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Data and R code accompanying article 10.3354/meps13886 in Marine Ecology Progress Series.

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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