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320 results for “community assembly”
Pawpaws prevent predictability: A locally-dominant tree alters understory beta-diversity and community assembly
<p>Data used in "Pawpaws Prevent Predictability: A locally-dominant tree alters understory beta-diversity and community assembly" (Wassel and Myers) accepted for publication in Ecosphere.<br><br><strong>Metadata for Zenodo.pdf </strong>contains more information on the following data files including descriptions of the columns. </p> <p>The file <strong>understory_abundance_data2021.csv</strong> contains all species abundances in 1x1m plots. This data was used for analyses in publication. Each row is a plot, each column is a speceis or plot descriptor, values for columns 5 and higher are species abundances. Data was collected July-August 2021 by Anna Wassel in Missouri, USA. </p> <p>The file <strong>understory_species_list2021.csv </strong>contains a list of the species codes used in the first file with their scientific names and their status as herbs or woody. This was used to filter out herbaceous species from the data set for herbaceous-only analyses. </p> <p> </p>
Long-term studies of secondary succession and community assembly in the prairie-forest ecotone of eastern Kansas, Hay meadow restoration experiment
Local and regional-scale processes interact to govern the assembly, diversity and functioning of ecological communities. Evaluating the interplay of these differently-scaled processes in the regulation of ecological systems is a challenging problem, but is crucial towards understanding and predicting the potential effects of accelerated human activity on biological diversity and ecosystem sustainability. Since 2000, two long-term field experiments have been underway in grasslands of eastern Kansas to investigate the interplay of soil resource availability, species interactions and regional processes governing plant secondary succession, community assembly, biodiversity, and ecosystem functioning. Both experiments involve manipulations of soil nutrients in permanent grassland study plots and employ multi-species seed addition treatments to evaluate the contribution of dispersal limitation and regional constraints on local species pools to the regulation of plant community dynamics. Hay meadow restoration experiment, previously funded by USDA, was established in 2000 in a section of the field that was left unplowed at the start of the experiment. Thus Experiment 2 was initiated in the context of secondary succession on recently abandoned cool-season hayfield where hay grass species were dominant at the start of the study. In this experiment we have been monitoring plant community change annually since 2001 in response to two aspects of hay management important in our area: annual fertilization and annual haying. The experimental design involves factorial manipulations of nutrient supply (two levels of NPK fertilization), annual haying (two levels: hayed; not hayed) and propagule input achieved by adding seeds of 41 native prairie species to half of the plots. Experiment 2 parallels Experiment 1 with manipulations of soil resources and species pools, but does so in the contexts of hay management and native prairie hay meadow restoration.
Data for "Ecosystem size filters life-history strategies to shape community assembly in lakes"
<p>Dataset 1. List of 71 fish species collected from north temperate lakes in Wisconsin USA. Data include critical life-history data used for strategy classifications according to Winemiller and Rose (1992), principal component scores, and strategy classification according to the cluster analysis.</p> <p>Dataset 2. Species occurrence data in all study lakes along with results from the 'soft classification" according to Euclidean distance.</p> <p>Dataset 3. Limnological and fish community characteristics of study lakes including species richness, lake area, estimated lake volume, and convex hull statistics for the overall fish community and each life-history strategy type.</p>
Dataset Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial Pseudomonas in the wheat rhizosphere
<p>This dataset is related to the paper "<strong>Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial <em>Pseudomonas </em>in the wheat rhizosphere</strong>" (Garrido-Sanz et al., 2023, doi: 10.1186/s40168-023-01660-5) and contains the data obtained from bacterial competition asays and plant-growth measurements.</p> <p>Sequencing data used in this study has been deposited in the NCBI Sequence Read Archive (RSA) under the BioProject accession number <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA948847">PRJNA948847</a>.</p> <p>The R script used to analyze the data generated in the paper is available at <a href="https://github.com/dgarrs/Pprotegens_proliferation_NatComs">GitHub </a>and <a href="https://doi.org/10.5281/zenodo.8322086">Zenodo</a>.</p>
FIG. 6 in Ecometrics and Neogene faunal turnover: the roles of cats and hindlimb morphology in the assembly of carnivoran communities in the New World
FIG. 6. — Ecometric plots of ankle gear ratio in carnivoran assemblages from the Arikareean (latest Oligocene and earliest Miocene) through the present. The mean and standard deviation of each assemblage is indicated by the broken line and grey bands respectively. Family-level classification of each species can be found in Appendix 6.
