Find research datasets worth reusing

opencc-zeroDec 2017View details →

Data from: Boreal tree growth exhibits decadal-scale ecological memory to drought and insect defoliation, but no negative response to their interaction

1. Interactions between drought and insect defoliation may dramatically alter forest function under novel climate and disturbance regimes, but remain poorly understood. We empirically tested two important hypotheses regarding tree responses to drought and insect defoliation: 1) trees exhibit delayed, persistent, and cumulative growth responses to these stressors; 2) physiological feedbacks in tree responses to these stressors exacerbate their impacts on tree growth. These hypotheses remain largely untested at a landscape scale, yet are critical for predicting forest function under novel future conditions given the connection between tree growth and demographic processes such as mortality and regeneration. 2. We developed a Bayesian hierarchical model to quantify the ecological memory of tree growth to past water deficits and insect defoliation events, derive antecedent variables reflecting the persistent and cumulative effects of these stressors on current growth, and test for their interactive effects. The model was applied to extensive tree growth, weather, and defoliation survey data from western and eastern regions of the Canadian boreal forest impacted by recent drought and defoliation events and characterized by contrasting tree compositions, climates, and insect defoliators. 3. Results revealed persistent negative tree growth responses to past water (all trees) and defoliation (host trees) stress lasting 3-6 and 10-12 years, respectively, depending on study region. Accounting for the ecological memory of tree growth to water and defoliation stress allowed for detection of interactions not previously demonstrated. Contrary to expectations, we found evidence for positive interactions among non-host trees likely due to reduced water stress following defoliation events. Regional differences in ecological memory to water stress highlight the role of climate in shaping forest responses to drought. 4. Synthesis. Study results suggest negative feedbacks in tree responses to drought and insect attack may be weaker than predicted for defoliator-dominated boreal forest systems. Instead, insect defoliation may offset the impacts of water deficit on boreal tree growth by reducing transpirational water demand. This offset mimics increased resistance to drought following forest thinning and may lessen growth and mortality losses due to increased aridity and more severe insect damage forecast for the boreal forest under global change.

opencc-zeroAug 2019View details →

Data from: Comparative analysis of the shape and size of the middle ear cavity of turtles reveals no correlation with habitat ecology

The middle ear of turtles differs from other reptiles in being separated into two distinct compartments. Several ideas have been proposed as to why the middle ear is compartmentalized in turtles, most suggesting a relationship with underwater hearing. Extant turtle species span fully marine to strictly terrestrial habitats, and ecomorphological hypotheses of turtle hearing predict that this should correlate with variation in the structure of the middle ear due to differences in the fluid properties of water and air. We investigate the shape and size of the air-filled middle ear cavity of 56 extant turtles using 3D data and phylogenetic comparative analysis to test for correlations between habitat preferences and the shape and size of the middle ear cavity. Only weak correlations are found between middle ear cavity size and ecology, with aquatic taxa having proportionally smaller cavity volumes. The middle ear cavity of turtles exhibits high shape diversity among species, but we found no relationship between this shape variation and ecology. Surprisingly, the estimated acoustic transformer ratio, a key functional parameter of impedance-matching ears in vertebrates, also shows no relation to habitat preferences (aquatic/terrestrial) in turtles. We suggest that middle ear cavity shape may be controlled by factors unrelated to hearing, such as the spatial demands of surrounding cranial structures. A review of the fossil record suggests that the modern turtle ear evolved during the Early to Middle Jurassic in stem turtles broadly adapted to freshwater and terrestrial settings. This, combined with our finding that evolutionary transitions between habitats caused only weak evolutionary changes in middle ear structure, suggests that tympanic hearing in turtles evolved as a compromise between subaerial and underwater hearing.

opencc-by-4.0Nov 2016View details →

Data alignment and phylogenetic trees from Phylogeny, ecology, morphological evolution, and reclassification of the diatom orders Surirellales and Rhopalodiales

Alignment and tree files from Ruck et al. 2016: Phylogeny, ecology, morphological evolution, and reclassification of the diatom orders Surirellales and Rhopalodiales

opencc-zeroJul 2016View details →

Data for article Pesticide seed dressings can affect the activity of various soil organisms and reduce decomposition rate of plant material, BMC Ecology

