Comparison of MetaDAVis and other popular microbiome analysis tools.

Contains data and code for peer review of the draft manuscript 'Two dominant forms of multisite similarity decline – their origins and interpretation' in review at Ecology and Evolution (Manuscript ID: ECE-2022-10-01523). The data are a subset of the metaCommunity Ecology: Species, Traits, Environment and Space; "CESTES" database reported in A global database for metacommunity ecology, integrating species, traits, environment and space by A. Jeliazkov, D. Mijatovic, S. Chantepie, N. Andrew, R. Arlettaz, L. Barbaro, et al. Scientific Data 2020 Vol. 7 Issue 1 Pages e6. Data were downloaded from the Figshare repository: https://doi.org/10.6084/m9.figshare.c.4459637 on 9 Nov 2021. Methods The 80 datasets in the original database were first filtered to select only abundance (or similar quantitative) estimate of species in each site. This yielded 69 datasets. Several of these were experimental treatments (e.g., logged vs unlogged) or were time series re-surveys of the same sites. Because our interest was in structures within a single habitat type and point in time, these datasets were subdivided into discrete units. In total, this (coincidentally) resulted in 80 datasets for analysis. These data are in the cestesAbSplit.RData object, with matching metadata in mdat_cestesSplit.csv. cestesAbSplit.RData - a list containing the sites x species matrices for the 80 datasets used for analysis. mdat_cestesSplit.csv - matching metadata for the 80 datasets (name and source of the data, taxonomic grouping, kingdom, realm, extent in km2, total sites, total species. This file is only included to run the R analysis. Data are repeated, with full description in Appendix S5 (see Readme tab). Appendix S5 Metadata.xlsx - metadata and values of standardized effect sizes from empirical analyses with ReadMe file explaining each field. The effect sizes were calculated using the scripts in Rcode_form_of_zeta.R (requires R_function.R) and can be reproduced by running the scripts (some very small numerical differences might occur in simulated values based on randomisation).

Field data for fishes sampled using bottom and surface gill nets during daylight hours in Clear Lake, California, USA. This data release includes all measured environmental parameters and fish taxa included in the analysis.

A. Area under the curve distributions for multiplicative spike-ins in dataset A1. Violin plot of distributions of area under the receiver operating characteristic curve (AUC) for spiked vs non-spiked p values from differential relative abundance (DA) tests. AUC distributions from 150 iterations for each combination of spike-in magnitude and case proportion (vertical panels) in dataset A1, analyzed with all differential relative abundance methods (horizontal panels). Black dots represent medians in each distribution. B. Area under the curve distributions for multiplicative spike-ins in dataset A2. Violin plot of distributions of area under the receiver operating characteristic curve (AUC) for spiked vs non-spiked p values from differential relative abundance (DA) tests. AUC distributions from 150 iterations for each combination of spike-in magnitude and case proportion (vertical panels) in dataset A2, analyzed with all differential relative abundance methods (horizontal panels). Black dots represent medians in each distribution. C. Area under the curve distributions for multiplicative spike-ins in dataset A3. Violin plot of distributions of area under the receiver operating characteristic curve (AUC) for spiked vs non-spiked p values from differential relative abundance (DA) tests. AUC distributions from 150 iterations for each combination of spike-in magnitude and case proportion (vertical panels) in dataset A3, analyzed with all differential relative abundance methods (horizontal panels). Black dots represent medians in each distribution. (ZIP 2685 kb)

