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328 results for “ecological community”
A practical approach to measuring the acoustic diversity by community ecology methods
<p>The study of the diversity of animal signals on within- and among-species levels is the key to uncover mechanisms that shape the evolution of communication systems. However, the methods used to quantify acoustic diversity (like repertoire size) lack to grasp several aspects of acoustic diversity. Here, we propose a new framework for the study of animal communication, in which we decompose the acoustic diversity with the methodological toolbox from community ecology.</p> <p>We explore how different diversity estimates reflecting different aspects of acoustic diversity can be applied to characterise the complexity of acoustic signals. We propose that this approach can be used in a wide range of animal taxa to derive further insights about the function and evolution of communication systems besides the traditional methods.</p> <p>To illustrate the use of our approach in a case study, we used the song of collared flycatcher (<em>Ficedula albicollis)</em> as a model system. Based on three frequency and time variables, we calculated three diversity indies (FRic, FEve, and FDiv) to characterise the distribution of song elements (syllables) in the acoustic parameter space. We aimed to uncover the interrelations of diversity indices, reveal the degree of among-individual consistency, and investigate their relationships with certain aspects of individual quality.</p> <p>We found that the chosen diversity indices were largely independent from each other and showed different consistency patterns that were timescale dependent indicating different signalling potential of individual-specific attributes. We also found that FEve strongly related to the age of males. Our case study showed that decomposing the diversity into different components can reveal additional biologically meaningful aspects of birdsong.</p>
Using local ecological knowledge as evidence to guide management: A community-led harvest calculator for muskoxen in Greenland
<p>Indigenous peoples manage or have tenure rights on over a quarter of the world's land surface. While there is growing interest in "evidence-based" natural resource management, there are few documented experiences with "evidence-based" practice in community-managed lands. We explore the evidence required for decisions about harvesting of a community-managed muskox herd in Greenland, and the collaboration needed to acquire this evidence. We present the development, application and outcome of a user-friendly demographic model - a harvest calculator - and we show how Local Ecological Knowledge was used throughout the process and combined with scientific knowledge. The community members identified suitable harvest scenarios with the use of the calculator. The calculator's predictions corresponded with their own perceptions of declining numbers of muskox bulls and suggested that reversal was possible under an alternative harvest scenario. As a result, the community members used the findings to request a revised muskox harvest quota, which gained immediate approval by the government. We draw on our experience to propose where community-led harvest calculators can be useful. Community-led harvest calculators can help Indigenous and local communities develop economically within environmentally sustainable limits, while at the same time providing community members a 'voice' in natural resource governance. An effective local management regime will require the sustained application of this tool.</p>
Data from: Elevated success of multispecies bacterial invasions impacts community composition during ecological succession
Successful microbial invasions are determined by a species' ability to occupy a niche in the new habitat whilst resisting competitive exclusion by the resident community. Despite the recognised importance of biotic factors in determining the invasiveness of microbial communities, the success and impact of multiple concurrent invaders on the resident community has not been examined. Simultaneous invasions might have synergistic effects, for example if resident species need to exhibit divergent phenotypes to compete with the invasive populations. We used three phylogenetically diverse bacterial species to invade two compositionally distinct communities in a controlled, naturalised in vitro system. By initiating the invader introductions at different stages of succession, we could disentangle the relative importance of resident community structure, invader diversity and time pre-invasion. Our results indicate that multiple invaders increase overall invasion success, but do not alter the successional trajectory of the whole community.
Data from: The challenges that spatial context present for synthesizing community ecology across scales
Accurately characterizing spatial patterns on landscapes is necessary to understand the processes that generate biodiversity, a problem that has applications in ecological theory, conservation planning, ecosystem restoration, and ecosystem management. However, the measurement of biodiversity patterns and the ecological and evolutionary processes that underlie those patterns is highly dependent on the study unit size, boundary placement, and number of observations. These issues, together known as the modifiable areal unit problem, are well known in geography. These factors limit the degree to which results from different metacommunity and macro-ecological studies can be compared to draw new inferences, and yet these types of comparisons are widespread in community ecology. Using aquatic community datasets, we demonstrate that spatial context drives analytical results when landscapes are sub-divided. Next, we present a framework for using resampling and neighborhood smoothing to standardize datasets to allow for inferential comparisons. We then provide examples for how addressing these issues enhances our ability to understand the processes shaping ecological communities at landscape scales and allows for informative meta-analytical synthesis. We conclude by calling for greater recognition of issues derived from the modifiable areal unit problem in community ecology, discuss implications of the problem for interpreting the existing literature, and identify tools and approaches for future research.
