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328 results for “ecological community”
Figure 3 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation
Figure 3. Species richness of pimplines against sampling intensity. (a) Estimates of total species richness against number of traps sampled (filled circles: observed data; open circles: bootstrap; diamonds: first-order jackknife; triangles: Chao; squares: second-order jackknife); (b) site-level rarefaction (±SD); (c) trap-level rarefaction (±SD); (d) mean individual-level rarefaction for the whole data (top line) and altitudinally-zoned subsets (from top to bottom, 332–549 m, 703–887 m, 952–1071 m, 110–150 m, and 1236–1482 m, which are superimposed, 1649–1812 m and 1935–2169 m), points are literature-based data covering the same span of sampling intensities for comparison from [45]. Note the log scale on the y-axis.
Figure 1 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation
Figure 1. (a) Location of the Serra dos Órgãos National Park (gray shaded area), a protected tropical Atlantic Rain Forest in the State of Rio de Janeiro, southeast Brazil. (b) Map of the 15 study sites and their respective altitudes along the elevational gradient in the Park, where four different phytophysiognomies are observed: (c) lower montane forest (up to 500 m), which presents a 20 m high canopy but normally no other well-defined forest layers; (d) montane forest (500 m to 1500 m), with its clear stratification into arboreal, shrub, and herb layers, and large emergent trees reaching 40 m covered with abundant lianas and epiphytes; (e) high montane forest (1500 m to 2000 m) with smaller trees of up to 10 m covered with mosses and epiphytes, and great diversity of shrubs; and (f) high-altitude grassland, also known as campos de altitude (above 2000 m), dominated by herbal vegetation growing around rocks and scattered shrubs.
Figure 5. Pimplinae wasp community metrics against mean monthly temperature across 15 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation
Figure 5. Pimplinae wasp community metrics against mean monthly temperature across 15 sites. (a) Abundance; (b) Log10 Species Richness; (c) Log10 Simpson's Index (1/D); and (d) Shannon Index. Lines are the equations of the model in Table 3 ± 95%CI. (a) cubic model; (b,d) quadratic models; and (c): linear model.
Data from: Ecological drivers of avian community assembly along a tropical elevation gradient
<p>Community assembly theory hypothesizes that two main niche-based processes act to shape composition and organization of biological assemblages: abiotic filtering and biological interactions. Here, we conducted repeated surveys of bird abundance along an undisturbed elevational gradient in the tropical Andes to investigate (1) signals of deterministic processes driving community assembly and (2) potential mechanisms by which these forces operate (temperature, habitat complexity, fruit and insect availability), while correcting for imperfect detection and modeling species abundances with N-mixture models. We observed strong signals of abiotic filtering driving functionally and phylogenetically clustered assemblages towards higher elevations, and a weaker signal of limiting similarity resulting in few overdispersed assemblages at lower elevations. Whereas the decay in species richness with increasing elevation was explained by temperature, trait and phylogenetic dispersion were explained by both temperature and vegetation structure, implying that an interplay of abiotic and biotic mechanisms determines abundance-based community structure in our montane assemblages. Interestingly, trait and phylogenetic dispersion consistently decreased until ~3000 m but increased above this elevation, highlighting a potential role of competition in resource-scarce habitats. Combined, our findings suggest abiotic filters are still the main process shaping montane biotas across elevations, whereas resource availability might act locally upon assemblages further modifying them. Our study challenges recent studies in tropical mountains that suggest that biotic filters are a stronger force than abiotic filters in shaping tropical montane assemblages, and exemplifies how accounting for imperfect detection might overcome potential biases in detecting environmental filtering signals in community assembly studies.</p>
Constructing a social-behavioral association network to study management impact on waterbird community ecology using digital video recording cameras
