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Data and R scripts for analyses of declines in invertebrate species from the Gulf of Maine, USA, 1997 - 2018
Data files and R scripts are for the analyses that are presented in an article that is under revision for Biology Communications. The title of the article is: Declines over the last two decades of five key invertebrate species found on rocky intertidal shores throughout the western North Atlantic. The three data files contain the abundances of four gastropod species and the recruitment of barnacles and mussels from 1997 to 2018, monthly temperature data from three buoys from 2001 to 2018, and pH and aragonite saturation state from 1997 to 2014. R scripts include details of Bayesian estimates for Poisson regressions of species over time, clean-up of environmental data, imputation of missing environmental data and analyses of species versus environmental parameters.
Effects of experimental manipulation of light and nutrients on establishment of seedlings of native and invasive woody species in Long Island, NY, USA forests 2000 - 2003
While several studies on the process of invasion often focused on single factors or on the general explanation of ‘disturbance,' recent work has attempted to move towards a more mechanistic understanding of the factors that promote plant community invasion. Manipulative experiments provide a means for discerning causal relationships and interactive effects of environmental factors in promoting invasion. This dataset contains the results of multifactor manipulative experiments in forest communities, which compared factors influencing early seedling establishment for native and invasive woody plants. In an earlier study, we found that in Long Island, NY, invasion patterns are correlated with forest community type (pine barrens or hardwood), light availability, and soil N and Ca. Therefore, we conducted manipulative field experiments in two different years to determine the relative importance and interaction of experimental gaps and N and Ca addition in pine barrens and hardwood forests in promoting invasion. We used seedlings of seven common native and invasive species in the first experiment, and 16 native and invasive species paired phylogenetically in the second experiment. This was done in the years 2000 and 2003 respectively.
High-Frequency Water Temperature Data at Lake Lillinonah, Connecticut, USA, 2018-current
An instrumented buoy maintained by Friends of the Lake and Fairfield University has been deployed on Lake Lillinonah (Connecticut, USA) during the summer months to collect high-frequency water quality data. The buoy is deployed early each summer and remains in the lake until late October. The instrumented buoy is equipped with an RBR temperature sensor chain, collected data every meter from a depth of 0.6 meters to 14.5 meters and every two meters to a depth of 18.5. meters. Data was collected every fifteen minutes. Included in this data package are data sets containing 15-minute data as well as daily averages. Prior to the deployment of the RBR temperature sensor, the instrumented buoy was equipped with a Nexsens T-node thermistor chain (2011-2015) with sensors at different depths. These data are available in the data package EDI557. Additional high-frequency water quality data for Lake Lillinonah including dissolved oxygen, specific conductance and pigment fluorescence are available in packages EDI559 and EDI560.
High-frequency water quality data for water temperature, dissolved oxygen, specific conductivity, pH, phycocyanin fluorescence and chlorophyll a fluorescence at Lake Lillinonah, Connecticut, USA, 2011-2017.
From 2011 to 2017, an instrumented buoy maintained by Friends of the Lake (FOTL, friendsofthelake.org) and Fairfield University was deployed on Lake Lillinonah (Connecticut, USA) during the summer months to collect high-frequency water quality data. The buoy was deployed early each summer and remained in the lake until late October. The instrumented buoy was equipped with a YSI 6600 sonde at a depth of 1 meter. The YSI 6600 collected water temperature, dissolved oxygen, specific conductivity, pH, chlorophyll a fluorescence and phycocyanin fluorescence data. Additionally, the instrumented buoy is equipped with an In-Situ RDO sensor which collects water temperature and dissolved oxygen readings at a depth of 15 meters. Included in this data package are datasets containing 15-minute data as well as daily averages from all sensors. Following the summer of 2017, the YSI 6600 sonde was replaced with a YSI EXO2 sonde which collected data on the same variables. Data from the YSIEXO2 sonde, as well as data from the In-Situ RDO sensor during the same period, are available in the EDI data package EDI560. Additionally, the instrumented buoy at Lake Lillinonah is equipped with a water temperature thermistor chain . These data can be found in data packages EDI557 (2011-2015) and EDI558 (2018-current).
High-frequency water quality data for water temperature, dissolved oxygen, specific conductivity, pH, phycocyanin fluorescence and chlorophyll a fluorescence at Lake Lillinonah, Connecticut, USA, 2018-current.
