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Eddy Covariance and Meteorological Data in the Clearcut Site at Harvard Forest 2009-2012
Clearcutting and other forest disturbances perturb carbon, water, and energy balances in significant ways, with corresponding influences on Earth’s climate system through biogeochemical and biogeophysical effects. Observations are needed to quantify the precise changes in these balances as they vary across diverse disturbances of different types, severities, and in various climate and ecosystem type settings. This dataset reports eddy covariance and micrometeorological measurements of surface-atmosphere exchanges that can be combined with related datasets from vegetation inventories and chamber-based estimates of soil respiration and leaf gas exchange to collectively quantify and understand how carbon, water, and energy fluxes changed during the first four years following forest clearing in a temperate forest environment of the northeastern US. Associated publications show rapid recovery with sustained increases in gross ecosystem productivity (GEP) over the first three growing seasons post-clearing, coincident with large and relatively stable net emission of CO2 because of overwhelmingly large ecosystem respiration. The rise in GEP was attributed to vegetation changes not environmental conditions (e.g. weather), but attribution to the expansion of leaf area versus changes in vegetation composition remains unclear. Soil respiration was estimated to contribute 44% of total ecosystem respiration during summer months and coarse woody debris accounted for another 18%. Evapotranspiration also recovered rapidly and continued to rise across years with a corresponding decrease in sensible heat flux. Gross shortwave and longwave radiative fluxes were stable across years except for strong wintertime dependence on snow covered conditions and corresponding variation in albedo. Overall, these findings underscore the highly dynamic nature of carbon and water exchanges and vegetation composition during the regrowth following a severe forest disturbance, and sheds light on both the
Imputed Forest Composition Map for New England Screened by Species Range Boundaries 2001-2006
Initializing forest landscape models (FLMs) to simulate changes in tree species composition requires accurate fine-scale forest attribute information mapped contiguously over large areas. Nearest-neighbor imputation maps have high potential for use as the initial condition within FLMs, but the tendency for field plots to be imputed over large geographical distances results in species frequently mapped outside of their home ranges, which is problematic. We developed an approach for evaluating and selecting field plots for imputation based on their similarity in feature-space, their species composition, and their geographical distance between source and imputation to produce a map that is appropriate for initializing an FLM. We applied this approach to map 13m ha of forest throughout the six New England states (Rhode Island, Connecticut, Massachusetts, New Hampshire, Vermont, and Maine). The map itself is a .img raster file of FIA plot CN numbers. To access FIA data from this map, one has to link the mapcodes in this map to FIA data supplied by USDA FIA database (https://apps.fs.usda.gov/fia/datamart/datamart.html). Due to plot confidentiality and integrity concerns, pixels containing FIA plots were always assigned to some other plot than the actual one found there.
Estimating Forest Productivity Using Carbon Isotopes in Tree Rings at Harvard Forest 1992-2010
We investigated relationships between tree-ring δ13C and growth, and flux tower estimates of gross primary productivity (GPP) at Harvard Forest from 1992 to 2010. Seasonal variations of derived photosynthetic isotope discrimination (Δ13C) and leaf intercellular CO2 concentration (ci) showed significant increasing trends for the dominant deciduous and coniferous species. Δ13C was positively correlated to growing-season GPP and is primarily controlled by precipitation and soil moisture indicating that site conditions maintained high stomatal conductance under increasing atmospheric CO2 levels. Increasing Δ13C over the 1992-2010 period is attributed to increasing annual and summer water availability identified at Harvard Forest and across the region. Higher Δ13C is coincident with an enhancement in growth and ecosystem-level net carbon uptake. This work suggests that tree-ring δ13C could serve as a measure of forest GPP and be used to improve the calibration and predictive skill of ecosystem and carbon cycle models.
Vascular Flora of the Harvard Farm at Harvard Forest 2014
The objectives of this study were to: (1) Inventory the vascular flora of the former Petersham Country Club (now the Harvard Farm). (2) Collect voucher specimens for the HF Herbarium of species that were not previously documented from Harvard Forest, or that were found historically at HF but were not recorded in 2004–2007 by Jenkins et al. (2008). (3) Establish and sample a series of permanent plots to characterize current vegetation composition, and to enable evaluation of vegetation change over time. (4) Sample soils within permanent plots to document initial conditions and to facilitate future work on soil dynamics and ecosystem processes.
