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MCR LTER: Coral Reef: Long-term Population and Community Dynamics: Fishes, ongoing since 2005 (Reformatted to the ecocomDP Design Pattern)

This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-mcr/6/58. The abstract below was extracted from the Level 0 data package and is included for context: These data describe the species abundance and size distributions of fishes surveyed as part of MCR LTER's annual reef fish monitoring program. This study began in 2005 and the dataset is updated annually. The abundances of all mobile taxa of fishes (Scarids, Labrids, Acanthurids, Serranids, etc.) observed on a five by fifty meter transect which extends from the bottom to the surface of the water column are recorded by a diver using SCUBA. The diver then swims back along a one by fifty meter section of the original transect line and records the abundances of all non-mobile or cryptic taxa of fishes (Pomacentids, Gobiids, Cirrhitids, Holocentrids etc). Surveys are conducted between 0900 and 1600 hours (Moorea time) during late July or early August each year. In 2006, divers also began to estimate the size (length) of each fish observed to the nearest half cm. Four replicate transects are surveyed in each of six locations on the forereef (two on each of Moorea's three sides), six locations on the backreef (two on each of Moorea's three sides) and on six locations on the fringing reef (two on each of Moorea's three sides) for a total of 72 individual transects. Transects are permanently marked using a series of small, stainless steel posts affixed to the reef. Transects on the forereef are located at a depth of approximately 12m, those on the backreef are located at a depth of approximately 1.5m and those on the fringing reef are located at a depth of approximately 10m. In addition to the biotic data collected, divers also record data on the date and time each transect was surveyed,

openCC (other)Jul 2021View details →

MCR LTER: Coral Reef: Long-term Population and Community Dynamics: Other Benthic Invertebrates, ongoing since 2005 (Reformatted to the ecocomDP Design Pattern)

MCR LTER: Coral Reef: Long-term Population and Community Dynamics: Corals, ongoing since 2005 (Reformatted to the ecocomDP Design Pattern)

This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-mcr/4/38. The abstract below was extracted from the Level 0 data package and is included for context: This dataset contains the percentage cover of the stony corals (Scleractinia) and other major groups analyzed from 0.5 x 0.5 m photographic quadrats in several reef habitats at the Moorea Coral Reef LTER, French Polynesia. This survey has been repeated annually in April since 2005. There are two tables available, providing different views of the same data: a long table having all values in one column and a wide table having a separate column for each dependent variable. Functional groups (i.e., dependent variables) counted are: Scleractinian Corals (by genus where appropriate, see methods), Macroalgae, Crustose Coralline Algae / Bare Space, Soft Corals, Hydrocorals (Millepora), Algal Turf and Sand. The coral community was sampled photographically in all habitats surrounding the island: Fringing Reef, Lagoon (Backreef), and Outer Reef (Forereef.) The sampling regime consists of a repeated-measures protocol in each habitat, and is structured by habitat to allow a statistical contrast of sites, shores, times, and in the case of the outer reef, depths. Detailed methods are available in the protocols section. This material is based upon work supported by the U.S. National Science Foundation under Grant No. OCE 16-37396 (and earlier awards) as well as a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2020). This work represents a contribution of the Moorea Coral Reef (MCR)

MCR LTER: Coral Reef: Long-term Population and Community Dynamics: Benthic Algae and Other Community Components, ongoing since 2005 (Reformatted to the ecocomDP Design Pattern)

This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-mcr/8/32. The abstract below was extracted from the Level 0 data package and is included for context: Coral reefs are comprised of scleractinian corals and many other benthic organims. The sampling described here quantifies the relative abundances of corals (aggregate abundance) and the other major benthic components including algal turfs, macroalgae, crustose corallines, and other sessile invertebrates. Abundance is estimated yearly at each of 6 sites (2 per shore) around the island. At each site, and in each of 4 habitats (fringing reef, backreef, forereef 10-m depth, forereef 17-m depth), 5 permanent 10-m long transects have been established and abundance estimates are made at fixed positions along each transect (n=10, 0.25 m2 quadrats per transect) allowing a repeated measures statistical analysis for the detection of temporal trends. This material is based upon work supported by the U.S. National Science Foundation under Grant No. OCE 16-37396 (and earlier awards) as well as a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2020). This work represents a contribution of the Moorea Coral Reef (MCR) LTER Site.