Raw data for article "Pesticide seed dressings can affect the activity of various soil organisms and reduce decomposition rate of plant material" published in BMC Ecology

opencc-by-4.0Mar 2017View details →

Data supplementing the article "Assessing ecological status with diatoms DNA metabarcoding : scaling-up on a WFD monitoring network (Mayotte island, France)" V. Vasselon, F. Rimet, K. Tapolczai, A. Bouchez submitted to Ecological Indicators journal

These data supplement the article"Assessing ecological status with DNA metabarcoding or microscopy? Comparison using benthic diatoms in tropical rivers" V. Vasselon, F. Rimet, K. Tapolczai, A. Bouchez submitted to Ecological Indicators journal. The directory contains the following files: 80 PGM sequencing libraries (raw data, fastq files).rar - contains the 80 fastq files provided by the sequencing platform with demultiplexed DNA reads (raw data prior any bioinformatics treatments). 80 fastq files information.xlsx - contains the information relative to the 80 samples including: the ID used in Mothur analyses (corresponding to the name of the fastq files), the sample name, the sampling site code, the name of the river, the monitoring network to which rivers belong, the year of sampling and the GPS coordinates of sampling sites. OTU (95 percent of similarity) list of 80 Mayotte samples.xlsx - contains the final OTU list obtained after applying all the bioinformatics treatments (trimming, clustering,...): OTUs created at 95% of similarity, the number of DNA reads per sample was normalized at 5710 reads (the smallest values obtained in one sample). A DNA representative sequence and the taxonomic assignment determined using Mothur (using classify.otu command) are also provided for each OTU.

opencc-zeroOct 2023View details →

Opening the museum's vault: Historical field records preserve reliable ecological data

Museum specimens have long served as foundational data sources for ecological, evolutionary, and environmental research. Continued reimagining of museum collections is now also generating new types of data associated with, but beyond physical specimens, a concept known as "extended specimens". Field notes penned by generations of naturalists contain first-hand ecological observations associated with museum collections and comprise a form of extended specimens with the potential to provide novel ecological data spanning broad geographic and temporal scales. Despite their data-yielding potential, however, field notes remain underutilized in research due to their heterogeneous, unstandardized, and qualitative nature. We introduce an approach for transforming descriptive ecological notes into quantitative data suitable for statistical analysis. Tests with simulated and real-world published data show that field notes and our transformation approach retain reliable quantitative ecological information under a range of sample sizes and evolutionary scenarios. Unlocking the wealth of data contained within field records could facilitate investigations into the ecology of clades whose diversity, distribution, or other demographic features present challenges to traditional ecological studies, improve our understanding of long-term environmental and evolutionary change, and enhance predictions of future change.

opencc-zeroNov 2023View details →

Data from: Hunting behavior and feeding ecology of Mojave Rattlesnakes (Crotalus scutulatus), Prairie Rattlesnakes (C. viridis), and their hybrids in southwestern New Mexico

Predators must contend with numerous challenges to successfully find and subjugate prey. Complex traits related to hunting are partially controlled by a large number of co-evolved genes which may be disrupted in hybrids. Accordingly, research on the feeding ecology of animals in hybrid zones has shown that hybrids sometimes exhibit transgressive or novel behaviors, yet for many taxa empirical studies of predation and diet across hybrid zones is lacking. We undertook the first such field study for a hybrid zone between two snake species, the Mojave Rattlesnake (Crotalus scutulatus) and Prairie Rattlesnake (C. viridis). Specifically, we leveraged established field methods to quantify hunting behaviors of animals, their prey communities, and diet of individuals across the hybrid zone in southwestern New Mexico, USA. We found that, even though hybrids had significantly lower body condition indices than snakes from either parental lineage, hybrids were generally similar to non-hybrids in hunting behavior, prey encounter rates, and predatory attack and success. We also found that, compared to C. scutulatus, C. viridis was significantly more active while hunting at night and abandoned ambush sites earlier in the morning, and hybrids tended to be more viridis-like in this respect. Prey availability was similar across the study sites, including within the hybrid zone, with Kangaroo Rats (Dipodomys spp.) as the most common small mammal both in habitat surveys and frequency of encounters with hunting rattlesnakes. Analysis of prey remains in stomachs and feces also showed broad similarity in diets, with all snakes preying primarily on small mammals and secondarily on lizards. Taken together, our results suggest that the significantly lower body condition of hybrids does not appear to be driven by differences in their hunting behavior or diet, and may instead relate to metabolic efficiency or other physiological traits we have not yet identified.

opencc-zeroNov 2023View details →

Data from: Functional trait plasticity diverges between sexes in African cichlids: a contribution toward ecological sexual dimorphism?

