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Stoichiometry of Bogs and Bog Plants in Massachusetts and Vermont 2002
Geographic trends in surface water chemistry and leaf tissue nutrients may reflect gradients of nutrient limitation and broad-scale anthropogenic inputs. In 24 bogs and poor fens in Massachusetts and Vermont, we measured nutrient and metal concentrations in pore-water and in leaf tissues of three common bog plants – leather leaf (Chamaedaphne calyculata), northern pitcher plant (Sarracenia purpurea), and peat moss (Sphagnum spp.). The concentrations of N, P, and K were low in leaf tissues of all three plant genera, as were the concentrations of many trace heavy metals, including Cr, Cu, Co, Cd, Mo, and Pb. Stoichiometric ratios of macronutrients (N:P, P:K, and N:K) in plant leaves suggested that plant growth in the sampled bogs was limited by P, or was co-limited by all three macronutrients. N:P and N:K nutrient ratios of Sarracenia purpurea and Sphagnum spp. increased toward the northwest and with elevation, but stoichiometric ratios of Chamaedaphne calyculata did not show any clear geographic trends. A principal components analysis revealed additional distinct differences among the three plant genera in their nutrient and metal concentrations. Furthermore, dissolved organic carbon (DOC), dissolved organic nitrogen (DON), Cu, Mg, NO3, Al, and K in porewater increased from the northwest (northwestern Vermont) to the southeast (Cape Cod and eastern Massachusetts near Boston), a gradient of increasing human population density and urbanization. In contrast, pore-water concentrations of SO4 and Al were highest in the western sites, and SO4 concentrations increased with elevations. These patterns may reflect atmospheric inputs from the Ohio River Valley leading to increased acidic deposition, causing Al to be leached from soils. Because bogs are naturally low in nutrients and do not receive substantial inputs from surrounding groundwater, the chemical signatures and nutrient stoichiometry of specific bog plant species or genera may provide useful indicators for assessing
Phenology and Vegetation Growth in Prospect Hill Soil Warming Experiment at Harvard Forest 1992-1993
As the mean annual temperature of northeast North America rises as a component of global climatic change, it is important to understand how the predominant vegetation of the region will be affected. Existing experimental and correlative evidence from field sites suggests that temperature rise will significantly modify soil processes, nutrient availability, and plant growth. We investigated the responses of temperate deciduous forest vegetation to artificial soil warming at 20 sampling dates during the 1992 and 1993 growing season. We explored whether soil warming measurably altered growth and the temporal dynamics of leaf and fruit production in 26 species of three contrasting plant growth forms (herbaceous perennials, shrubs, and canopy trees). We hypothesized that soil warming would exert differential effects on emergence, phenology, leaf expansion rates, growth, photosynthesis, and vegetative and sexual reproduction among species, with implications for changing community structure in these forests. Timing of leaf emergence and flower production was not affected by treatment in saplings; however, mature trees and shrubs leafed out slightly earlier and in larger numbers in heated plots. Soil warming significantly enhanced relative growth in stem diameters of woody plants, especially shrubs, in 1992. This effect was less pronounced in 1993. Species richness was lower in heated plots than in intact control plots in both years; disturbed but unheated control plots showed the lowest species richness of all plots. Changes in relative abundance of herbaceous species from 1992 to 1993 were not significantly affected by treatment. Rank abundances of species were more stable between years in the heated and disturbance-control plots than in the intact plots. Total density of herbaceous species was highest in heated plots during April and May of both years, reflecting greatly accelerated emergence of two dominant species, Maianthemum canadense and Uvularia sessilifolia, due t
Seed Dispersal and Seedling Establishment of Sarracenia Purpurea at Hawley Bog, MA 1998-1999
Plant ecologists continue to grapple with Reid’s paradox, the observation that dispersal distances of most herbs and trees are too limited to account for their recolonization of northern latitudes following glacial recession. As global climate changes and natural habitats become increasingly fragmented, understanding patterns of seed dispersal and the potential for long-distance colonization takes on new importance. We studied the dispersal and establishment of the northern pitcher plant Sarracenia purpurea, which grows commonly in isolated bogs throughout Canada and eastern North America. Median dispersal distance of S. purpurea is only 5 cm, which is insufficient to explain its occurrence throughout formerly glaciated regions of North America. Establishment probability of seeds in the field is approximately 5%, and juveniles are normally found clustered around adult plants. The large-scale population genetic structure of this species can be accounted for by rare long-distance dispersal events, but its predictable occurrence in isolated habitats requires additional explanation. Reid’s paradox remains an open question, and predicting long-range colonization into fragmented habitats by species with limited dispersal ability is a novel challenge.
