystem processes.

opencc-by-4.0Sep 2023View details →

The data used for the paper "Adapting a multiscale approach to assess the compositional diversity of landscapes" (Landscape Ecology)

The data consists of a single SimpleFeatures (sf) object with 267,813 rows, i.e. hexagons covering Hungary, and 89 variables. The following variables are contained by the data (Table 1.). <table> <caption>Table 1. Main attributes of the variables. For explanation of the vegetation type codes implied in the table by "XX", see the Supplementary Material S2 of Konrád et al. 2023.</caption> <thead> <tr> <th scope="col">Variable</th> <th scope="col">Description</th> </tr> </thead> <tbody> <tr> <td>id</td> <td>unique id of hexagons</td> </tr> <tr> <td>Bakony</td> <td>logical mask for subsetting the landscape Bakony</td> </tr> <tr> <td>Baranya</td> <td>logical mask for subsetting the landscape Baranya Hills</td> </tr> <tr> <td>ExternalSomogy</td> <td>logical mask for subsetting the landscape External Somogy</td> </tr> <tr> <td>HunGreatPlain</td> <td>logical mask for subsetting the landscape Hungarian Great Plain</td> </tr> <tr> <td>KorosMarosInterfluve</td> <td>logical mask for subsetting the landscape Körös-Maros Interfluve</td> </tr> <tr> <td>Mezofold</td> <td>logical mask for subsetting the landscape Mezőföld & Velence Hills</td> </tr> <tr> <td>NorthernHunMountains</td> <td>logical mask for subsetting the landscape Northern Hungarian Mountains</td> </tr> <tr> <td>Orseg</td> <td>logical mask for subsetting the landscape Őrség</td> </tr> <tr> <td>SouthernBukk</td> <td>logical mask for subsetting the landscape Southern Bükk</td> </tr> <tr> <td>binarized_potential_XX</td> <td>binarized potential vegetation data of the XX vegetation type</td> </tr> <tr> <td>binarized_actual_XX</td> <td> binarized potential vegetation data of the XX vegetation type </td> </tr> </tbody> </table>   References Konrád KD, Bede-Fazekas Á, Bartha S, Somodi I (2023) Adapting a multiscale approach to assess the compositional diversity of landscapes. Landscape Ecology.

opencc-zeroSep 2023View details →

Data from: Non-native mammals are weak candidates to substitute ecological function of native avian seed-dispersers in an island ecosystem

Although prominent examples exist of non-native species causing substantial ecological harm, many have neutral or positive effects, including filling surrogate roles once performed by extinct native organisms. We tested the ecological roles of two non-native mammals as seed dispersers or seed predators in Guåhan, which, due to invasive brown treesnakes (Boiga irregularis), is devoid of native seed dispersers – birds and bats. We conducted feeding trials with captive rats (Rattus spp.), which are present but uncommon due to predation by snakes, and pigs (Sus scrofa), which are abundant. We examined if and how they interacted with common forest fruits. We then compared how any gut-passed or handled seeds germinated compared to seeds left in whole fruit or depulped seeds. Rats and pigs interacted with most of the fruits and seeds (>80%) that they were fed. Of those, most seeds were destroyed – 78% for rats and 90% for pigs, across both native and non-native plant species. Compared to seeds germinating within whole fruits, rats improved germination of the seeds that they handled without ingesting, while pigs diminished the germination of seeds that they handled. The small percentage of seeds (approximately 1.5% for rats and 5% for pigs) that survived gut passage germinated in higher proportions than those in whole fruits. Percentages of seed survival to germination are lower than those found in similar studies with native avian frugivores. Our results indicate that pigs and rats have mixed effects on seeds, but are not suitable surrogates for native seed dispersers.

opencc-by-4.0Sep 2023View details →

Supplementary data for: "The demographic history of the wild crop relative Brachypodium distachyon is shaped by distinct past and present ecological niches"

Supplementary data to https://doi.org/10.1101/2023.06.01.543285

opencc-zeroSep 2023View details →

Data from: Genomic and transcriptomic analyses reveal polygenic architecture for ecologically-important functional traits in aspen (Populus tremuloides Michx.)

Intraspecific genetic variation in foundation species such as aspen (Populus tremuloides Michx.) shapes their impact on forest structure and function. Identifying genes underlying ecologically important traits is key to understanding that impact. Previous studies, using single-locus genome-wide association (GWA) analyses to identify candidate genes, have identified fewer genes than anticipated for highly heritable quantitative traits. Mounting evidence suggests that polygenic control of quantitative traits is largely responsible for this "missing heritability" phenomenon. Our research characterized the genetic architecture of 30 ecologically important traits using a common garden of aspen through genomic and transcriptomic analyses. A multilocus association model revealed that most traits displayed a highly polygenic architecture, with most variation explained by loci with small effects (likely below the detection levels of single-locus GWA methods). Consistent with a polygenic architecture, our single-locus GWA analyses found only 38 significant SNPs in 22 genes across 15 traits. Next, we used differential expression analysis on a subset of aspen genets with divergent concentrations of salicinoid phenolic glycosides (key defense traits). This complementary method to traditional GWA discovered 1,243 differentially expressed genes for a polygenic trait. Soft clustering analysis revealed three gene clusters (241 candidate genes) involved in secondary metabolite biosynthesis and regulation. Our work reveals that ecologically important traits governing higher-order community- and ecosystem-level attributes of a foundation forest tree species have complex underlying genetic structures and will require methods beyond traditional GWA analyses to unravel.