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Disturbance to monitoring plots at Altamaha River Plant Transition Sites SCSA, ZSC1, and ZSC2 from 2013 to 2025.
We established permanent vegetation monitoring plots at Altamaha River plant transition sites in 2012. Starting in 2013, when we recorded plant sizes, we also noted any disturbance to the plots. Plots were scored as normal (no visible disturbance), disturbed by wrack (wrack present in plots and stems dead or broken), disturbed by snails (>100 Littoraria per square meter and plant biomass low), disturbed by pigs (animal trail through the plot), initial slump (plot at the creekbank sliding into the creek based on movement of pvc poles or formation of a crevasse), and terminal slump (plot had slid far enough down that vegetation had drowned). Plots that experienced terminal slump or could not be found for any reason were scored as lost. Lost plots were replaced with a new plot in the same general area with the plot code incremented by 10. For example if plot 3 was lost, it was replaced by 13, and then in turn by 23.
Fall 2022 grasshopper monitoring -- mid-marsh grasshopper abundance and species diversity at eight GCE LTER sampling sites
Grasshopper abundance and species diversity were investigated at eight sampling sites within the Georgia Coastal Ecosystems (GCE) LTER study area in July 2022. Visual surveys were conducted along 8 2m by 10m transects randomly allocated within the mid-marsh zone at each site. All grasshoppers observed within each transect were counted and identified to species, if possible. This survey was conducted as part of the GCE invertebrate monitoring program, and will be performed annually to assess long-term changes in relative species abundances across the GCE study area.
Fall 2023 grasshopper monitoring -- mid-marsh grasshopper abundance and species diversity at eight GCE LTER sampling sites
Grasshopper abundance and species diversity were investigated at eight sampling sites within the Georgia Coastal Ecosystems (GCE) LTER study area in August 2023. Visual surveys were conducted along 8 2m by 10m transects randomly allocated within the mid-marsh zone at each site. All grasshoppers observed within each transect were counted and identified to species, if possible. This survey was conducted as part of the GCE invertebrate monitoring program, and will be performed annually to assess long-term changes in relative species abundances across the GCE study area.
Soil temperature at GCE core monitoring sites in the winter of 2019-2020
We deployed one hobo logger in each vegetation zone at each of the ten primary GCE monitoring sites, for a total of 20 loggers. The loggers were deployed at plot number 1 in each zone, to the “outside” (away from plot number 2), parallel in elevation with the middle of plot 1, buried 10 cm deep, lying horizontal, and tied with a string to the upper left hand (looking from the ocean towards the land) corner stake of the plot. Hobos were deployed during fall monitoring in October 2019, and set to start logging on October 15, 1 am, at 15 minute intervals, with the loggers set on Central Time (times were converted to UTC in post-processing). They were retrieved in April 2020 and files were trimmed to end on a standard date. Exact deployment and retrieval dates are on the attached adobe acrobat file.
Percent cover measurements of four site-dominant species from the GCE-LTER Seawater Addition Long-Term Experiment (SALTEx) Project
SALTEx (Seawater Addition Long-Term Experiment) is a field experiment designed to simulate saltwater intrusion in a tidal freshwater wetland to predict how chronic (Press) and acute (Pulse) salinization will affect this and other tidal freshwater ecosystems. The SALTEx experiment was initiated in 2012 and consists of 31 field plots, each 2.5 m on a side. There are three treatments (Press, Pulse, and Fresh) and two types of controls (with and without sides), each consisting of six replicates. The Press treatment plots receive regular (4 times each week) additions of a mixture of seawater and fresh river water. Pulse plots receive the same mixture of seawater and river water during September and October, which is historically a time of low flow in the river when natural saltwater intrusion occurs. The Fresh treatment plots receive regular additions of fresh river water. Treatment water is added during low tide to facilitate its infiltration into the soil, and all plots are inundated by astronomical tides at high tide. Percent cover was measured for four site-dominant species (Zizaniopsis miliacea, Pontederia cordata, Persicaria hydropiperoides, and Ludwigia repens) each July from 2013 to 2022.
Fall 2024 grasshopper monitoring -- mid-marsh grasshopper abundance and species diversity at eight GCE LTER sampling sites
Grasshopper abundance and species diversity were investigated at eight sites within the Georgia Coastal Ecosystems (GCE) LTER study area in August 2024. Visual surveys were conducted along eight 2m by 10m transects randomly located within the mid-marsh zone at each site. All grasshoppers observed within each transect were counted and identified to species, if possible. This survey is conducted annually to assess spatial patterns of grasshopper abundance and long-term changes in relative species abundances across the GCE study area. In 2024, only 3 sites were sampled due to time and weather constraints.