<p>Studying social behavior and species associations in ecological communities is challenging because it is difficult to observe the interactions in the field. Animal behavior is especially difficult to observe when selection of habitat and activities are linked to energy costs of long-distance movement. Migrating communities tend to be resource specific and prefer environments that offer more suitability for coexisting in a shared space and time. Given the recent advances in digital technologies, digital video recording systems are gaining popularity in wildlife research and management. We used digital video recording cameras to study social interactions and species-habitat linkages for wintering waterbird communities in shared habitats. Examining over 8,640 hours of video footages, we built tetrapartite social behavioral association network of wintering waterbirds over habitat (n=5) selection events in sites with distinct management regimes. We analyzed these networks to identify hub species and species role in activity persistence, and to explore the effects of hydrological regime on these network characteristics. Although the differences in network attributes were not significant at treatment level (<i>p</i> = 0.297) in terms of network composition and keystone species composition, our results indicated that network attributes were significantly different (<i>p </i>= 0.000, <i>r<sup>2</sup></i><sup> </sup>= 0.278) at habitat level. There were evidences suggesting that the habitat quality was better at the managed sites, where the formed networks had more species, more network nodes and edges, higher edge density, and stronger intra- and inter-species interactions. In addition, we also calculated the species interaction preference scores (SIPS) and behavioral interaction preference scores (BIPS) of each network. The results showed that species synchronize activities in shared space for temporal niche partitioning in order to avoid or minimize any potential competition for shared space. Our social network analysis (SNA) approach is likely to provide a practical use for ecosystem management and biodiversity conservation.</p>
Predicting habitat suitability for wild deer in relation to threatened ecological communities in south-eastern New South Wales, Australia
<p><strong>Context.</strong> High density deer populations can cause ecological damage, yet their distribution and impacts are poorly known across much of Australia. As a result, land managers rely on anecdotal reports to make decisions about management and control measures.</p> <p><strong>Aims.</strong> We aimed to model habitat suitability for deer in the South Coast of New South Wales (NSW), Australia, to be used as a baseline for future management and identify which threatened ecological communities (TECs) in the region are at greatest current risk of being occupied by deer.</p> <p><strong>Methods.</strong> We compiled 678 presence-only records of wild deer from online databases, observations made by National Parks and Wildlife Service field staff and field-based surveys. We combined these observations with eight environmental variables to model and map habitat suitability for deer across our study area using maximum entropy. Three spatial models of habitat suitability across our study area were produced: one for all deer species; and two species-specific models for fallow and sambar deer. Key results. Our models indicate that suitable habitat for deer exists throughout much of the South Coast of NSW. Of the TECs examined, Coastal Saltmarsh, Themeda Grassland, and Swamp Sclerophyll Forest had the highest proportion of area likely to be extremely suitable for deer and thus should be prioritised for protection within our study area.</p> <p><strong>Conclusions. </strong>Further systematic field-based surveys are needed to improve the quality of models in this region. Implications. We recommend that areas having high habitat suitability but are not yet occupied by deer be identified as sites where deer occupancy could be prevented.</p>
Data from: Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics
High-throughput DNA methods hold great promise for the study of taxonomically intractable mesofauna of the soil. Here, we assess species diversity and community structure in a phylogenetic framework, by sequencing total DNA from bulk specimen samples and assembly of mitochondrial genomes. The combination of mitochondrial metagenomics and DNA barcode sequencing of 1494 specimens in 69 soil samples from three geographic regions in southern Iberia revealed >300 species of soil Coleoptera (beetles) from a broad spectrum of phylogenetic lineages. A set of 214 mitochondrial sequences longer than 3000 bp was generated and used to estimate a well-supported phylogenetic tree of the order Coleoptera. Shorter sequences, including cox1 barcodes, were placed on this mitogenomic tree. Raw Illumina reads were mapped against all available sequences to test for species present in local samples. This approach simultaneously established the species richness, phylogenetic composition and community turnover at species and phylogenetic levels. We find a strong signature of vertical structuring in soil fauna that shows high local community differentiation between deep soil and superficial horizons at phylogenetic levels. Within the two vertical layers, turnover among regions was primarily at the tip (species) level and was stronger in the deep soil than leaf litter communities, pointing to layer-mediated drivers determining species diversification, spatial structure and evolutionary assembly of soil communities. This integrated phylogenetic framework opens the application of phylogenetic community ecology to the mesofauna of the soil, among the most diverse and least well-understood ecosystems, and will propel both theoretical and applied soil science.
