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Thresholds and Tipping Points in a Sarracenia Microecosystem at Harvard Forest 2012-2013
The primary goal of this project is to determine experimentally the amount of lead time required to prevent a state change. To achieve this goal, we will (1) experimentally induce state changes in a natural aquatic ecosystem - the Sarracenia microecosystem; (2) use proteomic analysis to identify potential indicators of states and state changes; and (3) test whether we can forestall state changes by experimentally intervening in the system. This work uses state-of-the art molecular tools to identify early warning indicators in the field of aerobic to anaerobic state changes driven by nutrient enrichment in an aquatic ecosystem. The study tests two general hypotheses: (1) proteomic biomarkers can function as reliable indicators of impending state changes and may give early warning before increasing variances and statistical flickering of monitored variables; and (2) well-timed intervention based on proteomic biomarkers can avert future state changes in ecological systems.
Microclimate at Harvard Forest HEM, LPH and EMS Towers since 2005
Microclimatic data are collected continuously within footprint areas of the flux towers in order to (1) understand relationships between climatic and microclimatic conditions and carbon dioxide and water vapor exchange between forest and atmosphere, (2) to develop predictive models for the exchange rates of these gases, based on microclimate data, (3) detect long-term trends in climate and microclimate at the sites and (4) determine whether the response of carbon dioxide and water vapor exchange processes to climate or microclimate is changing over time. The primary climatic and microclimatic variables measured at these sites include: above-canopy photosynthetically active radiation (PAR), forest understory PAR at 1 m height, total net radiation exchange measured above the forest canopy, air temperature and relative humidity above the forest canopy, forest understory air temperature at 20 cm and 1 m above ground level (shielded but not ventilated thermocouple sensors, used only to estimate nighttime understory air temperature), soil temperature at 10 cm depth, and soil moisture.
Fuel Loading in Simulated Hurricane Experiment at Harvard Forest since 1993
Wind disturbance profoundly shapes temperate forests but few studies have evaluated patterns and mechanisms of long-term forest dynamics following major windthrows. In 1990, we initiated a large hurricane simulation experiment in a 0.8 ha manipulation (pulldown) and 0.6 ha control area of a maturing Quercus rubra-Acer rubrum forest in New England. We toppled 276 trees in the pulldown, using a winch and cable, in the northwesterly direction of natural treefall from major hurricanes. Eighty percent of canopy trees and two-thirds of all trees greater than 5 cm dbh suffered direct and indirect damage. An enormous input of dead wood was one result of the manipulation. Many perceive an increased risk of wildfire after trees are blown down, but this depends on the amount, size, and persistence of the dead wood inputs.
Mark-Recapture of Rodent and Shrew Populations in a Declining Hemlock Stand at Harvard Forest 2012
Eastern Hemlocks (Tsuga canadensis) are foundation species, which are known to have a large influence on the species composition and ecosystem dynamics. The purpose of this study was to understand how rodent species richness and composition differed among different hemlock treatments consisting of intact forest, logged forest, and invaded hemlock stands in the Harvard Forest of Petersham, MA. Sherman live traps were arranged on 7x7m grids covering 0.49ha in four different hemlock treatments that were established in 2003: 1) the logged treatment, where commercial trees were removed 2) the girdled treatment, where the hemlocks were girdled using a chainsaw, thus killing the trees, and mimicking the effects of the woolly adelgid, an invasive insect 3) the hemlock control which is where hardwoods are at least 70% hemlocks, and 4) the hardwood control, where other hardwood species are dominate. Animals were marked and recaptured from June-July. Using Schnabel methods for population estimate, there appeared to be a shift in the population from more abundant Gapper’s Red-backed vole, Clethrionomys gapperi in the logged and girdled treatments to white-footed and deer mice (Peromyscus spp) in the hemlock and hardwood control plots. This shift in population may indicate that hemlocks support Peromyscus spp over voles. The species richness and overall population dynamic of these rodents surveyed may lead to a greater understanding as to the potential affect they may have on the seed dispersal in these plots and could account for many interactions between the vegetation and the animals also present.
Isotopic Composition of Net Ecosystem CO2 Exchange at Harvard Forest EMS Tower since 2011
This archive features long-term measurements of the eddy and storage fluxes of 16O12C16O, 16O13C16O, and 18O12C16O at the Harvard Forest EMS flux tower. Provided are the individual isotopologue fluxes, the total CO2 flux, the δ13C and δ18O isofluxes, and various ancillary flux and environmental data. The data are described in Wehr et al (2013), Long-term eddy covariance measurements of the isotopic composition of the ecosystem–atmosphere exchange of CO2 in a temperate forest, Agricultural and Forest Meteorology 181, 69–84. They are also analyzed in Wehr and Saleska (2015), An improved isotopic method for partitioning net ecosystem–atmosphere CO2 exchange, Agricultural and Forest Meteorology 214-215, 515–531, as well as in Wehr et al 2016, Seasonality of Temperate Forest Photosynthesis and Daytime Respiration, Nature (in press). The eddy (iso)fluxes were measured by eddy covariance (EC), with a 30- or 35-minute integration period on a 40- or 45-minute duty cycle (the precise duty cycle was changed during the record to accommodate various synergistic measurement campaigns). The storage fluxes were measured as the increase in storage below 29 m during the EC integration period, based on vertical integrations over 7 air sampling heights on the tower (0.2, 1.0, 7.5, 12.7, 18.1, 24.1, 29.0 m, prior to July 3, 2012), or over 6 air sampling heights on the tower (0.2, 1.0, 7.5, 12.7, 18.1, 29.0 m, after July 3, 2012). Some periods are missing at regular intervals because the system was being used for other measurements, not reported here. Corrected and uncorrected versions of the eddy (iso)fluxes are provided; the corrections account for high-frequency signal attenuation, and were made by comparing w-CO2 and w-T cospectra. The precise method is novel and complex and is described, along with all further details of the measurements, in Wehr et al (2013), Long-term eddy covariance measurements of the isotopic composition of the ecosystem–atmosphere exchange of CO2 in a temperat
Radiocarbon Measurements at Harvard Forest 1996-2010
Long-term datasets on soil C stocks, radiocarbon content, and CO2 efflux from the Harvard forest, MA were applied to the ForCent model to examine soil C dynamics over long term timescales and under warming and nitrogen amendments. The objective was to determine if manipulations of soil temperature and nitrogen supply affect the relative age of respired soil C substrates. Heating of the soil increased decomposition of all soil C pools, the absolute amount of increased decomposition from the older pools was not large enough to make a difference in 14C composition of respired C from model results. Further the high spatial variation observed in 14C from temperature and nitrogen amendments made it difficult to detect changes in respired C sources over this short a study period.