Phenotypic plasticity enables development to produce multiple phenotypes in response to environmental conditions. Plasticity driven variation has been suggested to play a key role in adaptive divergence, and plasticity itself can evolve. However, the interaction of plasticity with the multiple levels involved with adaptive divergence is less understood. For example, sexual dimorphism can contribute to adaptive variation through ecological sexual dimorphism (ESD), but the contribution of plasticity to this phenomenon is unknown. Therefore, to determine the potential contribution of plasticity to ESD, we used the adaptive radiation of Malawi cichlids. Two mouthbrooding species (Labeotropheus fuelleborni and Tropheops "Red Cheek", hereafter LF and TRC respectively) with differences in foraging tactics underwent foraging experiments using benthic and limnetic treatments while accounting for sex. Plasticity in craniofacial shape and three functionally important traits were measured. Plasticity was shown, but without any sex-based differences in shape. However, for mechanical advantage traits of the mandible sex by diet interactions were found. This suggests that ESD, may be influenced by phenotypic plasticity that diverges between sexes. Given the involvement of the mandible in parental care in cichlids this may indicate that sexual divergence in plasticity may trade-off against maternal care tactics.

opencc-zeroNov 2023View details →

Opsin data from: Multiple axes of visual system diversity in Ithomiini, an ecologically diverse tribe of mimetic butterflies

The striking structural variation seen in arthropod visual systems can be explained by the overall quantity and spatio-temporal structure of light within habitats coupled with developmental and physiological constraints. However, little is currently known about how fine-scale variation in visual structures arise across shorter evolutionary and ecological scales. In this study, we characterise patterns of interspecific (between species), intraspecific (between sexes) and intraindividual (between eye regions) variation in the visual system of four ithomiine butterfly species. These species are part of a diverse 26-Myr-old Neotropical radiation where changes in mimetic colouration are associated with fine-scale shifts in ecology, such as microhabitat preference. By using a combination of selection analyses on visual opsin sequences, in-vivo ophthalmoscopy, micro-computed tomography (micro-CT), immunohistochemistry, confocal microscopy, and neural tracing, we quantify and describe physiological, anatomical, and molecular traits involved in visual processing. Using these data, we provide evidence of substantial variation within the visual systems of Ithomiini, including: i) relaxed selection on visual opsins, perhaps mediated by habitat preference, ii) interspecific shifts in visual system physiology and anatomy, and iii) extensive sexual dimorphism, including the complete absence of a butterfly-specific optic neuropil in the males of some species. We conclude that considerable visual system variation can exist within diverse insect radiations, hinting at the evolutionary lability of these systems to rapidly develop specialisations to distinct visual ecologies, with selection acting at both the perceptual, processing, and molecular level.

opencc-zeroDec 2023View details →

Data from: Loss and recovery of ecological diversity associated with evolutionary rescue in abruptly and gradually deteriorating environments

Populations may survive environmental deterioration by evolutionary adaptation. However, such evolutionary rescue events may be associated with ecological costs, such as reduction in growth performance and loss of ecologically important genetic diversity. Those negative ecological consequences may be mitigated by additional adaptive evolution. Both the ecological costs and the opportunities for additional evolution are contingent on the severity of environmental deterioration. Here we hypothesize that populations evolutionarily rescued from faster, relative to slow, environmental deterioration suffer more severe long-term fitness decline and diversity loss. An experiment with the model adaptive radiation of bacterium Pseudomonas fluorescens exposed to abruptly or gradually increased antibiotic stress supported our hypothesis. The effect of additional adaptive evolution in recovering population size and ecological diversity was far from perfect. Cautions are therefore needed in predicting the role of rapid evolution for mitigating the impacts of environmental changes, in particular very fast environmental deterioration. We also found that bacterial populations rescued from gradually increased antibiotic stress evolved higher levels of antibiotic resistance, lending more support to aggressive chemotherapy in pathogen control.

