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Monitoring Amphibians in the Declined Hemlocks at Harvard Forest 2013-2014
Disturbances such as outbreaks of nonnative insects and pathogens can devastate unique habitats and directly reduce biodiversity. The foundation tree species Tsuga canadensis (eastern hemlock) is declining due to infestation by the nonnative insect Adelges tsugae (hemlock woolly adelgid). The decline and expected elimination of hemlock from northeastern US forests is changing forest structure, function, and assemblages of associated species. We assessed changes in occupancy, detection probability, and relative abundance of two species of terrestrial salamanders, Plethodon cinereus (eastern red-back salamander) and Notopthalmus viridescens viridescens (eastern red-spotted newt), in the experimental removal of T. canadensis at Harvard Forest. Four treatments (logging, girdling, hemlock control and hardwood control) have been applied and replicated in eight 0.81-ha plots. Salamanders were sampled under cover boards and using visual encounter surveys in June-July of 2013 and 2014. Removal of the hemlock canopy increased occupancy of P. cinereus but significantly reduced its estimated detection probability and abundance. Estimated abundance of N. v. viridescens also declined dramatically after canopy manipulations. Our results suggest that ten years after hemlock loss due to either the adelgid or pre-emptive salvage logging, and 50-70 years later when these forests have become mid-successional mixed deciduous stands, that the abundance of these salamanders likely will be less than 50% of their abundance in current, intact hemlock stands.
Phenology and Carbon Allocation of Roots at Harvard Forest 2011-2013
The objective of this study is to estimate the phenology and partitioning of C allocated belowground across the growing season at Harvard Forest in two hardwood stands dominated by Quercus rubra and Fraxinus americana, respectively, and one conifer stand dominated by Tsuga canadensis. The phenology of fine root production was characterized by multiple flushes of growth and mortality, especially in the red oak (Q. rubra) stand. Root exudation rate did not have a clear seasonal signal. The deciduous hardwood stands allocated C belowground earlier in the season compared to the conifer-dominated stand. Deciduous stands also allocated a greater proportion of total belowground C flux (TBCF) to root growth compared to the conifer-dominated hemlock (T. canadensis) stand. Of the three stands, red oak partitioned the greatest proportion of TBCF (~50%) to root growth, while hemlock partitioned the least.
Paleolimnology of Lakes in Central New England from 2000 BP to Present
Paleolimnological studies of three small watersheds in central New England were undertaken to determine the influence of deforestation and agriculture on lake systems, as well as the response of the lakes to agricultural abandonment and reforestation, or the cessation of disturbance. Sites were chosen to represent a range of past land-use activities, while keeping other site factors constant. The study was designed to complement the historical and paleoecological studies of the central Massachusetts area of Fuller et al. (1998) and Foster et al. (1998). Changes in terrestrial vegetation were documented using the pollen record from each lake, and changes in aquatic systems were documented through fossil chironomid assemblages (Chironomidae: Diptera) and sediment chemistry. Dated cores were analyzed for pollen, fossil chironomids, percent organic matter, carbon and nitrogen, and sedimentation changes. Increased sedimentation rates occurred in all lakes during the settlement period, and small increases in productivity changes resulted from the increased runoff. Productivity changes, as indicated by organic material, C:N ratios, and chironomid assemblages, are more pronounced in North Round and Wickett Ponds than in Pecker Pond, even though agricultural activity was most intense at Pecker Pond. North Round and Wickett Ponds are more shallow than Pecker, and were more affected by sediment and nutrient inputs from the watershed. North Round Pond was the least impacted site, with only minimal logging and no agriculture, but still significant changes occurred during the settlement period. The sedimentation rates and productivity continue to be higher than pre-settlement levels, indicating that the systems have not returned to pre-disturbance states. This is similar to the response of forest vegetation studied by Fuller et al. (1998) in the Central Massachusetts study. The low intensity agricultural practices of the 19th Century and small watershed sizes contributed to the f
Partitioning the Components of Soil Respiration in a Trenching Experiment at Harvard Forest 2011
Total soil respiration (Rt) is a combination of autotrophic (Ra) and heterotrophic respiration (Rh). We used a trenching method to sever the rooting system surrounding a plot to remove the Ra component within the plot. We used a custom-made automated chamber system to measure soil respiration within the trenched plot and the control in an oak dominated forest with the footprint of the LPH tower. 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.