FIG. 1 in Ecometrics and Neogene faunal turnover: the roles of cats and hindlimb morphology in the assembly of carnivoran communities in the New World
FIG. 1. — Ankle gear ratio in Carnivoramorpha: A, plantarflexion in the carnivoran ankle joint (medial view). Black dot marks the approximate centre of rotation. Distance between dot and insertion of gastrocnemius is the approximate out-lever for plantarflexion. Scans of astragalus and calcaneum from Puma concolor (WRAZL 0210086); B, calcaneal anatomy and gear ratio (dorsal view); C, ecometric distribution of ankle gear ratio (y-axis) for 215 carnivormorphan species in rank order (x-axis). Felid and barbourofelid ratios are highlighted with black circles and stem lines. Horizontal broken line, mean value; grey band, 1 standard deviation. Colour coding matches Figure 2.
Temporal dynamics of invertebrate community assembly in Lake Victoria since the Late Pleistocene based on chitinous remains
<p>Preserved assemblages of invertebrate remains in lacustrine sediment reveal temporal variations of community composition and environmental conditions. However, records for large tropical lakes are scarce. Lake Victoria, the largest tropical lake, has a dynamic history of changes in water level, biogeochemistry, and fish community composition over the past ~17,000 cal yr BP. In order to quantify changes in the invertebrate assemblage of Lake Victoria from the Late Pleistocene throughout the Holocene, we examined chitinous remains of Cladocera and larval dipterans (Chironomidae and Chaoboridae) from a sediment core (37 m water depth) dated from ~13,700 cal yr BP to present. We identified four major phases in the invertebrate assemblage throughout this period of lake history. First, Chironomidae and Chaoboridae appeared at low abundances during the earliest stages of the lake inundation in the late Pleistocene, at a time when Cladocera were notably absent. Second, chaoborids and chironomids increased in abundance during the Mid Holocene, which coincided with high diatom production towards the end of the Holocene African Humid Period. Third, starting ~4,700 cal yr BP, <i>Alona</i>, a predominantly littoral cladoceran genus, consistently appeared in the invertebrate assemblage alongside changes in mixing regimes and persisted throughout the Late Holocene to present. Fourth, the arrival of both <i>Chydorus</i> and <i>Bosmina longirostris</i> marked the establishment of an abundant cladoceran assemblage at ~1,350 cal yr BP. The assemblage then gradually shifted toward the increasing dominance of <i>B. longirostris</i>, a planktonic cladoceran. This study provides the first multi-millennial record of sedimentary invertebrate assemblages in Lake Victoria, and elucidates some of the temporal development of these communities throughout most of the modern ecosystem's dynamic history. Overall, we provide novel insights into the temporal dynamics of invertebrate community assembly in relation to climatic and environmental variability in tropical lakes.</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>
Functional biogeography of Neotropical moist forests: trait-climate relationships and assembly patterns of tree communities
<p>Aim: Here we examine the functional profile of regional tree species pools across the latitudinal distribution of Neotropical moist forests, and test trait-climate relationships among local communities. We expected opportunistic strategies (acquisitive traits, small seeds) to be overrepresented in species pools further from the equator due to long-term instability, but also in terms of abundance in local communities in currently wetter, warmer and more seasonal climates.</p> <p>Location: Neotropics.</p> <p>Time period: Recent.</p> <p>Major taxa studied: Trees.</p> <p>Methods: We obtained abundance data from 471 plots across nine Neotropical regions, including ~100,000 trees of 3,417 species, in addition to six functional traits. We compared occurrence-based trait distributions among regional species pools, and evaluated single trait-climate relationships across local communities using community abundance-weighted means (CWM). Multivariate trait-climate relationships were assessed by a double-constrained correspondence analysis that tests both how CWMs relate to climate and how species distributions, parameterized by niche centroids in climate space, relate to their traits.</p> <p>Results: Regional species pools were undistinguished in functional terms, but opportunistic strategies dominated local communities further from the equator, particularly in the northern hemisphere. Climate explained up to 57% of the variation in CWM traits, with increasing prevalence of lower-statured, light-wooded and softer-leaved species bearing smaller seeds in more seasonal, wetter and warmer climates. Species distribution were significantly but weakly related to functional traits.</p> <p>Main conclusions: Neotropical moist forest regions share similar sets of functional strategies, from which local assembly processes, driven by current climatic conditions, select for species with different functional strategies. We can thus expect functional responses to climate change driven by changes in relative abundances of species already present regionally. Particularly, equatorial forests holding the most conservative traits and large seeds are likely to experience the most severe changes if climate change triggers the proliferation of opportunistic tree species.</p>