Supporting Data for Ocean acidification drives global reshuffling of ecological communities
<p>The paradigm that climate change will alter global marine biodiversity is one of the most widely accepted. Yet, its predictions remain difficult to test because laboratory systems are inadequate at incorporating ecological complexity, and common biodiversity metrics have varying sensitivity to detect change. Here, we test for the prevalence of global responses in biodiversity and community-level change to future climate (acidification and warming) from studies at volcanic CO<sub>2</sub> vents across four major global coastal ecosystems and studies in laboratory mesocosms. We detected globally replicable patterns of species replacements and community reshuffling under ocean acidification in major natural ecosystems, yet species diversity and other common biodiversity metrics were often insensitive to detect such community change, even under significant habitat loss. Where there was a lack of consistent patterns of biodiversity change, these were a function of similar numbers of studies observing negative vs positive species responses to climate stress. Laboratory studies showed weaker sensitivity to detect species replacements and community reshuffling in general. We conclude that common biodiversity metrics can be insensitive in revealing the anticipated effects of climate stress on biodiversity – even under significant biogenic habitat loss – and can mask widespread reshuffling of ecological communities in a future ocean. Whilst the influence of ocean acidification on community restructuring can be less evident than species loss, such changes can drive the dynamics of ecosystem stability or their functional change. Importantly, species identity matters, representing a substantial influence of future oceans.</p>
Code and data sets analysed in: "Marine heatwave bleaching causes mass mortality and drives a microbial community reorganisation in an ecologically important temperate sponge" Bell et al. (2024). Global Change Biology
<p>The attached zipped folder contains in-situ, satellite, reanalysis and laboratory measurements, together with R and MATLAB scripts, to reproduce the results in Bell et al. (2024). Marine heatwave bleaching causes mass mortality and drives a microbial community reorganisation in an ecologically important temperate sponge. Global Change Biology. Each folder contains a read me file that describes the enclosed data sets and scripts.</p>
Seasonal Variations of Microbial Communities and Viral Diversity in Fishery-Enhanced Marine Ranching Sediments: Insights into Metabolic Potentials and Ecological Interactions
<p>Sediment samples were collected in four seasons from May 2022 to January 2023 from the Tian coastal marine ranching (36°91′ N and 122°15′ E) located along Jinghai Bay in Weihai City, Shandong Province, China. We employed amplicon (16S and 18S) and metagenomic approaches aiming to reveal the seasonal patterns of microbial communities, bacterial-eukaryotic interactions, whole metabolic potential, and their coupling mechanisms with carbon (C), nitrogen (N), and sulfur (S) cycling in marine ranching sediments. Additionally, the characterization and diversity of viral communities in different seasons were explored in marine ranching sediments. This dataset mainly includes amplicon sequencing (16S and 18S) generated ASV tables (after rarefied), corresponding taxonomic classification tables, metagenome assembly (Single assembly and Co-assembly), <span>metagenome-assembled genomes (MAGs)</span> sequences, and <span>viral operational taxonomic units (vOTUs)</span> sequences.</p>
Data from: Ecological drift and local exposures drive gastrointestinal bacterial community differences among Galápagos iguana populations
Diet strongly influences the intestinal microbial communities through species sorting. Alternatively, these communicates may differ because of chance variation in local microbial exposures or species losses among allopatric host populations (i.e. ecological drift). We investigated how these forces shape enteric communities of Galápagos marine and land iguanas. Geographically proximate populations shared more similar communities within a host ecotype, suggesting a role for ecological drift during host colonization of the islands. Additionally, evidence of taxa sharing between proximate heterospecific host populations suggests that contemporary local exposures also influence the gut community assembly. While selective forces such as host-bacterial interactions or dietary differences are dominant drivers of intestinal community differences among hosts, historical and contemporary processes of ecological drift may lead to differences in bacterial composition within a host species. Whether such differences in community structure translate into geographic variation in benefits derived from these intimate microbial communities remains to be explored.
Data from: Experimental parasite community ecology: intraspecific variation in a large tapeworm affects community assembly
Non-random species associations occur in naturally-sampled parasite communities. The processes resulting in predictable community structure (e.g. particular host behaviours, cross-immunity, interspecific competition) could be affected by traits that vary within a parasite species, like growth or antigenicity. We experimentally infected three-spined sticklebacks with a large tapeworm (Schistocephalus solidus) that impacts the energy needs, foraging behaviour, and immune reactions of its host. The tapeworms came from two populations, characterized by high or low growth in sticklebacks. Our goal was to evaluate how this parasite, and variation in its growth, affects the acquisition of other parasites. Fish infected with S. solidus were placed into cages in a lake to expose them to the natural parasite community. We also performed a lab experiment in which infected fish were exposed to a fixed dose of a common trematode parasite. In the field experiment, infection with S. solidus affected the abundance of four parasite species, relative to controls. For two of the four species, changes occurred only in fish harbouring the high-growth S. solidus; one species increased in abundance and the other decreased. These changes did not appear to be directly linked to S. solidus growth though. The parasite exhibiting elevated abundance was the same trematode used in the lab infection. In that experiment, we found a similar infection pattern, suggesting that S. solidus affects the physiological susceptibility of fish to this trematode. Associations between S. solidus and other parasites occur and vary in direction. However, some of these associations were contingent on the S. solidus population, suggesting that intraspecific variability can affect the assembly of parasite communities.