Butterfly, Dragonfly and Damselfly Species at Harvard Forest 2015
I report on preliminary observations of butterflies in small meadows in the vicinity of “Harvard Farm” (formerly Petersham Country Club) in Petersham, MA, from 16-20 July 2015. I sampled butterflies at 10 locations over five days, visiting some areas twice. I documented (with digital photography) a total of 17 recognizable species/morpho-species, as well as 2-8 additional “grass skippers” which could not be identified to species. Initially I had planned to conduct a more organized survey, but most of the property had been grazed by the time I arrived in mid-July. This, combined with the late start date, meant that flowers – and nearly all butterflies – were absent at the Harvard Farm property during my visit. Instead, I opted to opportunistically sample several un-grazed meadows in the Petersham area, including North Common Meadow near the center of town and small meadows on Harvard Forest property, to develop a species list and photographic database of as many local butterflies as possible. From these surveys, the most numerous species were clouded/orange sulfur (Colias spp.; 34 individuals observed), followed by great spangled fritillary (Speyeria cybele; n = 32) and unidentified grass-skippers (various genera; n = 32). Moderately common species (n = 8-12) included Common wood-nymph (Cercyonis pegala), American copper (Lycaena phlaeas) and cabbage white (Pieris rapae); fewer than 4 individuals were recorded of: black/spicebush swallowtail (Papilio sp.), banded hairstreak (Satyrium calanus), gray hairstreak (Strymon melinus), azure (Celastrina ladon), eastern tailed-blue (Everes comyntas), pearl crescent (Phycioides tharos), eastern comma (Polygonia comma), Appalachian brown (Satyodes appalachia), northern pearly-eye (Enodia anthedon), and silver-spotted skipper (Epargyreus claras). These observations should be taken as preliminary, but may serve as a list of the most common and conspicuous butterfly taxa during mid-summer in the Petersham area, and could inform st
Hemlock Woolly Adelgid and Elongate Hemlock Scale Surveys in Connecticut and Massachusetts 1997-2011
In the eastern USA, eastern hemlock (Tsuga canadensis) is the host plant for two invasive insect species - hemlock woolly adelgid (Adelges tsugae) and elongate hemlock scale (Fiorinia externa). We observed the density of adult hemlock woolly adelgid and elongate hemlock scale on eastern hemlock branches on five occasions over 14 years at 142 stands across a latitudinal transect encompassing 7,500 km2 in Connecticut and Massachusetts to assess whether there is a difference in the response to abiotic conditions (winter temperature, summer temperature, summer precipitation) between the two species, and whether the distribution and abundance of each insect species is dependent on biotic interactions with the co-occurring insect species.
Long-term Stand Dynamics in Central Massachusetts 1500-2000
The long-term impact of human land-use is among the most important factors influencing the development of vegetation in New England, a region which experienced extensive agricultural clearance in the 19th century and subsequent reforestation during this century. We employed stand-level pollen stratigraphies and tree-ring chronologies to examine the post-settlement dynamics of hemlock stands which have never been pastured or plowed, representing among the least disturbed parts of the central Massachusetts landscape. Although the sites are currently dominated by large Tsuga canadensis individuals and give the impression of great age and stability, our results indicate that they have dynamic developmental histories driven by exogenous disturbance factors, including logging, forest pathogens, catastrophic wind disturbance, and fire. Sites containing pre-settlement pollen assemblages indicate stand compositions at this time which were substantially different from each other and from modern assemblages. Pollen assemblages similar to those of modern stands were not established in any of our sites until the 20th century and the mechanisms by which these assemblages arose was considerably different in each stand, indicating great flexibility of forest response to a variety of disturbance types.
