DOI: 10.5061/dryad.fj6q573w0
title: A test of the gleaner-opportunist trade-off among photosynthetic traits in Cryptophyte algae

description: 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. 
description: # A test of the gleaner-opportunist trade-off among photosynthetic traits
 in Cryptophyte algae ###### MS Authors: Jake A. Swanson, Matthew J.
 Greenwold, Tammi L. Richardson, and Jeffry L. Dudycha ###### Read Me
 author: Jake A. Swanson #### **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.