Rapid ant community re-assembly in a Neotropical forest: recovery dynamics and land-use legacy
<p>Regrowing secondary forests dominate tropical regions today, and a mechanistic understanding of their recovery dynamics provides important insights for conservation. In particular, land-use legacy effects on the fauna have rarely been investigated. One of the most ecologically dominant and functionally important animal groups in tropical forests are ants. Here, we investigated the recovery of ant communities in a forest – agricultural habitat mosaic in the Ecuadorian Chocó region. We used a replicated chronosequence of previously used cacao plantations and pastures with 1 – 34 years of regeneration time to study the recovery dynamics of species communities and functional diversity across the two land use legacies. We compared two independent components of responses on these community properties: resistance, which is measured as the proportion of an initial property that remains following the disturbance; and resilience, which is the rate of recovery relative to its loss. We found that compositional and trait structure similarity to old-growth forest communities increased with regeneration age, whereas ant species richness remained always at a high level along the chronosequence. Land-use legacies influenced species composition, with former cacao plantations showing higher resemblance to old-growth forests than former pastures along the chronosequence. While resistance was low for species composition and high for species richness and traits, all community properties had similarly high resilience. In essence, our results show that ant communities of the Chocó recovery rapidly, with former cacao reaching predicted old-growth forest community levels after 21 years and pastures after 29 years. Recovery in this community was faster than reported from other ecosystems and was likely facilitated by the low-intensity farming in agricultural sites and their proximity to old-growth forest remnants. Our study indicates the great recovery potential for this otherwise highly threatened biodiversity hotspot.</p>
Semi‐quantitative metabarcoding reveals how climate shapes arthropod community assembly along elevation gradients on Hawaii Island
<p>Spatial variation in climatic conditions along elevation gradients provides an important backdrop by which communities assemble and diversify. Lowland habitats tend to be connected through time, whereas highlands can be continuously or periodically isolated, conditions that have been hypothesized to promote high levels of species endemism. This tendency is expected to be accentuated among taxa that show niche conservatism within a given climatic envelope. While species distribution modeling approaches have allowed extensive exploration of niche conservatism among target taxa, a broad understanding of the phenomenon requires sampling of entire communities. Species-rich groups such as arthropods are ideal case studies for understanding ecological and biodiversity dynamics along elevational gradients given their important functional role in many ecosystems, but community-level studies have been limited due to their tremendous diversity. Here, we develop a novel semi-quantitative metabarcoding approach that combines specimen counts and size-sorting to characterize arthropod community-level diversity patterns along two elevational gradients across two volcanoes on the island of Hawai`i. We find that arthropod communities between the two transects become increasingly distinct compositionally at higher elevations. Resistance surface approaches suggest that climatic differences between sampling localities are an important driver in shaping beta-diversity patterns, though the relative importance of climate varies across taxonomic groups. Nevertheless, the climatic niche position of OTUs between transects was highly correlated, suggesting that climatic filters shape the colonization between adjacent volcanoes. Taken together, our results highlight climatic niche conservatism as an important factor shaping ecological assembly along elevational gradients and suggest topographic complexity as an important driver of diversification.</p>
Geographical variation in the trait-based assembly patterns of multitrophic invertebrate communities