Snowpack in Hemlock, Hardwood, and Open Sites at Harvard Forest 2008-2014
Sub-forest canopy meteorological forcing and snowpack properties can profoundly influence the winter ecology. 3/4 inch graduated PVC snow stakes and web cams were installed at three Harvard Forest (HF) sites including: mixed-hardwood at the Little Prospect Hill (LPH) Eddy Flux Tower, near the Hemlock walk-up tower, and at the open area behind Shaler Hall. Web cameras connected to a laptop at the three sites provided daily images of snowpack surface depth. Snow density profiles were recorded during weekly to monthly site visits from December 2008 to April 2014. Gaps in the datasets were primarily caused by laptop malfunctions and lack of site visits necessary to maintain equipment and to obtain density measurements of the snowpack. There were no site visits to record snowpack properties during the 2011-2012 snow season, a year of unusually low snowfall. These datasets would prove useful for research related to snow ecology and hydrology projects at Harvard Forest.
Ants in the New York Pine Barrens 2012-2013
Ants are ecologically important, environmentally sensitive, widespread, and abundant, yet ant assemblages of many habitats remain poorly understood. This is true of inland pine barrens in the northeastern United States. In the Northeast, such barrens support uncommon ant species and high species density for the region. Ants in inland barrens of New York State barely have been studied. To increase knowledge of these assemblages, I systematically collected ants from three NY inland barrens and investigated how hiking trails--a common man-made disturbance--may be impacting ant assemblages in these early-successional, disturbance-dependent ecosystems. My data strongly indicate uncommonly high densities of ant species in NY pine barrens, including the most northern known occurrences of two species, and show that hiking trails alter ant assemblage composition and species density.
EXPOS Model for Estimating Topographic Exposure to Wind
EXPOS is a simple model of topographic exposure to wind that utilizes digital elevation data to predict which points on a landscape are exposed to or protected from a given wind direction. The model was developed to approximate the effects of topography on hurricane wind flow at a landscape scale (~ 10 km). The model requires an accurate digital elevation map and a specified wind direction. Each point on the elevation map is then classified as protected or exposed, depending on whether or not it falls within the wind shadow cast by points upwind. The wind shadow is estimated by assuming that the wind bends downward no more than a fixed inflection angle from the horizontal as it passes over a height of land. The effects of topographic features beyond the margins of the input elevation map are of course not predicted by the model. For a given landscape and wind direction, predicted protected areas decrease in size as the inflection angle increases. Application of the model in studies of two recent hurricanes suggests that the probability of wind damage in protected areas also decreases as the inflection angle increases. An inflection angle of about 5 to 10 degrees was found to give good results. For more information on the EXPOS model, please see the published paper (Boose, E. R., D. R. Foster, and M. Fluet. 1994. Hurricane impacts to tropical and temperate forest landscapes. Ecological Monographs 64: 369-400). Additional information is contained in the documentation that accompanies the program. For an updated version of the EXPOS model in R and Python, please see HF447.
Role of Moose and Deer Browsing in Unharvested Forests of Southern New England since 2011
In the past 25 years, moose have spread south from Vermont and New Hampshire and recolonized their pre-historical range limit in southern New England from which they had been extirpated almost 200 years earlier. Intensive moose browsing in the boreal forest has caused declines in forest density and shifts in species composition in some areas, generating considerable interest and concern among foresters, wildlife managers, and ecologists as to how moose along with white-tailed deer will impact forest regeneration, composition, and diversity in this region. Harvard Forest in collaboration with researchers at the USGS Massachusetts Cooperative Research Unit has initiated a long-term study of the role of moose and deer in SNE forests using experimental exclosures. The design is a randomized block with 3 factors -- full exclosure, partial exclosure, and control plot. Full exclosures exclude both moose and deer but allow access to small mammals such as mice, squirrels, and rabbits. Partial exclosures have a 60cm opening around the bottom perimeter of the fence, which excludes moose but allows access to deer and other small and medium-sized animals. The design enables us to quantify forest composition and structure in areas (1) exposed to moose and deer browsing, (2) protected from moose and deer browsing, and (3) exposed to deer browsing but protected from moose browsing.
Ungulate Browsing and Foundation Tree Regeneration in Central New England 2010
Large herbivores are important forest disturbances capable of altering community composition, biodiversity, tree density, successional pathways, and nutrient cycling. The extent to which browsers exert important impacts on forests, however, depends on the intensity and duration of browsing, the palatability and tolerance of the vegetation, available resources to plants, and the scale at which these factors are being investigated. Few studies have examined ungulate impacts at the landscape scale. Since the late-1980s moose have recolonized their pre-historical range in southern New England, joined white-tailed deer to create a potentially important new driver of forest dynamics in the region. Few, if any, studies have looked at combined deer and moose impacts on temperate forests in eastern North America. In the summer of 2010, we initiated a landscape-scale observational study on ungulate habitat use and browsing on foundation tree species (Quercus spp. and Tsuga canadensis) in unlogged forests. Seventy-two forest plots were sampled across several ecoregions in central and western Massachusetts, southern Vermont and New Hampshire and northern Connecticut. Tree seedlings, overstory characteristics, browsing, pellet piles, and shrub densities were sampled; and site attributes such as mean annual temperature and forest fragmentation were examined.
