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76 results for “Comparative ecology”
Data from: Comparative ecological and behavioral study of Macaca assamensis and M. mulatta in Shivapuri Nagarjun National Park, Nepal
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Reconstructing locomotor ecology of extinct avialans: a case study of Ichthyornis comparing sternum morphology and skeletal proportions
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Data from: Comparing traditional and Bayesian approaches to ecological meta-analysis
<p>1. Despite the wide application of meta-analysis in ecology, some of the traditional methods used for meta-analysis may not perform well given the type of data characteristic of ecological meta-analyses.</p> <p>2. We reviewed published meta-analyses on the ecological impacts of global climate change, evaluating the number of replicates used in the primary studies (ni) and the number of studies or records (k) that were aggregated to calculate a mean effect size. We used the results of the review in a simulation experiment to assess the performance of conventional frequentist and Bayesian meta-analysis methods for estimating a mean effect size and its uncertainty interval.</p> <p>3. Our literature review showed that ni and k were highly variable, distributions were right-skewed, and were generally small (median ni =5, median k=44). Our simulations show that the choice of method for calculating uncertainty intervals was critical for obtaining appropriate coverage (close to the nominal value of 0.95). When k was low (<40), 95% coverage was achieved by a confidence interval based on the t-distribution that uses an adjusted standard error (the Hartung-Knapp-Sidik-Jonkman, HKSJ), or by a Bayesian credible interval, whereas bootstrap or z-distribution confidence intervals had lower coverage. Despite the importance of the method to calculate the uncertainty interval, 39% of the meta-analyses reviewed did not report the method used, and of the 61% that did, 94% used a potentially problematic method, which may be a consequence of software defaults.</p> <p>4. In general, for a simple random-effects meta-analysis, the performance of the best frequentist and Bayesian methods were similar for the same combinations of factors (k and mean replication), though the Bayesian approaches had higher than nominal (>95%) coverage for the mean effect when k was very low (k<15). Our literature review suggests that many meta-analyses that used z-distribution or bootstrapping confidence intervals may have over-estimated the statistical significance of their results when the number of studies was low; more appropriate methods need to be adopted in ecological meta-analyses.</p>
Data from: Comparative ecological transcriptomics and the contribution of gene expression to the evolutionary potential of a threatened fish
Understanding whether small populations with low genetic diversity can respond to rapid environmental change via phenotypic plasticity is an outstanding research question in biology. RNA sequencing (RNA-seq) has recently provided the opportunity to examine variation in gene expression, a surrogate for phenotypic variation, in non-model species. We used a comparative RNA-seq approach to assess expression variation within and among adaptively divergent populations of a threatened freshwater fish, Nannoperca australis, found across a steep hydroclimatic gradient in the Murray-Darling Basin, Australia. These populations evolved under contrasting selective environments (e.g. dry/hot lowland; wet/cold upland) and represent opposite ends of the species' spectrum of genetic diversity and population size. We tested the hypothesis that environmental variation among isolated populations has driven the evolution of divergent expression at ecologically important genes using differential expression (DE) analysis and an ANOVA-based comparative phylogenetic expression variance and evolution model framework based on 27,425 de novo assembled transcripts. Additionally, we tested whether gene expression variance within-populations was correlated with levels of standing genetic diversity. We identified 290 DE candidate transcripts, 33 transcripts with evidence for high expression plasticity, and 50 candidates for divergent selection on gene expression after accounting for phylogenetic structure. Variance in gene expression appeared unrelated to levels of genetic diversity. Functional annotation of the candidate transcripts revealed variation in water quality is an important factor influencing expression variation for N. australis. Our findings suggest that gene expression variation can contribute to the evolutionary potential of small populations.
