Data Documentation

General Information
Name of data set: SNR_Nels_VegMonitoring_2001_12

Name of data files in data set:
SNR_Nels_Burn.csv
SNR_Nels_Canopy.csv
SNR_Nels_Environment.csv
SNR_Nels_HerbShrub.csv
SNR_Nels_Phenology.csv
SNR_Nels_SpeciesList.csv
SNR_Nels_R_Code.R

Date the data set was last modified: 9 Oct 2017

Funder: Missouri Botanical Garden's Center for Conservation and Sustainable Development

How to cite data: Reid, J.L., N. J. Holmberg, M. Albrecht, S. Arango-Caro, O. Hajek, Q. Long, & J. Trager. 2020.
Annual understory plant recovery dynamics in a temperate woodland mosaic during a decade of ecological restoration.
Natural Areas Journal 40.

Description of data collected: These data and code represent vegetation changes in a restored woodland at Shaw Nature Reserve,
Franklin County, Missouri, USA. Shaw Nature Reserve comprises 10 sq-km of woodland, prairie, wetland, and display garden
in Missouri’s Ozark Border division. This study occurred in the Dana Brown Woods management unit. Soil depth across 
Dana Brown Woods is variable with exposed Ordovician dolomite on hillsides and deeper soil in stream valleys. Some 
sandstone is exposed in streambeds. The climate is temperate (hardiness zone 6a; USDA 2012); average Jan air temperature
was -1° C, and average July air temperature was 25° C in 2014-2015 (Smith unpubl. data). Mean annual precipitation in
nearby Pacific, MO was 1090 mm/y in 1981-2010 (NOAA 2012). At the outset of the study, in 2000, Dana Brown Woods was
a closed-canopy woodland with high density of eastern red cedar (Juniperus virginiana). The precise fire history for 
this management unit is not known, but it is likely that the last fire was prior to 1925. Cool season fire was applied 
to Dana Brown Woods five times between Nov 2001 and Jan 2010, and cedars were largely removed in 2005-2006. 

Methodology for data collection: To monitor the influence of restoration activities on herbaceous vegetation, 30 
permanent 50-m transects were established in 2000, one year prior to the first prescribed burn. Transects were 
selected by placing a grid over a topographical map and choosing grid coordinates from a random number table. 
Transects were evenly distributed among three identifiable plant communities: an upland community dominated by 
white oak (Quercus alba), a mesic slope community dominated by northern red oak (Q. rubra), paw paw (Asimina triloba),
and spicebush (Lindera benzoin), and an invaded community dominated by eastern red cedar (Juniperus virginiana). 
Transects were separated by =5 m and were selected to maximize elevational gradient. Slope and aspect were uncontrolled.
Vegetation was sampled in three strata: ground layer (<0.5 m height), shrub layer (0.5-3 m), and canopy. Ground and 
shrub layer plant abundance and cover were sampled twice per year (Apr, Jun) in five nested quadrats along each transect.
Ground layer quadrats were 0.5 sq-m, and shrub quadrats were 1 sq-m in Apr and 2 sq-m in Jun. Quadrats were offset by 
five meters between seasons to reduce impact on the vegetation. Herbaceous and shrub layer sampling were conducted in 
all years 2000-2012 except 2006, when there was little vegetation due to restoration activities. Canopy composition and
 diameters at breast height were sampled along each transect using a crown line-intercept technique (Cox 1980). Canopy 
sampling was conducted in 2000, 2004, 2007, and 2012. Following prescribed fires, the percentage of each transect 
that had burned was also estimated. Plants were initially identified using Steyermark (1963), and taxonomy was 
subsequently updated to Yatskievych (1999, 2006, 2013). Voucher specimens were deposited at Missouri Botanical Garden.
In 2016, Olivia Hajek (a Research Experience Undergraduate) collected environmental data for each quadrat. She measured elevation
using a Garmin GPSmap. She measured aspect using a compass. She measured slope using a clinometer; slope was measured over a 3-m
distance centered on the quadrat. To calculate a relative radiation index (RRI), we used the formula 
RRI = cos (180° – O) x sin ß x sin ' + cos ß x cos ', where O = aspect, ß = slope, and ' = latitude (Maren et al. 2015). Canopy
cover was estimated using a spherical densiometer. The percent of exposed rock in each quadrat was also recorded based on 
subjective evaluation on a rank-transformed scale with 0=0% cover, 1=0-5%, 2=5-25%, 3=25-50%, 4=50-75%, 5=75-95%, and 6=95-100%. 
Burned or cut Juniper stumps were counted within a 2.5-m radius centered on each herb quadrat.    

Data collector(s): Nels Holmberg, Olivia Hajek

Date of data collection: April-July 2000-2012, June-July 2016 (SNR_Nels_Environment.csv)

Where collected: Dana Brown Woods Management Unit, Shaw Nature Reserve, Franklin County, Missouri, USA

Person to contact with questions: Nels Holmberg (nholmbrg@fidnet.com) or Leighton Reid (j.leighton.reid@gmail.com)

Data entry

Software (including version #) used to prepare data set: Microsoft Excel 2007, R version 3.2.4

Data processing that was performed: Data were proofed for transcription errors. Plant classifications were changed to match
Yatskievych (1999, 2006, 2013). Data from 2000 were excluded due to incomplete sampling, except for SNR_Nels_Canopy.csv.
For SNR_Nels_Canopy.csv, canopy cover for R6 in 2000 is excluded because it is not equivalent to other years. On 2017-10-09,
JLR fixed some problems with shrub data identified by NH, and JLR also removed duplicate rows (>600).