Land-Cover Change Scenarios for Massachusetts 2010-2060
Working with a panel of practitioners and regional experts, we developed and analyzed four plausible but divergent land-use scenarios that depict the future of Massachusetts from 2010 to 2060. We simulated the land-use scenarios and their interactions with anticipated climate change by coupling statistical models of land use to the LANDIS-II landscape model and then evaluated the outcomes in terms of the magnitude and spatial distribution of (1) direct human uses of the landscape (residential and commercial development, agricultural, timber harvest), (2) ecosystem services (carbon storage, flood regulation, nutrient retention), and (3) habitat quality (forest tree species composition, interior forest habitat). Across all scenarios, conflicts occurred between dispersed residential development and the supply of ecosystem services and habitat quality. In all but the scenario that envisioned a significant agricultural expansion, forest growth resulted in net increases in aboveground carbon storage, despite the concomitant forest clearing and harvesting. One scenario, called Forests as Infrastructure, showed the potential for synergies between increased forest harvest volume through the sustainable practices that encouraged the maintenance of economically and ecologically important tree species, and carbon storage. This scenario also showed trade-offs between development density and water quantity and quality at the watershed scale. The process of integrated scenario analysis led to important insights for land managers and policymakers in a populated forested region where there are tensions among development, forest harvesting, and land conservation. More broadly, the results emphasize the need to consider the consequences of contrasting land-use regimes that result from the interactions between human decisions and spatially heterogeneous landscape dynamics.
Red-backed Salamanders as Indicators of Hemlock Forest Health at Harvard Forest 2014
Species that react quickly to ecological changes are useful indicators for assessing forest health. Red-backed salamanders (Plethodontid cinereus) may be used as an indicator species in declining hemlock forests, allowing for assessment of soil quality and forest health. We hypothesized that decline of hemlock stands due to the effect of hemlock woolly adelgid would negatively impact the abundance of red-backed salamanders by altering soil quality. In the Hemlock Removal Experiment at Harvard Forest, eight-0.8ha plots were treated either with girdling to simulate adelgid invasion, logging to simulate preemptive logging strategies, no treatment in hemlock areas, or no treatment in hardwood areas. Within these treatments in June and July of 2014, P. cinereus relative abundance was determined from coverboard surveys. Soil quality was determined from core samples. Bulk density, pH, carbon-nitrogen ratio, moisture, soil temperature, and litter depth were measured, and ordination was used to create an index of soil quality from these. There was a significant correlation between plot treatment and soil quality (p less than 0.05). Temperature, CN ratio, and pH influenced a strong significant negative correlation between soil quality and salamander abundance (pless than 0.05). Soil quality affected by hemlock decline influenced salamander abundance. These data suggest that we could gain an understanding of forest health and soil quality by examining salamander abundance. Assessing adelgid invasion can be difficult and objective, whereas salamander abundances are easily measured; therefore, we suggest that salamander abundances could be useful in assessing the health of hemlock forest ecosystems.
Soil Carbon in a Hemlock Stand Infected by Hemlock Woolly Adelgid at Harvard Forest since 2015
The main objective of this research is to study changes in soil carbon stocks (soil C, root biomass) and fluxes (soil respiration) in a hemlock stand that is currently infested by the hemlock woolly adelgid, and where trees are declining in vigor and dying off. Soil respiration is measured throughout the growing season using an automated system, which produces a long-term, high-temporal-resolution series of soil respiration over multiple locations. Soil carbon stocks and root biomass are estimated by sampling soil in multiple locations throughout the hemlock stand following the sampling design used by Serita Frey at Harvard Farm (“Conant plots”). The large number of samples will be used to determine how many should be resampled in the future to be able to determine if any difference in soil C content or root biomass is statistically significant. Soil and roots will be sampled every 5 to 10 years to evaluate the trends in soil carbon stocks during and after the decline of hemlock caused by the hemlock woolly adelgid infestation.
