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Ground-truthing Phylotype Assignments for Antarctic Invertebrates
<p>Release from GitHub to Zenodo after proof correction (and branch merging). See article and README.md for further dataset descriptions.</p>
Fig. 39. Fossil invertebrates from a in Scaphites Of The ''Nodosus Group'' From The Upper Cretaceous (Campanian) Of The Western Interior Of North America
Fig. 39. Fossil invertebrates from a cold seep in the Pierre Shale, Didymoceras cheyennense Zone, AMNH loc. 3418, Custer County, South Dakota. A, B. Baculites corrugatus Elias, 1933, mature macroconch, AMNH 58552, uncoated. Note the series of small scalloped edges along the entire length of the body chamber on both sides (arrows), probably reflecting predation. A. Ventral, with apertural projection on top; B. right lateral, with apertural projection on top. C. Didymoceras cheyennense (Meek
Effects of nutrient enrichment on freshwater macrophyte and invertebrate abundance: A meta-analysis
<p>The zip-file contains the data and code accompanying the paper 'Effects of nutrient enrichment on freshwater macrophyte and invertebrate abundance: A meta-analysis'. Together, these files should allow for the replication of the results.</p> <p>The 'raw_data' folder contains the 'MA_database.csv' file, which contains the extracted data from all primary studies that are used in the analysis. Furthermore, this folder contains the file 'MA_database_description.txt', which gives a description of each data column in the database.</p> <p>The 'derived_data' folder contains the files that are produced by the R-scripts in this study and used for data analysis. The 'MA_database_processed.csv' and 'MA_database_processed.RData' files contain the converted raw database that is suitable for analysis. The 'DB_IA_subsets.RData' file contains the 'Individual Abundance' (IA) data subsets based on taxonomic group (invertebrates/macrophytes) and inclusion criteria. The 'DB_IA_VCV_matrices.RData' contains for all IA data subsets the variance-covariance (VCV) matrices. The 'DB_AM_subsets.RData' file contains the 'Total Abundance' (TA) and 'Mean Abundance' (MA) data subsets based on taxonomic group (invertebrates/macrophytes) and inclusion criteria.</p> <p>The 'output_data' folder contains maps with the output data for each data subset (i.e. for each metric, taxonomic group and set of inclusion criteria). For each data subset, the map contains random effects selection results ('Results1_REsel_<subset>.csv'), the fixed effects selection results ('Results2_FEsel_<subset>.csv'), the random variance components and R^2 values for the best models subset ('Results3_BestModels_<subset>.csv'), the parameter value estimations for the fixed effects ('Results4_Parameters_<subset>.csv'), the standard errors for the estimated parameter values ('Results5_SE_<subset>.csv'), and the consensus model parameter values ('Results6_ConsensusModel_<subset>.csv'). Furthermore, each map contains a file with the best-selected random effects model structure ('BestRanEf_<subset>.RData'), the model with the best-selected random effects structure without moderators (only for IA) ('BestRanEfModel_<subset>.RData'), and a file with the consensus model ('ConsensusModel_<subset>.RData').</p> <p>The 'scripts' folder contains all R-scripts that we used for this study. The 'PrepareData.R' script takes the database as input and adjusts the file so that it can be used for data analysis. The 'PrepareDataIA.R' and 'PrepareDataAM.R' scripts make subsets of the data and prepare the data for the meta-regression analysis and mixed-effects regression analysis, respectively. The regression analyses are performed in the 'SelectModelsIA.R' and 'SelectModelsAM.R' scripts to calculate the regression model results for the IA metric and MA/TA metrics, respectively. These scripts require the 'RandomAndFixedEffects.R' script, containing the random and fixed effects parameter combinations, as well as the 'Functions.R' script. The 'CreateMap.R' script creates a global map with the location of all studies included in the analysis (figure 1 in the paper). The 'CreateForestPlots.R' script creates plots showing the IA data distribution for both taxonomic groups (figure 2 in the paper). The 'CreateHeatMaps.R' script creates heat maps for all metrics and taxonomic groups (figure 3 in the paper, figures S11.1 and S11.2 in the appendix). The 'CalculateStatistics.R' script calculates the descriptive statistics that are reported throughout the paper, and creates the figures that describe the dataset characteristics (figures S3.1 to S3.5 in the appendix). The 'CreateFunnelPlots.R' script creates the funnel plots for both taxonomic groups (figures S6.1 and S6.2 in the appendix) and performs Egger's tests. The 'CreateControlGraphs.R' script creates graphs showing the dependency of the nutrient response to control concentrations for all metrics and taxonomic groups (figures S10.1 and S10.2 in the appendix).</p> <p>The 'figures' folder contains all figures that are included in this study.</p>
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>
F I G U R E 5 in Untangling the web: dynamics of Australia s online terrestrial invertebrate trade
F I G U R E 5 (a) Total number of invertebrate listings per State on the classifieds website, (b) classes of invertebrate for sale per State. Note: the Y axes are transformed to display less abundant classes.
F I G U R E 8 in Untangling the web: dynamics of Australia s online terrestrial invertebrate trade
F I G U R E 8 Reconstructed examples of classifieds listings with vague descriptions and poor-quality images.
F I G U R E 6 in Untangling the web: dynamics of Australia s online terrestrial invertebrate trade
F I G U R E 6 (a) Total number of invertebrate listings per State on online pet stores. (b) The classes of invertebrate each listing features. Y axis are log10 transformed to display less abundant classes.
F I G U R E 1 in Untangling the web: dynamics of Australia s online terrestrial invertebrate trade
F I G U R E 1 Species accumulation curve for invertebrate listings collected from the public classifieds website, representing the total cumulative number of species identified over time as listings were collected from the website.
