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158 results for “Metacommunity”
Metacommunity simulations for diatom assemblages residing in benthic cyanobacterial mats in Fryxell Basin in Taylor Valley in the McMurdo Dry Valleys, Antarctica
Here, we use MCSim, a spatially explicit metacommunity simulation package for R, to test alternative hypotheses about the roles of dispersal and species sorting in maintaining the biodiversity of diatom assemblages residing in black and orange mats in Fryxell Basin in Taylor Valley in the McMurdo Dry Valleys of Antarctica. The spatial distribution and patchiness of cyanobacterial mat habitats was characterized by remote imagery of the Lake Fryxell sub-catchment in Taylor Valley collected in January 2015. The available species pool for diatom metacommunity simulation scenarios was informed by the Antarctic Freshwater Diatoms Database, maintained by the McMurdo Dry Valleys Long Term Ecological Research program, representing samples collected between January 1994 and January 2013. We used simulation outcomes to test the plausibility of alternative community assembly hypotheses to explain empirically observed patterns of freshwater diatom biodiversity in the long-term record. The most plausible simulation scenarios suggest species sorting by environmental filters, alone, was not sufficient to maintain biodiversity in the Fryxell Basin diatom metacommunity. The most plausible scenarios included either (1) neutral models with different immigration rates for diatoms in orange and black mats or (2) species sorting by a relatively weak environmental filter, such that dispersal dynamics also influenced diatom community assembly, but there was not such a strong disparity in immigration rates between mat types. The results point to the importance of dispersal for understanding current and future biodiversity patterns for diatoms in this ecosystem, and more generally, provide further evidence that metacommunity theory is a useful framework for testing hypotheses about microbial community assembly. This dataset supports the paper: Sokol, E. Et al, 2020. Evaluating Alternative Metacommunity Hypotheses for Diatoms in the McMurdo Dry Valleys Using Simulations and Remote Sensing Data
Biodiversity and metacommunity structure of rocky intertidal invertebrates in some coastal ecosystems in Puerto Rico
The goals of this study were to determine the relative importance of environmental (wave power density, wave height) and habitat (e.g., algal cover, slope, complexity of rock surfaces) factors associated with the structure of local assemblages at multiple shore heights and the regional metacommunity of mobile invertebrates on oceanic rocky intertidal habitats. These characteristics and abundances of 41 species of invertebrate were estimated at 10 plots at each of three tidal heights at each of ten sites on the shoreline of Puerto Rico. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Environmental DNA captures signals of the internal structure of a pond metacommunity
<p>R Code for the study of "<strong>Environmental DNA captures signals of the internal structure of a pond metacommunity"</strong></p>
Trophic metacommunities in bromeliad-dwelling insects
<p>This data was collected by D. S. Srivastava and members of her research lab (including B. Gilbert, K. Kirby, J. Ngai, J. Petermann, B. Starzomski) at Estación Biológica Pitilla, in the Área de Conservación Guanacaste in north-western Costa Rica in 1997, 2000, 2002, 2004, 2010. Over these five years, we collected a total of 85 bromeliads between late September and early December. Specifically, this data relates to the abundance of the mosquitoes in the genus Wyeomyia and Culex, and their predator Mecistogaster modesta.</p> <p>Water depths were measured to the nearest mm in three marked leaves of 30 bromeliads, every two days for one year (8 October 2012 to 9 October 2013). The maximum volume of each bromeliad was measured at the inception of the survey. We assumed that mosquito larvae encountered in our invertebrate survey could be affected by water depths only from the period 15 September to 22 December, that is, at most three weeks before and after our survey (as a mosquito encountered at the beginning of the invertebrate survey may be already a late instar, and at the end of our invertebrate survey may be just an early instar). We trimmed our year of water level data to this 15 September-22 December period, and calculated the proportion of days each of the 30 bromeliads had standing water (defined as >5mm moisture, as the basal debris retains some moisture in the absence of standing water).</p>