An ongoing quest in ecology is understanding how species commonness influences compositional change. While each species’ contribution to beta diversity (SCBD) depends both on its abundance and how widespread it is (e.g., occupancy) a general expectation for these influences is lacking. Using published data for 9924 species across 177 metacommunities, we modeled relative SCBD as a function of abundance and occupancy using both correlative and mechanistic regression models (the latter derived from population demographic theory). Although the correlative model provided a superior fit to the data, both results suggest it is infrequent (high abundance and mid-high occupancy) species that make the dominant contribution to beta diversity. The nature of their interaction is most apparent when depicted in abundance-occupancy sample space, which shows the probability of making a dominant contribution to beta diversity is a concave-up function of abundance. Species found in an intermediate number ..., The dataset used for analysis was calculated from 177 different datasets in 117 different study systems collated from 3 published databases: (i) The metaCommunity Ecology:Species, Traits, Environment and Space (CESTES) database (Jeliazkov et al. 2020); (ii) Ulrich and Gotelli (2010), and, (iii) Deane et al. (2020). Each sites x species abundance dataset was analysed separately by calculating each species contribution to beta diversity (SCBD; Legendre and De Caceres 2013), which was the response variable. Raw SCBD scores were converted to normalised SCBD rank by dividing the rank (highest observed SCBD being rank 1) by the number of species in the metacommunity. Thus, SCBD.rnk was on the interval [0, 1). Explanatory variables extracted from the raw data were the number of individuals for all species across all sites (relative abundance) and the number of sites that each species was observed (occupancy). Jeliazkov, A., D. Mijatovic, S. Chantepie, N. Andrew, R. Arlettaz, L. Barbaro, N. Ba..., , # Data from: Species that dominate spatial turnover can be of (almost) any abundance

https://doi.org/10.5061/dryad.5dv41nsfs

Description of the data and file structure

Summary of experimental efforts underlying this dataset

All data used are observational ecological studies recording the abundance (number of individuals) of species within a defined ecological community (e.g., 'woodland birds') from multiple sampling sites (i.e., different locations). In total, 177 separate sites x species matrices are included, from 117 different study systems.Â

The manuscript analyses the data by first quantifying the contribution made by each species to changes in species composition across all sites in that dataset using the 'species contribution to beta diversity' (SCBD) metric of Legendre and de Caceres (2013). It then relates this contribution by each species to its relative abundance (the fraction of total individuals that species represents...

The Ants of New England project is a multi-investigator, multi-year effort to document the occurrence, distribution, and relative abundance of ants (Hymenoptera: Formicidae) in the six New England states (Connecticut, Rhode Island, Massachusetts, Vermont, New Hampshire, and Maine). The project was initiated in 1999 as a more narrowly-focused effort aimed at determining ant species diversity in bogs and surrounding forests in Massachusetts and Vermont using standard methods (pitfall trapping, timed baiting, litter collection, and visual searching; Gotelli and Ellison 2002, Ellison et al. 2002). Subsequent detailed analysis of collection methods revealed that reliable estimates of ant species occurrences, distribution, and abundance in this geographic region could be obtained using only visual searching and litter collection (Ellison et al. 2007). Following this analysis, we carried out an initial survey of ant occurrences, distribution, and abundances in Massachusetts in 2007. The 2007 survey was focused on ants living in natural community types as defined by the Massachusetts Natural Heritage and Endangered Species Program (Swain and Kearsley 2001) and located in properties of high conservation and education value owned by Massachusetts Audubon Society and The Trustees of Reservations. The primary goals for the 2007 survey were: (1) To describe and quantify patterns of distribution and abundance of ants across Massachusetts and to determine the regional "species pool" of ants that could ground local studies on ants (for example, the Warm Ants project at Harvard Forest). (2) To provide a baseline from which to assess long-term effects of climate change on species distributions. (3) To develop a set of indicator species to be used to determine efficacy of ongoing and proposed management strategies and to reveal effects of future disturbances and habitat degradation. (4) To compare with ongoing or planned quantitative surveys of birds and plants at sites owned by conservation partners (e.g., MAS, TTOR, NCF). (5) To lay the groundwork and develop capacity within partnering organizations for future sampling of additional sites and of the same sites in future years. As the Ant of Massachusetts project became more widely known, additional specimens were contributed by individuals working throughout the region. A longitudinal series (2004 - present) of collections of ants from pitfall traps on Nantucket Island was added to the database by Scott Smyers and Mark Mello. Volunteers with Friends of Mount Wachusett and the Massachusetts Audubon Society regularly contribute additional specimens. Additional specimens have accrued through regional BioBlitzes and through a Research Experience for Teachers collaboration with the J. R. Briggs Elementary School in Ashburnham, Massachusetts. In 2009, the PIs decided to expand the scope of the project to the six New England states. This expansion coincided with a regional effort to document ant diversity in bogs throughout New England (supported by an NSF award to the PIs) and the digitization of geographical records of 50 common New England ant species in the collection of Harvard's Museum of Comparative Zoology (MCZ) by Dave Lubertazzi. Work is now underway to digitize records of the remaining New England ant species housed in the MCZ collections; to identify and digitize records of New England ant species housed in other major museums (American Museum of Natural History, Smithsonian Institution); to make field collections in parts of New England that are poorly represented in museum collections. Data collected through the end of 2011 (datafile hf147-12) were used to create collection maps for A Field Guide to the Ants of New England, written by Aaron M. Ellison, Nicholas J. Gotelli, Elizabeth J. Farnsworth, and Gary D. Alpert, and published by Yale University Press. New ant species records for New England, the Mid-Atlantic States, and the Maritime Provinces of Canada accumulated since publication of A Field Guide to the Ants of New England are recorded in hf147-18. Revisions May 1, 2020: HF147-01 has been updated to reflect new and updated taxonomy and nomenclature since A Field Guide to the Ants of New England was published in 2012. Synonymy is provided in the data file.