Additional morphometrical and ecological data collected during the 2018 expedition of the UMMZ in Nicaragua

Nicaragua is a biodiverse country, but documented herpetological specimens are underrepresented when compared to other neighboring countries. In 2018 we conducted a collaborative expedition between the University of Michigan Museum of Zoology and Nicaraguan biologists. We visited three collection sites in the Pacific lowlands, Caribbean lowlands, and the Central Highlands, representing three major biogeographic regions. We collected specimens of 100 species from a total of 106 encountered. We provide accession numbers, morphological, genetic, and ecological information for these specimens. We recorded 23 new departmental and the first country record of Metlapilcoatlus indomitus (Smith & Ferrari-Castro, 2008), helping filling gaps in the known distribution of the species within Nicaragua and the Central American region. When available, we provide species range maps and comparative genetic tree including conspecific reference sequences from the region.

Data associated with: A phylogenetic perspective on ecological specialisation reveals hummingbird and insect pollinators have generalist diets

Specialisation in food resource use is a crucial process that fosters species coexistence in plant-animal networks, contributing to the maintenance of biodiversity, ecological complexity, and community stability. Notably, although there is a vast literature on ecological specialisation in pollination systems, the evolutionary similarity among the plant species visited by particular pollinators has been largely ignored. Here, we apply a robust phylogenetic approach to analyse whether the evolutionary relatedness of plant species is a significant factor in mediating pollinator visits and how it relates to the morphology of interacting species. We quantified ecological and clade specialisation of hummingbird and insect species in three mutualistic networks from the Costa Rican highlands and associated these metrics with species traits. We found that hummingbirds were overall ecologically more specialised than insects (i.e. visited a less diverse set of plant species). However, when evaluating the phylogenetic relatedness among the visited plant species, all hummingbird species and most insects had overdispersed diets, which indicates they visited phylogenetically distant plant species in the community. Moreover, a great proportion of these clade generalists visited plant species with a great variation in corolla length, showing a lack of preference for this morphological trait. Altogether, our results demonstrate that by incorporating plant phylogeny to network analysis, pollinator species were generalists and that corolla length weakly influences plant-pollinator interactions in the three studied networks. A phylogenetic perspective should occupy a central role in the study of specialisation since it contributes to understanding the interplay between ecological and evolutionary processes in mutualistic networks. Future research should focus on evaluating whether the phylogenetic structure of animal diets mediates patterns of interactions in different types of mutualisms and environmental contexts, linking these patterns to other floral traits. This knowledge may be valuable for deepening our comprehension of the underlying mechanisms shaping ecological networks.

Stem data from first three censuses on the University of California Santa Cruz Forest Ecology Research Plot

Here we present stem-based data from the first three censuses of the 16-ha UC Santa Cruz Forest Ecology Research Plot, located in the Mediterranean climate forest of coastal central California, USA. The forest includes both mixed evergreen forest and redwood-dominated forest, and is recovering from significant logging disturbance in the early 20th century. Each woody stem with diameter larger than 1 cm has been mapped, tagged, identified, and measured, with censuses on a ~5-year interval. The first census (FERP1) began in 2007, and included just 6 ha. During FERP2, begun in 2011, the plot was expanded to 16 ha. The FERP3 census was begun in 2017. The community includes 34 woody species, including 4 gymnosperm and 9 angiosperm tree species, 18 species of shrubs, and 3 species of lianas. Across the three censuses, we report identity, size, location, and mortality data from 48,556 stems of 31,206 mapped individuals.

