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17 results for “assembly rules”
Phylogenetic diversity and environment form assembly rules for Arctic diatom genera – a study on recent and ancient sedimentary DNA
<p><span><b>Aim</b></span></p> <p><span>This study investigates taxonomic and phylogenetic diversity in diatom genera to evaluate assembly rules for eukaryotic microbes across the Siberian treeline. We first analysed how phylogenetic distance relates to taxonomic richness and turnover. Second, we used relatedness indices to evaluate if environmental filtering or competition influences the assemblies in space and through time. Third, we used distance-based ordination to test which environmental variables shape diatom turnover.</span></p> <p><span><b>Location</b></span></p> <p><span>Yakutia and Taymyria, Russia: we sampled 78 surface sediments and a sediment core, extending to 7000 years before present, to capture the forest–tundra transition in space and time, respectively. </span></p> <p><span><b>Taxon</b></span></p> <p><span>Arctic freshwater diatoms.</span></p> <p><span><b>Methods</b></span></p> <p><span>We applied metabarcoding to retrieve diatom diversity from surface and core sedimentary DNA. The taxonomic assignment binned sequence types (lineages) into genera and created taxonomic (abundance of lineages within different genera) and phylogenetic datasets (phylogenetic distances of lineages within different genera).</span></p> <p><span><b>Results</b></span></p> <p><span>Contrary to our expectations, we find a unimodal relationship between phylogenetic distance and richness in diatom genera. We discern a positive relationship between phylogenetic distance and taxonomic turnover in spatially and temporally distributed diatom genera. Further, we reveal positive relatedness indices in diatom genera across the spatial environmental gradient and predominantly in time-slices at a single location, with very few exceptions assuming effects of competition. Distance-based ordination of taxonomic and phylogenetic turnover indicates that lake environment variables, like HCO<sub>3</sub><sup>–</sup> and water depth, largely explain diatom turnover. </span></p> <p><span><b>Main conclusion</b></span></p> <p>Phylogenetic and abiotic assembly rules are important in understanding the regional assembly of diatom genera across lakes in the Siberian treeline ecotone. Using a space–time approach we are able to exclude the influence of geography and elucidate that lake environmental variables primarily shape the assemblies. We conclude that some diatom genera have greater capabilities to adapt to environmental changes, whereas others will be putatively replaced or lost due to the displacement of the Arctic tundra biome under recent global warming.</p>
Data from: A test of community assembly rules using foliar endophytes from a tropical forest canopy
<p>Community assembly theory assumes that ecological communities are spatially delimited into patches. Within these patches, coexistence results from environmental filtering, competition, and immigration. Truly delineated communities exist in laboratory studies of microbial cultures in Petri dishes, yet empirical tests conducted in continuous environments often use patches defined by convention as opposed to realised boundaries. Here we perform a test of ecological community assembly rules using foliar endophyte communities from a tropical rainforest, where leaves are considered as patches for both fungal and bacterial communities. We determined the diversity of fungal and bacterial endophytes using environmental DNA sequencing of 365 top-canopy leaves, collected from 38 host trees belonging to 22 different species across a 4-hectare research plot. Three leaves were collected from three or more branches within each tree crown. We tested the effect of host tree species and their level of phylogenetic relatedness on community composition as well as the contribution of geographic distance between leaves to endophyte community diversity. Endophyte diversity significantly differed across host tree species, as did community composition. Within certain endophytic orders (Xylariales, Rhizobiales) species assemblages significantly differed across host tree species, but this trend was weaker or non-existent in other orders known to contain pathogens and saprotrophs (Polyporales, Solirubrobacterales). Phylogenetically related host tree species displayed more similar endophyte communities than expected by chance, but geographically close trees did not. Consistent with the finding of host-specificity, nearby leaves tended to host more similar communities than distantly positioned ones. These findings demonstrate that foliar endophytes are structured by dispersal across small spatial scales, but at the scale of the canopy they display patterns of neutral filtering, with only a small part of variation described by host tree differences. Endophyte communities thus act as a model system in evoking the rules predicted by theoretical community ecology.</p>
Rule-based generative design of translational and rotational interlocking assemblies
<p>Video illustrating the ideas and limitations developped in our eponymous article.</p>
Bryophyte assembly rules across scales
<ol> <li>Understanding how species assemble into communities is a central issue in community ecology. So far, most studies have focused on the assembly mechanisms of vascular plant communities, while the role of deterministic (environmental filtering and biotic interactions) and stochastic (e.g., dispersal limitation) processes structuring bryophyte assemblages remains poorly understood.</li> <li>To evaluate how different assembly processes shape bryophyte communities in mountain streams, we examined functional trait patterns across spatial scales and along environmental gradients. To do so, we sampled 754 microhabitat plots (0.25 m<sup>2</sup>) nested within 165 sites (100-m long stream segments) and 13 sub-basins, located in the northwest and central-west of Portugal. At each spatial scale, observed functional diversity indices (Functional Richness and Rao's quadratic entropy) were compared to random expectations derived from null models, followed by the analysis of changes in functional trait patterns along environmental gradients by fitting a series of generalized additive mixed models (GAMMs).