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Plant biomass dynamics following logging, burning, and thinning in Watersheds 6 and 7, Andrews Experimental Forest, 1979 to 2021
Watersheds 6 (WS06) and 7 (WS07) at the HJ Andrews are part of a three-watershed study initiated in the 1970’s to examine the response of hydrology and forest vegetation to logging. In 1974, Watershed 6 was clearcut logged; Watershed 7 was shelterwood cut, leaving 75-100 overstory trees per hectare (comprising about 40% of the original basal area). A nearby watershed (WS08) serves as an unlogged control. In 1975, all of Watershed 6 and the portion of WS07 below the road were broadcast-burned. In 1976, both watersheds were planted with Douglas-fir seedlings. Natural regeneration of Douglas-fir and western hemlock also established. In 1984, the remnant overstory trees in WS07 were harvested, and in 2001 the young stand in WS07 was thinned to about 550 trees per hectare. The thinning was not planned but provides an interesting twist to the study. The watersheds are located along the northern boundary of the HJA off the 327 and 328 roads, at elevations ranging from 850 to 1,160 m. Initial vegetation measurements were taken in the summer of 2002 in watersheds 6 and 7 for the purpose of characterizing plant succession after thinning in a small, high-elevation watershed. Understory vegetation plots are remeasured at approximately 6 year intervals.
Above ground plant biomass and leaf area of moist acidic tussock tundra 1981 experimental site (MAT81), Arctic LTER, Toolik Lake, Alaska.1995.
Above ground plant biomass and leaf area were measured in a tussock tundra experimental site. The plots were set up in 1981 and have been harvested in previous years (See Shaver and Chapin Ecological Monographs, 61, 1991 pp.1-31).
Long-term monitoring of seven high marsh plant mixtures on Sapelo Island GA
We set up plots (1x2m) in 1996 in mixtures or on vegetation borders at three sites. We set up 16 plots for each of seven mixtures - Marsh Landing (Juncus-Meadow, Spartina-Meadow, and Spartina-Batis mixtures), Teal Boardwalk (Juncus-Spartina mixture) and Shell Hammock (Juncus-Spartina, Juncus-Meadow, and Spartina-Meadow mixtures). Half were watered with fresh water 3 times per week (W) and half were controls (C). Watering stopped in April 2000. Plots were monitored to document changes in plant community composition (percent cover) over time.
Disturbance to monitoring plots at Altamaha River Plant Transition Sites SCSA, ZSC1, and ZSC2 from 2013 to 2025.
We established permanent vegetation monitoring plots at Altamaha River plant transition sites in 2012. Starting in 2013, when we recorded plant sizes, we also noted any disturbance to the plots. Plots were scored as normal (no visible disturbance), disturbed by wrack (wrack present in plots and stems dead or broken), disturbed by snails (>100 Littoraria per square meter and plant biomass low), disturbed by pigs (animal trail through the plot), initial slump (plot at the creekbank sliding into the creek based on movement of pvc poles or formation of a crevasse), and terminal slump (plot had slid far enough down that vegetation had drowned). Plots that experienced terminal slump or could not be found for any reason were scored as lost. Lost plots were replaced with a new plot in the same general area with the plot code incremented by 10. For example if plot 3 was lost, it was replaced by 13, and then in turn by 23.
GCE-LTER Altamaha River Plant Community Monitoring Survey in October 2021
A quadrat survey was conducted in October 2021 to measure the species and size distribution of plants at 3 sampling sites on the creekbank of the Altamaha River. The sites were chosen to capture the transition from Spartina alterniflora to Spartina cynosuroides (site SCSA) and the transition from Spartina cynosuroides to Zizaniopsis miliacea (sites ZSC1 and ZSC2). The quadrats were established as permanent plots in October 2012 by placing PVC stakes along the creekbank at each site. Plots were evenly spaced, but were not randomly located because the goal was to start with mixtures of vegetation in most of the plots, and vegetation was distributed in patches along the creekbanks. Therefore, these plots provide useful measures of vegetation change, but are not a random sample of the vegetation at the site. Plots will be replaced each year as necessary to replace any lost to disturbance. The plots were visually surveyed and the species, shoot height, and flowering status was recorded individually for each shoot over 10 cm in height present in each plot. Observations from plots exhibiting signs of disturbance were noted in a separate data set. This survey will be repeated annually to assess changes in plant distribution and biomass in relation to environmental changes documented by other GCE LTER monitoring efforts.