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.
Litter Decomposition in Response to Nitrogen Addition and Soil Warming at Harvard Forest 2010-2012
The purpose of this study is to examine whether two environmental change stressors (warming and nitrogen deposition) differentially impact litter decomposition. We investigated this using a two year litterbag decomposition experiment at the chronic N amendment experiment and the Barre Woods Soil warming experiment, and measured litter decay dynamics, enzyme activities and litter chemistry. In both years mass loss of the mixed litter was suppressed under N addition, with most of the mass loss observed in the first year compared to the second year (70% and 30% of total mass loss, respectively). Both years showed either increased activity for some hydrolytic enzymes (e.g. cellobiohydrolase) or no difference (e.g. ß-N-acetylglucosaminidase) with increased N. The lignolytic enzymes (e.g. peroxidases) showed no difference in activity in the first year, but had a highly reduced activity in year 2 under elevated N conditions. Soil warming did not significantly affect litter mass loss, and only had an effect on the activity of a few enzymes. In the oak reciprocal litterbag study, decay of oak litter originating from the highest N addition plot was negatively affected by simulated N deposition in the first year of decomposition, while after two years, simulated N deposition negatively affected all litter, and litter originating from the highest N addition plot decayed more slowly than control litter even without added N (i.e. in the control plot). In addition, in the first year of decomposition lignolytic enzyme activities were suppressed in litter originating from the N addition treatments, but due to simulated N deposition in year two.
Modeling Impacts of Climate Change on Mangroves Worldwide 2012-2080
Given the multitude of ecosystem services provided by mangroves, it is important to understand their potential responses to global climate change. Extensive reviews of the literature and manipulative experiments suggest that mangroves will be impacted by climate change, but few studies have tested these predictions over large scales using statistical models. We provide the first example of applying species and community distribution models (SDMs and CDMs, respectively) to coastal mangroves worldwide. Species projected to shift their ranges polewards by at least 2 degrees of latitude consistently experience a decrease in the amount of suitable coastal area available to them. Central America and the Caribbean are forecast to lose more mangrove species than other parts of the world. We found that the extent and grain size, at which continuous CDM outputs are examined, independent of the grain size at which the models operate, can dramatically influence the number of pseudo-absences needed for optimal parameterization. The SDMs and CDMs presented here provide a first approximation of how mangroves will respond to climate change given simple correlative relationships between occurrence records and environmental data. Additional, precise georeferenced data on mangrove localities and concerted efforts to collect data on ecological processes across large-scale climatic gradients will enable future research to improve upon these correlative models.
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
Water Chemistry and Well Levels at Upper Bigelow Brook, Harvard Forest 2009-2010
This dataset is the result of a full year of high-resolution monitoring of hydrologic event-driven export of stream dissolved organic matter from the Upper Pipe site on Bigelow Brook at Harvard Forest. In situ measurements of fluorescent dissolved organic matter (FDOM) and conductivity were collected from October of 2009 to December of 2010. Grab samples of water were collected during hydrological events and analyzed using standard methods for dissolved organic matter, nitrate, ammonium, and dissolved organic nitrogen. Water level measurements in wells at this study site were initiated in May of 2010.
Ant Mesocosm Experiment in Harvard Forest Lath Houses 2011-2012
Direct and indirect consequences of global warming on ecosystem functions and processes mediated by invertebrates remain understudied but are likely to have major impacts on ecosystems in the future. Among animals, invertebrates are taxonomically diverse, responsive to temperature changes, and play major ecological roles which also respond to temperature changes. We used a mesocosm experiment to evaluate impacts of two warming treatments (+3.5 and + 5 °C, set points) and the presence and absence of the ant Formica subsericea (a major mediator of processes in north-temperate ecosystems) on decomposition rate, soil movement, soil respiration, and nitrogen availability. Replicate 19-Litre mesocosms were placed outdoors in lath houses and continuously warmed for 30 days in 2011 and 85 days in 2012. Warming treatments mimicked expected temperature increases for future climates in eastern North America. In both years, the amount of soil displaced and soil respiration increased in the warming and ant presence treatments (soil movement: 73 to 119%; soil respiration: 37 to 48% relative to the control treatments without ants). Decomposition rate and nitrogen availability tended to decrease in the warmest treatments (decomposition rate: -26 to -30%; nitrate availability: -11 to -42%). Path analyses indicated that ants had significant short term direct and indirect effects on the studied ecosystem processes. These results suggest that ants may be moving more soil and building deeper nests to escape increasing temperatures, but warming may also influence their direct and indirect effects on soil ecosystem processes.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.