</li> <li>At local scales (site and microhabitat plot), coexisting species tended to be more functionally similar than expected, suggesting the prevalence of environmental filtering effects. In contrast, no significant deviations from random expectations were detected at the broadest spatial scale (sub-basin), indicating the prevalence of stochastic processes. We found contrasting assembly processes along environmental gradients: environmental filtering prevailed in stressful environments, while competitive interactions were more important in favourable conditions.</li> <li>Synthesis. Our results highlight the role of environmental filtering in bryophyte community assembly at fine spatial scales, emphasizing the importance of measuring environmental conditions at the same spatial scales where biotic interactions take place. In line with the stress-dominance hypothesis, the relative importance of environmental filtering increased with abiotic stress. Thus, analysing functional trait patterns across different spatial scales and environmental gradients may contribute to a better understanding of the mechanisms underlying community assembly.</li> </ol>
Scale-dependence of ecological assembly rules: insights from empirical datasets and joint species distribution modelling
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Bryophyte assembly rules across scales
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Invaders break assembly rules to beat the natives: How cheatgrass cheats
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Data from: A test of community assembly rules using foliar endophytes from a tropical forest canopy
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Data from: Phylogenetic diversity and environment form assembly rules for Arctic diatom genera—a study on recent and ancient sedimentary DNA
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Code and data for Assembly rules of helminth parasite communities in grey mullets: combining components of diversity
<p>Raw data analysed and a step-by-step summary of the R functions and packages used in Llopis-Belenguer, C., Pavoine, S., Blasco-Costa, I., Antonio Balbuena, J., 2020. Assembly rules of helminth parasite communities in grey mullets: combining components of diversity. International Journal for Parasitology. DOI: 10.1016/j.ijpara.2020.06.006</p>
Data from: Changes in assembly rules along a stress gradient from open dry grasslands to wetlands
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Data from: The rules for symbiont community assembly change along a mutualism-parasitism continuum
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Data from: Multifaceted functional diversity for multifaceted crop yield: towards ecological assembly rules for varietal mixtures
<p>Data and code for the study "Multifaceted functional diversity for multifaceted crop yield: towards ecological assembly rules for varietal mixtures"</p> <p>Two data files are available:</p> <ul> <li>"CWM_D.csv" contains one row per experimental plot with community-weighted mean (CWM) and Rao quadratic diversity (D) indices computed on the 19 functional traits.</li> </ul> <p>The first two columns ("genotype_1" & "genotype_2") are the identity of the two genotypes in the plot, which are identical in single-variety plots. The third column ("assoc") refers to the plot type: single-variety ("M") or mixed-variety ("P") plot. Then, all trait CWMs and Ds are reported as "CWM_trait_name" and "D_trait_name" , respectively. For single-variety plots, only CWMs are reported but in this case they correspond to unweighted-averaged trait values across replicated measurements within plots. Root trait names are followed by "sem" or "adv" depending if they were measured on seminal or adventitious roots. Reported traits are: "Angle_aer" (Aerial angle, °), "Angle_root" (Root angle, °), "Diam_sem/adv" (mean root diameter, mm), "SRL_sem/adv" (specific root length, m/g), "RTD_sem/adv" (root tissue density, g/cm3), "RBI_sem/adv" (root branching intensity, nb of root tips/cm), "RLD_sem/adv" (root length density, cm root/cm3 soil), "Till_nb" (tiller number per capita), "Ear_bio" (early biomass per capita, g), "SLA" (specific leaf area, m²/kg), "LNC" (leaf nitrogen content, %), "Height" (plant height, cm), "Heading" (heading date, Growing Degree Days), and "Maturity" (maturity date, Growing Degree Days).</p> <ul> <li>"RAW_RYT.csv" contains one row per experimental plot with absolute and relative measures of performance on several agronomic variables.</li> </ul> <p>The first two columns ("genotype_1" & "genotype_2") are the identity of the two genotypes in the plot, which are identical in single-variety plots. The third column ("assoc") refers to the plot type: single-variety ("M") or mixed-variety ("P") plot. Then, all absolute and relative measures of agronomic performance are reported as "RAW_performance_variable_name" and "RYT_performance_variable_name", respectively. For single-variety plots, only absolute performances are reported. Reported performance variable are "GY" (Grain yield, g/m²), "GNb" (Grain number per m²), "SY" (Spike yield, g/m²), "SNb" (Spike number per m²), "BY" (Biomass yield, g/m²), "PY" (Protein yield, g/m²), "TKW" (Thousand kernel weight, g), "SeY" (Semolina yield, %), "GPC" (Grain protein content, %), "TW" (Test weight, kg/hL), "RLVA" (Rate of loss of vitreous aspect, %), "YI" (Yellowness index), "GPD" (Grain protein deviation, %).</p> <p>One R code file is available:</p> <ul> <li>"Mu_FD_Mu_CY_Analysis.R" contains all statistical analysis performed to produce the results presented in the main text and in the Supplementary Information of the study. It uses "CWM_D.csv" and "RAW_RYT.csv" files as inputs.</li> </ul>
Trait-based approach confirms the importance of propagule limitation and assembly rules in old-field restoration
<p>Trait values for plant species present in our research.</p>
Data from: Spatial scale and intraspecific trait variability mediate assembly rules in alpine grasslands
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Dissect Assembly Rules of SPET12 Complex in the Mammalian Sperm
ClinicalTrials.gov study NCT04159402. IPD Sharing: Not stated. Countries: 0. Publications: 0.
Data from "Ecological assembly rules on arthropod community inhabiting mistletoes" publication.
<p>Field-collected data that support the findings of the study Lázaro-González et al. 2020.</p> <p>Lázaro-González, A., Hódar, JA & Zamora, R. (2020) Ecological assembly rules on arthropod community inhabiting mistletoes. Ecological Entomology.</p>
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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