Landscape Phenology from Unmanned Aerial Vehicle Photography at Harvard Forest 2013
This data set contains orthophotos in the vicinity of the EMS tower at Harvard Forest, as well as the flight logs from the unmanned aerial vehicle (UAV) used to obtain the digital images used in orthophoto creation. Orthophotos were created by mosaicking approximately 200 JPEG images from each date of observation. The orthophotos cover the spatial extent of the 250 meter resolution MODIS pixel that contains the EMS tower. Land cover types in the area of photography include deciduous and evergreen forest, and wetlands. The research goal of data collection for this data set was to observe spatial variance in plant phenology. Therefore, photos were taken from before leaf out until after leaf drop. Orthophotos were collected approximately every 5 days during spring and weekly during fall; see filenames for specific dates. The nominal spatial resolution of the orthophotos is 6 cm, however due to various factors including inaccuracy of the onboard GPS, wind-blown motion of trees, the automated orthophoto mosaicking process, and user error in final georeferencing, image analysis has been conducted at 10 m resolution. The orthophotos are available as GeoTIFF files.
Metaproteomic Analysis of Sarracenia Purpurea Pitcher Fluid at Harvard Forest 2012-2017
Aquatic ecosystem enrichment can lead to distinct and irreversible changes to undesirable states. Understanding changes in active microbial community function and composition following organic-matter loading in enriched ecosystems can help identify biomarkers of such state changes. In a field experiment, we enriched replicate aquatic ecosystems in the pitchers of the northern pitcher plant, Sarracenia purpurea. Shotgun metaproteomics using a custom metagenomic database identified proteins, molecular pathways, and contributing microbial taxa that differentiated control ecosystems from those that were enriched. The number of microbial taxa contributing to protein expression was comparable between treatments; however, taxonomic evenness was higher in controls. Functionally active bacterial composition differed significantly among treatments and was more divergent in control pitchers than enriched pitchers. Aerobic and facultative anaerobic bacteria contributed most to identified proteins in control and enriched ecosystems, respectively. The molecular pathways and contributing taxa in enriched pitcher ecosystems were similar to those found in larger enriched aquatic ecosystems and are consistent with microbial processes occurring at the base of detrital food webs. Detectable differences between protein profiles of enriched and control ecosystems suggest that a time series of environmental proteomics data may identify protein biomarkers of impending state changes to enriched states.
Widespread Sampling Biases in Herbaria Revealed from Large-Scale Digitization 1656-2016
Non-random collecting practices may bias conclusions drawn from analyses of herbarium records. Recent efforts to fully digitize and mobilize regional floras offer a timely opportunity to assess commonalities and differences in herbarium sampling biases. We determined spatial, temporal, trait, phylogenetic, and collector biases in ~5 million herbarium records, representing three of the most complete digitized floras of the world: Australia (AU), South Africa (SA), and New England, USA (NE) We identified numerous shared and unique biases among these regions. Shared biases included specimens i) collected close to roads and herbaria; ii) collected more frequently during spring; iii) of threatened species collected less frequently; and iv) of close relatives collected in similar numbers. Regional differences included i) over-representation of graminoids in SA and AU and of annuals in AU; and ii) peak collection during the 1910s in NE, 1980s in SA, and 1990s in AU. Finally, in all regions, a disproportionately large percentage of specimens were collected by a few individuals. These mega-collectors, and their associated preferences and idiosyncrasies, may have shaped patterns of collection bias via ‘founder effects’. Studies using herbarium collections should account for sampling biases and future collecting efforts should avoid compounding these biases.
