# Climate-driven shifts in kelp forest composition reduce carbon sequestration potential This repository contains data and annotated R code accompanying article 10.1111/gcb.16299 in *Global Change Biology*. The repository is split into five groups: **Assimilation**, **Export**, **Decomposition**, **Sequestration** and **Irradiance**. Below is a description of each file within those groups as well as the input and output of each R script. **Assimilation** 1. `Assimilation.csv`: Net and gross carbon assimilation data. - **species** = categorical variable with levels *Laminaria digitata* (d), *Laminaria hyperborea* (h) and *Laminaria ochroleuca* (o) - **bag** = random factor (categorical variable) with plants (P3...24) and mesh bags (B1...9) as levels - **age** = detrital age given in days - **R** = respiration rate given in µmol oxygen per gram of buoyant mass per hour (buoyant mass is practically identical to wet mass) - **NPP** = net photosynthesis rate given in µmol oxygen per gram of buoyant mass per hour - **GPP** = gross photosynthesis rate given in µmol oxygen per gram of buoyant mass per hour (NPP + R) - **d:w** = dry to wet mass ratio 2. `Assimilation.R`: Code to analyse and visualise carbon assimilation. - **Input** = `Assimilation.csv`, Figure 5b from `Decomposition.R` - **Output** = Figure 5, Figure S8, carbon assimilation functions and results **Export** 1. `Export.csv`: Carbon export data. - **month** = month and year given as MMM-YY - **season** = categorical variable with levels Spring, Summer, Autumn and Winter - **time** = numerical expression of months - **species** = categorical variable with levels *Laminaria digitata* (d), *Laminaria hyperborea* (h) and *Laminaria ochroleuca* (o) - **dw.export** = biomass export given in grams of dry mass per plant per day - **fw.export** = biomass export given in grams of wet mass per plant per day, converted from dry mass with plant-specific dry to wet mass ratios - **fw.export.avg** = biomass export given in grams of wet mass per plant per day, converted from dry mass with species- and month-specific dry to wet mass ratios - **C.export** = carbon export given in grams per plant per day, converted from dry mass with species- and month-specific carbon content (%) 2. `Carbon.csv`: Lamina carbon content data. - **month** = month and year given as MMM-YY - **season** = categorical variable with levels Spring, Summer, Autumn and Winter - **species** = categorical variable with levels *Laminaria digitata* (d), *Laminaria hyperborea* (h) and *Laminaria ochroleuca* (o) - **carbon** = carbon content (%) 3. `Mass.csv`: Sporophyte mass data. - **month** = month and year given as MMM-YY - **season** = categorical variable with levels Spring, Summer, Autumn and Winter - **species** = categorical variable with levels *Laminaria digitata* (d), *Laminaria hyperborea* (h) and *Laminaria ochroleuca* (o) - **mass** = whole plant wet mass given in grams 4. `DW.csv`: Dry to wet mass ratio data. - **month** = month and year given as MMM-YY - **season** = categorical variable with levels Spring, Summer, Autumn and Winter - **species** = categorical variable with levels *Laminaria digitata* (d), *Laminaria hyperborea* (h) and *Laminaria ochroleuca* (o) - **d.w** = dry to wet mass ratio 5. `Density.csv`: Sporophyte density data. - **month** = month and year given as MMM-YY - **season** = categorical variable with levels Spring, Summer, Autumn and Winter - **species** = categorical variable with levels *Laminaria digitata* (d), *Laminaria hyperborea* (h) and *Laminaria ochroleuca* (o) - **density** = number of plants per square metre. Note that *Laminaria hyperborea* and *Laminaria ochroleuca* share each quadrat while *Laminaria digitata* occurs spatially separated. 6. `Export.R`: Code to analyse and visualise carbon export. - **Input** = `Export.csv`, `Carbon.csv`, `Mass.csv`, `DW.csv`, `Density.csv` - **Output** = Figure S2, `Constants.csv`, carbon export results **Decomposition** 1. `Decomposition.csv`: Biomass decomposition data. - **species** = categorical variable with levels *Laminaria digitata* (d), *Laminaria hyperborea* (h) and *Laminaria ochroleuca* (o) - **site** = categorical variable with levels West Hoe (WH), Drake's Island (DI) and Jennycliff (JC) - **substratum** = categorical variable with levels Forest and Sediment - **mesh** = mesh diameter given in centimetres - **g.loss** = absolute biomass loss given in grams per day - **perc.loss** = relative biomass loss given in percentage of initial mass per day 2. `Biochemical.csv`: Elemental stoichiometry and phenols