GCE-LTER Altamaha River Plant Community Monitoring Survey in October 2022
A quadrat survey was conducted in October 2022 to measure the species and size distribution of plants at 3 sampling sites on the creekbank of the Altamaha River. The sites were chosen to capture the transition from Spartina alterniflora to Spartina cynosuroides (site SCSA) and the transition from Spartina cynosuroides to Zizaniopsis miliacea (sites ZSC1 and ZSC2). The quadrats were established as permanent plots in October 2012 by placing PVC stakes along the creekbank at each site. Plots were evenly spaced, but were not randomly located because the goal was to start with mixtures of vegetation in most of the plots, and vegetation was distributed in patches along the creekbanks. Therefore, these plots provide useful measures of vegetation change, but are not a random sample of the vegetation at the site. Plots will be replaced each year as necessary to replace any lost to disturbance. The plots were visually surveyed and the species, shoot height, and flowering status was recorded individually for each shoot over 10 cm in height present in each plot. Observations from plots exhibiting signs of disturbance were noted in a separate data set. This survey will be repeated annually to assess changes in plant distribution and biomass in relation to environmental changes documented by other GCE LTER monitoring efforts.
GCE-LTER Altamaha River Plant Community Monitoring Survey in October 2023
A quadrat survey was conducted in October 2023 to measure the species and size distribution of plants at 3 sampling sites on the creekbank of the Altamaha River. The sites were chosen to capture the transition from Spartina alterniflora to Spartina cynosuroides (site SCSA) and the transition from Spartina cynosuroides to Zizaniopsis miliacea (sites ZSC1 and ZSC2). The quadrats were established as permanent plots in October 2012 by placing PVC stakes along the creekbank at each site. Plots were evenly spaced, but were not randomly located because the goal was to start with mixtures of vegetation in most of the plots, and vegetation was distributed in patches along the creekbanks. Therefore, these plots provide useful measures of vegetation change, but are not a random sample of the vegetation at the site. Plots will be replaced each year as necessary to replace any lost to disturbance. The plots were visually surveyed and the species, shoot height, and flowering status was recorded individually for each shoot over 10 cm in height present in each plot. Observations from plots exhibiting signs of disturbance were noted in a separate data set. This survey will be repeated annually to assess changes in plant distribution and biomass in relation to environmental changes documented by other GCE LTER monitoring efforts.
GCE-LTER Altamaha River Plant Community Monitoring Survey in October 2024
A quadrat survey was conducted in October 2024 to measure the species and size distribution of plants at 3 sampling sites on the creekbank of the Altamaha River. The sites were chosen to capture the transition from Spartina alterniflora to Spartina cynosuroides (site SCSA) and the transition from Spartina cynosuroides to Zizaniopsis miliacea (sites ZSC1 and ZSC2). The quadrats were established as permanent plots in October 2012 by placing PVC stakes along the creekbank at each site. Plots were evenly spaced, but were not randomly located because the goal was to start with mixtures of vegetation in most of the plots, and vegetation was distributed in patches along the creekbanks. Therefore, these plots provide useful measures of vegetation change, but are not a random sample of the vegetation at the site. Plots will be replaced each year as necessary to replace any lost to disturbance. The plots were visually surveyed and the species, shoot height, and flowering status was recorded individually for each shoot over 10 cm in height present in each plot. Observations from plots exhibiting signs of disturbance were noted in a separate data set. This survey will be repeated annually to assess changes in plant distribution and biomass in relation to environmental changes documented by other GCE LTER monitoring efforts.
Baseline Plant Abundances on Garlic Mustard Experiment Plots at Harvard Forest 2013
This is a five year project that investigates the reassembly of soil fungi and native plants in forests affected by biological invasion. The experiment brings together regional land managers to create comparative eradications of garlic mustard at nine distinct sites along a natural climate and nitrogen deposition gradient in New England. This dataset represents baseline plant abundances from 2013 at nine study plots in Harvard Forest. Species richness, Shannon diversity, and Pielou’s evenness were not different between invaded and non-invaded plots at Harvard Forest.