Since 2011, an instrumented buoy maintained by Friends of the Lake (FOTL, friendsofthelake.org) and Fairfield University has been deployed on Lake Lillinonah (Connecticut, USA) during the summer months to collect high-frequency water quality data. The buoy is deployed early each summer and remains in the lake until late October. Since 2018, the instrumented buoy has been equipped with a YSI EXO2 sonde at a depth of 1 meter. The YSI EXO2 collects water temperature, dissolved oxygen, specific conductivity, pH, chlorophyll a fluorescence and phycocyanin fluorescence data. Additionally, the instrumented buoy is equipped with an In-Situ RDO sensor which collects water temperature and dissolved oxygen readings at a depth of 15 meters. Included in this data package are datasets containing 15-minute data as well as daily averages from both sensors from 2018 to present. Prior to 2018, the instrumented buoy was equipped with a YSI 6600 sonde, which collected data on the same variables (2011-2017). Data from the YSI 6600 sonde, as well as data from the In-Situ RDO sensor during the same period, are available in the EDI data package EDI559. Additionally, the instrumented buoy at Lake Lillinonah is equipped with a water temperature thermistor chain sensor. These data can be found in data packages EDI557 (2011-2015) and EDI558 (2018-current).
Water quality data collected by the Citizen-Led Environmental Observatory (CLEO) from multiple nearshore sites in Lake Lillinonah, Connecticut, USA, 2010-current
Included in this data package are water quality data from the Citizen-Led Environmental, a Observatory (CLEO) volunteer water quality monitoring program run by Friends of the Lake (FOTL) and Fairfield University at Lake Lillinonah, Connecticut, USA. The program has been operational since 2008 (data available 2010-current). Trained volunteer monitors collect data from dock locations across the lake on water temperature, Secchi disk depth, water color, presence of floating woody debris, recreation potential, trash, particle type and surface scum. Volunteers collect data between 3:00 and 7:00 PM three times per week from Memorial Day through Labor Day. In addition to the variables listed above, CLEO volunteers collect routine water samples on a biweekly basis, as well as any time there is a notable algal bloom. The routine samples are analyzed for nutrient (total nitrogen and total phosphorus) concentrations as well as concentrations of the cyanobacterial toxin microcystin. The blooms samples are analyzed for microcystin only. These data are available in EDI packages EDI568 (nutrients) and EDI569 (toxins).
Total nitrogen and total phosphorus concentrations from surface water samples collected by the Citizen-Led Environmental Observatory (CLEO) from multiple nearshore sites in Lake Lillinonah, Connecticut, USA, 2011-current
Included in this data package are water quality data from the Citizen-Led Environmental Observatory (CLEO), a volunteer water quality monitoring program run by Friends of the Lake (FOTL, friendsofthelake.org) and Fairfield University at Lake Lillinonah, Connecticut, USA. The program has been operational since 2008 (data available 2011-current). Trained volunteer monitors collect surface water samples from multiple nearshore sites twice a month from Memorial Day through Labor Day. These samples are analyzed for total nitrogen and total phosphorus concentrations. Water samples are also analyzed for levels of the toxin microcystin. Additionally, CLEO volunteers collect data on water temperature, Secchi disk depth, water color, presence of floating woody debris, recreation potential, trash, particle type and surface scum every 1-3 days during the same period. These additional data are available in EDI packages EDI567 (general water quality) and EDI569 (toxins).
A micro-environmental dataset exploring shrub-open climate contrasts in Cuyama Valley, California, USA,
A total of 62 Hobo micro-station data logger weather stations were deployed in Cuyama Valley, California drylands on public lands. Each station had 4 channels with two EC5 soil moisture smart sensors and two 12-Bit temperature smart sensors. The sensor arrays were deployed for two years or a total of 24 months. Key ecological variables included microsite, location, vegetation type, and extent of vegetation at each microsite. Temperature sensors were deployed 15 cm above the soil surface under the shrub canopy of Ephedra californica (sheltered from direct sunlight) or at adjacent, open paired-microsites within 1.5m of a focal shrub.Temperatures listed are in degrees Celsius. Soil moisture sensors were inserted into the soil near each temperature probe. The x,y,z columns are the width, perpendicular measure, and height in m respectively of each shrub at those microsites.