in relation to decomposition. - **species** = categorical variable with levels *Laminaria digitata* (d), *Laminaria hyperborea* (h) and *Laminaria ochroleuca* (o) - **bag** = random factor (categorical variable) with mesh bags (B1...9) as levels - **age** = detrital age given in days - **g.loss** = absolute biomass loss given in grams per day - **perc.loss** = relative biomass loss given in percentage of initial mass per day - **phenols** = final soluble polyphenolic content (%) - **N** = final nitrogen content (%) - **C** = final carbon content (%) - **CN** = final carbon to nitrogen ratio 3. `Grazing.csv`: Image analysis data of tissue damage on final retrieval. - **species** = categorical variable with levels *Laminaria digitata* (d), *Laminaria hyperborea* (h) and *Laminaria ochroleuca* (o) - **bag** = random factor (categorical variable) with mesh bags (B1...9) as levels - **excavation** = surface area of excavation scars relative to total tissue area (%) - **perforation** = surface area of holes relative to total tissue area plus holes (%) 4. `Decomposition.R`: Code to analyse and visualise carbon export. - **Input** = `Decomposition.csv`, `Biochemical.csv`, `Grazing.csv` - **Output** = Figure 3, Figure S3, decomposition results **Irradiance** 1. `L4.csv`: Physical and chemical data from station L4, compiled from data available at https://www.westernchannelobservatory.org.uk/l4_ctdf/index.php. - **Date** = date given as DD.M.YY - **Month** = month - **Year** = year given as YYYY - **Season** = categorical variable with levels Spring, Summer, Autumn and Winter - **Temp** = temperature (°C) - **Fluor** = fluorescence given in milligrams of chlorophyll *a* per cubic metre - **Depth** = depth given in metres - **Density** = water density given in kilograms per cubic metre - **Salinity** = salinity (‰) - **Trans** = transmission (%) - **PAR** = photosynthetically active radiation given in µmol photons per square metre per second - **Oxygen** = oxygen given in µM - **Sound** = sound velocity given in metres per second 2. `Irradiance.R`: Code to analyse the depth-irradiance relationship. - **Input** = `L4.csv` - **Output** = seasonal and annual exponential depth-irradiance relationships **Sequestration** 1. `Environmental.csv`: Physical data from the West Hoe decomposition experiment. - **date** = date given as DD/MM/YYYY - **time** = time given as HH:MM:SS - **d** = days from start of expeeriment given as integers - **day** = days expressed numerically - **sunrise** = time of sunrise given as HH:MM:SS - **sunset** = time of sunset given as HH:MM:SS - **daytime** = categorical variable with levels day and night based on sunrise and sunset times - **temp** = temperature (°C) - **lux** = light intensity given in lux 2. `Constants.csv`: Species-specific export and density data compiled in `Export.R`. - **period** = categorical variable with levels Year, Spring, Summer, Autumn and Winter - **species** = categorical variable with levels *Laminaria digitata* (d), *Laminaria hyperborea* (h) and *Laminaria ochroleuca* (o) - **biomass** = biomass export given in grams of dry mass per plant per year - **carbon** = carbon export given in grams per plant per year - **density** = number of plants per square metre - **bCI** = half 95% confidence interval (*z* × standard error) of the product of biomass export and density - **cCI** = half 95% confidence interval (*z* × standard error) of the product of carbon export and density 3. `Sequestration.R`: Code to analyse the depth-irradiance relationship. - **Input** = `Environmental.csv`, `Constants.csv`, gross carbon assimilation functions from `Assimilation.R`, photosynthesis-irradiance relationship for *Laminaria hyperborea* (doi 10.3354/ab00515), sunlight lux to µmol photons per square metre per second conversion, seasonal and annual exponential depth-irradiance relationships from `Irradiance.R`, seasonal and annual daylight hours for Plymouth, local carbon sink coordinates (doi 10.1002/ecm.1366), HadISST historical sea surface tempertaure data available at https://www.metoffice.gov.uk/hadobs/hadisst/data/download.html (doi 10.1029/2002jd002670), Bio-ORACLE representative concentration pathway sea surface temperature predictions available at https://www.bio-oracle.org/downloads-to-email.php (doi 10.1111/geb.12693), species-specific thermal tolerance data from Figure 2b and Table S4 - **Output** = Figure 4, Figure S4, Figure S5, Figure S6, Figure S7, carbon export estimates, carbon sequestration potential, cumulative detrital carbon assimilation Luka Seamus Wright, 10 July 2022