Data from: Disentangling the drivers of ground-dwelling macro-arthropod metacommunity structure at two different spatial scales
<p>The goal of this study was to explore the community assembly rules at local and regional scales.</p> <p> </p> <p><strong><em>Site description </em></strong></p> <p>All sampling locations were selected within the black soil region (Fig. 1), which is predominantly located in the temperate continental monsoon climatic zone in North China. It is characterized by a dry and cold winter and warm and humid summer. The soil was classified as black soil following the Chinese Soil Classification System, which is equivalent to a Typic Hapludoll in the USDA Soil Taxonomy. More specific details for this soil (such as black soil coverage area, geographical and ecological resources, etc.) can be obtained from Wen and Liang (2001). Samples were collected from three municipal districts: Bei'an, Hulan and Dehui.</p> <p> </p> <p><strong><em>Sampling design and setup</em></strong></p> <p>We conducted field sampling of ground-dwelling macro-arthropods and measured a set of environmental and spatial variables across all sampling locations three times: in May, July and September 2015. In total, 15 plots (five plots in each of the three municipal districts) were selected and sampled. At each plot, we further selected five sampling sites (approximately 10 m away from each other).</p> <p>We collected additional samples for estimating soil abiotic parameters at each site. Soil samples (5 × 5 cm and 10 cm depth) were collected near each pitfall trap site. The exact geographic coordinates of each sampling site were obtained by GPS.</p> <p>Ground-dwelling macro-arthropods were sampled by a pitfall trapping method. For pitfall traps, we used plastic cups (7 cm in diameter and 12 cm deep), which were partially filled with saturated salt water. The traps were exposed for one week in each sampling month. All collected ground-dwelling macro-arthropods were removed from the pitfall traps, sorted and preserved in a 95% alcohol solution. All adult macroarthropods from pitfalls were identified at the species or genus level using appropriate keys (e.g., Simon (1879), Martens (1978) and Barrientos (2004) for Opiliones; Roberts (1993, 1995) for Lycosidae; and Forel and Leplat (2001) and Ortuño and Marcos (2003) for Carabidae) and then were counted. Juvenile ground-dwelling arthropods were excluded from all analyses due to difficulties with their identification (Gao et al., 2016).</p> <p> </p> <p><strong><em>Environmental and spatial variables</em></strong></p> <p>Environmental variables used in our analysis included soil organic matter, soil total nitrogen, water content, pH, temperature. Soil water content (SWC%) was measured in the laboratory after the fresh soil was loaded into an aluminium box. Prior to estimating soil total nitrogen (TN) (Kjeldahl's method described by Duchaufour (1975)), soil organic matter (SOM) (Anne's method described by Duchaufour (1975)) and pH (Pansu and Gautheyrou, 2003), the collected soil samples were air-dried at 25℃ for one week and sieved (1 mm mesh size). Local temperature values were obtained from the publicly available datasets (The Local Chronicles of Bei’an, Hulan and Dehui). Geographic coordinates were recorded for further spatial modelling analysis.</p> <p> </p> <p>We have seven data files:</p> <p>env BAHLDH may.csv</p> <p>env BAHLDH july.csv</p> <p>env BAHLDH september.csv</p> <p>sp BAHLDH may.csv</p> <p>sp BAHLDH july.csv</p> <p>sp BAHLDH september.csv</p> <p>Geospatial coordinates.csv</p> <p> </p> <p>Explanation of the variables in the datasets:</p> <p>Site: Bei’an, Hulan, Dehui represent sampling district; I-V represent sampling plot; 1-5 represent replicate</p> <p>SOM: soil organic matter</p> <p>pH: soil pH</p> <p>SWC: Soil water content</p> <p>TN: soil total nitrogen</p>
Data from: Metacommunity theory review and its application in community assembly of soil animals