MCR LTER: Coral Reef: Long-term Community Dynamics: Backreef (Lagoon) Corals Annual Survey, ongoing since 2005 (Reformatted to the ecocomDP Design Pattern)

This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-mcr/1038/10. The abstract below was extracted from the Level 0 data package and is included for context: This dataset contains the percentage cover of all stony corals (Scleractinia, pooled among genera) and other major groups analyzed from 0.5 x 0.5 m photographic quadrats at the Backreef habitat at the Moorea Coral Reef LTER, French Polynesia. This survey time series began in 2005 and is repeated each year in April. Functional groups counted are: Scleractinian corals, Macroalgae, Crustose Coralline Algae / Bare Space, Soft Corals, Hydrocorals (Millepora), Algal Turf and Sand. The coral community was sampled photographically in all represented habitats surrounding the island: Fringing Reef, Lagoon, and Outer Reef. This dataset contains only Lagoon (Backreef) data (see knb-lter-mcr.4 for the other habitats) and is structured in a repeated-measures protocol to allow a statistical contrast of sites, shores and times. Community structure was determined through a coarse analysis of the benthic community, initially completed in situ (2005), but using photoquadrats from 2006. There are quadrats analyzed at each of five areas within each site, and the areas are revisited (but not the quadrats) each year to support the repeated measures design. There are two tables available, providing different views of the same data: a long table having all values in one column and a wide table having a separate column for each observed object. Detailed methods are available in the protocols section. This material is based upon work supported by the U.S. National Science Foundation under Grant No. OCE 16-37396 (and earlier awards) as well as a generous gift from the Gordon and Betty Moore Foundation. R

openCC (other)Jul 2021View details →

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SBC LTER: Reef: Kelp Forest Community Dynamics: Fish abundance (Reformatted to the ecocomDP Design Pattern)

This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-sbc/17/35. The abstract below was extracted from the Level 0 data package and is included for context: These data describe the abundance and size of fish species as part of SBCLTER's kelp forest monitoring program to track long-term patterns in species abundance and diversity. This study began in 2000 in the Santa Barbara Channel, California, USA. The abundance and size of all taxa of resident kelp forest fish encountered along permanent transects are recorded at nine reef sites located along the mainland coast of the Santa Barbara Channel and at two sites on the north side of Santa Cruz Island. These sites reflect several oceanographic regimes in the channel and vary in distance from sources of terrestrial runoff. In these surveys, fish were counted in either a 40x2m benthic quadrat, or in the water parcel 0-2m off the bottom over the same area. The two tables in this data package include: 1) The annual benthic fish community survey which was conducted on 11 reefs once a year around late July or early August; and 2) The monthly fish survey which was conducted once a month at a subset of the sites (3 of the annual sites) The time period of data collection for the annual benthic fish community survey varied among the 11 kelp forest sites. Sampling at BULL, CARP, and NAPL began in 2000, sampling at the other 6 mainland sites (AHND, AQUE, IVEE, GOLB, ABUR, MOHK) began in 2001 (transects 3, 5, 6, 7, 8 at IVEE were added in 2011). Data collection at the two Santa Cruz Island sites (SCTW and SCDI) began in 2004. The monthly fish survey at ABUR (Transect 1, 2, and 3), AQUE (Transect1), and MOHK (Transect 1) in 2002. The Transect 2 and 3 at ABUR were discontinued in June 2006. See Method

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Ground Arthropod Community Survey in Grassland, Shrubland, and Woodland at the Sevilleta National Wildlife Refuge, New Mexico (1992-2004) (Reformatted to the ecocomDP Design Pattern)

openOpenAug 2021View details →

opencc-by-4.0Nov 2020View details →

Data and code from: Insect biomass decline scaled to species diversity: General patterns derived from a hoverfly community