GEB_Budnick_DatasetsA zipfile containing the diatom, fish, and aquatic insect community and environmental data sets used for statistical analysis as described in Budnick et al., 2019, GEB

The objective of this study was to identify the patterns of juvenile salmonid distribution and relative abundance in relation to habitat correlates. It is the first dataset of its kind because the entire river was snorkeled by one person in multiple years.

During two consecutive summers, we completed a census of juvenile salmonids and stream habitat across a stream network. We used the data to...

Aim: We developed a new technique, utilizing species-specific counts of individuals from historical fish community samples, to examine landscape-level, spatiotemporal trends in relative abundance distributions. Abundance-based historical distribution analyses are often plagued by data comparability issues, but provide critical information about community composition trends inaccessible to those using analyses based only on species presence-absence. We established trends in native and non-native fish abundance and community homogenization, uniqueness, and diversity to help local conservation managers prioritize targets and motivate similar studies globally to support fish conservation.

Location: Upper and middle New River (UMNR) basin, Appalachian Mountains, USA.

Methods: We compiled catch data from 61 years of fish community surveys (1958-2019) and tested for community homogenization by comparing data from repeatedly sampled sites (1900s versus 2000s samples) using dispersion analyses. We measured community uniqueness (site contributions to beta diversity) and species diversity (Shannon index) at sampled streams to identify potential conservation hotspots. We then used regression analyses and Wilcoxon signed-rank tests to examine species-specific basin-wide and local abundance trends and identify species of potential conservation concern.

Results: Dispersion of sites in species-abundance space was significantly greater in the 1900s compared to the 2000s, indicating homogenization had occurred. Of 36 native species analyzed, 44.4% (16) showed basin-wide declines. Non-native species exhibited mixed patterns; site-level abundance increased in 2 of 15 species analyzed (13%).

Main conclusions: Our results indicate basin-wide community homogenization has occurred within the UMNR, but many unique and diverse communities persist. If conserved, these could help maintain regional fish diversity. We found basin-wide declines in four endemic species, as well as spread patterns of non-native and native species that were not detected by a presence-absence analysis applied within the same study area. This finding illustrates the importance of considering both species' abundance and occurrence patterns as separate dimensions of biodiversity to inform conservation planning.