<p>We were interested in community assembly of soil animals and performed a literature study to find out what is known about soil metacommunities. We aimed to study keywords co-occurrence relationships of scientific journal articles in the field of "metacommunity" research from 1992-2017 as a whole. We also investigated the co-occurrence of the top 20 most frequent keywords in five 5-year time periods.</p> <p> </p> <p> </p> <p>In September 2017 we searched the Web of Science with ‘metacommunity’ as the only keyword, and found 1226 English papers published in international journals between January 1992 and September 2017. And we exported these papers from Web of Science as a plain text file (.txt) with the option ‘Full Record and Cited References’, which is archived here. The text file thus contains full records and cited references (in a concise format, so without the titles of the cited papers), and each field is prefaced by a two-character field tag. Afterwards we used the software ‘Citespace’ to create Table 1 and Figure 2 in Guo et al. (2018). We created that Figure 2 using the following settings in Citespace: we choose the “co-occurrence” function and “keyword” as node types, then created keywords co-occurrence relationships (Figure 2). Next, we created lists of the top 20 keywords in different periods, which can reveal the research hotspots (Table 1). The method for extracting the top 20 most frequent keywords was as follows: We use the Web of Science database to retrieve scientific papers from 1992 to 2017, taking into account the relationship between citation and publication time. We calculated the percentage of 200 most cited papers published in each of the 5-year periods. To do so we followed the following steps:</p> <p>Step1: we selected the 200 most cited papers from the entire datset (1226 in the 1992-2017 period).</p> <p>Step 2: we calculated the percentage of those 200 papers published each 5-year period.</p> <p>Step 3: we also calculated an correction coefficient by taking, for each 5-year period, the number of top-200 most cited papers published in that period, and dividing that number by the total number of papers (out of the 1226 selected papers) published in that period.</p> <p>Step 4 Last, we calculate the real keyword frequency by multiplying the keyword frequency in specific 5-year periods with the correction coefficient.</p>
Guadeloupe Snails Metacommunity
<p><span>Metacommunity structure reflects the interplay of various processes, including niche filtering, extinction/colonization, and interspecific interactions. Spatial patterns of species distributions are often analyzed to infer these processes. However, such inferences rely on often unrealistic equilibrium assumptions, and remain ambiguous, as different processes can produce similar patterns. Temporal data may improve these inferences. For example, stochastic species turnover may occur in local communities, while, on the long run, temporal changes are kept within limits set by locally available niches. Our objective is to explore how the joint analysis of spatial and temporal patterns can clarify the contribution of different processes to metacommunity structure. We recorded the occurrences of 21 freshwater mollusc species, and environmental data, in 250 sites over 17 successive years in a network of ponds in Guadeloupe (Lesser Antilles). We analyzed variation in α and β-diversities in space and time, and used a joint-species distribution mode to characterize species-environment and species-species relationships. Local communities showed pronounced temporal variation reflecting both imperfect species detection and true stochastic species turnover. On the long term however, local communities were largely controlled by niche filtering along two main environmental gradients, one driven by site connectivity, the other by hydrological stability and aquatic vegetation. Two gastropod clades, caenogastropods and pulmonates, showed contrasted spatio-temporal distributions resulting from different responses to these gradients, and these distributions seemed little altered by interspecific competition. Our study illustrates the benefit of using spatiotemporal metacommunity data to discern long-term impacts of niche filtering and species interactions behind short-term stochasticity.</span></p>
Functional traits and metacommunity theory reveal that habitat filtering and competition maintain bird diversity in a human shared landscape