The influence of environmental factors on the distribution and density of invasive Centaurea stoebe across Northeastern USA, 2013 - 2018
Centaurea stoebe (Asteraceae; spotted knapweed) is an emerging invader in northeast US, and is a major invasive plant in the northern Midwest and western USA. Although it has been present in New York State (NYS) for over 100 years, its apparent recent population increases and spread provide a rare opportunity to study a plant in the early stages of invasion. Therefore, a study was carried out understand how distinct environmental factors influence the distribution, density and change in density C. stoebe at different spatial scales within its novel range in the northeastern USA. First, we collected field data on the occurrence, density and change in density of this species in North Eastern United States, from 2013 to 2014. Then, using species distribution models, we assessed the potential influence of environmental factors on the invasion of spotted knapweed in northeast US. Within different parts of C. stoebe‘s range, different factors explained its occurrence, density and change in density over 2 years. Across northeast US, climate and soil factors were the most influential predictors explaining C. stoebe‘s distribution, while within Long Island in southeastern NYS and the Adirondack Mountains in northern NYS, precipitation and disturbance respectively were the most important. These results are published in the paper titled The influence of environmental factors on the distribution and density of invasive Centaurea stoebe across Northeastern USA (Akin-Fajiye and Gurevitch, 2018).
Conifer seed delivery after the Berry Fire Grand Teton National Park, USA, 2018
These data were collected by NS Gill, TJ Hoecker, and MG Turner in Grand Teton National Park from July-October 2018. The dataset represents seed delivery and surrounding forest structure and demographics following the 2016 Berry Fire, used to examine the relationship between fire regime change and conifer seed delivery in Pinus contorta var. latifolia forests. Stand structure and cone abundance were quantified at 21 sites positioned at the edges of the burned area in 50-m transects. Seed delivery was measured in seed traps placed at distance intervals running out to 100 m into burned patches from the live forest edge over a period of three months. Pinus contorta, Picea engelmannii, and Abies lasiocarpa seeds were collected. Five meteorological stations were deployed throughout the study area. Wind speed and direction data were attributed to transects from the nearest of these deployed meteorological stations.
Ecosystem metabolism estimates from Lake Sunapee, NH, USA and meteorological driver data at the Newport, NH, USA NOAA NCDC weather station from August 2007 – December 2008
In August 2007, the Lake Sunapee Protective Association (LSPA) deployed a buoy in Lake Sunapee, NH with a meteorological station, dissolved oxygen sensor at 1 m, and a string of thermistor water temperature sensors collecting data every 10 minutes. For this dataset, the Lake Sunapee buoy was located at a location near Loon Island all year (August 2007–December 2008) including during the winter. We used high-frequency dissolved oxygen, photosynthetically active radiation (PAR), wind speed, and water temperature profile data to estimate daily rates of gross primary production, respiration, and net ecosystem production as metrics of ecosystem metabolism and carbon cycling. This dataset included under-ice data, and we compared seasonal changes in ecosystem metabolism rates for an entire lake year from the start of fall mixing in 2007 through the end of summer stratification in 2008. Under-ice and mixing periods are infrequently sampled due to logistical challenges and assumptions of low biological activity, resulting in limited understanding of the contribution of winter epilimnetic metabolism to annual carbon cycling. Using a continuous year of high-frequency dissolved oxygen data, we found that on average, under-ice net ecosystem production (NEP) was negative, in contrast to positive NEP for the spring and summer periods. Importantly, under-ice respiration was 1.2 times higher than summer respiration. Gross primary production was low but not absent under ice and increased during the last under-ice phase. Including winter metabolism estimates flipped annual NEP from autotrophy to heterotrophy, highlighting the importance of estimating metabolism year-round. Our methods for the data analysis are described in Brentrup et al. (accepted at Inland Waters) and were similar to Richardson et al. (2016) with some modifications described in the methods. This dataset also includes derived thermocline depth calculations from the water temperature thermistor data on the Lake Sunape
Native seedlings recorded on field plots with and without invasive buffel grass during the monsoon season of 2013 near Tucson, Arizona, USA
Although buffel grass (Cenchrus ciliaris) invasions on several continents have significant ecological impacts, little information is available on its effect on seedling emergence and establishment of native vegetation. In highly impacted areas of the Sonoran Desert of North America, perennial plants are particularly vulnerable during their seedling stage. We studied the impact of buffel grass on the emergence and early survival of native seedlings in a field experiment. We marked out 2m x 2m field plots at three locations near Tucson, Arizona, with and without buffel grass. We removed the buffel grass from half of those with the invasion, and censused and marked native perennial seedlings that emerged in each plot for ten weeks during July-September (monsoon season) of 2013. Emergence and survival of native perennials in the field were both significantly higher where mature buffel grass was removed or had never invaded than where it remained. Our results highlight the need for more manipulative studies of density to improve mechanistic understanding of population dynamics, and to forecast how populations and communities will respond in the long term to perturbations such as invasion.