Person/people who entered data: Christian Schwarz

Person/people who proofed data: Leighton Reid, Nels Holmberg

Person to contact with questions: Leighton Reid (j.leighton.reid@gmail.com)

Variables:
ABP = Plant species Annual (A), Biennial (B), or Perennial (P) [Factor]
ACRON = Plant species acronym [Factor]
Asp = Aspect (degrees from N) [Numeric]
Burn = Estimated percentage of each transect burned during prescribed fires [Numeric]
C = Coefficient of conservatism [Integer]; 99 = Adventive species
C34 = Photosynthetic system for grasses [Factor]. Sources: Baskin et al. (1995), Campbell (2004), Smith & Wu (1994), Towne (2002), Waller & Lewis (1979)
Cancov = Canopy cover (percent) [Numeric]
Cov = Percent Cover [Numeric]
D = Day [Integer]
DBH = Diameter at breast height (cm)[Numeric]
Elev = Elevation (m) above mean sea level [Numeric]
End = Last month of spore or pollen production [Integer]. Source: Yatskievych (1999, 2006, 2013)
Family = Plant family [Factor]
Genus = Plant genus [Factor]
H = Habitat [Factor] "J" = Juniper; "R" = Red oak; "W" = White oak
Int = Intercept or distance in meters along transect occupied by canopy cover of a given species [Numeric]
Jstump = Juniper stump density [Integer]
L = Layer [Factor] "H" = Herbaceous; "S" = Shrub
M = Month [Integer]
MO = Plant species wetness category [Factor]
Notes = Additional text clarifying data [Character]
NT = Plant species Native (Nt) or Adventive (Ad) [Factor]
PHYS = Plant species physiognamy [Factor]
Q = Quadrat [Integer] This is equivalent to the length (m) from the start of the transect
Rocks = Index of soil rockiness - see methods [Integer]
RRI = Relative radiation index - see methods [Numeric]
Ses = Season [Factor] "Sp" = Spring = April/May. "Su" = Summer = June/July
Slp = Slope measured in degrees over 3 m centered on the herb quadrat [Numeric]
Source = Plant species information source [Factor]. LT = Ladd & Thomas (2015). NH = Nels Holmberg expert opinion.
Species = Plant species [Factor]
Start = First month of spore or pollen production [Integer]. Source: Yatskievych (1999, 2006, 2013)
Stems = Number of stems [Integer]
T = Transect [Factor]
Y = Year [Integer]

Literature:
Baskin, J.M., Webb, D.H. & Baskin, C.C. 1995. A Floristic Plant Ecology Study of the Limestone Glades of Northern Alabama.
Bulletin of the Torrey Botanical Club 122: 226-242.
Campbell, J. 2005. Comparative ecology of warm-season (C4) versus cool-season (C3) grass species in Kentucky, with special 
reference to Bluegrass Woodlands. In:  Proceedings of the 4th Eastern Native Grass Symposium. University of Kentucky,
Department of Forestry. Lexington, Kentucky, pp. 95-115.
Ladd, D. & Thomas, J.R. 2015. Ecologist checklist of the Missouri flora for floristic quality assessment. Phytoneuron 12: 1-274.
Maren, I.E., Karki, S., Prajapati, C., Yadav, R.K., Shrestha, B.B.  2015.  Facing north or south:  does slope aspect impact 
forest stand characteristics and soil properties in a semiarid trans-Himalayan valley?”  Journal of Arid Environments 121:  112-123.  
Smith, M. & Wu, Y. 1994. Photosynthetic characteristics of the shade-adapted C4 grass Muhlenbergia sobolifera (Muhl.) Trin.:
control of development of photorespiration by growth temperature. Plant, Cell & Environment 17: 763-769.
Towne, E.G. 2002. Vascular plants of Konza Prairie Biological Station: an annotated checklist of species in a Kansas tallgrass
prairie. SIDA, Contributions to Botany 20: 269-294.
Waller, S.S. & Lewis, J.K. 1979. Occurrence of C3 and C4 photosynthetic pathways in North American grasses. Journal of Range
Management 32: 12-28.
Yatskievych, G.A. 1999. Steyermark's Flora of Missouri, revised edition. Missouri Department of Conservation with Missouri 
Botanical Garden Press, Saint Louis, Missouri.
Yatskievych, G.A. 2006. Steyermark's Flora of Missouri, revised edition. Missouri Botanical Garden Press with Missouri Department 
of Conservation, Saint Louis, Missouri.
Yatskievych, G.A. 2013. Steyermark's Flora of Missouri, revised edition. Missouri Botanical Garden Press with Missouri Department
 of Conservation, Saint Louis, Missouri.