This data set provides information on species type, abundance, and distribution, and sediment description for the Phase IIIA survey area of the Long Island Sound Cable Fund (LISCF) Seafloor Habitat Mapping Initiative. This data set contains the results of image analyses of frame captures of video collected by the Ponar Imaging and Sampling System for Assessing Habitat (PISSAH) developed by the Long Island Sound Mapping and Research Collaborative (LISMaRC) to obtain both physical sediment grab samples and ultra-high definition (4K) video using the latest version of GoPro cameras. A four-day survey using the PISSAH deployed from the Research Vessel Weicker was conducted from June 12-16, 2023 including mobilization and demobilization. The PISSAH was used to acquire both physical sediment grab samples as well as the GoPro video from 60 sites in the Phase III area of the Long Island Sound Cable Fund (LISCF) Seafloor Habitat Mapping Initiative. These sites were identified in the Phase IIIA area based upon an analysis of existing acoustic backscatter data obtained from multiple surveys by NOAA that exhibited what appeared to be inconsistent gray scale settings. Multiple GoPro cameras with lights captured both forward-looking and down-looking points of view. The down-looking video files were reviewed and two to five still images (frame grabs) were captured in the .tiff format for image analysis. The images were color corrected using the IrfanView software. Each image was then analyzed using the ImageJ software for point count and percent cover of observed taxa, biogenic features and sediment type. The results of this analysis and attendant maps were provided to the team led by Roger Flood from the Stony Brook University to assist with the interpretation of new and existing acoustic backscatter data in the area. The data file is in ESRI Shapefile format. Funding was provided by the Long Island Sound Cable Fund Seafloor Habitat Mapping Initiative administered cooperatively by the EPA Long Island Sound Study and the Connecticut Department of Energy and Environmental Protection (DEEP).

The Caddo Madtom, Noturus taylori, is a small catfish endemic to the Ouachita Mountain ecoregion in Arkansas, with habitat altered by land use practices and reservoir dams. We examined aspects of distribution, abundance, habitat, and life history of N. taylori during seasonal sampling from winter 2016 through fall 2017. Our sampling data were concordant with previous studies that suggested N. taylori is more widespread and has higher catch per unit effort in the Caddo River drainage when compared to the upper Ouachita River drainage. We did not detect N. taylori in the Little Missouri River drainage, where it is presumed extirpated. A total of 370 individuals ranging from 14–76 mm (mean = 45.1 mm) standard length (SL) were collected during seasonal samples. Length-frequency analyses estimated a maximum age of 3 years for N. taylori, and we identified three discernable age classes with the emergence of young-of-year (age 0 cohort) in summer: age 0 (up to ~40 mm SL); age 1 (~41–60 mm SL); and age 2+ (>60 mm SL). Sites where N. taylori was captured had an average depth of 20.6 cm, an average base velocity of 0.18 m/sec, and were dominated primarily by a mix of gravel, pebble, and cobble. Despite the relatively higher abundances of N. taylori in the Caddo River, we recommend that long-term, periodic monitoring of N. taylori would be an important conservation tool to assess potential future changes in distribution, habitat, occurrence, and abundance. Future studies that implement occupancy and habitat suitability modeling are needed to better understand suitable and preferred habitat of N. taylori.

This data set contains the documentation of the BALTIC data set analysis as a part of the manuscript 'Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale' by

Kissling, W. D., et al. (2018), Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale. Biol Rev, 93: 600-625. doi:10.1111/brv.12359

The data set contains input and output files, geographic locations, and R scripts.

This data set contains the documentation of the BALTIC data set analysis as a part of the manuscript 'Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale' by

Kissling, W. D., et al. (2018), Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale. Biol Rev, 93: 600-625. doi:10.1111/brv.12359

The data set contains input and output files, geographic locations, and R scripts.