Species, DBH, and height of overstory trees in a chronosequence of reforested urban sites, Lexington, KY, USA
Urban reforested areas located in Lexington, Kentucky were evaluated over the course of summer 2020. This dataset contains information on tree species, height, DBH, and snag class across twenty urban reforestation sites planted as part of the Reforest the Bluegrass program in Lexington, KY. At least three plots (and up to nine plots) were established in each site, with additional plots added if forested patches were sufficiently large. At each plot, we established a 0.008-ha (0.02-ac) circular sampling plot and recorded the species, diameter at breast-height (DBH), and total height of each tree ≥2.5 cm (1 in) DBH. DBH was measured to the nearest 0.25 cm (0.1 in) using a DBH tape, and tree height was measured to the nearest 0.1 m using a laser hypsometer (Nikon Forestry Pro II) or telescoping height pole. These data provide a critical baseline for understanding tree growth on reforested urban sites.
Chemical and physical characteristics of soil samples collected from a chronosequence of reforested urban sites in Lexington, KY USA.
This dataset contains information on soil physical and chemical characteristics across twenty urban reforestation sites planted as part of the Reforest the Bluegrass program in Lexington, Kentucky, USA. At least three plots (and up to nine plots) were established in each site, with additional plots added if forested patches were sufficiently large. Soil samples were collected from each plot in summer 2020. Samples were composited from five subsamples collected from plot center and approximately 1 m from plot center in the four cardinal directions. Subsamples were collected to a depth of approximately 10 cm using a sampling spade. Composite samples were air-dried and passed through a 2cm sieve, and then sent to the University of Kentucky Regulatory Services soils lab for analysis for pH, P, K, Ca, Mg, Zn, particle size distribution, total C, and total N.
Species and height of understory trees and shrubs in a chronosequence of reforested urban sites, Lexington, KY USA.
This dataset contains information on soil physical and chemical characteristics across twenty urban reforestation sites planted as part of the Reforest the Bluegrass program in Lexington, KY. Urban reforested areas located in Lexington, Kentucky were evaluated over the course of summer 2020. At least three plots (and up to nine plots) were established in each site, with additional plots added if forested patches were sufficiently large. At each plot, we established a 0.002-ha (0.005-ac) circular sampling plot to survey woody understory species, respectively. Height and species of all woody plants <2.5 cm DBH and ≥30 cm tall were tallied to the nearest 0.5 cm with a telescoping height pole. These data will contribute to understanding of understory stand dynamics in developing urban forests.
Stream Metabolism in Marsh Creek, Idaho, USA 2016-2017
Most research on stream metabolism uses a single reach to characterize a stream. We aimed to characterize variation in stream metabolism rates and the controls on metabolism along a 75-km agricultural stream. We continuously measured dissolved oxygen, discharge, conductivity, temperature, light, and turbidity using a variety of sensors deployed at 6 locations along Marsh Creek, a stream in southeastern Idaho. Monthly grab samples were collected for water chemistry throughout the study period, and aquatic vegetation was surveyed from May through September. Data were collected from October 2016 through October 2017.
Mammalian herbivores restrict the altitudinal range limits of three alpine grass species (transplant and herbivore exclusion experiment and demographic data from natural populations), West Elk Mountains, Colorado, USA 2015-2018
Though rarely experimentally tested, biotic interactions have long been hypothesized to limit low-elevation range boundaries of species. We tested the effects of herbivory on three alpine-restricted plant species by transplanting plants below (novel), at the edge (limit), or in the center (core) of their current elevational range and factorially fencing-out above- and belowground mammals in the West Elk Mountains, Colorado, USA from 2015-2018. Herbivore damage was greater in range limit and novel habitats than in range cores. Exclosures increased plant biomass and reproduction more in novel habitats than in range cores, suggesting demographic costs of novel interactions with herbivores. We then used demographic models to project population growth rates, which increased 5-20% more under herbivore exclosure at range limit and novel sites than in core habitats. Our results identify mammalian herbivores as key drivers of the low-elevation range limits of alpine plants and indicate that upward encroachment of herbivores could trigger local extinctions by depressing plant population growth.
Extracellular enzyme activities in plots dominated by trees that associate with arbuscular mycorrhizal or ectomycorrhizal fungi in the nitrogen fertilized and reference watershed at the Bear Brook Watershed in Maine, USA during the final year of N fertilization (2016) and during the year after N fertilization ceased (2017).