Thresholds and Regime Shifts at Four LTER Sites (CCE, JRN, PAL, SBC) 1951-2009
The existence and causes of abrupt transitions, thresholds, or regime shifts between ecosystem states is of great concern because the likelihood of such transitions is predicted to increase. The science for measuring and responding to state changes, however, is not well developed. This limitation stems from a lack of data-supported case studies of abrupt transitions in all but a few well-studied ecosystems. We used 30-60 years of data on biological responses and putative drivers from ocean, coastal, polar, and dryland ecosystems to illustrate general approaches to analysis of abrupt transitions. The analyses indicate one case in which the state or response variable (krill abundance) tracked abrupt changes in the driver (Pacific Decadal Oscillation) in a linear fashion. Response variables in other cases (sea cucumber abundance, penguin abundance, and perennial grass production) exhibited hysteretic relationships to drivers (wave intensity, sea ice duration, and monsoonal rainfall amounts, respectively) through a variety of response mechanisms. The analyses illustrate that 1) a suite of common concepts and approaches can be used across disparate systems, 2) there are generally insufficient data for the use of leading indicators, particularly considering the abruptness of transition relative to the lifespan of long-lived organisms, 3) information on spatiotemporal context is useful for comparing transitions in similar systems, and 4) ancillary information from associated experiments and observations is critical for interpreting response-driver relationships.
Canopy Phenology and Greenness Indices at 13 Sites across North America 2003-2012
This data set contains camera-derived color index data, which serve as a proxy for canopy phenology. The data set spans 13 geographically distinct research sites, including 17 different cameras it total, each of which was mounted on a eddy flux tower for intercomparison of canopy and photosynthesis phenology. Each site was dominated by one of three PFTs: deciduous broadleaf forest, evergreen needleleaf forest, and grassland/crops (see HF215-01 for details). On each eddy covariance tower, a digital camera was installed in a fixed position, with a view across the top of the canopy. Most cameras collected photos, which were saved in 24-bit JPEG format, at 30-60 minute intervals, 12-24 hours a day. Time series were first visually inspected for camera shifts and changes in field of view. Noting these changes, we processed the image archives to extract regions of interest (ROI) that encompassed all portions of the full canopy within the foreground. To quantify canopy greenness, we calculated the green chromatic coordinate (GCC), which is widely used to monitor canopy development and identify phenological phase changes, as follows: GCC = DNG / (DNR + DNG + DNB) where DN is the digital number and R, G and B denote the red, green and blue channels, respectively. The Excess Green (ExG) index was then calclated as follows: ExG = 2 * DNG - (DNR + DNB) To characterize canopy coloration in fall, the red chromatic coordinate (RCC) was calculated using the same form as GCC, substituting DNR in the numerator. Indices have been smoothed along a 3-day interval, using a 90th percentile filter (Sonnentag et al. 2012). For each deciduous broadleaf site, there are three files – one each for GCC, ExG and RCC. For the grassland and evergreen needleleaf sites, there are two files, one each for GCC and ExG.
Vegetation Cover in the Clearcut Site at Harvard Forest 2010-2013
We used the line-intercept method to monitor the expansion of vegetation cover at our site, post-clearcut. This dataset was also used to calculate leaf area at the site from 2010 to 2012 and also in upscaling leaf gas exchange measurements collected during the 2010 and 2012 growing seasons. The data was used in two publications listed below (as of June 2014) and numerous poster presentations. Data collection was done during the REU summer programs, with Prof. William’s graduate students and postdocs acting as guides/mentors to the REU students.
Soil Gas Exchange in the Clearcut Site at Harvard Forest 2011-2013
Soil CO2 efflux was measured at the clear cut site beginning in 2011. That year a nearby spruce site was also measured for comparison. Soil respiration was measured in 2011 and 2012 with the LI-COR 6200 instrument and soil efflux was calculated later in the lab. In 2013 soil respiration was measured with the LI-COR 6400 instrument, which computed the fluxes internally. In 2012 three trenched plots were established at the clear cut site. Those were established by trenching a 2 x 2 meter perimeter to a depth of about 50 cm, severing any roots. The trenches were lined with heavy duty landscaping cloth and backfilled. Soil collars were installed in the middle of the trenched plots and measured in 2012 (1 large one used with the LI-6200 machine) and in 2013 (two smaller ones used with the LI-6400 machine). Sampling points were scattered around the site, along vegetation transects (near the EC tower, across the fire access road).