<p>Human shared landscapes cover much of Earth, yet their conservation value is contested. This controversy may persist because previous studies have examined species diversity, rather than the processes through which such diversity is maintained. For example, a site exhibiting high diversity may not actually bolster populations if the diversity is only maintained through net immigration. Recent research has begun to isolate the processes that maintain metacommunities and develop functional trait methods to identify these processes. However, the processes underlying bird communities remain obscure. Here, we leverage metacommunity theory, functional trait partitioning, and a Bayesian multispecies abundance model to assess whether a shared landscape – woody perennial polyculture farms – bolsters bird diversity. Such farms grow multiple species of food-producing woody perennials together with vegetative groundcover. We surveyed birds and their <em> in situ </em> functional traits across the US Midwest in traditional agriculture, woody perennial polyculture, prairie, and woods. We found that woody perennial polycultures exhibited the highest bird diversity and were the most preferred by many species (including threatened ones). Moreover, our functional trait analysis suggests that this diversity is maintained through habitat filtering and competition, rather than merely immigration. Thus, shared landscapes can likely conserve birds by providing a distinct habitat. These results suggest that woody perennial polyculture farms offer substantial potential to support bird populations in the US Midwest. Our study demonstrates the utility of <em> in situ </em> functional trait partitioning within a Bayesian framework to unmask ecological processes and help assess the conservation value of landscapes.</p>
Animal metacommunities of temporary ponds in a flat grassland landscape of Uruguay
<p>The database comprises a survey of an animal metacommunity of temporary ponds carried out in October 2008, in a grassland landscape of Uruguay. The animal groups involve macroinvertebrates, fishes, and amphibians. Individual occurrence, taxonomic affiliation, and traits associated with diet and body size are provided. The metacommunity is located in a flat landscape surrounded by hills, where a maximum of 61 ponds, every year, are filled with water in winter and dry out in summer in the same spatial locations. Information on species and morphospecies abundances at the sampling unit level was recorded in 18 ponds, the number of ponds that were active (i.e., with water) at the sampling date. These ponds are part of the metacommunity for which plants have been sampled every year since 2005 in all ponds and for which environmental information was also compiled—data available in this same Dryad entry. Further surveys are being processed and will be available in the future. Data are provided for promoting the advancement of metacommunity theory, corroborating published studies, and generating novel ones. We are incorporating all the available information about the studied metacommunity that now comprises 20 years of continuous monitoring. The database includes animal species and morphospecies abundances at the sampling unit level for 18 temporary ponds sampled in October 2008. The species traits related to body sizes (measured for each individual) and trophic guild (obtained from literature) are presented together with the individual taxonomy. Note that species Order or family can also be used as a proxy of many conserved attributes like life history, resistance strategy, dispersal mode, or vulnerability to predators.</p>
Fig. 1 in Extinction Disorders The Species Composition Of Metacommunities
Fig. 1. Changes of nestedness in relation to the exclusion of the rarest species from the metacommunity. A = orthopterans, B = butterflies, C = beetles, D = birds, D(st) is the standardized difference between the average temperature of 100 random matrices and the actual matrix temperature, divided by the standard deviation of the random matrices. Triangles indicate non-significant nestedness
Fig. 2 in Helminths of sigmodontine rodents in an agroforestry mosaic in the Brazilian Atlantic Forest: Patterns and processes of the metacommunity structure
Fig. 2. Ordinated matrices for the helminths metacommunity at Pratigi Environmental Protection Area, municipality of Igrapiúna, state of Bahia, northeast Brazil. A) Infracommunities and B) Component Communities.
Fig. 1 in Helminths of sigmodontine rodents in an agroforestry mosaic in the Brazilian Atlantic Forest: Patterns and processes of the metacommunity structure
Fig. 1. The bipartite network analysis illustrating the rodent–helminth association at Pratigi Environmental Protection Area, municipality of Igrapiúna, state of Bahia, northeast Brazil. The brackets separate the rodent tribes.
Pre-exposure of abundant species to disturbance improves resilience in microbial metacommunities. Zenodo fileset.