Phenology of Woody Species at Harvard Forest since 1990
Starting in the spring of 1990 we have observed the timing of woody vegetation development during the growing season. For the first twelve years (1990-2001) we observed bud break (50% leaf emergence) and leaf development (75% final size) on two to five permanently tagged individuals of 33 woody species at 3-7 day intervals from April through June. All individuals are located within 1.5 km of the Harvard Forest headquarters at elevations between 335 and 365 m, in habitats ranging from closed forest, through forest-swamp margins, to dry, open fields. For most species both overstory and understory individuals are represented. Bud break is defined as when 50% of the buds on the individual have recognizable leaves emerging from them. Leaf development (75%) is defined as when at least 75% of the leaves on the individual have reached 75% of their final (mature) size. This point is used rather than "fully developed" because the leaves are functional but still developing rapidly during this period, which permits better estimation of a date between observations. Flowering and fruit development are also recorded if they occurred during the observation period. Through 2001 these observations documented substantial (up to three weeks difference) inter-annual variation in the timing of leaf emergence (50%) and leaf development (75% final size), but good relative consistency among species and among individuals within species during these twelve years. Therefore, starting in 2002 we maintained the same observation protocol, but reduced the number of species observed to nine, including striped maple (Acer pensylvanicum), red maple (A. rubrum), sugar maple (A. saccharum), yellow birch (Betula alleghaniensis), beech (Fagus grandifolia), white ash (Fraxinus americana), witch hazel (Hamamelis virginiana), white oak (Q. alba) and red oak (Q. rubra). This subset of important, representative species allows us to continue to characterize leaf development each spring, and document inter-annu
Harvard Forest Climate Data since 1964
This dataset provides daily minimum, maximum, and mean air temperature and 24-hour precipitation data from Harvard Forest for long-term climate studies. It combines measurements from the original manual weather station (Shaler Met Station, 1964-2002, 42.53167 N, 72.18937 W, dataset HF000) with measurements from the current automated weather station (Fisher Met Station, since 2001, 42.53311 N, 72.18968 W, dataset HF001). Gaps in the Shaler data were filled using data from nearby stations. Data from a 12-month period when both stations were operational were used to adjust the Shaler data to account for differences in microclimate at the two sites. This dataset is updated annually.
Effects of Warming on Soil Microbial Oxidative Activity at Harvard Forest 2013
As Earth’s climate warms, the massive stores of carbon found in soil are predicted to become depleted, and leave behind a smaller carbon pool that is less accessible to microbes. At a long-term forest soil-warming experiment in central Massachusetts, soil respiration and bacterial diversity have increased, while fungal biomass and microbially-accessible soil carbon have decreased. Here, we evaluate how warming has affected the microbial community’s capability to degrade chemically-complex soil carbon using lignin-amended BioSep beads. We profiled the bacterial and fungal communities using PCR-based methods and completed extracellular enzyme assays as a proxy for potential community function. We found that lignin-amended beads selected for a distinct community containing bacterial taxa closely related to known lignin degraders, as well as members of many genera not previously noted as capable of degrading lignin. Warming tended to drive bacterial community structure more strongly in the lignin beads, while the effect on the fungal community was limited to unamended beads. Of those bacterial operational taxonomic units (OTUs) enriched by the warming treatment, many were enriched uniquely on lignin-amended beads. These taxa may be contributing to enhanced soil respiration under warming despite reduced readily available C availability. In aggregate, these results suggest that there is genetic potential for chemically complex soil carbon degradation that may lead to extended elevated soil respiration with long-term warming.
Atmospheric Oxygen and Carbon Dioxide at Harvard Forest EMS Tower since 2006
This archive features long-term measurements of the atmospheric mixing ratios of O2 and CO2 at two heights on the Harvard Forest EMS flux tower. The data fields include the time of data collection, the height from which the samples were drawn, the O2 mixing ratio and the CO2 mixing ratio.