F I G U R E 4 The top 10 in Untangling the web: dynamics of Australia s online terrestrial invertebrate trade
F I G U R E 4 The top 10 most popular invertebrate species in online pet stores, and those that also feature in the top 10 most popular species on the Australian classifieds website. Note that Urodacus elongatus (Flinders Ranges scorpion) has the same relative abundance in online pet stores as Exatosoma tiaratum (giant prickly stick insect), the overall most traded species online.
F I G U R E 7 in Untangling the web: dynamics of Australia s online terrestrial invertebrate trade
F I G U R E 7 (a) Histogram of mean species price-per-unit differences (AUD) between classifieds and online pet stores (classifieds price minus pet store price, i.e., negative price difference indicates that classifieds species are less expensive). Median value of 7.442 is represented by the red line. (b) Examples of species with large price differences on the two e-commerce platforms. Photo credits: (a) Rosie Steinberg, (b) Ajay Narendra, (c) Stephan Höhne.
F I G U R E 3 in Untangling the web: dynamics of Australia s online terrestrial invertebrate trade
F I G U R E 3 Bar graph of the top 10 most popular invertebrate species on the classifieds website by proportion of total listings, and those that also feature in the top 10 most popular species in online pet stores.
F I G U R E 2 in Untangling the web: dynamics of Australia s online terrestrial invertebrate trade
F I G U R E 2 (a) Total number of invertebrate orders traded on the classifieds website. (b) Total number of species within each invertebrate order traded on the classifieds website.
Fig. 2 in A closer look at the main actors of Neotropical floodplain food webs: functional classification and niche overlap of dominant benthic invertebrates in a floodplain lake of Paraná River
Fig. 2. Cluster plot depicting trophic similarity (Morisita index) among species of dominant benthic invertebrates in a floodplain lake of ParanÁ River, Argentina. Dotted line depicts the threshold similarity of 0.6.
Fig. 3 in A closer look at the main actors of Neotropical floodplain food webs: functional classification and niche overlap of dominant benthic invertebrates in a floodplain lake of Paraná River
Fig. 3. Non Metric Multidimensional scaling plot. Circles depicts taxa classified as gatherer collectors (Aulodrilus pigueti, Pristina leidyi, Dero vagus, Nais communis, Pelomus sp., Cladopelma sp., Endotribelos sp., Polypedilum sp., Chironomus sp., Parachironomus sp., Phaenopsectra sp., Americabaetis sp., Baetis sp., Campsurus violaceus, Hyalella curvispina, Crynellus sp.) [Triangles: Tanypodinae (Coelotanypus sp., Procladius sp. and Ablabesmyia (Karelia); inverted triangle: Sympetrum sp.; square: Monopelopia sp.; cross: Pomacea canaliculata].
Fig. 1 in A closer look at the main actors of Neotropical floodplain food webs: functional classification and niche overlap of dominant benthic invertebrates in a floodplain lake of Paraná River
Fig. 1. Relative importance (IRI) of food items for analyzed taxa of dominant benthic invertebrates in a floodplain lake of ParanÁ River, Argentina (parenthesis indicate sample size).
Fig. 2 in Invertebrate Fauna Associated with Floating Sargassum horneri (Fucales: Sargassaceae) in the East China Sea
Fig. 2. Density of total taxa of epibionts on floating algae (A), abundance of total taxa (B), and Simpson's diversity index (C) presented as box plots. The number above each box indicates the number of examined algal rafts per station. The black line in each box shows the median and the whiskers show the range except for the outlier (black dot).
Fig. 3 in Invertebrate Fauna Associated with Floating Sargassum horneri (Fucales: Sargassaceae) in the East China Sea
Fig. 3. Correlations between number of total taxa and examined algal wet weight (A) (n=53, R2=0.21); abundance of total taxa and examined algal wet weight (B) (n=53, R2=0.41); and Simpson's diversity index and examined algal wet weight (C) (n=53, R2 = 0.10).
Plecoptera of the Daniel L. Gustafson Aquatic Invertebrate Collection, Montana Entomology Collection, Montana State University
<p>The adults and nymphs of Plecoptera, an order of aquatic insects commonly named stoneflies, are emulated in fly fishing patterns and the nymphs are used in water quality assessments. They are encountered in the flowing freshwaters of Montana and the state has relatively high species richness for this group. From 2018 to 2022, Montana Entomology Collection (MTEC), funded by the Council on Library and Information Resources “Hidden Collections” grant, digitized stonefly (Insecta: Plecoptera) specimens housed in its museum. This produced over 2000 records detailing sampling localities, collecting dates, number of individuals, and identifications of stoneflies collected mainly from Montana, USA. The records reveal the efforts of 40 collectors, spanning 60 years of sampling. This dataset makes information associated with 22,600 individual specimens from over 90 species stored in the MTEC available.</p>
Ephemeroptera of the Daniel L. Gustafson Aquatic Invertebrate Collection, Montana Entomology Collection, Montana State University
<p>Ephemeroptera (commonly called mayflies) is an order of insects well-recognized by fishing enthusiasts and regularly used in water quality assessments. From 2018 to 2022, Montana Entomology Collection (MTEC), funded by the Council on Library and Information Resources “Hidden Collections” grant, digitized mayfly specimens housed in its museum. Digitization of label data produced over 2900 records detailing sampling localities, collecting dates, number of individuals, and identifications of mayflies collected mainly from Montana, USA. The records reveal the efforts of 29 collectors, contributing specimens since the 1970s. The digital records make information associated with 37,000 individual specimens from approximately 100 species stored in the MTEC available.</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>
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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.