Leaf Gas Exchange in the Clearcut Site at Harvard Forest 2010-2012
Clearcutting a forest ecosystem can result in a drastic reduction of the stand’s productivity. Despite the severity of this disturbance type, past studies have found that the productivity of young regenerating stands can quickly rebound, approaching that of mature undisturbed stands within a few years. One of the obvious reasons is increased leaf area with each year of recovery. However, a less obvious reason may be the variability in species composition and distribution during the natural regeneration process. The purpose of this study was to investigate to what extent the increase in GEP, observed during the first four years of recovery, in a naturally regenerating clearcut stand was due to 1) an overall expansion of leaf area, and 2) an increase in the canopy’s photosynthetic capacity stemming from either species compositional shifts or drift in physiological traits within species. We found that the multi-year rise in GEP following harvest was clearly attributed to the expansion of leaf area rather than a change in vegetation composition. Sizeable changes in relative abundance of species were masked by remarkably similar leaf physiological attributes for a range of vegetation types present in this early successional environment. Comparison of upscaled leaf-chamber to eddy-covariance-based light-response curves revealed broad consistency in both maximum photosynthetic capacity and quantum yield efficiency. The approaches presented here illustrate how chamber- and ecosystem-scale measurements of gas exchange can be blended with species-level leaf area data to draw conclusive inferences about changes in ecosystem processes over time in a highly dynamic environment.
Soil Characteristics in the Clearcut Site at Harvard Forest 2012
Soil properties (C:N ratio, pH, soil moisture, bulk density, litter layer thickness) were measured at the clear cut site in December 2012. Measurements were taken inside the large PVC collars that were used to measure soil respiration at the sites during the 2012 growing season. The collars were removed for storage thereafter. 15 locations in total were sampled: 3 collars were in trenched plots, and 12 on untrenched soil. Soil properties were collected in order to help interpret spatial variability in the corresponding soil CO2 fluxes measured at the site.
Leaf Area in the Clearcut Site at Harvard Forest 2010-2012
This dataset contributed to an estimate of leaf area by species at the Prospect Hill clearcut regeneration site, used in a publication to attribute measured changes in gross primary productivity over time to either changes in species composition and associated traits versus changes in total leaf area. The file reports data on leaf area by species from destructive harvest in select plots. It also reports leaf area and leaf weight from destructive harvest of the foliage of select individual species to characterize the vertical distribution of foliage for those species. Corresponding measurements of total plant area recorded with a LAI-2000 before and after harvest of this foliage is reported as well, useful for inferring the leaf versus stem/branch portions of light interception as needed for improved estimates of LAI with the light-interception method. Lastly, below we report the result of an August 2012 site-level survey of plant area index measured with the LAI-2000 and converted to leaf area index.
Specific Leaf Area in the Clearcut Site at Harvard Forest 2012
Clearcutting a forest ecosystem can result in a drastic reduction of the stand’s productivity. Despite the severity of this disturbance type, past studies have found that the productivity of young regenerating stands can quickly rebound, approaching that of mature undisturbed stands within a few years. One of the obvious reasons is increased leaf area with each year of recovery. However, a less obvious reason may be the variability in species composition and distribution during the natural regeneration process. The purpose of this study was to investigate to what extent the increase in GEP, observed during the first four years of recovery, in a naturally regenerating clearcut stand was due to 1) an overall expansion of leaf area, and 2) an increase in the canopy’s photosynthetic capacity stemming from either species compositional shifts or drift in physiological traits within species. We found that the multi-year rise in GEP following harvest was clearly attributed to the expansion of leaf area rather than a change in vegetation composition. Sizeable changes in relative abundance of species were masked by remarkably similar leaf physiological attributes for a range of vegetation types present in this early successional environment. Comparison of upscaled leaf-chamber to eddy-covariance-based light-response curves revealed broad consistency in both maximum photosynthetic capacity and quantum yield efficiency. The approaches presented here illustrate how chamber- and ecosystem-scale measurements of gas exchange can be blended with species-level leaf area data to draw conclusive inferences about changes in ecosystem processes over time in a highly dynamic environment.