Partitioning the Components of Soil Respiration in a Trenching Experiment at Harvard Forest 2009-2010
Total soil respiration (Rt) is a combination of autotrophic (Ra) and heterotrophic respiration (Rh). Several methods have been developed to tease out the components of Rt, such as isotopic analyses, and removing Ra input through tree girdling and root exclusion experiments. Trenching involves severing the rooting system surrounding a plot to remove the Ra component within the plot. This method has some potential limitations. Reduced water uptake in trenched plots could change soil water content, which is one of the environmental controllers of Rt in many ecosystems. Eliminating root inputs could reduce heterotrophic decomposition of SOM via lack of priming. On the other hand, the severed dead roots may temporarily increase available carbon substrate for Rh. We utilized the trenching method to partition the autotrophic and heterotrophic components of soil respiration in an oak dominated forest with the footprint of the LPH tower.
Land-Use Impacts on Ecosystem Services Provisioning in Massachusetts 2001-2011
Meeting fundamental human needs while also maintaining ecosystem function and services is the central challenge of sustainability science. In the densely populated state of Massachusetts, USA, abundant forests and other natural land cover convey a range of ecosystem services. However, after more than a century of reforestation following an agrarian past, Massachusetts is again losing forests, this time to housing and commercial development. We used land-cover maps, ecosystem process models, and land-use data bases to map changes (2001, 2006, 2011) in eight ecosystem service variables and to identify “hotspots,” or areas that produce a high value of five or more services, at three policy-relevant spatial scales. Water-related services (clean water provisioning and flood regulation) experienced local declines in response to shifting land uses, but changed little when measured at the state-level. General habitat quality for terrestrial species declined state-wide during the study period as a consequence of forest loss. In contrast, climate regulation (carbon storage) and cultural services (outdoor recreation) increased, driven by continued forest biomass accrual and land protection, respectively. Timber harvest volume had high inter-annual variability, but no temporal trend. The scale at which hotspots are delineated greatly affects their quantity and spatial configuration, with a higher density in eastern Massachusetts and 10–12% more hotspots overall when they are identified at a town scale as compared to a watershed or state scale. Ecosystem service hotspots cover a small percentage of land area in Massachusetts (2.5–3.5% of the state), but are becoming more abundant as urbanization concentrates ecosystem service provisioning onto a diminished natural land base. This suggests that while ecosystem service hotspots are valuable targets for conservation, more are not necessarily better since hotspot proliferation can reflect the bifurcation of the landscape into servic
Calibrating Abundance Indices of Red Back Salamanders at Harvard Forest 2014
Herpetologists and conservation biologists frequently use convenient and cost-effective, but less accurate, abundance indices (e.g. artificial cover boards or natural objects surveys) in lieu of more accurate but costly and destructive population size estimators to detect and monitor size, state, and trends of amphibian populations. Despite advantages and disadvantages to each approach, studies calibrating abundance indices so they can be used as reliable population estimators are rare. We calibrated indices based on surveys under artificial cover boards and natural objects with a more accurate estimator of population sizes of red back salamanders (Plethodon cinereus (Green)) in a New England forest. Plethodon cinereus is an ecologically significant indicator species of forest dynamics, and accurate calibration of these indices should increase their reliability for monitoring programs. Average density/m2, capture probability, relative density of both natural objects searches, and cover board observations of P. cinereus in 30 × 30-m plots at the Harvard Forest (Petersham, Massachusetts, USA) were similar in stands dominated by Tsuga canadensis (eastern hemlock) and deciduous hardwood species (predominantly Quercus rubra [red oak] and Acer rubrum [red maple]). Abundance indices based on both cover board and natural object surveys were able to be calibrated using density estimates of P. cinereus derived from depletion (removal) surveys. The cover board index underestimated the estimated density of P. cinereus by 40%, but the natural object survey underestimated it by about 55%. We conclude that when calibrated and used appropriately, abundance indices can provide cost-effective and reliable measures of P. cinereus abundance that may be used in conservation assessments and long-term monitoring of northeastern USA forests.