Data from: Does adaptive radiation of a host lineage promote ecological diversity of its bacterial communities? A test using gut microbiota of Anolis lizards
Adaptive radiations provide unique opportunities to test whether and how recent ecological and evolutionary diversification of host species structures the composition of entire bacterial communities. We used 16S rRNA gene sequencing of faecal samples to test for differences in the gut microbiota of six species of Puerto Rican Anolis lizards characterized by the evolution of distinct 'ecomorphs' related to differences in habitat use. We found substantial variation in the composition of the microbiota within each species and ecomorph (trunk-crown, trunk-ground, grass-bush), but no differences in bacterial alpha diversity among species or ecomorphs. Beta diversity analyses revealed subtle but significant differences in bacterial composition related to host phylogeny and species, but these differences were not consistently associated with Anolis ecomorph. Comparison of a trunk-ground species from this clade (A. cristatellus) with a distantly related member of the same ecomorph class (A. sagrei) where the two species have been introduced and are now sympatric in Florida revealed pronounced differences in the alpha diversity and beta diversity of their microbiota despite their ecological similarity. Comparisons of these populations with allopatric conspecifics also revealed geographic differences in bacterial alpha diversity and beta diversity within each species. Finally, we observed high intraindividual variation over time and strong effects of a simplified laboratory diet on the microbiota of A. sagrei. Collectively, our results indicate that bacterial communities are only weakly shaped by the diversification of their lizard hosts due to the strikingly high levels of bacterial diversity and variation observed within Anolis species.
Data from: Your infections are what you eat: how host ecology shapes the helminth parasite communities of lizards
1. Understanding how parasite communities are assembled, and the factors that influence their richness, can improve our knowledge of parasite-host interactions and help to predict the spread of infectious diseases. Previous comparative analyses have found significant influences of host ecology and life history, but focused on a few select host taxa. 2. Host diet and habitat use play key roles in the acquisition of parasitic helminths as many are trophically-transmitted, making these attributes potentially key indicators of infection risk. Given the paucity of comparative studies with non-piscine, non-avian or non-mammalian hosts, it is critical to examine the degree to which host ecology influences parasite communities in other host taxa in order to identify common drivers. 3. We examined helminth diversity in over 350 species of lizards in relation to their body mass, ecology (diet and habitat use), and life history (clutch size, and ovo- or viviparity) using previously published data. 4. Overall, lizard species with herbivorous diets harboured fewer types of helminths (especially larval stages), with similar results for traits that were ultimately strongly associated with diet (host mass and habitat use). Large hosts tended to be herbivores with few helminth types whereas species utilizing arboreal habitats typically consumed some animal matter and hosted more helminths. 5. Understanding how host ecology and life history are related to their parasite assemblages has significant implications for the risk of acquiring novel parasites. Our results indicate an overwhelming influence of host diet such that many helminths may be relatively easily acquired by hosts in new ranges, or through dietary shifts.
Data from: Parasites structuring ecological communities: the mistletoe footprint in Mediterranean pine forests
1. The capacity of parasitic plants in structuring natural communities is increasingly recognized. These plants can affect the structure, composition and productivity of plant communities by modifying the competitive balance between hosts and non-host species and by altering the quantity and quality of resources entering the soil. Despite the progress made in this field, there is still a lack of integrative studies showing the structuring capacity of parasitic plants in forest ecosystems, where their effect may be less detectable due to the long lifespan of the system. 2. In this study we evaluate the long-term impact of Viscum album subsp. austriacum on the woody-plant community of a Mediterranean pineland. This mistletoe remains several years on the same host, exerting long-lasting, spatially concentrated effects on community and ecosystem characteristics. Mistletoe concentrates zoochorous seeds and induces changes in the soil fertility and light availability beneath the canopy of parasitized trees, which have the potential to facilitate zoochorous-plant colonization, recruitment, and growth at the same time as it weakens the host. Here, we analyse whether mistletoe-driven changes could result in a nucleus of zoochorous woody plants nourished by the abundant organic detritus accumulated under the host. We also analyse whether mistletoe effects can expand after host death. 3. We selected unparasitized, parasitized, and dead parasitized Pinus nigra trees, in which we studied the joint effect of mistletoe-mediated changes in soil nutrient and light availability, with the seed rain, seed predation, seedling establishment, plant recruitment, and plant growth. Light- and soil-nutrient resources were greater under parasitized trees, and intensified after host death. The seed rain was maximum under parasitized trees, where seedling recruitment proved more likely. Sapling density, richness, and growth increased with the development of parasitism. 4. Our findings show that Viscum album exerts a strong and lasting impact on the structure and dynamics of Mediterranean pinelands, with parasitized trees acting as centres for the establishment and growth of colonizing fleshy-fruited woody species, which, over the long term, promote vegetation shifts by limiting dominant pine trees and facilitating less represented fleshy-fruited shrubs.