<p><span>It has been argu</span><span>ed that the mechanisms structuring ecological communities may be more generalizable when based on traits than on species identities. If so, patterns in the assembly of community-level traits along environmental gradients should be similar in different places in the world. Alternatively, geographic change in the species pool and regional variation in climate might result in site-specific relationships between community traits and local environments. These competing hypotheses are particularly untested for animal communities. </span><span>Here we test the geographic constancy of trait-based assembly patterns using a widespread multi-trophic community: aquatic macroinvertebrates within bromeliads. We used data on 615 invertebrate taxa from 1656 bromeliads in 26 field sites from Mexico to Argentina. We summarized invertebrate traits with four orthogonal axes, and used these trait axes to examine trait convergence and divergence assembly patterns along three environmental gradients: detrital biomass and water volume in bromeliads, and canopy cover over bromeliads. </span><span>We found no overall signal of trait-based assembly patterns along any of the environmental gradients. However, individual sites did show trait convergence along detrital and water gradients, and we built predictive models to explore these site differences. </span><span>Sites that showed trait convergence along detrital gradients were all north of the Northern Andes. This geographic pattern may be related to phylogeographic differences in bromeliad morphology. Bromeliads with low detritus were dominated by detritivorous collectors and filter feeders, where those with high detritus had more sclerotized and predatory invertebrates. </span><span>Sites that showed the strongest trait convergence along gradients in bromeliad water were in regions with seasonal precipitation. In such sites, bromeliads with low water were dominated by soft-bodied, benthic invertebrates with simple life cycles. In less seasonal sites, traits associated with short-term desiccation resistance, such as hard exoskeletons, were more important.</span><span> In summary, we show that there are strong geographic effects on the trait-based assembly patterns of this invertebrate community, driven by the biogeography of their foundational plant species as well as by regional climate. We suggest that inclusion of biogeography and climate in trait-based community ecology could help make it a truly general theory. (excerpted from Srivastava, DS et al. 2022. Geographical variation in the trait-based assembly patterns of multitrophic invertebrate communities. Functional Ecology)</span></p>
OTU level 16s sequence data for "Algae drive convergent bacterial community assembly when nutrients are scarce"
<p>16s sequence data at the OTU level for the experiments conducted in "Algae drive convergent bacterial community assembly when nutrients are scarce"</p> <p>The file is in fasta format, which can be read by many software packages including biopython, R, and SILVA's alignment, classification and tree service.</p> <p>The sequence ids can be used to find the phylogeny and OTU ID of the sequences from Supplementary dataset 4. </p>
Opposing community assembly patterns for dominant and non-dominant plant species in herbaceous ecosystems globally
<p>Biotic and abiotic factors interact with dominant plants —the locally most frequent or with the largest coverage— and non-dominant plants differently, partially because dominant plants modify the environment where non-dominant plants grow. For instance, if dominant plants compete strongly, they will deplete most resources, forcing non-dominant plants into a narrower niche space. Conversely, if dominant plants are constrained by the environment, they might not exhaust available resources but instead may ameliorate environmental stressors that usually limit non-dominants. Hence, the nature of interactions among non-dominant species could be modified by dominant species. Furthermore, these differences could translate into a disparity in the phylogenetic relatedness among dominants compared to the relatedness among non-dominants. By estimating phylogenetic dispersion in 78 grasslands across five continents, we found that dominant species were clustered (e.g., co-dominant grasses), suggesting dominant species are likely organized by environmental filtering, and that non-dominant species were either randomly assembled or overdispersed. Traits showed similar trends for those sites (<50%) with sufficient trait data. Furthermore, several lineages scattered in the phylogeny had more non-dominant species than expected at random, suggesting that traits common in non-dominants are phylogenetically conserved and have evolved multiple times. We also explored environmental drivers of the dominant/non-dominant disparity. We found different assembly patterns for dominants and non-dominants, consistent with asymmetries in assembly mechanisms. Among the different postulated mechanisms, our results suggest two complementary hypotheses seldom explored: (1) Non-dominant species include lineages adapted to thrive in the environment generated by dominant species. (2) Even when dominant species reduce resources to non-dominant ones, dominant species could have a stronger positive effect on some non-dominants by ameliorating environmental stressors affecting them, than by depleting resources and increasing the environmental stress to those non-dominants. These results show that the dominant/non-dominant asymmetry has ecological and evolutionary consequences fundamental to understand plant communities.</p>