Soil Microbial Community Effects on Quercus Rubra Seedling Survival at Harvard Forest 2016-2017
Feedbacks between plants and their soil microbial communities often drive negative density dependence in tropical forests, but their importance for tree demographics in temperate forests remains unclear. Additionally, the relative contribution of intraspecific seedling competition and soil pathogens to density-dependent patterns has rarely been assessed. We assessed how the soil microbial community influenced Quercus rubra seedling survival by growing seedlings in a greenhouse inoculated with soil collected from beneath conspecific and heterospecific mature trees. We found that seedlings grown with soil from beneath conspecific adults had a higher mortality rate than seedlings grown with soil from beneath heterospecific adults; therefore adult plant-soil feedbacks decrease seedling survival in Q. rubra.
Evaluation of Mask R-CNN Model for Counting Reproductive Structures of Six Plant Species 1895-2018
Phenology––the timing of life-history events––is a key trait for understanding responses of organisms to climate. The digitization and online mobilization of herbarium specimens is rapidly advancing our understanding of plant phenological response to climate and climatic change. The current common practice of manually harvesting data from individual specimens greatly restricts our ability to scale data collection to entire collections. Recent investigations have demonstrated that machine-learning models can facilitate data collection from herbarium specimens. However, present attempts have focused largely on simplistic binary coding of reproductive phenology (e.g., flowering or not). Here, we use crowd-sourced phenological data of numbers of buds, flowers, and fruits of more than 3000 specimens of six common wildflower species of the eastern United States (Anemone canadensis, A. hepatica, A. quinquefolia, Trillium erectum, T. grandiflorum, and T. undulatum} to train a model using Mask R-CNN to segment and count phenological features. A single global model was able to automate the binary coding of reproductive stage with greater than 90% accuracy. Segmenting and counting features were also successful, but accuracy varied with phenological stage and taxon. Counting buds was significantly more accurate than flowers or fruits. Moreover, botanical experts provided more reliable data than either crowd-sourcers or our Mask R-CNN model, highlighting the importance of high-quality human training data. Finally, we also demonstrated the transferability of our model to automated phenophase detection and counting of the three Trillium species, which have large and conspicuously-shaped reproductive organs. These results highlight the promise of our two-phase crowd-sourcing and machine-learning pipeline to segment and count reproductive features of herbarium specimens, providing high-quality data with which to study responses of plants to ongoing climatic change.
Impacts of Deer and Moose on Soil Carbon, Soil Respiration, and Root Biomass at Harvard Forest since 2017
Over the past decade, several deer and moose exclosures have been built at Harvard Forest to study the effect of ungulate browsing on tree regeneration, species diversity, and composition. We built on the existing infrastructure to study the impacts of deer and moose browsing on soil carbon stocks (soil C, root biomass) in regenerating forests.
Sap Flow in Red Maple and Red Oak in the Harvard Forest Snow Removal Study 2011
The climate is changing in mid and high latitude environments with the depth and duration of snowpack shrinking for many temperate forest ecosystems. A reduced snowpack and increased depth and duration of soil frost can injure fine roots, which are essential for plant water uptake. Water uptake is a crucial component of ecosystem functioning because this process strongly impacts other biological processes, such as primary productivity and nutrient uptake. We evaluated the effects of changing winter climate, including snow and soil frost dynamics, on rates of water uptake (i.e. sap flow) in a snow manipulation study at Harvard Forest. We had three reference and tree plots from which we removed snow and induced soil freezing.