Litterfall in the Clearcut Site at Harvard Forest 2012
Clearcutting a forest ecosystem can result in a drastic reduction of the stand’s productivity. Despite the severity of this disturbance type, past studies have found that the productivity of young regenerating stands can quickly rebound, approaching that of mature undisturbed stands within a few years. One of the obvious reasons is increased leaf area with each year of recovery. However, a less obvious reason may be the variability in species composition and distribution during the natural regeneration process. The purpose of this study was to investigate to what extent the increase in GEP, observed during the first four years of recovery, in a naturally regenerating clearcut stand was due to 1) an overall expansion of leaf area, and 2) an increase in the canopy’s photosynthetic capacity stemming from either species compositional shifts or drift in physiological traits within species. We found that the multi-year rise in GEP following harvest was clearly attributed to the expansion of leaf area rather than a change in vegetation composition. Sizeable changes in relative abundance of species were masked by remarkably similar leaf physiological attributes for a range of vegetation types present in this early successional environment. Comparison of upscaled leaf-chamber to eddy-covariance-based light-response curves revealed broad consistency in both maximum photosynthetic capacity and quantum yield efficiency. The approaches presented here illustrate how chamber- and ecosystem-scale measurements of gas exchange can be blended with species-level leaf area data to draw conclusive inferences about changes in ecosystem processes over time in a highly dynamic environment.
Photosynthetically Active Radiation in the Clearcut Site at Harvard Forest 2013
The purpose of these measurements was to capture the light attenuation of the canopy throughout the growing season, which can help in determining leaf area/canopy openness at the site. Measurements were done along a 50-m-long transect (one of the ones used for line-intercept vegetation surveys, on the side of the EC-tower). Eight measurement locations were established along the transect, equidistant, and marked with a bright orange flag. Measurements were taken with a LI-COR LI-191 Line quantum sensor as described below. Before and after measurements along the transect, PAR-readings were taken in an open area (away from canopy cover) either at a log along the access road to the site or up on the fire tower nearby. At each location along the transect, two measurements were taken – one at the ground surface and one at a height of 1.3m (diameter at breast height).
Survey of Native American Archaeological Sites in Massachusetts 12000-300 BP
The interpretation that pre-contact Native American land-use played an increasing role in landscape dynamics through the Holocene is prevalent in historical, scientific and popular literature. This exerts a strong influence on modern conservation practices especially the use of prescribed fire (Cronon 1984, Abrams 2002, Pyne 1984, Mann 2002) and yet there has never been a robust analysis of relevant archaeological and paleoecological data on the subject. This data is used in the archaeological component of a larger National Science Foundation (NSF)-funded research project intended to analyze the triggers and drivers of ecosystem dynamics. More specifically, the research aims to determine the role of human activity (fire, land clearance, horticulture) in shaping vegetation dynamics. Some of the alternative hypotheses examined in the archaeological analysis include: (1) do we see progressively intensive cultural development and increasingly intensive land use throughout the pre-Contact period?; (2) do we see cultural continuity with fairly passive responses to environmental change and minimal ecological impact of people?; or (3) is cultural adaptation environmental and/or cultural specific, with clear influence of human agency? Our collaborative ecological and social research (Duranleau 2009, Foster and Aber 2004, Chilton et al. 2010) position us to undertake such a regional synthesis as one critical element of the proposed study on ecological dynamics and regime shifts. This synthesis will allow us to consider basic ecological questions concerning interactions among climate, disturbance and human activity in ecosystem dynamics; provide a landscape and regional test of a hypothesis put forth by Munoz et al. (2010) concerning the link between environmental change and cultural development in northeastern North America; and position our archaeological community to apply new ecological perspectives to their research. The archaeological component is derived from intensive
Coastal Native American Archaeological Sites in New York and Southern New England 12000-400 BP
