DOI: 10.5281/zenodo.13329229
title: Selected data sets for Marsh et al. 2024 'Tropical forest clearance impacts biodiversity and function whereas logging changes structure'

description: Data sets used in the for the manuscript Marsh et al. 2024 'Tropical forest clearance impacts biodiversity and function whereas logging changes structure'. The DOIs that link to all other data sets used in the publication are available in Tables S2-5 of the supplementary information. The z-score standardised data, and outputs of RMarkdown documents outline all the steps in the processing and analysis of the data are available at https://zenodo.org/uploads/13161799.

 

This repository contains data used for:

Mean canopy height

Canopy height and vertical profiles of forest structure were compiled using airborne remote sensing with LiDAR collected by NERC’s Airborne Research Facility (ARF) in November 2014, using a Leica ALS50-II LiDAR. A Beer-Lambert approximation was used to convert point clouds to plant area density (PAD) distributions, a similar measure to leaf-area index, but where methods do not distinguish between leaves and branches or trunks. LiDAR measurements for the carbon plots were converted to rasters with 0.5 × 0.5 m cell size. Plots were rotated to a North-South axis if necessary

Spectral diversity

Spectral measurements were made on five leaves attached to tree branches used to measure leaf chemical traits. Leaves were randomly selected but we avoided damaged and young plant material to avoid potential confounding factors. Reflectance spectra (350–2500 nm) were acquired using a FieldSpec 4, produced by Analytical Spectral Devices (ASD, Boulder, Colorado, USA). The spectroradiometer's contact probe was mounted on a clamp and firmly pushed down onto the sample against a black background so that no extraneous light was included in the measurement. Spectral measurements were taken halfway between the petiole and leaf tip, and between the main vein and the leaf edge, with the abaxial surface pointing towards the probe. The readings were calibrated against a Spectralon white reference panel every five samples. Leaf reflectance measured at 430 nm, 660 nm, 1450, 1980 nm and 2350 nm align closely with absorption features for pigments, water content, proteins and cellulose. Spectral diversity calculated from these absorption features can provide an integrated measure of the functional trait variability within plant communities and may be used as a proxy for functional diversity.

 

Liana abundance

Percentage liana cover for large canopy and emergent trees. The four quadrants of the canopy were scored as 0 (no lianas), 1 (1-20%), 2 (20-40%), 3 (40-60%), 4 (60-80%) and 5 (80-100%).

 

Leaf-area index

Leaf area index (LAI) for carbon plots was derived from hemispherical photos (Sigma 8mm SRL fish eye lens and Canon EOS 600D digital camera, mounted on a tripod at 1 m height). Between 5-27 photos were taken over time in each subplot. Images were processed with Hemisfer® software (www.wsl.ch/dienstleistungen/produkte/software/hemisfer/index_EN). LAI was calculated with the method by Thimonier et al. (2010) European Journal of Forest Research 129, 543–562 (2010), with a canopy clumping correction applied from Chen & Cihlar (1995) IEEE Transactions on Geoscience and Remote Sensing 33, 777–787.

 

Funding

Analyses were carried out, and data were collected, as part of the BALI (Biodiversity And Land-use Impacts on tropical ecosystem function) using the following funding:



NERC's Human Modified Tropical Forests research programme (grant number NE/K016377/1 awarded to the BALI consortium)

MHN was supported by a PhD scholarship from the Conselho Nacional de Pesquisa e Desenvolvimento (CNPq, grant No. 201516/2014-4) from Brazil