A test of the gleaner-opportunist trade-off among photosynthetic traits in Cryptophyte algae
Data files
May 30, 2024 version files 129.53 KB
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BStree_photsyn35P_B.dated.tre
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Crypto_Intercept_Estimates.csv
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PE_Curves_Raw_Data_clean.xlsx
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PE_RLC_PGLS_Data.csv
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Photosynthesis_trade_offs_read_me.Rmd
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PS_Rates_All.csv
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README.md
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RLC_Rates_All.csv
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RLC_Raw_Data_clean.xlsx
Abstract
As photosynthetic producers, phytoplankton form the foundation of aquatic food webs. Understanding the relationships among photosynthetic traits in phytoplankton is essential to revealing how diversification of these traits allows phytoplankton to harvest energy from different light environments. We investigated whether the diversification of 15 species of cryptophytes, a phylum of phytoplankton with diverse light-capturing pigments, showed evidence of trade-offs among photosynthetic performance traits as predicted by the gleaner-opportunist resource exploitation framework. We constructed photosynthesis vs. irradiance (P-E) curves and rapid light curves (RLCs) to estimate parameters characterizing photosynthetic performance and electron transport rate. We inferred the evolutionary relationships among the 15 species with ultraconserved genomic elements and used a phylogenetically controlled approach to test for trade-offs. Contrary to our prediction, we observed a positive correlation between maximum photosynthetic rate, Pmax, and P-E α, an indicator of a species’ sensitivity to increases in light intensity when light is a scarce resource. This result could not be explained by electron transfer traits, which were uncorrelated with photosynthetic rate. Together, our results suggest that ecological diversification of light exploitation in cryptophytes has escaped the constraints of a gleaner-opportunist tradeoff. Photosynthetic trade-offs may be context- or scale-dependent, thereby only emerging when investigated in situations different from the one used here.
README: A test of the gleaner-opportunist trade-off among photosynthetic traits in Cryptophyte algae
Data Files
File: PS_Rates_All.csv
Contains the measurements of photosynthetic rate across a range of 16 irradiances for all 15 cryptophytes used in the study. Each species has a column for the irradiance and photosynthetic rate as irradiance is not constant between each species. Units are µmol photons /meters squared/ second.
I_nord: Irradiance levels at which the photosynthetic rate of Chroomonas nordstedtii was measured at
I_ovata: Irradiance levels at which the photosynthetic rate of Cryptomonas ovata was measured at
I_placoidea: Irradiance levels at which the photosynthetic rate of Chroomonas placoidea was measured at
I_336: Irradiance levels at which the photosynthetic rate of Cryptomonas sp. CPCC 336 was measured at
I_theta: Irradiance levels at which the photosynthetic rate of Guillardia thetra was measured at
I_cryptochromatica: Irradiance levels at which the photosynthetic rate of Hemiselmis cryptochromatica was measured at
I_pacifica: Irradiance levels at which the photosynthetic rate of Hemiselmis pacifica was measured at
I_tepida: Irradiance levels at which the photosynthetic rate of Hemiselmis tepida was measured at
I_1623: Irradiance levels at which the photosynthetic rate of Crpytomonas sp. K-1623 was measured at
I_sulcata: Irradiance levels at which the photosynthetic rate of Proteomonas sulcata was measured at
I_minuta: Irradiance levels at which the photosynthetic rate of Rhodomonas minuta was measured at
I_minuta_15: Irradiance levels at which the photosynthetic rate of Rhodomonas minuta was measured at, but with an outlier dropped so only 15 irradiance-photosynthetic rate pairings are shown
I_salina_15: Irradiance levels at which the photosynthetic rate of Rhodomonas salina was measured at, but with an outlier dropped so only 15 irradiance-photosynthetic rate pairings are shown
I_salina: Irradiance levels at which the photosynthetic rate of Rhodomonas salina was measured at
I_teleaulax: Irradiance levels at which the photosynthetic rate of Teleaulax sp. was measured at
I_zigy: Irradiance levels at which the photosynthetic rate of Unidentified sp. ZIGY was measured at
I_meso_16: Irradiance levels at which the photosynthetic rate of Chroomonas mesostigmatica was measured at
I_meso_15: Irradiance levels at which the photosynthetic rate of Chroomonas mesostigmatica was measured at, but with an outlier dropped so only 15 irradiance-photosynthetic rate pairings are shown
The columns labeled PS_“species designation” contain the photosynthetic rate measured at a specific irradiance level. Column B is labeled PS_nord and is the photosynthetic rate of Chroomonas nordstedtii at each of the 16 irradiances that are listed in the I_nord column (Column A). In this data file, the units for photosynthetic rate are scaled to chlorophyll a, which is ((µg C / µg chl a) /h).