Data from: Comparative feeding behaviour of native and introduced terrestrial snails tracks their ecological impacts
A developing body of theory and empirical evidence suggest that feeding behaviour as measured by the functional response (FR) can assist researchers in assessing the relative potential ecological impacts and competitive abilities of native and introduced species. Here, we explored the FRs of two land snails that occur in SW Ontario, one native (Mesodon thyroidus) and one non-indigenous (Cepaea nemoralis) to Canada. The non-indigenous species appears to have low ecological impact and inferior competitive abilities. Consistent with theory, while both species conformed to Type II functional responses, the native species had a significantly higher attack rate (5.30 vs 0.41, respectively) and slightly lower handling time (0.020 vs. 0.023), and hence a higher maximum feeding rate (50.0 vs 43.5). The non-indigenous species exhibited a significantly longer time to contact for a variety of food types, and appeared less discriminating of paper that was offered as a non-food type. The non-indigenous species also ate significantly less food when in mixed species trials with the native snail. These feeding patterns match the known low ecological impact of the introduced snail and are consistent with the view that it is an inferior competitor relative to the native species. However, field experimentation is required to clarify whether the largely microallopatric distributions of the two species in SW Ontario reflect competitive dominance by the native species or other factors such as habitat preference, feeding preferences or predator avoidance. The relative patterns of feeding behaviour and ecological impact are, however, fully in line with recent functional response theory and application.
Data from: Comparative multi-locus phylogeography of two Palaearctic spruce bark beetles: influence of contrasting ecological strategies on genetic variation
While phylogeographic patterns of organisms are often interpreted through past environmental disturbances, mediated by climate changes, and geographic barriers, they may also be strongly influenced by species-specific traits. To investigate the impact of such traits, we focused on two Eurasian spruce bark beetles that share a similar geographic distribution, but differ in their ecology and reproduction. Ips typographus is an aggressive tree-killing species characterized by strong dispersal, whereas Dendroctonus micans is a discrete inbreeding species (sib mating is the rule), parasite of living trees and a poor disperser. We compared genetic variation between the two species over both beetles' entire range in Eurasia with five independent gene fragments, to evaluate whether their intrinsic differences could have an influence over their phylogeographic patterns. We highlighted widely divergent patterns of genetic variation for the two species and argue that the difference is indeed largely compatible with their contrasting dispersal strategies and modes of reproduction. In addition, genetic structure in I. typographus divides European populations in a northern and a southern group, as was previously observed for its host plant, and suggests past allopatric divergence. A long divergence time was estimated between East Asian and other populations of both species, indicating their long-standing presence in Eurasia, prior to the last glacial maximum. Finally, the strong population structure observed in D. micans for the mitochondrial locus provides insights into the recent colonization history of this species, from its native European range to regions where it was recently introduced.
Data from: Selection and genomic differentiation during ecological speciation: isolating the contributions of host association via a comparative genome scan of Neochlamisus bebbianae leaf beetles
This study uses a comparative genome scan to evaluate the contributions of host plant related divergent selection to genetic differentiation and ecological speciation in maple- and willow-associated populations of Neochlamisus bebbianae leaf beetles. For each of 15 pairwise population comparisons, we identified "outlier loci" whose strong differentiation putatively reflects divergent selection. Of 447 AFLP loci, 15% were outliers across multiple population comparisons, and low linkage disequilibrium indicated that these outliers derived from multiple regions of the genome. Outliers were further classified as "host-specific" if repeatedly observed in "different-host" population comparisons but never in "same-host" comparisons. Outliers exhibiting the opposite pattern were analogously classified as "host-independent." Host-specific outliers represented 5% of all loci and were more frequent than host-independent outliers, thus revealing a large role for host-adaptation in population genomic differentiation. Evidence that host-related selection can promote divergence despite gene flow was provided by population trees. These were structured by host-association when datasets included host-specific outliers, but not when based on neutral loci, which united sympatric populations. Lastly, three host-specific outliers were highly differentiated in all nine different-host comparisons. Because host-adaptation promotes reproductive isolation in these beetles, these loci provide promising candidate gene regions for future molecular studies of ecological speciation.
Data from: Comparing convenience and probability sampling for urban ecology applications
1. Urban forest ecosystems confer multiple ecosystem services. There is thus a need to quantify ecological characteristics in terms of community structure and composition so that benefits can be better understood in ecosystem service models. Efficient sampling and monitoring methods are crucial in this process. 2. Full tree inventories are scarce due to time and financial constraints, thus a variety of sampling methods exist. Modern vegetation surveys increasingly use stratified-random plot-based sampling to reduce the bias associated with convenience sampling, even though the latter can save time and increase species richness scores. The urban landscape, with a high degree of conspecific clustering and high species diversity, provides a unique biogeographical case for comparing these two methodological approaches. 3. We use two spatially extensive convenience samples of the urban forest of Meran (Italy) and compare the community structure, tree characteristics and ecosystem service provision with 200 random circular plots. 4. The convenience sampling resulted in a higher species diversity, incorporating more rare species. This is a result of covering more area per unit sampling time. Pseudorandom sub-plots were compared to the random plots revealing similar Shannon diversity and sampling comparability indices. Measured tree variables (diameter at breast height, height, tree-crown width, height to crown base) were similar between the two methods, as were ecosystem service model outputs. 5. Synthesis and applications. The results suggest that convenience sampling may be a time and money saving alternative to random sampling as long as stratification by land-use type is incorporated into the design. The higher species richness can potentially improve the accuracy of urban ecological models, which rely on species-specific functional traits.