Data from: Different taxonomic and functional indices complement the understanding of herb-layer community assembly patterns in a southern-limit temperate forest
<p><span>The efficient conservation of vulnerable ecosystems in the face of global change requires a complete understanding of how plant communities respond to various environmental factors. We aim to demonstrate that a combined use of different approaches, traits, and indices representing each of the taxonomic and functional characteristics of plant communities will give complementary information on the factors driving vegetation assembly patterns. We analyzed variation across an environmental gradient in taxonomic and functional composition, richness, and diversity of the herb-layer of a temperate beech-oak forest that was located in northern Spain. We measured species cover and four functional traits: leaf dry matter content (LDMC), specific leaf area (SLA), leaf size, and plant height. We found that light is the most limiting resource influencing herb-layer vegetation. Taxonomic changes in richness are followed by equivalent functional changes in the diversity of leaf size but by opposite responses in the richness of SLA. Each functional index is related to different environmental factors even within a single trait (particularly for LDMC and leaf size). To conclude, each characteristic of a plant community is influenced by different and even contrasting factors or processes. Combining different approaches, traits, and indices simultaneously will help us understand how plant communities work.</span></p>
Supporting data: Land-use change alters the mechanisms assembling rainforest mammal communities in Borneo
<p>These supporting data files were used in the analyses for a forthcoming<em> </em>paper (DOI to be confirmed). The two files consist of: </p> <p>1. Combined camera trap and live trap species-abundance matrix. Each row corresponds to a separate location, with species in different columns. Old-growth forest, logged forest and oil palm plantation locations have the prefixes "Old", "Log" and "Palm", respectively. Values in each cell are the number of independent captures (as defined in the paper) per seven days summed over the camera- and live-trapping protocols.</p> <p>2. Covariate data for each location, covering habitat structure, topography and local landscape context (covariates as defined in the paper). </p>
Data for: Community assembly of the human piercing microbiome
<p>Predicting how biological communities respond to disturbance requires understanding the forces that govern their assembly. We propose using human skin piercings as a model system for studying community assembly after rapid environmental change. Local skin sterilization provides a 'clean slate' within the novel ecological niche created by the piercing. Stochastic assembly processes can dominate skin microbiomes due to the influence of environmental exposure on local dispersal, but deterministic processes might play a greater role within occluded skin piercings if piercing habitats impose strong selection pressures on colonizing species. Here we explore the human ear-piercing microbiome and demonstrate that community assembly is predominantly stochastic but becomes significantly more deterministic with time, producing increasingly diverse and ecologically complex communities. We also observed changes in two dominant and medically relevant antagonists (<em>Cutibacterium acnes </em>and <em>Staphylococcus epidermidis</em>), consistent with competitive exclusion induced by a transition from sebaceous to moist environments. By exploiting this common yet uniquely human practice, we show that skin piercings are not just culturally significant but also represent ecosystem engineering on the human body. The novel habitats and communities that skin piercing produce may provide general insights into biological responses to environmental disturbance with implications for both ecosystem and human health.</p>
Data from: Mycorrhizal symbiosis increases plant phylogenetic diversity and regulate community assembly
<p>The intricate mechanisms shaping plant diversity and community composition are the cornerstone of ecological understanding. Yet, the role of mycorrhizal symbiosis, the fundamental partnership between fungi and plant roots, in influencing community composition has often been underestimated. Here, we use extensive species survey data from 1,315 terrestrial ecosystem sites to elucidate the influence of mycorrhizal symbiosis on plant phylogenetic diversity and its implications for community assembly processes. Our findings demonstrate that increasing mycorrhizal symbiotic potential leads to greater phylogenetic dispersion within plant communities. Furthermore, we unveil a distinct dichotomy in the assembly processes governed by mycorrhizal status. Mycorrhizal species predominantly influence deterministic processes, suggesting a role in niche-based community assembly. Conversely, non-mycorrhizal species exert a stronger influence on stochastic processes, highlighting the importance of random events in shaping community structure. These results underscore the crucial but often hidden role of mycorrhizal symbiosis in driving plant community diversity and assembly. This study provides valuable insights into the complex mechanisms shaping ecological communities and the way for more informed conservation and management practices that acknowledge the complex interplay between symbiosis and ecological community dynamics.</p>