PS_nord: The photosynthetic rate of Chroomonas nordstedtii at the aforementioned irradiance values
PS_nord: The photosynthetic rate of Chroomonas nordstedtii at the aforementioned irradiance values
PS_ovata: The photosynthetic rate of Cryptomonas ovata at the aforementioned irradiance values
PS_placoidea:The photosynthetic rate of Chroomonas placoidea at the aforementioned irradiance values
PS_336: The photosynthetic rate of Cryptomonas sp. CPCC 336 at the aforementioned irradiance values
PS_theta: The photosynthetic rate of Guillardia thetra at the aforementioned irradiance values
PS_cryptochromatica: The photosynthetic rate of Hemiselmis cryptochromatica at the aforementioned irradiance values
PS_pacifica: The photosynthetic rate of Hemiselmis pacifica at the aforementioned irradiance values
PS_tepida: The photosynthetic rate of Hemiselmis tepida at the aforementioned irradiance values
PS_1623: The photosynthetic rate of Crpytomonas sp. K-1623 at the aforementioned irradiance values
PS_sulcata: The photosynthetic rate of Proteomonas sulcata at the aforementioned irradiance values
PS_minuta: The photosynthetic rate of Rhodomonas minuta at the aforementioned irradiance values
PS_minuta_15: The photosynthetic rate of Rhodomonas minuta at the aforementioned irradiance values with an outlier dropped
PS_salina_15: The photosynthetic rate of Rhodomonas salina at the aforementioned irradiance values with an outlier dropped
PS_salina: The photosynthetic rate of Rhodomonas salina at the aforementioned irradiance values
PS_teleaulax: The photosynthetic rate of Teleaulax sp. at the aforementioned irradiance values
PS_zigy: The photosynthetic rate of Unidentified sp. ZIGY at the aforementioned irradiance values
PS_meso_16: The photosynthetic rate of Chroomonas mesostigmatica at the aforementioned irradiance values
PS_meso_15: The photosynthetic rate of Chroomonas mesostigmatica at the aforementioned irradiance values but with an outlier dropped
Chroomonas mesostigmatica, Rhodomonas minuta, and Rhodomonas salina have irradiance and photosynthetic rate data with both 16 points and 15 points. The 15 point datasets have an outlier dropped; these are what were used to generate PE curves for figures and parameter estimates for these species
This data file was used to generate PE curves for all 15 species, which are included in the supplemental material.
File: RLC_Rates_All.csv
Contains the electron transport rate data for 14 cryptophyte species used in this part of the study. Column A (Irradiance) contains the irradiance at which all species had their electron transport rate measured. The irradiance levels are the same for each species. Each column thereafter contains the mean electron transport rate of three replicates for each species at each irradiance level. Column names are representative of a single species with either the first letter of the genus followed by an underscore and the whole or part of the species name (i.e. C_nord for Chroomonas nordstedtii) while K_1623 represents Chroomonas sp. K1623, Teleaulax represents Teleaulax sp. 4857, and ZIGY represents Unid. sp. ZIGY 001. The units of irradiance are µmol photons /meters squared/ second. The units for mean electron transport rate are µmol electrons /meters squared/ second.
This data file was used to generate the rapid light curve figures for all 14 species, which are included as a supplemental file.
Columns in the data file are:
Irradiance: Light levels at which electron transport rates were measured. These are the same for each species.