Assessing Plant Phenological Patterns in the Eastern United States Over the Last 120 Years
Phenology is a key biological trait of an organism’s success and is one of the best indicators of its response to recent climate change. Plants are among the most well-studied organisms in this regard, but observational data bearing on this topic are largely restricted to woody species of the northern hemisphere, mostly from ca. the last three decades. Recent research has demonstrated that mobilized online herbarium specimens provide important, albeit mostly neglected, information on plant phenology. Here, we use the web tool CrowdCurio to crowdsource phenological data from more than 10,000 herbarium specimens representing 30 flowering plant species broadly distributed across the eastern United States. Our results, spanning 120 years and generated from over 2,000 crowdsourcers, clarify numerous aspects of plant phenology. First, they reveal that plant reproductive phenology is significantly advancing in response to warming, which is consistent with previous studies. Second, among those species with broad latitudinal ranges, populations from more southern latitudes are significantly more phenologically sensitive to temperature than those from northern populations. Last, contrary to some recent findings, plants in warmer, less variable climates may be much more dynamic, on average, in their phenological sensitivity. Our results are robust to a variety of confounding factors and span large phylogenetic distances and myriad life histories. These may represent more global trends in the latitudinal gradient of phenological response with myriad potential ecological and evolutionary consequences, and leads us to hypothesize that phenological sensitivity across species' ranges is driven by adaptation to local climates.
Leaf and Flower Phenology of Woody Plant Species at Harvard Forest and Southern Quebec 2015
Accurate predictions of spring plant phenology with climate change are critical for projections of growing seasons, plant communities and a number of ecosystem services, including carbon storage. Progress towards prediction, however, has been slow because the major cues known to drive phenology – temperature (including winter chilling and spring forcing) and photoperiod – generally covary in nature and may interact, making accurate predictions of plant responses to climate change complex and nonlinear. Alternatively, recent work suggests many species may be dominated by one cue, which would make predictions much simpler. Here, we manipulated all three cues across 28 woody species from two North American forests. Study sites were Harvard Forest and St. Hipplolyte, Quebec. Species were selected for this study based on their prevalence at the study sites; 28 species are included in this study. At each site, multiple cuttings of six or more representative individuals were collected. In total, we tracked the phenology of 2,137 cuttings from 275 individual source plants. All species responded to all cues examined. Chilling exerted a strong effect, especially on budburst (-15.8 d), with responses to forcing and photoperiod greatest for leafout (-19.1 and -11.2 d, respectively). Interactions between chilling and forcing suggest that each cue may compensate somewhat for the other. Cues varied across species, leading to staggered leafout within each community and supporting the idea that phenology is a critical aspect of species’ temporal niches. Our results suggest that predicting the spring phenology of communities will be difficult, as all species we studied could have complex, nonlinear responses to future warming.
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
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.
Root Systems of Individual Plants Worldwide 2022
The above- and below-ground sizes and shapes of plants strongly influence plant competition, community structure, and plant-environment interactions, but the plant size and shape across climate regimes remain incompletely understood. In this study I seek to understand how plant geometries respond to varying climates via trade-offs in shoot height and width, and root depth and spread. I more than doubled the Root Systems of Individual Plants (RSIP) database to contain 5,647 observations, to our knowledge the largest database describing the maximum rooting depth, lateral spread, and shoot size of terrestrial plants in the world. Shoot size and root system size strongly covary. Across climatic gradients woody plants show deeper-narrower root systems in arid climates and taller shoots in humid climates. Phylogeny greatly influences shoot size. Rooting depth is primarily influenced by climate seasonality and lateral root spread is strongly influenced by shoot size. Using our newly expanded global database I found that shoot size covaries strongly with rooting system size; however, these relationships are not static across the climate space, as the geometries of plants shift considerably.
Plant species-level responses to functional group and species removals in biodiversity experiment plots at the Jornada Basin LTER site, 1999
This dataset contains individual species size data in vegetation plots that have had various plant functional groups or species experimentally removed at the Jornada Basin LTER site in southern New Mexico, USA. This data was collected with the objective to distinguish the differential effects of plant community biomass, functional groups, and biodiversity within functional groups on ecosystem and plant community function. To make these distinctions, treatments were established by the selective removal of plant species or functional groups within experimental plots. There are eight treatments: control (C, no removals); four functional group removal treatments (PG, perennial grass removed; S, shrubs removed; SSh, subshrubs removed; Succ, succulents removed), and three species richness manipulation treatments. Richness manipulations included a simplified treatment (Simp), where only the single most abundant species of each growth form is preserved and all other species in the growth form are removed, a reduced‐Larrea treatment (rL), where the Larrea is assumed to be the dominant and is removed while minority components remain, and a reduced-Prosopsis treatment (rP), where Prosopis rather than Larrea is removed as the shrub dominant. In 1999, this pilot study attempted to assess individual species responses of representative individuals in these treatments. Ten randomly selected individuals of eight plant species were measured in each experimental plot, and this dataset reports volumetric data (diameters and height) for each. The study was designed as an individual-based complement to the transect data in EDI dataset knb-lter-jrn.210121001 but was not continued past 1999. This dataset is complete.