FIA Modeled Abundance:�This dataset portrays the live tree mean basal area (square feet per acre) of the species across the contiguous United States. The underlying data publication contains raster maps of live tree basal area for each tree species along with corresponding assessment data. An efficient approach for mapping multiple individual tree species over large spatial domains was used to develop these raster datasets. The method integrates vegetation phenology derived from MODIS imagery and raster data describing relevant environmental parameters with extensive field plot data of tree species basal area to create maps of tree species abundance and distribution at a 250-meter (m) pixel size for the contiguous United States. The approach uses the modeling techniques of k-nearest neighbors and canonical correspondence analysis, where model predictions are calculated using a weighting of nearest neighbors based on proximity in a feature space derived from the model. The approach also utilizes a stratification derived from the 2001 National Land-Cover Database tree canopy cover layer.�This data depicts current species abundance and distribution across the contiguous United States, modeled by using FIA field plot data. Although the absolute values associated with the maps differ from species to species, the highest values within each map are always associated with darker colors. The Little's Range Boundaries show the historical tree species ranges across North America. This is a digital representation of maps by Elbert L. Little, Jr., published between 1971 and 1977. These maps were based on botanical lists, forest surveys, field notes and herbarium specimens.Forest-type Groups:This dataset portrays the forest type group. Each group is a subset of the National Forest Type dataset which portrays 28 forest type groups across the contiguous United States. These data were derived from MODIS composite images from the 2002 and 2003 growing seasons in combination with nearly 100 other geospatial data layers, including elevation, slope, aspect, ecoregions, and PRISM climate data.Harvest Growth:This data shows the percentage of timber that is harvested when compared to the total live volume, at a county-by-county level. Timber volume in forests is constantly in flux, and harvest plays an important role in shaping forests. While most counties have some timber harvest, harvest volumes represent low percentages of standing timber volume.Carbon Harvest:The Carbon Harvest raster dataset represents Mg of annual pulpwood harvested (carbon) by county, derived from the Forest Inventory Analysis in 2016.This record was taken from the USDA Enterprise Data Inventory that feeds into the https://data.gov catalog. Data for this record includes the following resources: ISO-19139 metadata ArcGIS Hub Dataset ArcGIS GeoService For complete information, please visit https://data.gov.

Comparison of canonical ordination models for abundance and presence–absence data using simulations.

We present a detailed abundance analysis for 21 elements based on high-dispersion, high spectral resolution Keck spectra for four members of the outer halo "young" Galactic globular cluster Palomar 12. All four stars show identical abundance distributions with no credible indication of any star-to-star scatter. However, the abundance ratios of the Pal 12 stars are very peculiar.

The species composition of Amphipoda (Crustacea: Malacostraca: Peracarida) of the Greenland shelf south of 65°N was investigated by means of 18 epibenthic samples over a sampling period of three years (2001, 2002, 2004). The samples were taken using a Rauschert sledge in depths between 106 and 251 m. In total, 62,205 specimens were identified belonging to 154 species. The amphipods from the South Greenland shelf represent in general a homogeneously distributed community with respect to evenness (J’), diversity (H’) and Hurlbert’s rarefaction E (S500). Multivariate analyses of the species abundances divided the amphipods into a southeastern and southwestern fauna. Among the species most contributing to the separation between East and West, Hardametopa nasuta, Photis reinhardi and Phoxocephalus holboelli were identified. With respect to evenness and diversity, the amphipod community was stable over the three years. We used the WORMS database to present species in this metadata.

The National Marine Fisheries Service's Northeast Fisheries Science Center conducted standardized ichthyoplankton surveys from 1977-1988 along the continental shelf between Cape Hatteras, North Carolina and Cape Sable, Nova Scotia. These data were collected as part of a comprehensive fisheries ecosystem study to identify changes in fish community structure and investigate recruitment mechanisms. During this time period 25,000 bongo samples were collected within this broad area. In this analysis, a subset of the data were used to model ichthyoplankton abundance and distribution within the Gulf of Maine from Cape Sable, Nova Scotia to southern Massachusetts. Overall, 6,406 samples were used to model abundance and distribution within a seasonal time series (Figure 3.2.1). Additionally, samples conducted within Stellwagen Bank National Marine Sanctuary were analyzed to determine species composition abundance within the Sanctuary.