Data from: Ecological character displacement among Nothobranchius annual killifishes in Tanzania

Divergent ecological character displacement (ECD) is the competition-driven divergence in resource use-related phenotypic traits between coexisting species. It is considered one of the primary drivers of ecological diversification and adaptive radiation. We analyzed phenotypic and ecological variation in two African annual killifish species of the genus Nothobranchius; N. eggersi and N. melanospilus in sympatry and N. melanospilus in allopatry. Our aim was to test if allopatric and sympatric populations of N. melanospilus differ morphologically from each other and from N. eggersi, and examine if these differences are consistent with the predictions of ECD. We find that sympatric N. melanospilus differ from allopatric N. melanospilus and differ from N. eggersi more strongly than the latter. Our data satisfy four criteria for demonstrating ECD: Differences in phenotypes between allopatric and sympatric N. melanospilus are greater than expected by chance; the divergence pattern between allopatric and sympatric N. melanospilus results from an evolutionary shift rather than from ecological sorting; morphological differences observed reflect differences in resource use and, lastly, sites of allopatry and sympatry do not differ in food resource availability or other ecological conditions. Our results suggest that competition is the main driver of the observed divergence between two N. melanospilus populations.

opencc-zeroFeb 2024View details →

Data for: Coherent long-term body-size responses across all Northwest Atlantic herring populations to warming and environmental change despite contrasting harvest and ecological factors

Body size is a key component of individual fitness and an important factor in the structure and functioning of populations and ecosystems. Disentangling the effects of environmental change, harvest, and intra- and inter-specific trophic effects on body size remains challenging for populations in the wild. Herring in the Northwest Atlantic provide a strong basis for evaluating hypotheses related to these drivers given that they have experienced significant warming and harvest over the past century, while also having been exposed to a wide range of other selective constraints across their range. Using data on mean length-at-age 4 for the sixteen principal populations over a period of 53 cohorts (1962-2014), we fitted a series of empirical models for temporal and between-population variation in the response to changes in sea surface temperature. We find evidence for a unified cross-population response in the form of a parabolic function according to which populations in naturally warmer environments have responded more negatively to increasing temperature compared with those in colder locations. Temporal variation in residuals from this function was highly coherent among populations, further suggesting a common response to a large-scale environmental driver. The synchrony observed in this study system, despite strong differences in harvest and ecological histories among populations and over time, clearly indicates a dominant role of environmental change on size-at-age in wild populations, in contrast to commonly reported effects of fishing. This finding has important implications for the management of fisheries as it indicates that a key trait associated with population productivity may be under considerably less short-term management control than currently assumed. Our study, overall, illustrates the need for a comparative approach within species for inferences concerning the many possible effects on body size of natural and anthropogenic drivers in the wild.

opencc-by-4.0Jan 2024View details →

Data and Code for "Urban socioeconomic variation influences the ecology and evolution of trophic interactions"

Data and code required for all analyses in Urban socioeconomic variation influences the ecology and evolution of trophic interactions.  <a href="../api/files/5ca97a29-9947-482a-9095-5a54c40c57f0/Gall_Data_2022_new.csv">Gall_Data_2022_new.csv</a> contains data for gall predation and diameter measurements. <a href="../api/files/5ca97a29-9947-482a-9095-5a54c40c57f0/Goldrod_Gall_Density.csv">Goldrod_Gall_Density.csv</a> contains goldenrod and gall density measurements for each site. <a href="../api/files/5ca97a29-9947-482a-9095-5a54c40c57f0/GallSitesFinal.csv">GallSitesFinal.csv</a> contains location data for all study sites. <a href="../api/files/5ca97a29-9947-482a-9095-5a54c40c57f0/DisseminationAreaCodes.csv">DisseminationAreaCodes.csv</a> contains codes for each site location needed to obtain census data. Full descriptions of data are included in <a href="../api/records/10702694/draft/files/README.txt/content" target="_blank" rel="noopener noreferrer">README.txt</a> The script <a href="../api/records/10640975/draft/files/DataCleaning.R/content" target="_blank" rel="noopener noreferrer">DataCleaning.R</a> assembles the above four datasets with environmental and census data to produce the final dataset: <a href="../api/files/5ca97a29-9947-482a-9095-5a54c40c57f0/MartinElGalmady%26Johnson2023_cleandataset.csv">MartinElGalmady&Johnson2023_cleandataset.csv</a> and the supplemental dataset with galls with early larval death removed: <a href="../api/records/10640975/draft/files/NoELD_dataset.csv/content" target="_blank" rel="noopener noreferrer">NoELD_dataset.csv</a> <a href="../api/records/10640975/draft/files/Analysis.R/content" target="_blank" rel="noopener noreferrer">Analysis.R</a> provides the code for conducting analyses and producing figures using the <a href="../api/files/5ca97a29-9947-482a-9095-5a54c40c57f0/MartinElGalmady%26Johnson2023_cleandataset.csv">MartinElGalmady&Johnson2023_cleandataset.csv</a> dataset (or the <a href="../api/records/10640975/draft/files/NoELD_dataset.csv/content" target="_blank" rel="noopener noreferrer">NoELD_dataset.csv</a> for supplemental analyses with early larval death removed). Detailed descriptions of the final dataset are included in <a href="../api/records/10702694/draft/files/cleandataset_metadata.csv/content" target="_blank" rel="noopener noreferrer">cleandataset_metadata.csv</a> (NoELD_dataset has the same rows and columns as the full dataset).  All code was run in R verison 4.2.2

