Harvard Forest

Data Archive

HF355

Seedling Survey of the CTFS-ForestGEO Plot at Harvard Forest since 2017

Related Publications

Data

• hf355-01: taxonomic table (preview)
• hf355-02: seedling survey (preview)
• hf355-03: mass regressions (preview)
• hf355-04: basal diameters and dbh (preview)
• hf355-05: canopy photograph data (preview)

Overview

• Lead: Sydne Record
• Investigators: John Grady, Fiona Jevon
• Contact: Information Manager
• Start date: 2017
• End date: 2023
• Status: ongoing
• Location: Prospect Hill Tract (Harvard Forest)
• Latitude: +42.54 degrees
• Longitude: -72.18 degrees
• Elevation: 340 to 368 meter
• Datum: WGS84
• Taxa: Acer pensylvanicum, Acer rubrum, Amelanchier alnifolia, Amelanchier arborea, Betula alleghaniensis, Betula lenta, Betula papyrifera, Betula sp., Fagus grandifolia, Gaultheria procumbens, Hamamelis virginiana, Kalmia latifolia, Nyssa sylvatica, Picea abies, Picea rubens, Pinus strobus, Prunus serotina, Quercus rubra, Quercus velutina, Rhododendron prinophyllum, Sorbus americana, Tsuga canadensis, Vaccinium angustifolium, Vaccinium corymbosum, Vaccinium sp., Viburnum cassinoides, Viburnum lantanoides
• Release date: 2024
• Language: English
• EML file: knb-lter-hfr.355.4
• DOI: digital object identifier
• EDI: data package
• DataONE: data package
• Related links:
• Harvard Forest CTFS-ForestGEO Mapped Forest Plot since 2014
• Study type: long-term measurement
• Research topic: physiological ecology, population dynamics and species interactions
• LTER core area: primary production, population studies
• Keywords: aboveground biomass, abundance, canopy cover, community composition, demography, forest dynamics, seedlings, trees
• Abstract:

  Within a species, trees can vary in size by many orders of magnitude, from tiny seedlings to multi-ton adults. This intraspecific variation in tree size has important consequences for forest structure and function, as it governs patterns of tree abundance, growth rate and energy flux. Recent theoretical models make predictions about size-energy patterns of forests but available evidence indicates deviation from predictions for the smallest and largest trees. The goal of this project is to examine seedling and canopy tree demography at Harvard Forest and explore their theoretical implications. We will link early remote sensing data from the National Ecological Observatory Network (NEON) with boots-on-the-ground measurements at Harvard Forest plots. We will also fit demographic models of the trees of this forest in transition.

• Methods:

  Throughout the MegaPlot, 1m x 1m plots were set up, 81 plots (transects including plots 0101-0124, 1101-1124, 2101-2124 and 3101-3124) were set at 20 m intervals along transects running 460 m from location markers across the MegaPlot in a N-S orientation. Plots were named based on their proximity to markers previous placed within the MegaPlot at 20 m intervals. At the time the study commenced, most of the MegaPlot was represented by low-light conditions in the understory. To capture seedling responses to light variability, an additional 53 plots were selected from a stratified random sample of plots representing four light categories (Clark and Clark 1992). Each individual below 1 cm diameter at breast height was measured for height (length of the largest stem in multiple stemmed individuals) down to the nearest half-centimeter increment, tagged and subsequently identified down to the lowest possible taxonomic unit. In the case where one individual had multiple stems of notable size, ramets were counted as distinct individuals if and only if, the stem or stolon was buried under the ground. Individuals that were large enough, had their diameters measured at two different angles at the base of the stem to the nearest hundredth of a millimeter (smaller individuals would be easily damaged by the calipers).

  To convert height estimates into estimates of mass and basal diameter, ~15 individuals of the most prevalent species were harvested (removed from the ground at the base of the stem) from the Simes tract over the entire range of sizes that were observed within the MegaPlot (less than 1cm DBH). Once harvested, their height and basal diameter were determined (same methods were used as described above) and each plant was weighed to the nearest hundredth of a gram. Subsequently, these individuals were dried in a heating oven at 60 °C for a minimum of 72 hours, after which they were weighed to the nearest hundredth of a gram again to determine their dry biomass.

  To convert DBH measurements from the MegaPlot census to basal diameter for proper comparison with the seedling data, ~15 individuals of the most common species were non-destructively measured at both breast height (1.3 m) where possible and the plant’s base, to a minimum of the nearest 20th of an inch (measurements are converted into mm in the data file).