Conservation and Economic Data for New England Towns 1990-2015
Land protection, whether public or private, is often controversial at the local level because residents worry about lost economic activity. We used panel data and a quasi-experimental impact-evaluation approach to determine how key economic indicators were related to the percentage of land protected. Specifically, we estimated the impacts of public and private land protection based on local area employment and housing permits data from 5 periods spanning 1990-2015 for all major towns and cities in New England. To generate rigorous impact estimates, we modeled economic outcomes as a function of the percentage of land protected in the prior period, conditional on town fixed effects, metro-region trends, and controls for period and neighboring protection. Contrary to narratives that conservation depresses economic growth, land protection was associated with a modest increase in the number of people employed and in the labor force and did not affect new housing permits, population, or median income. Public and private protection led to different patterns of positive employment impacts at distances close to and far from cities, indicating the importance of investing in both types of land protection to increase local opportunities. The greatest magnitude of employment impacts were due to protection in more rural areas, where opportunities for both visitation and amenity-related economic growth may be greatest. Overall, we provide novel evidence that land protection can be compatible with local economic growth and illustrate a method that can be broadly applied to assess the net economic impacts of protection.
Leaf Traits of Darlingtonia Californica in Oregon and California 2001
Scaling relationships among photosynthetic rate, foliar nutrient concentration, and leaf mass per unit area (LMA) have been observed for a broad range of plants. Leaf traits of the carnivorous pitcher plant Darlingtonia californica, endemic to southern Oregon and northern California, USA, differ substantially from the predictions of these general scaling relationships; net photosynthetic rates of Darlingtonia are much lower than predicted by general scaling relationships given observed foliar nitrogen (N) and phosphorus (P) concentrations and LMA. At five sites in the center of its range, leaf traits of Darlingtonia were strongly correlated with elevation and differed with soil calcium availability and bedrock type. The mean foliar N : P of 25.2 6 15.4 of Darlingtonia suggested that these plants were P-limited, although N concentration in the substrate also was extremely low and prey capture was uncommon. Foliar N : P stoichiometry and the observed deviation of Darlingtonia leaf traits from predictions of general scaling relationships permit an initial assessment of the "cost of carnivory" in this species. Carnivory in plants is thought to have evolved in response to N limitation, but for Darlingtonia, carnivory is an evolutionary last resort when both N and P are severely limiting and photosynthesis is greatly reduced.
Nitrogen Deposition and Pitcher Plant Morphology in Massachusetts and Vermont 1998-1999
Atmospheric transport and deposition of nutrients, especially nitrogen, is a global environmental problem with well-documented consequences for ecosystem dynamics. However, monitoring nitrogen deposition is relatively expensive, monitoring stations are widely spaced, and estimates and predicted impacts of nitrogen deposition are currently derived from spatial modeling and interpolation of limited data. Bogs are nutrient-poor ecosystems that are especially sensitive to increasing nutrient input, and carnivorous plants, which are characteristic of these widespread ecosystem types, may be especially sensitive indicators of N deposition. Botanical carnivory is thought to have evolved in nutrient-poor and well-lit habitats such as bogs because the marginal benefits accruing from carnivory exceed the marginal photosynthetic costs associated with the maintenance of carnivorous organs. However, the production of carnivorous organs can be a phenotypically plastic trait. The northern pitcher plant, Sarracenia purpurea, produces leaves specialized for prey capture and nutrient uptake (pitchers) and leaves that are more efficient at photosynthesis (phyllodia). We hypothesized that relative allocation to these two types of leaves reflects ambient nitrogen availability. We manipulated nutrient availability to plants with leaf enrichment and whole-plot fertilization experiments. Increased nitrogen, but not phosphorus, reduced production of pitchers relative to phyllodia; this result provided empirical support for the cost–benefit model of the evolution of botanical carnivory. Because this phenotypic shift in leaf production occurs in ecological time, our results suggest that S. purpurea could be a reliable and inexpensive biological indicator of nitrogen deposition rates. This suggestion is supported by field observations across a geographic gradient of nitrogen deposition.
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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)
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.