opencc-by-4.0Oct 2023View details →

Supporting data for the paper "Investigating Potential Ecological Benefits from Mariculture"

This dataset provides the parameter data used for calculation, the generated resulting data, and data files uploaded as Supporting Information.

opencc-zeroDec 2023View details →

Data from: Geography and ecology shape the phylogenetic composition of Amazonian tree communities

Aim: Amazonia hosts more tree species, from numerous evolutionary lineages both young and ancient, than any other biogeographic region. Previous studies have shown that tree lineages colonised multiple edaphic environments and dispersed widely across Amazonia, leading to a hypothesis, which we test, that lineages should not be strongly associated with either geographic regions or edaphic forest types. Location: Amazonia. Taxon: Angiosperms (Magnoliids; Monocots; Eudicots). Methods: Data for the abundance of 5,082 tree species in 1,989 plots were combined with a mega-phylogeny. We applied evolutionary ordination to assess how phylogenetic composition varies across Amazonia. We used variation partitioning and Moran's eigenvector maps (MEM) to test and quantify the separate and joint contributions of spatial and environmental variables to explain the phylogenetic composition of plots. We tested the indicator value of lineages for geographic regions and edaphic forest types and mapped associations onto the phylogeny. Results: In the terra firme and várzea forest types, phylogenetic composition varies by geographic region, but the igapó and white-sand forest types retain a unique evolutionary signature regardless of region. Overall, we find that soil chemistry, climate, and topography explain 24% of the variation in phylogenetic composition, with 79% of that variation being spatially structured (R 2 = 19% overall for combined spatial/environmental effects). Phylogenetic composition also shows substantial spatial patterns not related to the environmental variables we quantified (R 2 = 28%). A greater number of lineages were significant indicators of geographic regions than forest types. Main conclusions: Numerous tree lineages, including some ancient ones (>66 Ma), show strong associations with geographic regions and edaphic forest types of Amazonia. This shows that specialization on specific edaphic environments has played a long-standing role in the evolutionary assembly of Amazonian forests. Furthermore, many lineages, even those that have dispersed across Amazonia, dominate within a specific region, likely because of phylogenetically conserved niches for environmental conditions that are prevalent within regions.

opencc-zeroApr 2024View details →

Data from: Historical field records reveal habitat as an ecological correlate of locomotor phenotypic diversity in the radiation of Neotropical Geophagini fishes

Phenotypic macroevolutionary studies provide insight into how ecological processes shape biodiversity. However, the complexity of phenotype-ecology relationships underscores the importance of also validating phenotype-based ecological inference with direct evidence of resource use. Unfortunately, macroevolutionary scale ecological studies are often hindered by the challenges of acquiring taxonomically and spatially representative ecological data for large and widely distributed clades. The South American cichlid fish tribe Geophagini represents a continentally distributed radiation whose early locomotor morphological divergence suggests habitat as one ecological correlate of diversification, but an association between locomotor traits and habitat preference has not been corroborated. Field notes accumulated over decades of collecting across South America provide first-hand environmental records that can be mined for habitat data in support of macroevolutionary ecological research. In this study, we applied a newly developed method to transform descriptive field note information into quantitative habitat data, and used it to assess habitat preference and its relationship to locomotor morphology in Geophagini. Field note-derived data shed light on geophagine habitat use patterns and reinforced habitat as an ecological correlate of locomotor morphological diversity. Our work emphasizes the rich data potential of museum collections, including often overlooked material such as field notes, for evolutionary and ecological research.