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The datasets in this repository include plant community surveys, hyperspectral reflectance data at the leaf and canopy level, leaf trait data, and soil chemistry data collected at five sites along an elevation gradient of 2400m-3500m in the Chilean Andes (33°S, 70°W). The purpose of this study was to evaluate the environmental drivers of community assembly processes along the elevation gradient.

Description of the Data and file structure

trait_dat_comb.csv
Summary of the data in this file: Leaf traits measured on individuals along an elevation gradient in Chile (33°S, 70°W). Traits were measured on fresh tissue using a spectroradiometer along the transect (every 0.5 m) using a SVC HR 1023i spectroradiometer and leaf clip foreoptic and calculated as spectral indices. In the case of leaf percent nitrogen, traits were predicted by spectral models developed from leaf nitrogen measured from dried leaf tissue.

Site_ID: elevation in m of the site and the transect number (elevation_transect)
species_name: Genus species
Elevation: elevation of the site in m
PRI: Photochemical reflectance index, estimated using spectral index (R531 - R570)/(R531 +R570) (Gamon, Serrano, and Surfus 1997)
ChlNDI: Chlorophyll A normalized difference index, estimated using spectral index (R750 - R705) /(R750 +R705) (Gitelson and Merzlyak 1994)
LMA: leaf mass per area, estimated using spectral index (R860/R1240) (Zhang, Li, and Zhang 2012)
leafNperc: percent nitrogen in the leaf tissue, predicted from spectra using models developed from spectra and measured leaf percent N from tissue collected from Chile

note: cells containing “?” are species we were not able to identify

Citations:
Gamon, J. A., L. Serrano, and J. S. Surfus. 1997. “The Photochemical Reflectance Index: An Optical Indicator of Photosynthetic Radiation Use Efficiency across Species, Functional Types, and Nutrient Levels.” Oecologia 112(4): 492–501.
Gitelson, Anatoly, and Mark N. Merzlyak. 1994. “Quantitative Estimation of Chlorophyll-a Using Reflectance Spectra: Experiments with Autumn Chestnut and Maple Leaves.” Journal of Photochemistry and Photobiology, B: Biology 22(3): 247–52.
Zhang, Qianxuan, Qingbo Li, and Guangjun Zhang. 2012. “Rapid Determination of Leaf Water Content Using VIS/NIR Spectroscopy Analysis with Wavelength Selection.” Spectroscopy (New York) 27(2): 93–105.

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enviro.var.csv
Summary of the data in this file: Soil properties and chemistry sampled from transects along an elevation gradient in Chile (33°S, 70°W).

Site_ID: elevation in m of the site and the transect number (elevation.transect)
Site: Elevation (m)
Water_content: gravimetric water content (g water/g soil)
pH: soil pH
Nitrogen: bulk nitrogen content (mg N/g soil)
Carbon: bulk carbon content (mg C/g soil)
CN_weight_ratio: bulk ratio of carbon to nitrogen in soil
N.Min.rate: rate of net nitrogen mineralization (ug N g Soil -1 d-1)

note: NA value indicates where we were not able to successfully acquire a pH value from the meter

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spectra.csv
Summary of the data in this file: Hyperspectral data measured on fresh leaf tissue along an elevation gradient in Chile (33°S, 70°W).
sample_name: ID of sample
Transect: Transect number
Site_ID: elevation in m of the site and the transect number (elevation_transect)
Elevation: Elevation of site (m)
species_name: species name
402.2-2399.4: spectral reflectance measured at a given wavelength (nm)

note: Cells containing “x” in the transect column indicates these were extra samples taken outside of the transects

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spectra_abundances.csv
Summary of the data in this file: Species abundance matrix of species counted along an elevation gradient in Chile (33°S, 70°W). Rows contain elevation sites in m, columns contain species names. Values indicate abundance of species at a given site.

note: cells containing “?” are species we were not able to identify

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ALLMB.CCESR.tre
Summary of the data in this file: Phylogenetic tree constructed using field-collected and herbarium samples.

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Transect_species.csv
Summary of data in this file: Surveys of plant species along an elevation gradient in the Chilean Andes

Date: date of observation
Site: Site number
Transect: transect number
Distance: meter number along the transect
Genus_species: Species name
code: species code used in survey
Location: site name
Elevation: elevation in meters
site_ID: elevation in m of the site and the transect number (elevation_transect)

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R scripts:
taxo_div_clean.R: Taxonomic diversity analysis (species richness, Shannon Index, ordination)
Phylo_div_clean.R: Phylogenetic diversity analysis (phylogenetic species richness, phylogenetic species evenness, ordination)
Blomberg_sK_clean.R: Calculate Blomberg’s K for traits to determine phylogenetic signal in traits. Adapted code from Jesus Pinto Ledezma: https://github.com/jesusNPL/PhyloSignal
FunDiv_clean.R: Functional diversity analysis (Functional dispersion, ordination)
SpecDiv_clean.R: Spectral diversity analysis (Spectral dispersion, ordination)
trait_soil and elevation.R: Analysis of plant traits across elevation and soil variables

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