Plant and litter cover estimates derived from overhead microplot photos in the Cross-Scale Interactions Study (CSIS) at Jornada Basin LTER, 2013-ongoing
This dataset contains plant and litter cover estimates derived from overhead photos collected from microplots in a long-term experiment (2013-present) of cross-scale interactions (CSIs) at the Jornada Basin LTER site in southern New Mexico, U.S.A. Experimental treatments were initiated in 2013 at 15 experimental blocks, each with 4 treatment plots: plant-scale herbicide of mesquite shrubs, patch-scale connectivity modifiers (ConMods), herbicide + ConMods, control without manipulations. Repeat, overhead (downward-looking) photographs of ten "microplots" in each plot were taken for estimation of litter, soil, and vegetation cover in the experimental treatment and control plots over time. Photographs were rotated and then cropped to provide standardized areas, and then were analyzed with USDA SamplePoint software to determine coverage by ~27 plant, litter or other cover classes on a 100 point grid. Raw and corrected cover estimates are provided. This study is ongoing and new data will be added annually. Cover estimates are derived from photos in EDI dataset knb-lter-jrn.210413004.
GLBRC Aboveground Plant Biomass at the Kellogg Biological Station, Hickory Corners MI (2008 to 2023), and the Arlington Research Station,Arlington, WI (2008 to 2014)
Dataset Abstract Aboveground biomass of BCSE herbaceous perennial crop treatments (G4 starting in 2021, G5-G7, G9-G10). Peak biomass samples were sorted to species from 2009-2017 but are left “unsorted” from 2018 onward. original data source http://lter.kbs.msu.edu/datasets/82
Plant species list for Niwot Ridge and Green Lakes Valley, 1970 - ongoing.
A plant species list was created for Niwot Ridge and Green Lakes Valley from species identified in those areas by NWT scientists, working primarily at the Saddle and Martinelli sites. Additions to this list included species identified by Komarkova (1979) in the Indian Peaks Wilderness area but not on Niwot Ridge or in the Green Lakes Valley because of the likelihood that those species might exist within the LTER research area. Additions to the list were also provided by Terry Theodose, Leeanne Lestak, Teresa Nettleton, Susan Sherrod, Laura Mujica-Crapanzano (2004), Hope Humphries (2006), and Jane G. Smith (2019-2025). The list was revised to remove duplicate entries, correct typos, and resolve synonymy problems. Species and non-species categories received USDA PLANTS database names and codes.
Bridging data silos to holistically model plant macrophenology data, Contiguous United States, 2013-2021
Phenological responses to climate change can have dire implications for ecosystem functions. Despite the availability of diverse datasets (e.g., herbarium specimens, community science initiatives, observatory networks, and remote sensing), holistic modeling of plant events across scales remains limited due to fragmented data and disciplinary silos. This is an important topic that has been overdue for attention. Here we use two different plant phenological datasets, herbarium and USA-NPN (includes NEON), to look at the overall flowering period of Acer rubrum between 2013-2021, distributed across the Contiguous United States. We harmonize the data to demonstrate its use to leverage the spatial and biological organizational scales at which these data are captured. Both datasets include phenophase status (presence or absence) across the flowering season (day of year). These harmonized data exemplify their usefulness to holistically model plant phenology using an integrated species distribution model framework, while accounting for the heterogeneity across data types (presence-only, presence-absence). These data can be used to explore general questions about intraspecific synchrony of Acer rubrum flowering phenology across populations, or questions with coarser scales of interest (e.g., community level, global scales).
Demographic census data for four perennial plants under experimental pollination treatments
These demographic data were collected to measure the effects of manipulated pollination treatments on the population dynamics of four iteroparous perennial plant species: Delphinium nuttallianum (Ranunculaceae), Hydrophyllum fendleri (Boraginaceae [Hydrophyllaceae]), Erigeron speciosus (Asteraceae), and Potentilla pulcherrima (Roseaceae). The pollination treatments consisted of Control corresponding to ambient pollination, Reduced for which 50% of open flowers on each individual were enclosed in mesh to exclude pollinators, Supplemented for which all receptive flowers were hand pollinated with outcross pollen, and Variable for which individuals received the Reduced treatment in ca. 50% of years. The full life cycle was characterized from at least four annual demographic censuses of tagged plants between 2017-2022, germination rates estimated in seed addition plots, and soil seed bank survival estimated from buried seed bags.
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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.