Land Owner Decisions and Consequences in North Central Massachusetts 1950-2009
Landscapes dominated by private ownership experience change as properties change hands, change monetary value, undergo land use conversion, become isolated or lose road access, or are divided and hence smaller in size. The future ecological integrity, connectivity, and function of landscapes dominated by private ownership depend on the speed or frequency with which decisions are made, the kinds of decisions, and their outcomes or consequences. One way to study this human behavior on land is through attitudinal surveys of owners investigating their motivations, beliefs, and values. Another is to pose hypothetical circumstances and query owners about potential response or reactions. Another involves the study of social networks around owners, and determining the extent to which information flows between owners and may influence decisions. We proposed instead to study or monitor decisions made and resulting circumstances, and to establish a long-term framework or network of points at which land owner decisions will be sampled over time. In essence, we proposed to study behavior enacted on the landscape, rather than individual people. Data derived from this network and sampling will inform land use scenario modeling efforts to forecast the future trajectory of the landscape, its rate of change, and subsequent potential provision of ecosystem services. The network was established to monitor change over time in the future, but an important aspect was to establish the baseline and antecedent circumstances that led to existing conditions. A classic historic study following specific decision-making over time on land ownership over generations is told in the Sanderson Farm story at the Harvard Forest: http://www.foresthistory.org/Publications/FHT/FHT1997/SandersonsFarm.pdf Establishment of the baseline and historic circumstances will inform models of future decisions. The summer 2009 project was a proof-of-concept to test the extent to which points could be established and an
Radiometric and Meteorological Data from Harvard Forest Barn Tower 2011-2017
To better quantify the seasonal changes in canopy structure and physiological status (e.g. photosynthetic capacity or efficiency), and provide a more rigorous context for interpretation of the camera data, we installed an extensive set of radiometric instruments on the Harvard Forest Barn Tower beginning in 2011. A complete list of sensors is given in the Methods section. Note that these include both broad-band and narrow-band sensors, and sensors with hemispherical, narrow, and multi-angular fields of view.
HURRECON Model for Estimating Hurricane Wind Speed, Direction and Damage
HURRECON is a simple meteorological model that estimates hurricane surface wind speed and direction based on the track, size, and intensity of a hurricane and the surface type (land or water). The model also estimates Fujita-scale wind damage as a function of peak 1/4 mile wind speed and wind gust factor. Estimates can be generated for a single site or a rectangular region. The model is based on published empirical studies of many hurricanes. HURRECON can be used to study the impacts of individual hurricanes or to reconstruct the hurricane disturbance regime for a particular region. For more information on the most recent version of the model please see the published paper (Boose, E. R., K. E. Chamberlin and D. R. Foster. 2001. Landscape and regional impacts of hurricanes in New England. Ecological Monographs 71: 27-48). Additional information is contained in the documentation that accompanies the program. For an updated version of the HURRECON model in R and Python, please see HF446.
Climate Change Impacts on Forest Biodiversity at Harvard Forest since 2011
Climate change is rapidly transforming forests over much of the globe in ways that are not anticipated by current science. Large-scale forest diebacks, apparently linked to interactions involving drought, warm winters, and other species, are becoming alarmingly frequent. Models of biodiversity and climate have not provided guidance on if/where/when such responses will occur. Instead models often predict potential numbers of extinctions, but these forecasts not are linked in any mechanistic way to the processes that could cause them. Both modeling and field studies rely on aggregate metrics of species presence/absence or relative abundance at regional scales, but climate affects individuals. Aggregation of individual data to the species level, hides or even qualitatively changes climate effects. By sampling and analysis at the individual scale across continental variation in climate, this study can link the individual scale processes to regional responses. This study will exploit existing research sites and the new NEON platform of sites for synthesis of models and data to determine when and where predicting climate impacts on biodiversity is a plausible goal, understand where surprises are likely to occur, and attribute those predictions back to individual tree health and vulnerability to climate risk factors. The study will provide climate vulnerability forecasts for forest biodiversity that are directly linked to the process scale. Our goal is provide probabilistic forecasts for the joint distribution of forest responses to climate change, including growth, reproduction, and mortality risk. For scientists, US Forest Service researchers, and policy makers predictions will anticipate combined risks of increasing drought and longer growing seasons. Methods developed under this project will be disseminated through training workshops for postdoctoral associates at other universities and resource managers.