Functional traits and habitat use: investigating community assembly in a montane community (Carabidae: Nebria)
<p>The processes that influence community assembly, such as competition for resources and environmental filtering, are often scale-dependent and vary across ecotones. Trait-based ecology provides a useful framework for testing which ecological processes most strongly influence local community composition, especially across environmental gradients where species diversity varies. Where environmental filtering dominates, species distributions are expected to be defined by strong turnover along environmental gradients, with more similar species occupying more similar habitats. Where interspecific competition dominates, species are expected to diverge in relative abundance and resource utilization at sites, so species can co-occur. Here, we integrate measurements of functional traits, microhabitat usage, isotopic composition (δ<sup>15</sup>N and δ<sup>13</sup>C), and abundance to test the importance of environmental filtering and resource/habitat partitioning in shaping a montane ground beetle species assemblage (Carabidae: Nebriini: <em>Nebria</em>) in the isolated, volcanic peaks of the northern Cascades Range, U.S.A. Across species of <em>Nebria</em>, body size, pronotal shape, temperature preference, and isotopic enrichment varied across habitats [gravel, rocks 10 cm – 50 cm in diameter), large rocks (>50 cm in diameter), vegetation-covered rocks, and alpine (snowfields and talus)], and habitat/microhabitat features were reliable predictors of species presence. Resource consumption among mid-elevation species on Mt. Rainier – the peak with the greatest species diversity – is highly overlapping. Species turnover and nestedness varied significantly across habitat gradients and peaks throughout this region and varied nearly significantly across sites. Across habitat types and sites, more similar species are more likely to coexist. These results suggest that environmental filtering is the primary process structuring this species assemblage, although we find detailed evidence for microhabitat niche partitioning among species of <em>Nebria</em> at the site-scale.</p>
Data and scripts for "The role of stochasticity in fungal community assembly – explaining apparent stochasticity with field experiments"
<p>The results presented in the manuscript “The role of stochasticity in fungal community assembly – explaining apparent stochasticity by field experiments” can be reproduced by the data and scripts provided in this repository.</p> <p>Concerning the analysis of observational data:</p> <p>· The file ObservationalData.RData includes all data: XData is the dataframe including the predictors, and t is the vector of responses (F. rosea occurrences).</p> <p>· The script O1_model_observational_data.R defines the models, fits the models, and computes model fits based on cross-validation. The results are saved into a file.</p> <p>· The script O2_show_results_observational_data.R loads the results saved by the previous script, and outputs the results reported in the manuscript.</p> <p>Concerning the analysis of experimental data:</p> <p>· The file ExperimentalData.RData includes all data: the dataframe meta includes the relevant predictors, otu.table the matrix of samples x OTU read counts, and the dataframe taxonomy the taxonomic placement of those OTUs.</p> <p>· The script E1_compute_model_based_ordinations.R precomputes the gllvm-ordinations needed both for the colonization success model as well as the community divergence model. The precomputed ordinations are saved into a file.</p> <p>· The script E2_model_colonization_success.R defines the colonization success model, fits the model, and computes model fit based on cross-validation. The results are saved into a file.</p> <p>· The script E3_show_colonization_model_results.R loads the results saved by the previous script, and outputs the results reported in the manuscript.</p> <p>· The script E4_model_community_divergence defines the community divergence model and fits the model. The results are saved into a file.</p> <p>· The script E5_show_community_divergence_model_results.R loads the results saved by the previous scripts, and outputs the results reported in the manuscript, including Table 1 and Figure 2.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.