Data from: No evidence for larger leaf trait plasticity in ecological generalists compared to specialists
Aim: Phenotypic plasticity is hypothesized to contribute to a species' capacity to occupy broader ranges of conditions and to optimally exploit resource-rich environments. Although this is supported by case studies of individual species, we do not know whether larger plasticity in functional traits is generally associated with ecological characteristics of species such as their niche breadth or niche position. Here, we test whether there is such a relationship for plasticity in leaf functional traits. Location: Central Europe. Methods: We surveyed 110–132 grassland plant species for plasticity in five leaf traits [leaf thickness, leaf greenness, specific leaf area, leaf dry matter content (LDMC) and plant height] and for biomass changes in response to experimental fertilization, shading and waterlogging. Trait plasticity and changes in biomass were compared with species niche characteristics along three environmental axes (light, nutrient and soil moisture) derived from a vegetation-plot database. Results: Although response of several traits to experimental treatments correlated with niche position and breadth (change in leaf thickness, greenness and biomass in response to fertilization; change in LDMC due to shading; and change in plant height and biomass due to waterlogging), we did not find evidence that species with broader niches or species from resource-rich environments are more plastic. Ecological generalists even turned out to be less plastic in some traits, including leaf thickness after fertilization and waterlogging. Generalists also displayed smaller plastic response averaged across all five traits ('composite plasticity'), though the relationship was not statistically significant. This composite plasticity was positively related to absolute change in biomass in all experimental treatments. Main conclusions: Our results suggest that larger species-level plasticity in leaf traits is not necessarily associated with a capacity to occupy a broader range of environments or with growth in resource-rich habitats; rather, it may indicate species' sensitivity to environmental changes.
Data, Metadata, R-codes and R data files for publication "Comparative ungulate diversity and biomass change with human use and drought: implications for community stability and protected area prioritization in African savannas" by Bartzke et al. in Ecology and Evolution
<p>These files contain data and metadata for modeling ungulate diversity and biomass in the Maasai Mara ecosystem in Kenya in the drought year of 1999 and a year with normal rainfall, 2002. The files also contain R codes and R data files.</p> <p>Metadata.pdf: Metadata for files "mc_333m.csv" and "mc_1km.csv"</p> <p>mc_333m.csv: A data file for 333-meter-by-333-meter sub-blocks.</p> <p>prepare_data.r: R code to impute missing vegetation records in 333-meter-by-333-meter subblocks and summarize the data over 1-kilometer-by-1-kilometer blocks for analysis.</p> <p>krige_vegetation.RData: An R data file containing the imputed vegetation records.</p> <p>mc_1km.csv: A data file for 1-kilometer-by-1-kilometer blocks for analysis.</p> <p>mc_1km.r: R code for modeling ungulate diversity and biomass; mc_1km_mod.RData: An R data file for loading the ungulate diversity and biomass models.</p> <p>mc_1km.RData: An R data file containing model predictions of ungulate diversity and biomass.</p> <p>mc_1km_plots.r: R code for plotting model predictions of ungulate diversity and biomass.</p> <p>MMNR_boundary.shp: A shapefile of the Maasai Mara National Reserve boundary in Kenya and associated files. These files are used for plotting the predictions of ungulate diversity and biomass.</p> <p>MMNR_border.zip: A shapefile and associated files for the Maasai Mara National Reserve border with Tanzania. These files are also used for plotting predictions of ungulate diversity and biomass.</p>
Fig. 5 in Comparative Analysis of the Ecological Functions of Dung Removal and Seed Dispersal among Two Telecoprid and Two Paracoprid Dung Beetles (Coleoptera: Scarabaeidae: Scarabaeinae)
Fig. 5. Box plots of the median, first, and third quartile, and lower and upper limits of dung removal by standardized 1-g biomass of Canthon rutilans cyanescens, Deltochilum multicolor, Dichotomius sericeus, and Phanaeus splendidulus exposed to dog feces for two and seven days. Plots with the same letter are not significantly different (Tukey test, P> 0.05).
