Photosynthetic pigments of co-occurring Northeast Atlantic Laminaria spp. are unaffected by decomposition

This repository contains data and R code accompanying article 10.3354/meps13886 in Marine Ecology Progress Series, split into two folders: Analysis and Deconvolution. The former contains all files to perform the statistical analysis. The latter contains all files to perform the spectral deconvolution adapted from article 10.1371/journal.pone.0137645 in Public Library of Science One. Below is a description of each file within those folders. For sake of completeness, the published Manuscript.pdf, Supplement.pdf and Figures are also provided.

Analysis

1. Environmental.csv|Environmental.R: In situ light and temperature data.
   • d = day from start of experiment as an integer
   • day = day from start of experiment as a numeric
   • lux = irradiance in lumens per square metre
2. Decomposition.csv|Decomposition.R: Biomass loss data.
   • species = Laminaria digitata (d), Laminaria hyperborea (h) or Laminaria ochroleuca (o)
   • bag = ID of galvanised steel mesh bag
   • age = detrital age in days
   • loss = biomass loss per day (%)
3. Extraction.csv|Extraction.R: Comparison of pigment extraction from fresh and lyophilised tissue. All pigment concentrations are given in micrograms per gram.
   • id = sample ID
   • pigment = Chlorophll a, Chlorophyll c or Carotenoids
   • wet = fresh extract pigment concentration
   • dry = lyophilised extract pigment concentration
4. Pigments.csv|Pigments.R: Main pigment data. All pigment concentrations are given in micrograms per gram of dry mass.
   • id = sample ID
   • site = Mount Batten (MB) or West Hoe (WH)
   • species = Laminaria digitata (d), Laminaria hyperborea (h) or Laminaria ochroleuca (o)
   • bag = ID of plant (P) or galvanised steel mesh bag (B)
   • age = detrital age in days
   • bb.Car = β,β-carotene
   • Chl.a = Chlorophll a
   • Chl.c1 = Chlorophll c₁
   • Chl.c2 = Chlorophll c₂
   • Fuco = Fucoxanthin
   • Phe.a = Pheophytin a
   • Viola = Violaxanthin
   • Zea = Zeaxanthin
5. Map.R: R code to plot the base map of Europe used to build Figure 1.

Deconvolution

1. gaussian.peak.parameters.txt: Gaussian peak parameters for 28 common algal pigments that determine the shape of the absorbance curve for each individual pigment (this file was left unchanged so see 10.1371/journal.pone.0137645 for details).
2. specific.absorption.coefficients.txt: Customised set of core pigments to be deconvoluted from Laminaria spp. pigment mixture absorbance spectra (details were obtained from the literature for acetone extractions since 10.1371/journal.pone.0137645 used ethanol)
   • pigment = pigment abbreviation as used in 10.1371/journal.pone.0137645
   • nm = absorbance maximum or the wavelength at which absorbance is highest given in nanometres
   • L.g.cm = absorption coefficient (sometimes also called the specific extinction coefficient) at the absorbance maximum given in litres per gram per centimetre
   • solvent = only values for acentone were used since this was the solvent we extracted our samples with
3. pigment.function.R: List of R functions required for spectral deconvolution. This file requires the above datasets.
4. Wet.csv|wet.mass.csv|Wet.R: Customised R code and raw spectrophotometric data from fresh tissue extractions required to obtain estimates of individual pigment concentrations.
   • wavelength = wavelength given in nanometres
   • d1A etc. = sample ID
   • id = sample ID
   • g = fresh mass of each sample in grams
5. Dry.csv|Dry.R: Same as above but for lyophilised tissue extraction. There is no equivalent of wet.mass.csv since sample weight was standardised to 100 ± 1 milligrams.
6. Spectrum.R: R code to visualise the deconvolution procedure on the basis of a single lyophilised Laminaria digitata sample (Figure S2).

Luka Seamus Wright, 4 September 2021