Crown Geometry Measurements of 14 Species in the CTFS-ForestGEO Plot at Harvard Forest 2013
Tree crown geometry and height, especially when coupled with remotely sensed data, can aid in the characterization of tree and forest structure. In this study, we collected crown geometry data (tree height, crown radius, and crown depth) in order to develop mixed-effects model allometric equations. We leveraged the already existing Center for Tropical Forest Science (CTFS) and Smithsonian Institute’s Forest Global Earth Observatory (ForestGEO) MegaPlot on Prospect Hill at Harvard Forest, Massachusetts to apply allometric equations. In total, we sampled 374 trees across 14 species. Developed allometry was applied to 2014 CTFS-ForestGEO census data to develop allometric canopy height models, which were compared to a lidar canopy height model acquired by NASA’s G-LiHT.
Longitudinal Streamflow in Headwater Streams on Prospect Hill Tract at Harvard Forest 2003
We have initiated long-term monitoring of streamflow in headwater streams on the Prospect Hill Tract at the Harvard Forest. In addition, we have periodically recorded summer flow conditions longitudinally along the length of headwaters within Harvard Forest to obtain information about spatial heterogeneity of flow and of availability of aquatic habitat within these headwaters. In summer of 2003, we recorded streamflow each week at 20-m intervals along the length of two tributaries of Nelson Brook, Tributary A, from Route 32 to its outlet from the Black Gum Swamp, and Tributary B, from its junction with Tributary A to its origin in wetlands north of Prospect Hill Road.
Synthesis of Sarracenia Research in North America 1982-2018
This archive includes the raw data and code (R scripts) required to reproduce all of the analyses and figures in the book Scaling Sarracenia: Ecology of a Model System by Aaron M. Ellison and Nicholas J. Gotelli. The book is a synthesis of our 25 years of research on the northern (a.k.a. purple) pitcher plant Sarracenia purpurea viewed through the conceptual lens of “scale”: scaling ecological phenomena through levels of biological organization with a model organism, across time and space, and using macroecological relationships.
Age of Nonstructural Carbohydrates in Four Tree Species at Harvard Forest 2015
We estimated the mean age of sugars within and between different organs of four temperate tree species using the radiocarbon (carbon-14) bomb spike approach. Radial patterns of carbon-14 in the stemwood and coarse roots showed that sugars tended to became older when moving towards the pith.
Gene Expression and Tree Growth in the CTFS-ForestGEO Plot at Harvard Forest 2017-2019
Major goals in ecosystem ecology have been to scale from leaves to canopies and to determine whether individual-level, intra-species and inter-specific variation is critical for models projecting ecosystem processes now and in the future. The project is important in that it examines these issues in detail considering genotypes and levels of gene expression all the way up to canopy level CO2 flux. Ecological genomics and transcriptomics are nascent fields that have been primarily restricted to model species in natural and (mostly) controlled environments. To date, we have very few studies of non-model organisms in nature and/or studies of functional genomics through space and time. The research is producing extraordinarily rich datasets regarding the gene expression of trees across populations, through space in each population, across the growing season and across years and linking this information to growth and gas exchange. It will, therefore, provide tremendous insights into how much variation exists in nature thereby guiding sampling designs in future ecological 'omics projects. More importantly, it will provide unusually detailed phenotypic information for important non-model species that have large impacts on the CO2 flux of eastern US forests.