C_meso: Mean electron transport rate data for Chroomonas mesostigmatica
C_nord: Mean electron transport rate data for Chroomonas nordstedtii
C_placoidea:Mean electron transport rate data for Chroomonas placoidea
K_1623: Mean electron transport rate data for Chroomonas sp. K-1623
C_ovata: Mean electron transport rate data for Cryptomonas ovata
G_theta: Mean electron transport rate data for Guillardia theta
H_crypto: Mean electron transport rate data for Hemiselmis cryptochromatica
H_pacifica: Mean electron transport rate data for Hemiselmis pacifica
H_tepida: Mean electron transport rate data for Hemiselmis tepida
P_sulcata: Mean electron transport rate data for Proteomonas sulcata
R_minuta: Mean electron transport rate data for Rhodomonas minuta
R_salina: Mean electron transport rate data for Rhodomonas salina
Teleaulax: Mean electron transport rate data for Teleaulas sp. 4857
ZIGY: Mean electron transport rate data for Unidientified sp. ZIGY 001
File: PE_RLC_PGLS_Data.csv
Contains data used in the PGLS analyses mentioned in the manuscript.
Cell_Volume is the average cell volume of 200 or 400 individuals of each species in units of microns cubed.
Marine is a binary column indicating habitat of each species, with 0 meaning the habitat is freshwater and 1 meaning the habitat is marine.
PBP is the absorption peak of each phycobiliprotein for each species. Units are nanometers.
Alpha is the estimate of alpha, the initial slope of a PE curve, for each species. Units are (µg C/µg chl a)/ h/µmol photons /meters squared/ second.
Pmax is the maximum photosynthetic rate, estimated from a PE curve, for each species. Units are (µg C/µg chl a)/ h.
Mean_Alpha_RLC is the mean value of three replicates of the initial slope of the RLC for each species. Units are µmol electrons/photons.
ETRm is the mean maximum electron transport rate of each species, estimated from RLCs. Units are µmol electrons /meters squared/ second.
I_10, I_25, and I_50 are the irradiance at which the photosynthesis rate of each species is 10%, 20%, and 50% of its maximum, respectively. Units are µmol photons /meters squared/ second.
File: BStree_photosyn35P_B.dated.tre
Phylogenetic tree used in PGLS analyses.
File: PE_Curves_Raw_Data.xlsx
A workbook containing all the raw photosynthetic rate data. Each sheet contains data on 1-3 species, depending on the day data were collected. The photosynthetron used in this experiment was divided into three blocks, which allowed us to run up to three species together at a time. These blocks were given the names Alfred, Batman, and Catwoman, which are used as identifiers in the datasheet to indicate where in the photosynthetron each species was placed. The name of the species run in a given block is listed next to the block names in the data sheet. When fewer than three species were run at the same time empty positions within the photosynthetron are shown as blank cells in the data.
Date is the date on which the data were collected. Experiment and sample are rows for identifying information that were left blank.
SampVol is the total volume, in microliters, of sample added to each scintillation vial.
TcVol is the volume, in microliters, in each total count vial.
Time and incubation time are the same, how long (in minutes) the samples were allowed to photosynthesize.
ml 14C Added is the amount of C14 added to the sample of a given species.
Chl indicates the chlorophyll concentration for a species on the day of measurement, units are µg/L.
DIC indicates the dissolved inorganic carbon in a culture on the day of measurement, units are µg/L.
Position indicates the position within the photosynthetron for a specific scintillation vial.
Irradiance is the light intensity that each vial in a given position was exposed to in units of µmol photons /meters squared/ second.
CPM are counts per minute, which are the number of flashes of light detected by the scintillation counter.
H# is the spectral index of the external standard, which describes the amount of quenching in a sample.
The column labeled Efficiency is the counting efficiency of the scintillation counter. It is calculated following a formula that has been left in the cells.
Cell H11 labeled Efficency is calculated by subtracting background disintegrations per minute (cell O8, Background) from the measured disintegrations per minute of the external standard (cell M8, Standard) and dividing by the disintegrations per minute of the external standard when it was made (cell M9, DPM). This Efficency value is not used in any further calculations and is 0 on sheets where the Standard and Background values were not entered.
DPM are disintegrations per minute,which are the number of nuclear decays per minute, calculated by dividing the CPM by the efficiency.
Pb/Chl is photosynthetic rate normalized to chlorophyll biomass. The formula to calculate it remains in the cell. Units are (µg C/µg chl a)/ h.
TcAvg is the average of the DPM of all the total count vials for a run.
T0Avg is the average of the DPM of all the time zero samples for a run.
File: RLC_Raw_Data.xlsx
A workbook containing all of the raw RLC data. The species label is in cell A1 and also the name of the sheet.