Harvard Forest CTFS-ForestGEO Mapped Forest Plot since 2014
To investigate the forest dynamics across a larger range of scales in which many processes operate, Harvard Forest (HF) researchers, with assistance from the Center for Tropical Forest Science (CTFS) and the Smithsonian Institute’s Forest Global Earth Observatory (ForestGEO), completed an initial census of all woody stems within a 35 ha plot located at the Harvard Forest in 2014. The HF MegaPlot is part of a global array of large-scale plots established by CTFS whose goals are to increase sampling efforts into temperate forests to explore ecosystem processes beyond population dynamics and biodiversity. The geography and size of the HF MegaPlot (500 m x 700 m) is designed to include a continuous, expansive, and varied natural forest landscape. The strategic plot location will yield opportunities for the study of forest dynamics and demography while capturing a large amount of existing NSF funded LTER (Long Term Ecological Research) science infrastructure (e.g. eddy flux towers, gauged sections of a small watershed, existing smaller permanent plots) and a century of observations and studies. The HF MegaPlot will enable an integrated study of ecosystem processes (e.g., biogeochemistry, hydrology, carbon dynamics) and forest dynamics by melding the past with current and future forest research. The second census was conducted during the summers of 2018 and 2019 but did not contain the central swamp portion of the plot.
Vegetation Patterns in Northeastern North America 1500-2000
Over the last few centuries, human activities have changed the landscape of northeastern North America from mostly forested to a patchwork of forest, farmland and logged areas, back in many areas to mostly forested. Meanwhile, there have been many rapid changes in the composition of the remaining forests, for example, the amounts of hemlock (Tsuga canadensis) and beech (Fagus grandifolia) have decreased while the amount of birch (Betula spp.) has increased. How stable have been the basic vegetational patterns under the onslaught of these landscape and compositional changes? In preliminary analyses, the assemblages of major tree taxa have been zoned for every other century, using optimal splitting by information content and other techniques, to study changes in vegetation groupings over the last 500 years. Several patterns seem to be emerging on a centennial scale: First, vegetation patterns were changing in the centuries before European colonization of the area. Second, the number of zones (vegetation types, based on pollen), was greater in 1700 and 1900 than in 1500 or now. Third, the zone boundaries have moved north from 1500 to the present. Further analyses, including several more data sets will be used to refine these conclusions and to suggest explanations for the changes.
Diurnal Patterns of Cavitation in Red Maple, Paper Birch and White Ash at Harvard Forest 2011-2012
Previous work at Harvard Forest has suggested that woody plants cavitate and re-dissolve embolisms in xylem on a daily basis. Here we investigated the common assumption that severing stems and petioles under water preserves the hydraulic continuity in the xylem conduits opened by the cut when the xylem is under tension. In red maple and white ash, higher PLC in the afternoon occurred when the measurement segment was excised under water at native xylem tensions, but not when xylem tensions were relaxed prior to sample excision. Bench drying vulnerability curves in which measurement samples were excised at native versus relaxed tensions showed a dramatic effect of cutting under tension in red maple, a moderate effect in sugar maple, and no effect in paper birch. These results suggest that sampling methods can generate PLC patterns indicative of repair under tension by inducing a degree of embolism that is itself a function of xylem tensions at the moment of sample excision.
Long-term Dynamics of Vegetation and Environment in Central Massachusetts 1000-2000
Historical and ecological data from north-central Massachusetts suggest that widespread and intensive human disturbance after European settlement led to a shift in forest composition and obscured regional patterns of species abundance. A paleoecological approach was required to place recent forest dynamics in a long-term context. Pollen and charcoal data from 11 small lakes in north-central Massachusetts were used to reconstruct local vegetation dynamics and fire histories across the region over the past 1000 years. The sites are located across an environmental gradient. Paleoecological data indicate that prior to European settlement, there was regional variation in forest composition corresponding to differences in climate, substrate, and fire regime. Oak, chestnut and hickory were abundant at low elevations, whereas hemlock, beech, sugar maple, and yellow birch were common at high elevations. Fire appears to have been more frequent and/or intense at lower elevations, maintaining high abundances of oak, and archaeological data suggest Native American populations were greater in these areas. A change in forest composition at higher elevations, around 550 years before present, may be related to the Little Ice Age (a period of variable climate), fire, and/or activity by Native Americans, and led to regional convergence in forest composition. After European settlement, forest composition changed markedly in response to human disturbance and there was a sharp increase in rates of vegetation change. Regional patterns were obscured further, leading to homogenization of broad-scale forest composition. There is no indication from the pollen data that forests are returning to pre-European settlement forest composition, and rates of vegetation change remain high, reflecting continuing disturbance to the landscape, despite regional reforestation.
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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.