Soil Carbon and Nitrogen at the Harvard Farm at Harvard Forest since 2015
These data represent baseline soil bulk density and total soil carbon and nitrogen concentrations for the three grazing treatments at Harvard Farm: hay (no grazing), rotational grazing, and intensive grazing. These samples were collected at the beginning of the study, so any differences across plots or treatments are due to inherent soil variability at the site rather than the treatments themselves. These data were collected to establish the starting conditions with which to compare potential treatment effects at later sampling dates.
Leaf and Soil Nitrogen Following Lymantria dispar Defoliation in Central Massachusetts 2018-2019
In this study we investigated relationships between ecosystem nitrogen (N) cycling and tree defoliation during a recent 2015-2018 irruption of invasive Lymantria dispar caterpillars, which can cause tree stress and sometimes mortality following multiple years of defoliation. Nitrogen is a critical nutrient that limits the growth of caterpillars and plants in temperate forests. We assessed the associations between N concentrations, soil solution inorganic N availability, and defoliation intensity by L. dispar at the scale of individual trees in the Amherst, MA area and forest plots in the Quabbin Reservoir area.
Foundation Species in Forest Dynamics Plots of China 2004-2014
Foundation species structure forest communities and ecosystems but are difficult to identify without long-term observations or experiments. We used statistical criteria---outliers from size-frequency distributions and scale-dependent negative effects on alpha diversity and positive effects on beta diversity---to identify candidate foundation woody plant species in 12 large forest-dynamics plots spanning 26 degrees of latitude in China. We used these data to: [1] identify candidate foundation species in Chinese forests; [2] test the hypothesis---based on observations of a mid-latitude peak in functional trait diversity and high local species richness but few numerically dominant species in tropical forests---that foundation woody plant species are more frequent in temperate than tropical or boreal forests; and [3] compare these results with data from the Americas to suggest candidate foundation genera in Northern Hemisphere forests. Using the most stringent criteria, only two species of Acer, the canopy tree Acer ukurunduense and the shrubby treelet Acer barbinerve, were identified in temperate plots as candidate foundation species. Using more relaxed criteria, we identified four times more candidate foundation species in temperate plots (including species of Acer, Pinus, Juglans, Padus, Tilia, Fraxinus, Prunus, Taxus, Ulmus, and Corlyus) than in (sub)tropical plots (the shrubs or treelets Aporosa yunnanensis, Ficus hispida, Brassaiopsis glomerulata, and Orophea laui). Species diversity of co-occurring woody species was negatively associated with basal area of candidate foundation species more frequently at 5- and 10-m spatial grains (scale) than at a 20-m grain. Conversely, Bray-Curtis dissimilarity was positively associated with basal area of candidate foundation species more frequently at 5-m than at 10- or 20-m grains. Using either stringent or relaxed criteria supported the hypothesis that foundation species are more common in mid-latitude temperate forests. Com
Ants in an Induced Drought Experiment at the Caxiuana National Forest in Brazil 2011-2012
Environmental change scenarios caused by low precipitation forecast species loss in tropical regions. We used one year of data from a rainwater exclusion experiment in primary Amazonian rainforest to test whether induced water stress, and covarying changes in humidity, soil respiration, and tree species richness, size, and total biomass and its diversity affected species richness and composition (relative abundance) of ground-dwelling ants. Induced drought reduced ant richness, whereas increased humidity and variability in biomass increased it. Species composition differed between control and rainfall-excluded plots. Occurrence of many ant species was strongly reduced, but some generalist groups of ants were favored by induced drought. The expected loss of ant species and changes in ant species composition in tropical forests likely will lead to cascading effects on ecosystem processes and services they mediate.