Cells labeled Rep 1, Rep 2, and Rep 3 indicate which replicate the corresponding data belongs to.REG 1referstoheoutput
F is the minimum fluorescence level when the sample is excited by low intensity light, units are relative.
Fm’ is the maximum fluorescence level during treatment that is induced by a saturating light pulse, units are relative.
PAR is light intensity, units are µmol photons /meters squared/ second.
Y(II) is the estimate of photochemical use of excitation energy in the light, units are
ETR is electron transport rate, units are µmol electrons /meters squared/ second.
Fv/Fm is the maximum photochemical quantum yield of PSII, units are relative.
Alpha is the initial slope of the RLC, units are electrons/photons.
ETRm is the maximum electron transport rate, units are µmol electrons /meters squared/ second.
Ik is the minimum saturating irradiance, units are µmol photons /meters squared/ second.
Beta is the photoinhibition parameter, units are electrons/photons.
ETRmPot is the potential maximum electron transport rate, units are µmol electrons /meters squared/ second.
REG 1 refers to the parameter estimates that are generated by the PAM fluorometer, which fits the data to Equations 3 and 4 in the manuscript (from Platt et al., 1980, see References in the main manuscript). For R.salina and ZIGY, the instrument did not generate all the estimates, so for both species estimates of alpha, beta, and ETRmPot were done in R and fitted to the same equations as above. We included those R estiamtes in the datasheets as well and labeled them to indicate they were done in R.
File: Bouman_JS_Comparison.csv
A csv file with PE data from Bouman et al., 2018 and the authors used to create Figure S2 in Appendix S1.
Type refers to which study an alpha value came from. This can either be MAPPS Alpha or Crypto Alpha (authors’ data).
Column Alpha is all the alpha (initial slope of PE curve) values from Bouman et al., 2018 and the authors. Units are (µg C/µg chl a)/ h/µmol photons /meters squared/ second for the authors and (mg C/mg chl a)/ h/µmol photons /meters squared/ second for Bouman et al.
Study refers to the source of Pmax (photosynthetic maximum) data, either MAPPS Pmax or Crypto Pmax.
Pmax column is the Pmax values from Bouman et al., 2018 and the authors. Units are (µg C/µg chl a)/ h. for the authors and (mg C/mg chl a)/ h for Bouman et al.
File: Crypto_Intercept_Estimates.csv
A .csv file with data used to create Figure S3 in Appendix S_1. Columns are:
Species: Identifies which cryptophyte species data is associated with
Alpha: Alpha (initial slope of PE curve) values for all cryptophyte species, units are (µg C/µg chl a)/ h/µmol photons /meters squared/ second.
Beta: Beta (photoinhibition parameter) values for all cryptophyte species, units are (µg C/µg chl a)/ h/µmol photons /meters squared/ second.
Pbs: Maximum photosynthetic rate without photoinhibition, units are (µg C/µg chl a)/ h.
Pmax: Maximum photosynthetic rate for all cryptophyte species, units are (µg C/µg chl a)/ h.
PS_10: 10% of a species photosyntheic maximum (Pmax)
PS_25: 25% of a species photosyntheic maximum
PS_50: 50% of a species photosyntheic maximum
I_10: Irradiance at which a species reaches 10% of its photosynthetic maximum, units are µmol photons /meters squared/ second
I_25: Irradiance at which a species reaches 25% of its photosynthetic maximum
I_50: Irradiance at which a species reaches 50% of its photosynthetic maximum
File: PE_Curves_Supp_Info.docx
Document with all PE curve figures.
File: RLC_Curves_Supp_Info.docx
Document with all RLC curve figures.
R Code
All_PE_Curve_Figures_SI.R
Code to create figures of PE curves for all 15 species, figures are in supplemental material.
All_RLC_SI.R
Code to create figures of rapid light curves for all 14 species, figures can be found posted on Dryad.
MS_Figures.R
Code to create all figures displayed in main text of the manuscript.
pgls_check_fncs.R
Code to generate diagnostic plots for PGLS models.
Photo_trade_offs_pgls.R
Code used for all PGLS analyses in the manuscript. Code includes single predictor models reported in the manuscript and the full predictor models reported in the supplemental material.