  Additionally, hemispherical canopy photos were taken for each plot (about 0.5 m above the plot) and analyzed for canopy openness using WinSCANOPY software. In the case where there were larger saplings covering much of the plot, individual photos were taken for the larger individuals at their crown level, in addition to the representative photo for the plot. Canopy photos were taken with a SONY ILCE-6000 ILCE-6000 v3.20 with settings provided by Regent Instruments Inc. in conjunction with WinSCANOPY software. Photos were taken on a self-leveling device and tripod such that the top of the camera was perpendicular to magnetic north. Most photos were taken on a cloudy day or within 3 hours of sunrise or sunset as to minimize glare from the sun, photos with glare were identified and removed manually from the dataset prior to submission. The WinSCANOPY software was used to conduct the analysis. Threshold settings for pixel classification was set to automatic, and all other settings were left untouched.

• Organization: Harvard Forest. 324 North Main Street, Petersham, MA 01366, USA. Phone (978) 724-3302. Fax (978) 724-3595.

• Project: The Harvard Forest Long-Term Ecological Research (LTER) program examines ecological dynamics in the New England region resulting from natural disturbances, environmental change, and human impacts. (ROR).

• Funding: National Science Foundation LTER grants: DEB-8811764, DEB-9411975, DEB-0080592, DEB-0620443, DEB-1237491, DEB-1832210.

• Use: This dataset is released to the public under Creative Commons CC0 1.0 (No Rights Reserved). Please keep the dataset creators informed of any plans to use the dataset. Consultation with the original investigators is strongly encouraged. Publications and data products that make use of the dataset should include proper acknowledgement.

• License: Creative Commons Zero v1.0 Universal (CC0-1.0)

• Citation: Record S. 2024. Seedling Survey of the CTFS-ForestGEO Plot at Harvard Forest since 2017. Harvard Forest Data Archive: HF355 (v.4). Environmental Data Initiative: https://doi.org/10.6073/pasta/6c4f69748959fff364ecf89fc293922f.

Detailed Metadata

hf355-01: taxonomic table

1. taxonCode: taxon code
2. latin: full scientific binomial name
3. genus: genus name
4. species: species name
5. family: scientific family
6. authority: authority for the identification, currently set to NA for all taxa
7. IDLevel: whether a TaxonCode can be ascribed to a single species or may represent multiple species. Based off Orwig et al., 2022.
   • multiple: multiple species
   • species: single species
8. synonyms: Latin name synonyms of the listed Latin name

hf355-02: seedling survey

1. coordinate: code denoting the 1m x 1m plot of the seedling. Can be used to link other data such as canopy photos and gps coordinates to individual locations. Coordinates are based on the quadrats used in the ForestGEO survey (e.g. Coordinate 0101 is near marker 0101).
2. color: tag color
   • BLU: blue tag
   • GRN: green tag
   • ORG: orange tag
   • RED: red tag
   • UNT: untagged, used to denote seedlings without a tag likely due to being killed by accident during the first observations
   • WHT: white tag
   • YLW: yellow tag
3. tag: tag number (UT means the individual was not tagged)
4. taxonCode: code for taxon assigned to the seedling ID. See hf355-01-taxa-codes.csv for definitions
5. yrFirstObs: year that the seedling is first observed or recorded. Note that this does not necessarily correspond to the year it germinated.
6. trueRecrt: whether or not the seedling is interpreted as being a “true recruit”. All seedlings first recorded in 2017 were recorded as 0 since this was the first year of the census. All subsequent years when an untagged seedling was encountered were set to 1 unless observations suggested otherwise (e.g. unexpected degree of secondary growth lacking cotyledons etc.).
   • 0: false
   • 1: true
7. seedlingID: unique code used to identify seedling
8. flag: whether or not the seedling needs to be inspected more closely upon next survey. Used to flag possible misidentifications, unusual data situations, etc.
   • 0: false
   • 1: true
9. status: current status of the seedling
   • ID: Invalid Data, seedlings outside of the plot or otherwise should be excluded from any analysis
   • IH: Invalid Herbaceous, previously tagged seedlings that upon a revisit are believed to be herbaceous and should be excluded from analysis
   • VA: Valid Active, seedlings that are actively in the survey and are still being searched for in the field
   • VG: Valid Graduated, seedlings that have survived to be greater than 1cm DBH, no longer active in the census
   • VI: Valid Inactive, seedlings that are no longer actively searched for in the field survey, due to being missing for more than 3 years, or the seedling’s tag has been removed upon death.
10. otherTagInfo: currently set to NA for all observations, meant for future expansion to include more tag information as different types of tags are introduced to the survey
11. yearOfOb: year of observation
12. alive: status of the individual
    • MISS: seedling was not found at plot (tag not encountered when plot surveyed). Quality warning: in 2022, MISS values not distinguished from NA
    • N: dead
    • NA: missing data, also used in years before the seedling was first observed
    • Y: alive
13. collector: initials of data collector
14. height: height of seedling (unit: millimeter / missing value: NA)
15. date: date of observation
16. sampled: whether or not the seedling was sampled (or an attempt to sample was made) during that yearOfOb
    • 0: seedling not sampled, and no attempt was made to sample it that year (e.g., seedling exited the census or was before the first observation of the seedling).
    • 1: True, seedling was sampled (or an attempt was made if not found)
17. notes: notes and comments about the seedling made in the field or made during data cleaning