Fig. 4 in Comparative Analysis of the Ecological Functions of Dung Removal and Seed Dispersal among Two Telecoprid and Two Paracoprid Dung Beetles (Coleoptera: Scarabaeidae: Scarabaeinae)
Fig. 4. Comparative analysis of dung removal and secondary dispersal of small and large seeds by single male/ female pair of Canthon rutilans cyanescens (Cr), Deltochilum multicolor (Dm), Dichotomius sericeus (Ds), and Phanaeus splendidulus (Ps) exposed to dog feces for two and seven days. Squares with the same letter and color are not significantly different (Tukey test, P> 0.05).
Fig. 3 in Comparative Analysis of the Ecological Functions of Dung Removal and Seed Dispersal among Two Telecoprid and Two Paracoprid Dung Beetles (Coleoptera: Scarabaeidae: Scarabaeinae)
Fig. 3. Box plots of the median, first, and third quartile, and lower and upper limits of dung removal and secondary seed dispersal by two paracoprid dung beetles as single male/female pair and three male/female pairs exposed to dog feces for two, seven, and 21 days. A) Dung removal capacity, B) Small seed dispersal, and C) Large seed dispersal by Dichotomius sericeus. D) Dung removal capacity, E) Small seed dispersal, and F) Large seed dispersal by Phanaeus splendidulus. Plots with the same letter are not significantly different (Tukey test, P> 0.05).
Fig. 1 in Comparative Analysis of the Ecological Functions of Dung Removal and Seed Dispersal among Two Telecoprid and Two Paracoprid Dung Beetles (Coleoptera: Scarabaeidae: Scarabaeinae)
Fig. 1. Arenas for the study of dung removal and secondary seed dispersal by dung beetles. A) Arena for telecoprids with 30 g of dyed feces divided into three portions of 10 g each with a variable number of artificial seeds, B) Closed arena covered with veil-type fabric, C) Arena protected from rain. D, E, and F show the same sequence for the arenas for paracoprids.
Fig. 2 in Comparative Analysis of the Ecological Functions of Dung Removal and Seed Dispersal among Two Telecoprid and Two Paracoprid Dung Beetles (Coleoptera: Scarabaeidae: Scarabaeinae)
Fig. 2. Box plots of the median, first, and third quartile, and lower and upper limits of dung removal and secondary seed dispersal by two telecoprid dung beetles as single male/female pair and three male/female pairs exposed to dog feces for two, seven, and 21 days. A) Dung removal capacity, B) Small seed dispersal, and C) Large seed dispersal by Canthon rutilans cyanescens. D) Dung removal capacity, E) Small seed dispersal, and F) Large seed dispersal by Deltochilum multicolor. Plots with the same letter are not significantly different (Tukey test, P> 0.05).
Identifying environmentally-comparable cities across the globe for urban ecology studies
<p>Defining a comprehensive and quantitative framework for comparing urban areas is a priority for conducting research in urban ecology and related fields. In this study, we use unsupervised learning on a matrix of climate- and human-related features to estimate the number of groups explaining the characteristics of ~6,000 cities across the globe. Using estimates of city-level stability within clusters, we estimate that cities can be clustered in 5–7 clusters, with 6 being the most likely and stable number of groups. Groups of cities are primarily defined by climatic and geographical features (e.g. elevation), with population-level and land use parameters being less relevant for structuring cities. City clusters generally correspond with a continental-based partitioning. However, geographic distances between cities do not necessarily reflect their position in the examined multivariate space. The analytical framework presented in this paper can be extended to accounting for alternative features to describing cities and their characteristics. We implement an online web application for comparing cities across the globe based on the results presented in this study. This application is expected to inform decisions on where to sample populations or species in cities with either similar or divergent climatic conditions.</p>
Data from: Natural enemy ecology: comparing the effects of predation risk, infection risk and disease on host behavior
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Data from: Comparative multi-locus phylogeography of two Palaearctic spruce bark beetles: influence of contrasting ecological strategies on genetic variation
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Data from: Comparative feeding behaviour of native and introduced terrestrial snails tracks their ecological impacts
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High-intensity flight feather molt and comparative molt ecology of warblers of eastern North America
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.