Data from: Bacterial adaptation to sublethal antibiotic gradients can change the ecological properties of multitrophic microbial communities
Antibiotics leak constantly into environments due to widespread use in agriculture and human therapy. Although sublethal concentrations are well known to select for antibiotic-resistant bacteria, little is known about how bacterial evolution cascades through food webs, having indirect effect on species not directly affected by antibiotics (e.g. via population dynamics or pleiotropic effects). Here, we used an experimental evolution approach to test how temporal patterns of antibiotic stress, as well as migration within metapopulations, affect the evolution and ecology of microcosms containing one prey bacterium, one phage and two protist predators. We found that environmental variability, autocorrelation and migration had only subtle effects for population and evolutionary dynamics. However, unexpectedly, bacteria evolved greatest fitness increases to both antibiotics and enemies when the sublethal levels of antibiotics were highest, indicating positive pleiotropy. Crucially, bacterial adaptation cascaded through the food web leading to reduced predator-to-prey abundance ratio, lowered predator community diversity and increased instability of populations. Our results show that the presence of natural enemies can modify and even reverse the effects of antibiotics on bacteria, and that antibiotic selection can change the ecological properties of multitrophic microbial communities by having indirect effects on species not directly affected by antibiotics.
Data from: Inferring species interactions in ecological communities: a comparison of methods at different levels of complexity
1. Natural communities commonly contain many different species and functional groups, and multiple types of species interactions act simultaneously, such as competition, predation, commensalism or mutualism. However, experimental and theoretical investigations have generally been limited by focusing on one type of interaction at a time or by a lack of a common methodological and conceptual approach to measure species interactions. 2. We compared four methods to measure and express species interactions. These approaches are, with increasing degree of model complexity, an extinction-based model, a relative yield model and two generalized Lotka-Volterra (LV) models. All four approaches have been individually applied in different fields of community ecology, but rarely integrated. We provide an overview of the definitions, assumptions and data needed for the specific methods and apply them to empirical data by experimentally deriving the interaction matrices among 11 protist and rotifer species, belonging to three functional groups. Furthermore, we compare their advantages and limitations to predict multispecies community dynamics and ecosystem functioning. 3. The relative yield method is, in terms of final biomass production, the best method in predicting the 11-species community dynamics from the pairwise competition experiments. The LV model, which is considering equilibrium among the species, suffers from experimental constraints given the strict equilibrium assumption, and this may be rarely satisfied in ecological communities. 4. We show how simulations of a LV stochastic community model, derived from an empirical interaction matrix, can be used to predict multispecies community dynamics across multiple functional groups. 5. Our work unites available tools to measure species interactions under one framework. This improves our ability to make management-oriented predictions of species coexistence/extinction and to compare ecosystem processes across study systems.
Data from: Patterns and processes in complex landscapes: testing alternative biogeographic hypotheses through integrated analysis of phylogeography and community ecology in Hawai'i
The Island of Hawai'i is a dynamic assemblage of five volcanoes with wet forest habitat currently existing in four distinct natural regions that vary in area, age, and geographic isolation. In this complex landscape, alternative assumptions of the relative importance of specific habitat characteristics on evolutionary and ecological processes predict strikingly different general patterns of local diversity and regional similarity. In this study we compare alternative a priori hypotheses against observed patterns within two distinct biological systems and scales: community composition of wet forest vascular plant species and mitochondrial and nuclear genes of Drosophila sproati, a wet forest restricted endemic. All observed patterns display strong and similar regional structuring, with the greatest local diversity found in Kohala and the windward side of Mauna Loa, the least in Ka'ū and Kona, and a distinctive pattern of regional similarity that likely reflects the historical development of this habitat on the island. These observations largely corroborate a biogeographic model that integrates multiple lines of evidence, including climatic reconstruction, over those relying on single measures, such as current habitat configuration or substrate age. This method of testing alternative hypotheses across biological systems and scales is an innovative approach for understanding complex landscapes and should prove valuable in diverse biogeographic systems.