<p>Data and code for downstream analyses for journal article entitled "Disturbance pre-exposure of abundant species improves community and metacommunity resilience"</p>
Self-organized pattern formation increases local diversity in metacommunities: code and data
<p>Code and data to reproduce the results published in the article "Self-organized pattern formation increases local diversity in metacommunities" (Ecology Letters, https://doi.org/10.1111/ele.13880).</p>
Mutualistic coevolution and community diversity favor persistence in metacommunities under environmental changes
<p>Linking local to regional ecological and evolutionary processes is key to understand the response of Earth's biodiversity to environmental changes. Here we integrate evolution and mutualistic coevolution in a model of metacommunity dynamics to understand how coevolution can shape species distribution and persistence in landscapes varying in space and time. Using simulations, we show that coevolution and species richness can synergistically shape distribution patterns by increasing colonization and reducing extinction of populations in metacommunities. Although conflicting selective pressures emerging from mutualisms may increase mismatches with the local environment and the rate of local extinctions, coevolution increases trait matching among mutualists at the landscape scale, counteracting local maladaptation and favoring colonization and range expansions. Our results show that by facilitating colonization, coevolution can also buffer the effects of environmental changes, preventing species extinctions and the collapse of metacommunities. Our findings reveal the mechanisms whereby coevolution can favor persistence under environmental changes and highlight that these positive effects are greater in more diverse systems that retain landscape connectivity.</p>
Priority effects determine how dispersal affects biodiversity in seasonal metacommunities
<p><span>The arrival order of species frequently determines the outcome of their interactions. This phenomenon, called the priority effect, is ubiquitous in nature and determines local community structure, but we know surprisingly little about how it influences biodiversity across different spatial scales. Here, we use a seasonal metacommunity model to show that biodiversity patterns and the homogenizing effect of high dispersal depend on the specific mechanisms underlying priority effects. When priority effects are only driven by positive frequency dependence, dispersal-diversity relationships are sensitive to initial conditions but generally show a hump-shaped relationship: biodiversity declines when dispersal rates become high and allow the dominant competitor to exclude other species across patches. When spatiotemporal variation in phenological differences alters species' interaction strengths (trait-dependent priority effects), local, regional, and temporal diversity are surprisingly insensitive to variation in dispersal, regardless of the initial numeric advantage. Thus, trait-dependent priority effects can strongly reduce the effect of dispersal on biodiversity, preventing the homogenization of metacommunities. Our results suggest an alternative mechanism that maintains local and regional diversity without environmental heterogeneity, highlighting that accounting for the mechanisms underlying priority effects is fundamental to understanding patterns of biodiversity.</span></p>
Scripts of data selection and analysis: role of community size in driving spatial variation in riverine fish metacommunities around the world
<p>Here we describe how we obtained and analyzed data for the manuscript: High compositional dissimilarity among small communities is decoupled from environmental variation, accepted for publication in Oikos. (10.1111/oik.09802). A preprint is also available: https://doi.org/10.32942/osf.io/vngse</p> <p>We investigated the role of community size in mediate the strength of ecological drift and environmental selection in driving community spatial variation in metacommunities. </p>
Plants metacommunity from temporary ponds
<p>The database comprises a long-term survey of a plant metacommunity of temporary ponds. The metacommunity is <span><span>located in a flat landscape surrounded by hills, where a maximum of 61 ponds, every year</span><span>,</span><span> are filled with water in winter and dry out in summer in the same spatial locations. Information on species occurrences at the sampling unit level was recorded since 2005 (until 2022 and continuous). </span></span></p> <p><span>The database includes: </span></p> <ol> <li><span>Species occurrences at the sampling unit level for 61 temporary ponds along 14 years (to be periodically updated). </span></li> <li><span>Species traits database and functional description of traits. </span></li> <li><span>Environmental information of each pond including connectivity, area, heterogeneity and hydroperiod.</span></li> </ol>
The interplay between abiotic and biotic factors on dispersal decisions: evidence and implications for metacommunities
<p>Suitable conditions for species to survive and reproduce constitute their ecological niche, which is built by abiotic conditions and interactions with conspecifics and heterospecifics. Organisms should ideally assess and use information about all these environmental dimensions to adjust their dispersal decisions depending on their own internal conditions. Dispersal plasticity is often considered through its dependence to abiotic conditions or conspecifics density, and to a lesser extent with the effects of interactions with heterospecifics, potentially leading to misinterpretation of dispersal drivers. Here, we first review the evidence for effects of, and the potential interplays between abiotic factors, biotic interactions with conspecifics and heterospecifics, and phenotype on dispersal decisions. We then present an experimental test of these potential interplays, testing the effects of density and interactions with conspecifics and heterospecifics on temperature-dependent dispersal in microcosms of <i>Tetrahymena </i>ciliates. We found significant differences in dispersal rates depending on temperature, density, and presence of another strain or species. However, the presence and density of conspecifics and heterospecifics had no effects on the thermal-dependency of dispersal. We discuss the causes and consequences of the (lack of) interplay between the different environmental dimensions and the phenotype for metacommunity assembly and dynamics.</p>
Plants metacommunity from temporary ponds
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Allen Brain Atlas
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