Our objective was to detect possible differences in N fertilization responses of extracellular enzymes in plots dominated by trees that associate with arbuscular mycorrhizal fungi (AM) or ectomycorrhizal fungi (ECM). To do this, we established a plot network of 6 AM and 6 ECM dominated (>65% diameter at breast height) 10 x 10 m plots in the lower elevation hardwood zone of both the reference and N fertilized watersheds (N=24 plots) at Bear Brook Watershed, in Maine USA. We assayed the potential activity of hydrolytic enzymes that release N (N-acetylglucosaminidase; NAG), phosphorus (acid phosphatase; AP), and simple carbon (ß-glucosidase; BG). The activities of these enzymes were measured separately in bulk mineral, rhizosphere, and organic horizon soils in the final year of N fertilization at Bear Brook in 2016 and during the year after N fertilization ceased in 2017.
SGS-LTER Standard Production Data: 1983-2008 Annual Aboveground Net Primary Production on the Central Plains Experimental Range, Nunn, Colorado, USA 1983-2008, ARS Study Number 6 (Reformatted to a Darwin Core Archive)
This data package is formatted as a Darwin Core Archive (DwC-A, event core). For more information on Darwin Core see https://www.tdwg.org/standards/dwc/. This Level 2 data package was derived from the Level 1 data package found here: https://pasta.lternet.edu/package/metadata/eml/edi/325/2, which was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-sgs/700/1. The abstract below was extracted from the Level 0 data package and is included for context: This data package was produced by researchers working on the Shortgrass Steppe Long Term Ecological Research (SGS-LTER) Project, administered at Colorado State University. Long-term datasets and background information (proposals, reports, photographs, etc.) on the SGS-LTER project are contained in a comprehensive project collection within the Digital Collections of Colorado (http://digitool.library.colostate.edu/R/?func=collections&collection_id=3429). The data table and associated metadata document, which is generated in Ecological Metadata Language, may be available through other repositories serving the ecological research community and represent components of the larger SGS-LTER project collection. The objective of the long-term ANPP study is to monitor long-term net above ground primary production of the shortgrass steppe community by species. There are 6 sites: ridgetop (ridge), midslope (mid), swale, ESA (replicate 1 not 2), Section 25 (SEC 25), and owl-creek (OC). Each site is located in a different landscape position or soil type on the shortgrass steppe and may be grazed or not. Ridgetop, midslope and swale are grazed and are sampled along a catena. Section 25 is grazed and is located in an upload grassland. ESA is an ungrazed upland grassland an is the control from the Ecosystem Stress Area experiment. Owl Creek is ungrazed and is located in the lowland along the owl creek drainage. There are 3 transects with 5 plots in each transect. Plots in the grazed
SGS-LTER Long-Term Monitoring Project: Vegetation Cover on Small Mammal Trapping Webs on the Central Plains Experimental Range, Nunn, Colorado, USA 1999 -2006, ARS Study Number 118 (Reformatted to a Darwin Core Archive)
This data package is formatted as a Darwin Core Archive (DwC-A, event core). For more information on Darwin Core see https://www.tdwg.org/standards/dwc/. This Level 2 data package was derived from the Level 1 data package found here: https://pasta.lternet.edu/package/metadata/eml/edi/326/2, which was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-sgs/140/17. The abstract below was extracted from the Level 0 data package and is included for context: This data package was produced by researchers working on the Shortgrass Steppe Long Term Ecological Research (SGS-LTER) Project, administered at Colorado State University. Long-term datasets and background information (proposals, reports, photographs, etc.) on the SGS-LTER project are contained in a comprehensive project collection within the Digital Collections of Colorado (http://digitool.library.colostate.edu/R/?func=collections&collection_id=3429). The data table and associated metadata document, which is generated in Ecological Metadata Language, may be available through other repositories serving the ecological research community and represent components of the larger SGS-LTER project collection. Additional information and referenced materials can be found: http://hdl.handle.net/10217/83458. The abundance and diversity of small mammals in shortgrass steppe is strongly influenced by the structure and composition of vegetation. Vegetation structure provides cover from predators and harsh abiotic conditions. Plant species composition affects the types of seeds and herbaceous material available to granivores and herbivores, and influences arthropod populations, which are important prey for the omnivorous species that dominate in shortgrass steppe. Both vegetation structure and plant community composition are sensitive to the availability of precipitation as well as the activity of large mammalian herbivores. In 1999, we began measuring vegetation structure and p
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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