Data from: Linking intra-specific trait variation to community abundance dynamics improves ecological predictability by revealing a growth-defence trade-off
1.Intraspecific trait change, including altered behaviour or morphology, can drive temporal variation in inter-specific interactions and population dynamics. In turn, variation in species' interactions and densities can alter the strength and direction of trait change. The resulting feedback between species′ traits and abundance permits a wide range of community dynamics that would not be expected from ecological theories purely based on species abundances. Despite the theoretical importance of these interrelated processes, unambiguous experimental evidence of how intraspecific trait variation modifies species interactions and population dynamics and how this feeds back to influence trait variation is currently required. 2.We investigate the role of trait-mediated demography in determining community dynamics and examine how ecological interactions influence trait change. We concurrently monitored the dynamics of community abundances and individual traits in an experimental microbial predator-prey-resource system. Using this data, we parameterized a trait dependent community model to identify key ecologically relevant traits and to link trait dynamics with those of species abundances. 3.Our results provide clear evidence of a feedback between trait change, demographic rates and species dynamics. The inclusion of trait-abundance feedbacks into our population model improved the predictability of ecological dynamics from r-squared of 34% to 57% and confirmed theoretical expectations of density dependent population growth and species interactions in the system. 4.Additionally, our model revealed that the feedbacks were underpinned by a trade-off between population growth and anti-predatory defence. High predator abundance was linked to a reduction in prey body size. This prey size decrease was associated with a reduction in its rate of consumption by predators and a decrease in its resource consumption. 5.Modelling trait-abundance feedbacks allowed us to pinpoint the underlying life history trade-off which links trait and abundance dynamics. These results show that accounting for trait-abundance feedbacks has the potential to improve understanding and predictability of ecological dynamics.
Database and source code for the article "epistemic communities and political ecology" https://doi.org/10.2458/jpe.4702
<p>This document supports a review of the field of political ecology, detailing the methods applied to two of the databases used in the study: a quantitative bibliometric content of Scopus indexed publications referring to political ecology (1951-2019), and a focus on the publications by the review Journal of political ecology. </p> <p>This database has been downloaded in 2019 and it can be updated from the Scopus database, using the keyword "political ecology".</p>
Figure 4 from: Mammola S, Piano E, Giachino PМ, Isaia M (2017) An ecological survey of the invertebrate community at the epigean/hypogean interface. Subterranean Biology 24: 27-52. https://doi.org/10.3897/subtbiol.24.21585
Figure 4 - Annual trends of temperatures in the Pugnetto hypogean complex. The shade of blues indicate the relative position of the dataloggers at each cave-triplet, from the outermost (lighter blues) to the innermost sections (darker blues). Records from only one MSS-triplet are shown.
Figure 3 from: Mammola S, Piano E, Giachino PМ, Isaia M (2017) An ecological survey of the invertebrate community at the epigean/hypogean interface. Subterranean Biology 24: 27-52. https://doi.org/10.3897/subtbiol.24.21585
Figure 3 - a sampling holes (details) b Blocking screw c installation of an MSS-triplet d SSD of three different length e MSS-triplet buried in the ground f, g renewing the pitfall trap inside the SSD. Photo credits: Elena Piano.
Figure 2 from: Mammola S, Piano E, Giachino PМ, Isaia M (2017) An ecological survey of the invertebrate community at the epigean/hypogean interface. Subterranean Biology 24: 27-52. https://doi.org/10.3897/subtbiol.24.21585
Figure 2 - Map of the study area. The shape and the topographic position of the four caves (Borna Maggiore di Pugnetto, Tana del Lupo, Creusa d'le Tampe, Tana della Volpe) was obtained from the original planimetric drawings of Muratore (1946). The position of the sampling plots in caves ("cave triplets", C1–C8), in the MSS ("MSS triplets", M1–M8) and in the leaf litter ("epigean", L1–L6) are represented by coloured dots. The different sectors of the cave are coloured with different shades of grey representing the subjacency – i.e., vertical distance from the surface – according to Motta and Motta (2015).
Figure 6 from: Mammola S, Piano E, Giachino PМ, Isaia M (2017) An ecological survey of the invertebrate community at the epigean/hypogean interface. Subterranean Biology 24: 27-52. https://doi.org/10.3897/subtbiol.24.21585
Figure 6 - Predicted values (black line) and 95% confidence intervals (grey surface) of the effect of the sampling series (Serie_i) on the abundance of external elements in the MSS (a), on the species richness of external elements in the MSS (b) and on the abundance of external elements in the cave at subjacency of 0–20m (c) derived from GAMM analyses. Only fixed effects are shown.
Figure 1 from: Mammola S, Piano E, Giachino PМ, Isaia M (2017) An ecological survey of the invertebrate community at the epigean/hypogean interface. Subterranean Biology 24: 27-52. https://doi.org/10.3897/subtbiol.24.21585
Figure 1 - a Main entrance of the Borna di Pugnetto (photo credit: Alberto Chiarle and Mauro Paschetta, 2014) b Main entrance of the Creusa d'le Tampe (photo credit: Elena Piano, 2013) c exposed soil/MSS profile in a fresh-cut along a slope in the vicinity of the Borna di Pugnetto (photo credit: Jacopo Orlandini, 2014) d the typical cave geo-morphology within the Borna di Pugnetto (photo credit: Alberto Chiarle and Mauro Paschetta, 2014) e detail of the MSS geo-morphological structure (photo credit: Jacopo Orlandini, 2014).