Data from: Bringing ecology blogging into the scientific fold: measuring reach and impact of science community blogs
The popularity of science blogging has increased in recent years, but the number of academic scientists who maintain regular blogs is limited. The role and impact of science communication blogs aimed at general audiences is often discussed, but the value of science community blogs aimed at the academic community has largely been overlooked. Here, we focus on our own experiences as bloggers to argue that science community blogs are valuable to the academic community. We use data from our own blogs (n = 7) to illustrate some of the factors influencing reach and impact of science community blogs. We then discuss the value of blogs as a standalone medium, where rapid communication of scholarly ideas, opinions, and short observational notes can enhance scientific discourse, and discussion of personal experiences can provide indirect mentorship for junior researchers and scientists from underrepresented groups. Finally, we argue that science community blogs can be treated as a primary source and provide some key points to consider when citing blogs in peer-reviewed literature.
Data from: Successional dynamics of the bee community in a tropical dry forest: insights from taxonomy and functional ecology
Despite the recent rapid growth of tropical dry forest succession ecology, most studies on this topic have focused on plant community attribute recovery, whereas animal community successional dynamics has been largely overlooked, and the few existing studies have used taxonomic approaches. Here, we analyze the successional changes in the bee community in a Mexican tropical dry forest, by integrating taxonomic (species, genus, and family diversity) and functional (sociability, nesting strategy, and body size) information for bees. Over one year, in a successional chronosequence (2–67 years after abandonment) we collected 469 individual bees, representing five families, 36 genera and 69 species. Linear modeling showed decreases in taxonomic diversity with succession, more strongly so for species. Bee species turnover along succession ranged from moderate to high, decreasing slightly at intermediate stages. An RLQ analysis (ordination method that allows relating environmental variables with functional attributes) revealed clear relations between bee functional traits and the plant community. RLQ axis 1 was positively related to vegetation structural and diversity variables, and to eusociality, whilst solitary, parasociality and ground nesting were negatively associated with it. Early successional fallows attract mostly solitary and parasocial bees; older fallows tend to attract eusocial bees with aerial nesting. The continuous taxonomic turnover observed by us and the functional analysis suggest that the disappearance of old fallows from agricultural landscapes would likely result in significant reductions and even local extinctions of particular bee guilds. Considering the low viability of preserving large mature tropical dry forest tracts, the conservation of older successional stands emerges as a crucial component of landscape management.
Morphology and mini-barcodes: The inclusion of larval sampling and NGS-based barcoding improves robustness of ecological analyses of mosquito communities
<p class="Normal0">A significant proportion of vector-borne diseases are transmitted by blood-sucking dipterans, including mosquitoes. Understanding transmission risks requires accurate identification of species across heterogenous habitats, but many cryptic and polymorphic species are overlooked when using morphological identification. Estimates of mosquito diversity are typically based on adult female trapping methods which tend to target host-seeking species and may represent a biased snapshot of community structure. Unfortunately, diversity estimates based on larval data are rarely included in mosquito ecological analyses. We carried out adult and larval sampling over six months in Singapore using an integrative approach of morphological identification and molecular delineation with mini-barcodes (313 bp) generated on a Next Generation Sequencing platform to obtain species estimates. We collected 3201 mosquitoes across 58 species (14 genera). Notably, 16 species were collected only through larval sampling and 22 species were only resolved using mini-barcodes. Of the latter we identified three morphologically similar species groups and documented several intraspecific polymorphisms. We compared adult-only data against a full dataset (adult + larval + mini-barcode). The species accumulation curves reached an asymptote for all but one site when using the latter; non-metric multidimensional scaling (NMDS) revealed that mosquito communities were only well separated when using the full dataset. Overall, the latter reflects a more defined and accurate community structure across all sites. We find that several mosquito species were generally influenced by tree cover, rainfall and presence of large water bodies, further supporting the idea that many species are niche-specific. <i>Synthesis and applications</i>. We report the first successful use of mini-barcodes on mosquitoes and demonstrate its utility in delineating multiple challenging species groups. We recommend the use of both morphological and molecular identification methods for ecological studies and vector surveillance. Misidentification in species estimation, especially for medically relevant insect groups can lead to conflicting reports and slows down vector control efforts. We provide evidence that varying sampling techniques, particularly of the larval stages for holometabolous insects, is important in generating a robust dataset for downstream analyses. Together with DNA barcoding, this integrative approach helps to minimize error cascades when designing management strategies.</p>
Figure 1 in Environmental humidity and leaf-litter depth affecting ecological parameters of a leaf-litter frog community in an Atlantic Rainforest area
Figure 1. Map showing the location of the study area of Serra das Torres mountains (the star), municipality of Atílio Vivacqua, State of Espírito Santo, south-eastern Brazil.