To study changes in flying insect communities, and hoverflies in particular, malaise trap samples from a German site were compared between two years (Hallmann et al. 2020). The data files deposited here contain data obtained from six malaise traps in the Wahnbachtal (North Rhine-Westphalia, Germany, 50.851944N, 7.320833E) that were deployed in 1989 and again in 2014, at the exact same locations. Traps were situated in wet meadows as well as tall perennial meadows, in close proximity to shrub corridors, to forest–grassland borders, and to the Wahnbach River and surrounded by agricultural land, essentially a rather heterogeneous habitat. The Wahnbach River and the greater part of the valley are protected for watershed purposes and are subject to nature conservation management by the Wahnbach Talperrenverband. Hence, several restrictions apply to safeguard against water contamination. Total insect biomass collected with these traps was already included in Hallmann et al. (2017), but here we focus on additional information: the abundance and richness of hoverflies (Syrphidae) in each of the collected samples (pots). Methodologies of collection are described in Sorg (1990), Schwan et al. (1993), Sorg et al. (2013), Hallmann et al. (2017), and Ssymank et al. (2018).  In brief, malaise traps were deployed throughout the growing season and operated continuously (day and night). Malaise trap construction (e.g., size, material, colouring, and ground sealing) and placing (e.g., positioning, orientation, and slope of the locations) were standardised in all aspects. Insect samples were preserved in 80% ethanol solution. Catches of the six traps investigated in the present study were emptied regularly: On average exposure intervals were 7.0 d (SD = 0.5) in 1989 and 16.7 d (SD = 5.6) in 2014. Across the six traps in 2014 the total exposure time (in number of days) was 42% higher compared to 1989. All collected samples (n = 196) were used in the present analysis with in total 19,604 individual hoverflies counted, distributed over 162 species and 59 genera. To assess how environmental conditions have changed over the 25 year, several additional datasets were assembled. Climatic data were obtained from 169 climatic stations and were used to interpolate daily weather variables to each trap location, using spatiotemporal kriging. These steps are described in detail in Hallmann et al. (2017). Our analysis (see R code) consists of three components. First, we considered total abundance, species richness, and species diversity, at two temporal scales: pooled per year, i.e., across the sampling season, and seasonally (i.e., per day), and we compared these metrics between 1989 and 2014. Second, we examined how total flying biomass (i.e., the weight of all trapped insects, of which hoverflies are only a small proportion) related to total abundance as well as species richness of hoverflies. Third, we derived persistence probabilities and population growth rate trends per species, to examine interspecific variation in these parameters. Descriptions of the deposited files: Groups.csv MF_NR = identifier of each of the six malaise trap locations yrf = year of sampling pot = sample identifier dt = number of sampling days from.dnr = day-of-the-year on which a pot was attached to a malaise trap to.dnr = day-of-the-year on which a pot was collected from a malaise trap mean.daynr = mean day-of-the-year of the sampling period Nspec = number of different hoverfly species found in a pot Nind = number of hoverfly individuals found in a pot Counts.csv A matrix of counts of individual hoverflies per pot per species. The 196 rows represent the pots in the same order as in the file 'Groups.csv'. The columns represent the 162 different hoverfly species found. The scientific species names are indicated in the column headers. PairedData.csv pot = sample identifier JAHR = year of sampling MF_NR = identifier of each of the six malaise trap locations dt = number of sampling days from.dnr = day-of-the-year on which a pot was attached to a malaise trap to.dnr = day-of-the-year on which a pot was collected from a malaise trap NI = number of hoverfly individuals found in a potbiomass.daily NSP = number of different hoverfly species found in a pot biomass.daily = daily fresh weight [gram] of flying insects: total fresh weight in a pot divided by the number of sampling days. ModelFrame.csv MF_NR = identifier of each of the six malaise trap locations yrf = year of sampling pot = sample identifier dt = number of sampling days from.dnr = day-of-the-year on which a pot was attached to a malaise trap to.dnr = day-of-the-year on which a pot was collected from a malaise trap mean.daynr = mean day-of-the-year of the sampling period plot = identifier of each of the six malaise trap locations date = date for which the weather variables are interpolated daynr = day-of-the-year for which the weather variables are interpolated altitude = altitude [m] of the malaise trap locations year = year of sampling temperature = interpolated temperature [degrees Celsius] precipitation = interpolated precipitation [mm per day] wind.speed = interpolated wind speed [m/s] Data_Rcode.pdf This pdf provides the R-code behind the analysis of the Hoverfly data. Three datasets are provided along with this R-code document, namely "Counts.csv", "Groups.csv", "PairedData.csv" and "ModelFrame.csv". Additionally, the BUGS-code ""syrphidModel.jag" is required for running the daily-activity model in JAGS. syrphidModel.jag This BUGS-code is required for running the daily-activity model in JAGS.