Figure 5 from: Mammola S, Piano E, Giachino PМ, Isaia M (2017) An ecological survey of the invertebrate community at the epigean/hypogean interface. Subterranean Biology 24: 27-52. https://doi.org/10.3897/subtbiol.24.21585
Figure 5 - Boxplots showing the results of the regression analysis of the MSS (a–c) and the cave (d–f) data. Outlying values are not shown. Significance codes: < 0.001 ***; < 0.005 **; < 0.05 *.
Input data and Supplementary Results for "Community-level signatures of ecological succession in natural bacterial communities"
<p> </p> <p><strong>README<br> ======</strong></p> <p><br> This file describes the content of the different files included in this repository to<br> reproduce results from [1] and some of its supplementary results.</p> <p> </p> <p><strong>## Input files ##</strong></p> <p><strong>* 20151016_Functions_remainder.csv</strong></p> <p> Functions measured in [2]. The relevant quantities used in [1] are labelled with "7", and include:<br> <br> * Community: Id of the sample<br> * Replicate<br> * Plate<br> * mgCO2.7: CO2 measured along 7 days of experiment<br> * CPM7: Cell counts at the end of the experiment<br> * pgRPC.7: CO2 per cell<br> * ATP7: ATP measured (nM)<br> * mG7: beta glucosidase (mM)<br> * mN7: beta chitinase (mM)<br> * mX7: xylosidase (mM)<br> * mP7: phosphatase (mM)<br> <br> <strong>* samples_metadata_time0.tsv</strong></p> <p> * Samples: Id of the sample <br> * Part.dates: Date of sampling<br> * Part.GPS.PAM: Optimal sampling sites <br> * Part.SparCC.PAM.t0: Optimal partition using SparCC<br> * Part.SJD.PAM.t0: Optimal partition using Jensen-Shannon Divergence<br> * Part.Dir.t0: Optimal partition using Dirichlet mixtures<br> * Part.month: Month in which the community was sampled<br> <strong>* Dist_GPS-Haversine.dat</strong></p> <p> Haversine (spatial) distances between samples</p> <p><strong>* corMat-SparCC_20151016_OTU_remainder.clean.samples.txt</strong></p> <p> Matrix of correlations between samples computed with SparCC<br> <br> <strong>* distMat_ShannonJensen_Samples_Time0.clean.dat</strong></p> <p> Distance matrix computed with Jensen-Shannon divergence.</p> <p> </p> <p><br> <strong>## Supplementary results ##</strong></p> <p><strong>* SEMmodels.zip</strong></p> <p> Results for the Structural Equation Models analysed. The structure of the folders follows the one<br> available at the repository of the [project ](https://github.com/apascualgarcia/TreeHoles_descriptive).<br> <br> <strong>* TaxaSummaries.zip</strong></p> <p> The file contains one folder for each community-class, with matrices in different formats (biom and txt) computing the relative abundances of the OTUs at different taxonomic levels (labelled L2 being the proxy for Phylum to L6, the proxy of species). These matrices can be visualized interactively opening with a web browser the files area_charts.html.</p> <p><strong>#### References ####</strong></p> <blockquote> <p> [1] Pascual-García, A., & Bell, T. (2019). Community-level signatures of ecological succession in natural bacterial communities. Nature Communications (In press)</p> </blockquote> <blockquote> <p> [2] Rivett, Damian W., and Thomas Bell. Abundance determines the functional role of bacterial phylotypes in complex communities." Nature microbiology 3.7 (2018): 767.</p> </blockquote> <p> </p>
Fig. 4 in Protocol for collecting Mutillidae (Hymenoptera, Aculeata) in ecological studies: species-area effects on Mutillidae communities
Fig. 4. Canonical Variable Analysis (CVA) from the multivariate analysis of variance (MANOVA) of the species composition of Mutillidae between the Cerrado fragments (Pillai Trace = 0.7078, F(1.314) = 51.81, p = 0.02). Matas do Segredo State Park (Segredo), Prosa State Park (Prosa), Private Natural Heritage Reserve of Universidade Federal de Mato Grosso do Sul (UFMS) and Private Natural Heritage Reserve of Universidade Católica Dom Bosco (UCDB).
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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.