Figure 3 in Environmental humidity and leaf-litter depth affecting ecological parameters of a leaf-litter frog community in an Atlantic Rainforest area
Figure 3. Relationship between body mass and abundance of leaf-litter frogs sampled in the Atlantic Rainforest area of Serra das Torres, municipality of Atilio Vivacqua, State of Espírito Santo, south-eastern Brazil.
Figure 2 in Environmental humidity and leaf-litter depth affecting ecological parameters of a leaf-litter frog community in an Atlantic Rainforest area
Figure 2. Rarefaction curve (solid line) and corresponding 95% limits of confidence (dashed lines), using the Sobs Mao Tau estimator (n = 330 plots sampled; predicted richness = 12) (Colwelll 2005), in terms of the frog species in the plots sampled in the Atlantic Rainforest area of Serra das Torres, municipality of Atílio Vivacqua, State of Espírito Santo, south-eastern Brazil.
Ecomorphological relationships and invasion history of non-native terrestrial bird species on O'ahu, Hawai'i suggests ecological fitting during community assembly
The widespread introduction of species has created novel communities in many areas of the world. Since introduced species tend to have generalized ecologies and often lack shared evolutionary history with other species in their communities, it would be expected that the relationship between form and function (i.e. ecomorphology) may change in novel communities. We tested this expectation in a subset of the novel bird community on O'ahu, Hawai'i. By relating foraging behavior observations to morphology obtained from live birds at four sites across the island, we found many relationships between species' morphology and foraging ecology that mirrored relationships found in the literature for native dominated bird communities. Both movement and certain foraging behaviors were related to a species' tarsus to wing ratio. Further, bill morphology was related to gleaning, frugivory, and flycatching behaviors. The commonness of significant ecomorphological relationships suggests that, within O'ahu's novel bird community, form is strongly related to function. We hypothesize that ecological fitting likely played a major role in the assembly of this novel community conserving the relationships between form and function found in many other bird communities. To further support this hypothesis, we used niche data from EltonTraits 1.0 to determine if the establishment of bird species introduced to O'ahu was related to the distinctiveness of their ecological niche from the incumbent community. Introduced species were more likely to establish on O'ahu if their diets were less similar to the bird species already present on the island. Our results support the idea that ecological fitting is an important mechanism in shaping ecological communities, especially in the Anthropocene, thereby influencing novel community assembly and functioning.
Social-ecological cascade effects of land-use on vertebrate pest dynamics in arid agricultural communities
<p>Extensive land conversion to agriculture in drylands and associated resource use have wide-ranging impacts on desert ecosystems globally. Incorporating the impacts of human-social aspects is thus imperative in examining ecological interactions. The provision of agricultural inputs in these resource-scarce regions supports invasive and pest species, negatively impacting both agricultural productivity and native desert ecosystems. Understanding the spatial dynamics of invasive and pest species requires analyzing both bottom-up resource availability factors underlying animal distributions and top-down biological controls. Here, we evaluate the social-ecological cascading effects of dryland agriculture on vertebrate pest communities in dryland agricultural communities of Israel. Our study region is characterized by 18 agricultural cooperatives with distinct crop regimes due to contrasting social decision-making and resource allocation schemes (i.e., communal Kibbutzim vs. privatized Moshavim). Crop choices further affect land management (e.g., enclosed vs. open farm systems) and resource intensity. This system is ideal to study trophic mechanisms underlying animal assemblages between agricultural regimes. We examine the role of agricultural land-use practices on pest spatial distributions based on multi-year vertebrate pest observations with agricultural datasets. We use structural equation modelling (SEM) to quantify the relative importance of added agricultural resources underlying bottom-up and top-down trophic processes regulating vertebrate pest assemblages. Results reveal that crop choices determine pest distributions through bottom-up processes directly, while simultaneously driving pest competitive interactions through indirect top-down cascades impacting pest communities. For example, due to the indirect negative effect of wolves on meso-predators (foxes and jackals) mediated by livestock, the total positive effect of livestock on the abundance of meso-predators is reduced. Our study illustrates the social-ecological cascading effects of agricultural regimes on pest community assemblages mediated by contrasting agricultural land-use practices. Considering the expansion of dryland agro-ecological systems globally, understanding the intricate cascading pathways of predator- and prey-pest communities has important implications for agricultural management, biological invasions in drylands and fragile desert environments.</p>
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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.