Information on coastal Native American archaeological sites in New York and southern New England was compiled from various state historical commissions. The data include the following characteristics: Project Area, Project Size, and Cultural Remains, which identifies the presence of either pre-Contact (PRE) or historic (HI) material, or the lack of cultural material (NCM). Site type Site Type delineates the type of pre-Contact site represented by the artifacts and features identified at a location, which ranges from a Find Spot (FS) (a tool or piece of chipping debris found on the surface or found alone), and a Short-term Site (ST) (presence of artifacts indicating temporary use of a location), to a Seasonal Site (SE) (a site containing evidence of repeated occupation over long periods of time and with features and evidence for a broad range of activities), and a Sedentary Site (SD) (evidence of year-round habitation in form of botanical, faunal, fish and shellfish remains; presence of hearths, storage pits and middens; large variety and great quantity of tool types). Time periods Time Periods include: the Paleoindian Period (P) (12,000-10,000 BP); Early Archaic (EA) (10,000-8000 BP), Middle Archaic (MA) (8000-6000 BP), Late Archaic (LA) (6000-3000 BP), Transitional Archaic (TA) (3500-2500 BP), Early Woodland (EW) (3000-2000 BP), Middle Woodland (MW) (2000-1000 BP), Late Woodland (LW) (1000-500 BP), Contact period (C) (A.D. 1500-1620), and sites of unknown temporal affiliation (U). Activities The activities represented by the artifacts recovered from the sites include: lithic tool repair (LTR) (chipping debris), lithic workshop (LTW) (chipping debris, hammerstones, cores), hunting (HU) (faunal material and/or projectile points), fishing (FI) (net weights, fish hooks, fish bone), shellfish gathering (SG) (presence of shell), plant gathering (PG) (presence of charred seeds and/or nuts), food processing (FP) (bifaces, scrapers, knives, blades, and other lithic tools, f
Seasonal non-destructive vegetation measurements at 15 net primary production (NPP) study sites at Jornada Basin LTER, 1989-ongoing
This data package contains non-destructive quadrat measurements collected for the long-term Net Primary Production (NPP) study at the Jornada Basin LTER. Data here include measurements of horizontal cover and vertical height of plants observed at permanent NPP quadrats at 15 study sites. Sites were selected to represent the 5 major ecosystem types in the Chihuahuan Desert (upland grasslands, playa grasslands, mesquite-dominated shrublands, creosotebush-dominated shrublands, tarbush-dominated shrublands). For each ecosystem type, three sites were selected to represent the range in variability in production and plant diversity; thus the locations are not replicates. All sites are excluded from domestic grazing. Eleven sites are in non-grazed pastures, and at the other four sites 1 hectare areas around the observational plots were fenced in 1988. At all sites a grid of 49 (48 at one playa location) 1m x 1m replicate quadrats was laid out when sampling began in 1989. Grids consist of 49 quadrats arranged in a square 7 x 7 pattern, with quadrats 10 m apart (P-COLL has 48 quadrats in a 3 x 16 pattern). Standing vegetation in quadrats is sampled three times a year: in winter (February - March), before shrubs begin spring growth; in spring (May), when shrubs and spring annuals have reached peak biomass; in fall (late summer; October), when summer annuals have reached peak biomass but before killing frosts. Additional observations of plant count and phenological stage are also made. This dataset is subsequently used to determine quadrat biomass and net primary production. Details and linked data packages are described in the methods element. This is an ongoing dataset with new quadrat measurements collected in the spring, fall and winter of each year. Attention: 1) For most species, these data are not appropriate for estimates of percentage cover because of the way the data are collected. See Note 1 in the methods element for further details.
Soil volumetric water content calculated from neutron hydroprobe data at 15 NPP study locations at the Jornada Basin LTER site, 1989-ongoing
This data package contains soil water content data calculated from monthly neutron hydroprobe count measurements made at 15 net primary production (NPP) study locations on Jornada Experimental Range (JER) and Chihuahuan Desert Rangeland Research Center (CDRRC) lands. Once a month, neutron probe measurements are made at 10 depths (where possible) at each of 10 access tubes at each of the 15 NPP sites using a neutron probe (CPN Model 503DR Hydroprobe and CPN Model 503 Elite Hydroprobe). The raw dataset, also on EDI (knb-lter-jrn.210013001), consists of the count of thermalized neutrons at 30 cm depth intervals to a maximum depth of 300 cm. In this data package, the raw neutron counts have been adjusted for radioactive decay of the neutron source, then converted to volumetric water content (VWC) to a maximum depth of 270 cm using calibration equations (deepest probe depths are excluded from VWC calculations). The NPP sites these measurements are made at represent the 5 dominant vegetation types of the Jornada Basin, which consist of 3 shrub (creosotebush, mesquite dune, and tarbush) and 2 grass (upland grassland and playa) types. Three NPP sites are located in each of the types. This data collection is ongoing with new data collected monthly (updates to the EDI package may occur less frequently). NOTE: This version of the dataset includes calibrated data from a new hydroprobe unit that has recently been put into service. Repair parts were no longer available for the older unit.
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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)
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DANDI Archive for NWB datasets
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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.