opencc-by-4.0Jun 2024View details →

Community science approach reveals temporal and eutrophication-related spatial patterns in bladderwrack-associated invertebrate fauna

Data related to the "Community science approach reveals temporal and eutrophication-related spatial patterns in bladderwrack-associated invertebrate fauna" paper by Salo, Nieminen, Salovius-Laurén and Rinne published in Estuarine, Coastal and Shelf Science in 2024. <a href="https://doi.org/10.1016/j.ecss.2024.108822">https://doi.org/10.1016/j.ecss.2024.108822</a> The data describes the community data collected with the community science method described in the paper.

opencc-by-4.0Mar 2023View details →

Fruit-feeding butterfly community data analysed in "Recovery patterns in community composition of fruit-feeding butterflies following 26 years of active forest restoration"

Community data of fruit-feeding butterflies collected from Kibale National Park, Uganda, in the periods 2011-2012 and 2020-2021 analysed in our paper Korkiatupa et al. 2023: "Recovery patterns in community composition of fruit-feeding butterflies following 26 years of active forest restoration" (Ecosphere 14(5): e4514. <a href="https://doi.org/10.1002/ecs2.4514">https://doi.org/10.1002/ecs2.4514</a>). The table consists of two parts. First part shows counts of individuals of butterfly species in each study site. Second part shows the metadata: code of studysite, census (2011-2012/2020-2021), planting year (planting year or "Primary forest"), and coordinates (WGS 84 coordinate system).

opencc-by-4.0Sep 2022View details →

Data from: Pathogen community composition and co-infection patterns in a wild community of rodents

ABSTRACT Rodents are major reservoirs of pathogens that can cause disease in humans and livestock. It is therefore important to know what pathogens naturally circulate in rodent populations, and to understand the factors that may influence their distribution in the wild. Here, we describe the incidence and distribution patterns of a range of endemic and zoonotic pathogens circulating among rodent communities in northern France. The community sample consisted of 713 rodents, including 11  host species  from diverse habitats. Rodents were screened for virus exposure (hantaviruses, cowpox virus, Lymphocytic choriomeningitis virus, Tick-borne encephalitis virus) using antibody assays. Bacterial communities were characterized using 16S rRNA amplicon sequencing of splenic samples. Multiple correspondence (MCA), regression and association screening (SCN) analyses were used to determine the degree to which extrinsic factors contributed to pathogen community structure, and to identify patterns of associations between pathogens within hosts. We found a rich diversity of bacterial genera, with 36 known or suspected to be pathogenic. We revealed that host species is the most important determinant of pathogen community composition, and that hosts that share habitats can have very different pathogen communities. Pathogen diversity and co-infection rates also vary among host species. Aggregation of pathogens responsible for zoonotic diseases suggests that some rodent species may be more important for transmission risk than others. Moreover we detected positive associations between several pathogens, including Bartonella, Mycoplasma species, Cowpox virus (CPXV) and hantaviruses, and these patterns were generally specific to particular host species. Altogether, our results suggest that host and pathogen specificity is the most important driver of pathogen community structure, and that interspecific pathogen-pathogen associations also depend on host species. FILE DESCRIPTION: MiSeq raw sequences of the 16Sv4 rRNA gene from spleen rodent samples This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each spleen rodent sample using the MiSeq platform. The 749 multiplexed PCR products were indexed using both forward and reverse indices. Information of the multiplexed samples (n=363 in replicate) and positive (n= 6) & negative controls (n= 17) is provided in the following XLSX file titled: 16S_raw_abundance_data.xlsx File name: MiSeq raw sequences of the V4 region 16S rRNA gene.zip Raw input and output files generated by the mothur program This ZIP file contains all the input and output files generated during the MiSeq sequence analysis with the mothur program. File name: Raw input and output files generated by the mothur program.zip Log file generated by the mothur program This TXT file contains is the history of all the command lines and parameters used during the MiSeq sequence analysis with the mothur program. File name: mothur.1428506786.logfile Raw abundance table of the 16v4 rRNA gene from spleen rodent samples before data filtering This XLSX file contains the number of reads for each distinct Operational Taxonomic Unit (OTU) and each of the PCR products, including the 332 spleen rodent samples analyzed in the study and the negative & positive controls, sequenced in the MiSeq run before the data filtering. This file contains also the following information: Study_site, Study_year, Sample_habitat, Host_species, Host_age, Host_sex, PCR_ID and the taxonomic classification (Kingdom to Genus) of each OTU. File name: 16S_raw_abundance_data.xlsx Occurrence table of the 16v4 rRNA gene from spleen rodent samples after data filtering This XLSX file contains the occurrences (presence: 1 ; absence: 0) after data filtering of each putative pathogenic Operational Taxonomic Unit (OTU) for each of the 332 spleen rodent samples analyzed in the study. File name: 16S_presence_absence_data.xlsx Statistical Analysis Scripts and Data File This ZIP file contains the R scripts for performing statistical analyses reported in the main text and supplemental materials. There is one main file (Analyses.R), as well as two source scripts required for association screening analyses (SCN.txt and FctTestScreenENV.txt). It also includes an R-legible data file containing occurrences (presence: 1 ; absence: 0) for all pathogen exposure variables on which statistical analyses were conducted (PA_DATA.csv) for each of the 332 spleen rodent samples analyzed in the study. The column names for bacterial exposures correspond to the “Pathogen Code” given in the 16S_presence_absence_data.xlsx file. File name: Statistical Analysis Scripts and Data File.zip

