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Understory vegetation of thermophilous oak forest (1-ha permanent plot near Němčičky, Czech Republic)

Source of data

Chudomelová, Zelený & Li (2019)

Description of the dataset

We established a square plot of 100 × 100 m with 100 subplots of 2 × 2 m. The subplots were organized in a regular grid with 10-m lags between adjacent subplots. At each 2 × 2 m subplot, we recorded a list of vascular plant species along with visual estimates of species cover using the nine-degree Braun-Blanquet scale (Westhoff & van der Maarel 1978). Woody seedlings and saplings were later excluded from the analyses. In the center of each subplot, we took a hemispherical photograph of the canopy at the height of 1.3 m (using Nikon Coolpix 4500 camera with FC-E8 fishey lens). We also measured the slope inclination (using Silva ClinoMaster), aspect (using compass) and relative elevation of each subplot using the Field-Map device (IFER, Ltd., Jílové u Prahy, Czech Republic) with accuracy up to 0.2 m. At four locations within each subplot, we measured the soil depth using 30 cm long iron probe, and collected a mixed soil sample from the top 5 cm.

Sampling design within the 1-ha permanent plot (from the Appendix B of Chudomelová et al. 2017).
An example of a 2 m × 2 m sampling plot (photo credit: David Zelený).


The study took place in a thermophilous oak forest dominated by Quercus petraea. The forest is located close to the village of Němčičky, south Moravia, Czech Republic, in low hills at the fringe of the flysch Carpathians (48.948° N, 16.837° E). The sampling area spreads over the upper part of an inconspicuous hill (322 m a.s.l.), in a forested complex surrounded by arable fields and pastures. The most prominent feature of the site is a pronounced fine-scale heterogeneity of soil pH and related variables (Ca and Mg concentration, conductivity, C:N). Although built of flysch, the hill is covered in partly decalcified loess deposits. The pH values can differ up to two units over a distance of 5 m (e.g. from about 5 to above 7) and the character of the ground herb layer obviously relates to them: patches with base-rich soil are densely overgrown by herb understorey, whereas patches with acid soil are almost bare. (From Chudomelová & Zelený, 2020).

Environmental variables

Name of variable Description
FIELD_N Field number (composed of X and Y coordinate separated by comma)
X X coordinate of the subplot
Y Y coordinate of the subplot
AUTOR Author of species composition record (Marketa Chudomelova, David Zeleny, Helena Prokesova)
TREE Presence of tree inside the plot (visual estimate)
MD Presence of deadwood (visual estimate)
Z Relative elevation [m]; within plot relative elevation measured by Field-Map device
ASPECT_NE Folded aspect [°]; difference from north-eastern direction
SLOPE Slope [°]; inclination measured by clinometer
RADIATION Radiation; computation based on field measurements of slope and aspect (McCune & Keon 2002, Eq. 3)
HEAT Heat load; computation based on field measurements of slope and aspect (McCune & Keon 2002, Eq. 3)
E3 Tree layer cover [%] (visual estimate)
E2 Shrub layer cover [%] (visual estimate)
COND_I Conductivity [μ]; measured in water extract
COND_II Conductivity [μ]; measured in water extract
pH Soil pH; measured in water extract
TC_S Total carbon []; measurement based on solid sample ignition
TOC Total organic carbon []; measurement from water extract
TC Total carbon []; measurement from water extract
IC Inorganic carbon []; measurement from water extract
TN Total nitrogen []; measurement from water extract
C/N C/N; ratio of total carbon and total nitrogen concentrations
Ca Ca []; concentration in water extract
Mg Mg []; concentration in water extract
K K []; concentration in water extract
Fe Fe []; concentration in water extract
P P []; concentration of PO43- in Mehlich III extract
Fe_M Fe []; concentration in Mehlich III extract
PCAN_OP Canopy openness [%]; percentage of open sky calculated from hemispherical photographs
PSIT_OP Site openness [%]; percentage of open sky given the influence of topographic shading, calculated from hemispherical photographs
LAI_4 Leaf Area Index 4 Ring; effective leaf area index integrated over zenith angles 0 to 60°, calculated from hemispherical photographs
LAI_5 Leaf Area Index 5 Ring; effective leaf area index integrated over zenith angles 0 to 75°, calculated from hemispherical photographs
TRA_DIR Direct transmitted radiation [MJ.m-2.d-1]; amount of direct solar radiation transmitted by the canopy, calculated from hemispherical photographs
TRA_DIF Diffuse transmitted radiation [MJ.m-2.d-1]; amount of diffuse solar radiation transmitted by the canopy, calculated from hemispherical photographs
TRA_TOT Total transmitted radiation [MJ.m-2.d-1]; the sum of direct and diffuse transmitted radiation, calculated from hemispherical photographs
PTRA_DIR Direct transmitted radiation [%]; percentage of direct radiation transmitted by the canopy from the amount of direct radiation above the canopy
PTRA_DIF Diffuse transmitted radiation [%]; percentage of diffuse radiation transmitted by the canopy from the amount of diffuse radiation above the canopy
PTRA_TOT Total transmitted radiation [%]; percentage of total radiation transmitted by the canopy from the amount of total radiation above the canopy

Species attributes (Ellenberg values, from Ellenberg et al. 1992)

SPE Species name (the same as in the “spe” sheet)
LIGHT Ellenberg indicator value for light
TEMP Ellenberg indicator value for temperature
CONT Ellenberg indicator value for continentality
MOIST Ellenberg indicator value for moisture
SOIL_REACT Ellenberg indicator value for soil reaction
NUTR Ellenberg indicator value for nutrients

Data for download

File name File type Description
nemcicky.xlsx Excel file Contains species × sample matrix, environmental variables, explanation of species abbreviations and metadata
nemcicky_spe.txt tab-delimited txt format Sample × species matrix (97 samples in rows, 274 species in columns)
nemcicky_env.txt tab-delimited txt format Environmental variable matrix (samples in rows, variables in columns)
nemcicky_ell.txt tab-delimited txt format Ellenberg indicator values for all species (species in rows, indicator values in columns)

Script for importing data into R

nemcicky_spe <- read.delim ('', row.names = 1)
nemcicky_env <- read.delim ('')
nemcicky_ell <- read.delim ('', row.names = 1)


  • Ellenberg, H., Weber, H.E., Düll, R., Wirth, V., Werner, W. & Paulissen, D. 1992. Zeigerwerte von Pflanzen in Mitteleuropa. 2nd ed. Scripta Geobotanica, 18: 1–248.
  • Chudomelová M., Zelený D. & Li C.-F. (2017): Contrasting patterns of fine-scale herb layer species composition in temperate forests. Acta Oecologica, 80: 24–31.
  • Chudomelová M. & Zelený D. (2020): Tracing the signs of local dispersal in the temperate forest understorey using spatially structured vegetation data. Journal of Vegetation Science, 31, 84–94.
  • McCune B. & Keon D. 2002. Equations for potential annual direct incident radiation and heat load. Journal of Vegetation Science, 13: 603–606.
en/data/nemcicky.txt · Last modified: 2022/04/09 14:31 by David Zelený

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