Density Anomalies in White Pine at Harvard Forest 2019
The density of wood is a primary determinant of the amount of carbon sequestered in forests. For boreal and Mediterranean ecosystems, anomalies from the typical intra-annual density increase in radial growth of conifers are predominantly related to drought. We took 41 wood samples at breast height, ten additional samples near branches, and seven samples from the top of 41 white pines to determine the spatial distribution of density anomalies throughout the stem. We measured the ring width, density anomaly presence, position within a ring, and arc of density anomalies at multiple heights. Even in a mesic forest density anomalies in white pine are predominantly occurring during drier growing seasons. Moreover, we examined the spatial extent of density anomalies within the stems of white pines and discovered density anomalies are more likely to occur near branches, at the top of the tree, and in wider rings. Furthermore, the position of the density anomalies within the rings was remarkably consistent with the anomalies occurring roughly 80% into the fully formed ring at all heights for high-frequency years only as well as all years Density anomalies seem to be triggered by exogenous factors but their distribution within the stem varies along endogenous gradients, thus better understanding these systematic anomalies can help us to understand how wood formation has reacted and will respond to the environment and changes therein.
White Pine Girdling and Compression Experiment at Harvard Forest 2017-2019
Wood formation is a crucial process for carbon sequestration on land, yet how variations in phloem-transported carbon affect wood formation, respiration and nonstructural carbon pools remains poorly understood. To better understand the role of carbon supply on allocation to wood formation, we constrained phloem transport using girdling and compression around the stem of 40 mature white pines to monitor the effects of contrasting carbon supply (enriched above and reduced below the manipulations) on local wood formation and respiration, as well as on nonstructural carbon pools in needles, stems, and roots. This data set contains all data measured during the experiment. This includes wood anatomy, xylogenesis, stem respiration, nonstructural carbon measurements in coarse roots, stems and needles, as well as pre-dawn water potential measurements and pressure measurements from underneath the phloem compression collars. Furthermore, we provide allometric measurements for all trees. The code to process these data and reproduce our results is available in hf348-14-density-anomaly-analysis-code.zip. For more details pertaining to the methods see Rademacher et al. (2021).
Scaling Sarracenia in North America 1900-2100
Scaling in Ecology with a Model System synthesizes central theories from ecology, biogeography, and macroecology through the lens of scale and scaling across spatiotemporal extents and grains, levels of biological organization, and with dimensionless ratios. In this book, we link 25 years of detailed natural history observations and laboratory and field experiments on the “Sarracenia microecosystem” (the northern pitcher plant, Sarracenia purpurea, and its associated food web of microbes and macrobes) with new models and analyses to generate novel insights into ecophysiology and stoichiometry; demography and species distribution models; food webs and trophic dynamics; and tipping points and regime shifts. Our work addresses the Sarracenia microecosystem at a hierarchy of spatial scales: individual pitchers within plants, plants within bogs, and bogs within landscapes, all of which can be treated as replicate “island” ecosystems that can be studied throughout the United States east of the Mississippi River and Canada east of the Rocky Mountains. Through integrated studies of its proteomics, physiology, population dynamics, community ecology, and ecosystem processes, the Sarracenia microecosystem has emerged as a model system for experimental ecology. Our synthetic work clearly illustrates that working with the Sarracenia microecosystem can yield new results and understanding of the importance of ecosystem-wide disturbances and anthropogenically-driven environmental and climatic change. They also show that research with the experimentally tractable Sarracenia microecosystem proceeds much more rapidly than studies of larger, more slowly changing ecosystems such as forests, grasslands, lakes, and streams that are more difficult to replicate and experimentally manipulate.
Ants of the Adirondack Mountains High Peaks 2016
The ants of the Adirondack Mountains are rarely sampled, and it was of interest to inventory their diversity as part of a general biodiversity survey of the Adirondack Park in New York State. A first set of collections were done in 2016 in the “High Peaks” region (mountains over 1200 meters (4000 feet) high). Ants were collected haphazardly from nests encountered by Adirondack Mountain trail stewards during June and July 2016 when they were doing regular botanical inventories and trail maintenance. Eleven species were collected, with the cold-climate species Formica neorufibarbis and Camponotus herculeanus accounting for 75% of the nests encountered. The species composition of ants in the Adirondack High Peaks is similar to that of other alpine and subalpine habitats in adjacent New England.
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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.