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[DEPRECATED] CFC01 Kings Creek long-term fish and crayfish community sampling at Konza Prairie (Reformatted to ecocomDP Design Pattern)

This data package has been deprecated due to several issues in the L0 source dataset that prohibits the creation of an L1 ecocomDP dataset. This data package is formatted according to the "ecocomDP", a data package design pattern for ecological community surveys, and data from studies of composition and biodiversity. For more information on the ecocomDP project see https://github.com/EDIorg/ecocomDP/tree/master, or contact EDI https://environmentaldatainitiative.org. This Level 1 data package was derived from the Level 0 data package found here: https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-knz&identifier=130&revision=4 The abstract below was extracted from the Level 0 data package and is included for context:

openCC0Jul 2021View details →

opencc-by-4.0Feb 2015View details →

Figure 4 in Year-round activity patterns in a hyperdiverse community of rainforest amphibians in Madagascar

Figure 4. Canonical correspondence biplot relating amphibian species abundance along the study transect and five environmental predictors (italics, labelled as in Figure 3). Circles identify the sampling units (days) and crosses identify species. Species occurring more frequently at extreme environmental conditions are labelled using the codes presented in Table 1.

Fig. 5 in Habitat Preferences And Activity Patterns Of The Larger Mammal Community In Phnom Prich Wildlife Sanctuary, Cambodia

Fig. 5. Mean Relative Abundance Indice (± SEM) for 12 most frequently encountered mammal species in PPWS at camera trap locations closer (black bars) and further (open bars) than 11-km from nearest village. RM red muntjac; EWP Eurasian wild pig; B banteng; E Asian elephant; LIC large Indian civet; EAP east Asian porcupine; L leopard; CPC common palm civet; D dhole; LC leopard cat; G gaur; and PTM pig-tailed macaque.

Fig. 4 in Habitat Preferences And Activity Patterns Of The Larger Mammal Community In Phnom Prich Wildlife Sanctuary, Cambodia

Fig. 4. Mean Relative Abundance Indices (± SEM) for 12 most frequently encountered mammal species in PPWS at camera trap locations in DDF (black bars) and SEGF (open bars). RM red muntjac; EWP Eurasian wild pig; B banteng; E Asian elephant; LIC large Indian civet; EAP east Asian porcupine; L leopard; CPC common palm civet; D dhole; LC leopard cat; G gaur; and PTM pig-tailed macaque.

Fig.6 in Habitat Preferences And Activity Patterns Of The Larger Mammal Community In Phnom Prich Wildlife Sanctuary, Cambodia

Fig.6. Activity patterns, % of all encounters within each hour, of red muntjacs and Eurasian wild pigs from camera-traps in PPWS.

Fig. 2 in Habitat Preferences And Activity Patterns Of The Larger Mammal Community In Phnom Prich Wildlife Sanctuary, Cambodia

Fig. 2. Increase in species richness (species recorded) with total cumulative number of camera trap nights within Phnom Prich Wildlife Sanctuary (Dec 08–Aug 09).