hf355-03: mass regressions

1. genus: specimen genus
2. species: specimen species
3. binomial: Latin binomial
4. year: year of collection
5. date: date of collection
6. location_collected: where specimen was collected (either off of the ForestGEO MegaPlot or at the Simes Tract of Harvard Forest)
7. identifying_code: context specific identifying code of individual. Individuals measured in 2018 were harvested and thus this value was not recorded
8. basal_diameter1_mm: first basal diameter measurement (unit: millimeter / missing value: NA)
9. basal_diameter2_mm: second basal diameter measurement (unit: millimeter / missing value: NA)
10. avg_basal_diam_mm: midpoint of basal_diameter1_mm and basal_diameter2_mm (unit: millimeter / missing value: NA)
11. diameter_mm: diameter at 1.2 m (unit: millimeter / missing value: NA)
12. height_mm: height (unit: millimeter / missing value: NA)
13. wetmass_g: mass after collection (unit: gram / missing value: NA)
14. drymass_g: mass after drying (unit: gram / missing value: NA)
15. collectors: initials of who collected the data
16. notes: notes made by the collectors

hf355-04: basal diameters and dbh

1. genus: specimen genus
2. species: specimen species
3. binomial: Latin binomial
4. date: date of sample collection
5. basal_diameter1_mm: first basal diameter measurement (unit: millimeter / missing value: NA)
6. basal_diameter2_mm: second basal diameter measurement (unit: millimeter / missing value: NA)
7. avg_basal_diam_mm: midpoint of basal_diameter1_mm and basal_diameter2_mm (unit: millimeter / missing value: NA)
8. dbh1_mm: first diameter measured at 1.3 m (unit: millimeter / missing value: NA)
9. dbh2_mm: second diameter measured at 1.3 m (unit: millimeter / missing value: NA)
10. avg_dbh_mm: midpoint of dbh1_mm and dbh2_mm (unit: millimeter / missing value: NA)
11. collectors: initials of who collected the data (NR – Nia Riggins, JMR – Marcos Rodriguez)
12. notes: notes made by the collectors

hf355-05: canopy photograph data

1. file_name: name of the image file
2. year: year in which the photo was taken
3. analysis_date_time: time and date that the image was analyzed
4. datetime: date and time that the image was acquired
5. plot: plot number which the photo represents
6. included_individuals: individuals that the light measurements correspond to (see methods)
7. gap_fraction: proportion of open pixels, unweighted based on location (unit: dimensionless / missing value: NA)
8. openness: proportion of open pixels, weighted by location in photo (directly above pixels are weighted more) (unit: dimensionless / missing value: NA)
9. ppfd_directoverperday_mj_m2day: measurement of direct solar radiation experienced by the canopy (unit: megajoulePerMeterSquaredPerDay / missing value: NA)
10. ppfd_diffuseoverperday_mj_m2day: measurement of direct solar radiation experienced by the canopy (unit: megajoulePerMeterSquaredPerDay / missing value: NA)
11. ppfd_totaloverperday_mj_m2day: measurement of all solar radiation experienced by the canopy (unit: megajoulePerMeterSquaredPerDay / missing value: NA)
12. ppfd_directunderperday_mj_m2day: measurement of direct solar radiation experienced by the plot (unit: megajoulePerMeterSquaredPerDay / missing value: NA)
13. ppfd_diffuseunderperday_mj_m2day: measurement of indirect solar radiation experienced by the plot (unit: megajoulePerMeterSquaredPerDay / missing value: NA)
14. ppfd_totalunderperday_mj_m2day: measurement of all solar radiation experienced by the plot (unit: megajoulePerMeterSquaredPerDay / missing value: NA)
15. comments: comments made by data processor