Employing high-resolution spectra obtained with the near-UV-sensitive detector on the Keck I HIRES, supplemented by data obtained with the McDonald Observatory 2d-coude, we have performed a comprehensive chemical composition analysis of the bright r-process-rich metal-poor red giant star HD 221170. Analysis of 57 individual neutral and ionized species yielded abundances for a total of 46 elements and significant upper limits for an additional five. Model stellar atmosphere parameters were derived with the aid of ~200 Fe peak transitions. From more than 350 transitions of 35 neutron-capture (Z>30) species, abundances for 30 neutron-capture elements and upper limits for three others were derived. Utilizing 36 transitions of La, 16 of Eu, and seven of Th, we derive ratios of log{epsilon}(Th/La)=-0.73 ({sigma}=0.06) and log{epsilon}(Th/Eu)=-0.60 ({sigma}=0.05), values in excellent agreement with those previously derived for other r-process-rich metal-poor stars such as CS 22892-052, BD +17 3248, and HD 115444. Based on the Th/Eu chronometer, the inferred age is 11.7+/-2.8Gyr. The abundance distribution of the heavier neutron-capture elements (Z>=56) is fitted well by the predicted scaled solar system r-process abundances, as also seen in other r-process-rich stars. Unlike other r-process-rich stars, however, we find that the abundances of the lighter neutron-capture elements (37<Z<56) in HD 221170 are also in agreement with the abundances predicted for the scaled solar r-process pattern.

Correlation between the Azooxantellate Scleractinian coral distribution and abundance of zooplankton in the Atlantic Ocean was discussed. The analysis was based on a dataset of 943 specimens (82 species) sampled at 87 stations during cruises of Russian research vessels in the Atlantic. A hypothesis concerning correlation of coral biodiversity and population density with zooplankton abundance was tested. Relationships between these parameters were contradictory. High coral biodiversity and population density were registered for areas of low and average zooplankton abundance in surface waters.

Various biodiversity indicators, such as species richness, total abundance, and species diversity indices, have been developed to capture the state of ecological communities over space and time. As biodiversity is a multifaceted concept, it is important to understand the dimension of biodiversity reflected by each indicator for successful conservation and management. Here we utilised the responsiveness of biodiversity indicators’ dynamics to environmental changes (i.e. environmental responsiveness) as a signature of the dimension of biodiversity. We present a method for characterising and classifying biodiversity indicators according to environmental responsiveness and apply the methodology to monitoring data for a marine fish community under intermittent anthropogenic warm water discharge. Our analysis showed that ten biodiversity indicators can be classified into three super-groups based on the dimension of biodiversity that is reflected. Group I (species richness and community mean of centre of distribution latitude (cCOD)) showed the greatest robustness to temperature changes; Group II (species diversity and total abundance) showed an abrupt change in the middle of the monitoring period, presumably due to a change in temperature; Group III (species evenness) exhibited the highest sensitivity to environmental changes, including temperature. These results had several ecological implications. First, the responsiveness of species diversity and species evenness to temperature changes might be related to changes in the species abundance distribution. Second, the similar environmental responsiveness of species richness and cCOD implies that fish migration from lower latitudes is a major driver of species compositional changes. The study methodology may be useful in selecting appropriate indicators for efficient biodiversity monitoring. Methods A long-term monitoring dataset for a marine fish community on the coast of Uchiura Bay (35 °32' N, 135 °30' E) was used. The monitoring area was located 2 km from the discharge outlet of the Takahama Nuclear Power Plant (NPP). The Takahama NPP started operation in 1974 and was shut down for two periods: 4 years from February 2012 to January 2016, and 14 months from March 2016 to May 2017 (Kansai Electric Power Group 2021). During operation, Takahama NPP drains a maximum thermal discharge of 238 m3s-1, which is 7 °C higher than the water temperature in the natural environment (Kokaji 1995). As a result, the temperature increase in the survey area due to the NPP operation is approximately 2 °C (Masuda 2020). Abundance data for each fish species were obtained by direct visual underwater surveys, covering an area of approximately 1200 m2 (2 m wide by 600 m long). These surveys were conducted once a month from January 18, 2012, to April 26, 2019. The fish identification procedure followed that described by Nakabo et al. (2013). The survey method was previously described by Masuda (2020). Data were obtained at 88 time-points over 7 years. A total of 95 fish species were recorded during the survey periods (Figure 1: Examples of fish species observed in the survey). Using time-series data, ten biodiversity indicators were calculated for each survey, including species richness (i.e., number of species), relative abundance of species, and differences in fish taxonomy and geographic distribution.