DOI: 10.5061/dryad.v6wwpzh6m
title: Adaptive phenotypic evolution of Skeletonema costatum to ocean acidification and warming with trade-offs from a multi-year outdoor experiment

description: Human-induced climate change is increasing variability in marine
 environments, significantly affecting marine organisms and ecosystems.
 While marine diatoms can adapt to ocean acidification and warming in
 stable laboratory settings, their responses to long-term environmental
 changes under natural variability remain unclear. To investigate this, we
 cultivated Skeletonema costatum in outdoor semi-continuous cultures for
 over three years, exposing them to fluctuating natural light and
 temperature that tracked the in situ sea surface temperatures. We
 simulated current and future ocean conditions through four treatments:
 ambient CO2 and temperature (LTLC), elevated CO2 (LTHC), elevated
 temperature (+ 4°C, HTLC), and combined increases (HTHC). After 1,396
 days, we assessed populations in two assay environments (20°C, 400 ppm CO2
 and 24°C, 1,000 ppm CO2) for adaptations in growth rate, pigment
 composition, and photosynthesis. The HTLC-selected group showed highest
 growth rates in the HTHC assay environment, while the LTLC-selected group
 grow fastest in the LTLC assay environment, indicating adaptive evolution.
 Furthermore, populations selected under elevated conditions exhibited
 lower fitness in LTLC environments, highlighting a trade-off and
 underscoring the complexity of evolutionary adaptation in marine diatoms.
 Understanding these mechanisms is crucial for predicting phytoplankton
 dynamics and their role in marine ecosystems, especially in response to
 climate change.
description: # Adaptive phenotypic evolution of Skeletonema costatum to ocean
 acidification and warming with trade-offs from a multi-year outdoor
 experiment Dataset DOI: [10.5061/dryad.v6wwpzh6m](10.5061/dryad.v6wwpzh6m)
 ## Description of the data and file structure The uploaded data files
 provide the original empirical results from both the long-term selection
 experiment and the short-term assay experiment described in the
 manuscript. The dataset includes: * **.csv files** containing raw and
 processed data such as recorded environmental variables (e.g., temperature
 and light intensity), growth rates, and other physiological and
 experimental parameters. * **.R files** with annotated scripts used for
 data cleaning, statistical analyses, and figure generation, enabling full
 reproducibility of the results presented in the paper. ### Files and
 variables #### File: all.csv **Description:** All parameters used for the
 figures of the long-term experiment and the assay experiment. #####
 Variables * Selection: Four selection treatments (LTLC, LTHC, HTLC, and
 HTHC); * Assay: Two assay treatments (LTLC and HTHC); * qy: Quatumn yield
 of PSII, unitless; * chla: Chlorophyll a content (pg/cell); * car:
 Carotenoid content (pg/cell); * cartochla: Ratio of Chlorophyll a content
 to Carotenoid content, unitless; * ik: Saturation light (μmol
 photons/m2/s); * a: Light utilization efficiency, unitless; * retrmax:
 Maximum relative election transfer rate, unitless; * dark: Dark
 respiration rate (pmol O2/cell/h); * ox: Net oxygen evolution rate (pmol
 O2/cell/h); * cue: Carbon use efficiency, unitless; * grow: Ralative
 growth rate (μ); * pgross: Gross oxygen evolution rate (pmol O2/cell/h) *
 ratio: Relative fitness, unitless. #### File:
 Code_growth_dynamics_and_gen.R **Description:** R code for the growth
 dynamics and accumulated generations during the long-term experiment. R
 packages required: ggplot2, dplyr, reader, mgcv, ggnewscale. #### File:
 Code_other_figures.R **Description:** R code for other parameters during
 the assay experiment. R packages required: ggplot2, grid, broom, cowplot,
 dplyr. #### File: Data_HTHC_assay.csv **Description:** Parameters from the
 HTHC assay experiment. ##### Variables * Selection: Four selection
 treatments (LTLC, LTHC, HTLC, and HTHC); * Assay: Two assay treatments
 (LTLC and HTHC); * qy: Quatumn yield of PSII, unitless; * chla:
 Chlorophyll a content (pg/cell); * car: Carotenoid content (pg/cell); *
 cartochla: Ratio of Chlorophyll a content to Carotenoid content, unitless;
 * ik: Saturation light (μmol photons/m2/s); * a: Light utilization
 efficiency, unitless; * retrmax: Maximum relative election transfer rate,
 unitless; * dark: Dark respiration rate (pmol O2/cell/h); * ox: Net oxygen
 evolution rate (pmol O2/cell/h); * cue: Carbon use efficiency, unitless; *
 grow: Ralative growth rate (μ); * pgross: Gross oxygen evolution rate
 (pmol O2/cell/h) * ratio: Relative fitness, unitless. #### File:
 Data_combined_Growth_long-term.csv **Description:** Detailed data from the
 long-term experiment, including the records of dilution cycle, ambient
 temperature, and growth rate et al. ##### Variables * time: Dilution cycle
 (number); * time.real: Time recorded from the experiment started (day); *
 temperature: Temperature treatments (LT and HT); * CO2: CO2 treatments (LC
 and HC); * temp.real: Ambient temperature (℃); * treatment: Selestion
 treatments (LTLC, LTHC, HTLC, and HTHC); * growth: Relative growth rate
 (μ); * replicate: Replicates (number); * id: Sample ID (number); * season:
 Seasons that the time belongs to (S1 represents autum when the experiment
 started and the coming seasons are recorded as S2, S3, S4, and so on); *
 PAR: Ambient light intensity (μmol photons/m2/s). #### File:
 Data_LTLC_assay.csv **Description:** Parameters from the LTLC assay
 experiment. ##### Variables #### Selection: Four selection treatments
 (LTLC, LTHC, HTLC, and HTHC); * Assay: Two assay treatments (LTLC and
 HTHC); * qy: Quatumn yield of PSII, unitless; * chla: Chlorophyll a
 content (pg/cell); * car: Carotenoid content (pg/cell); * cartochla: Ratio
 of Chlorophyll a content to Carotenoid content, unitless; * ik: Saturation
 light (μmol photons/m2/s); * a: Light utilization efficiency, unitless; *
 retrmax: Maximum relative election transfer rate, unitless; * dark: Dark
 respiration rate (pmol O2/cell/h); * ox: Net oxygen evolution rate (pmol
 O2/cell/h); * cue: Carbon use efficiency, unitless; * grow: Ralative
 growth rate (μ); * pgross: Gross oxygen evolution rate (pmol O2/cell/h) *
 ratio: Relative fitness, unitless. **File:
 Data_temperature_record_long-term.csv** **Description:** The recorded
 ambient temperature from the long-term experiment. ##### Variables * day:
 Days from the beginning of the experiment (day); * temperature: Ambient
 temperature (℃); * group: Group of the temperature treatment (LT and HT);
 * year: Years from the beginning of the experiment (year); *
 season: Seasons that the time belongs to (S1 represents autum when the
 experiment started and the coming seasons are recorded as S2, S3, S4, and
 so on). #### File: gen.csv **Description:** Accumulated generations from
 the long-term experiment. ##### Variables * day: Days from the beginning
 of the experiment (day); * gen: Generations accumulated from the start of
 the experiment (number); * treatment: Selection treatments (LTLC, LTHC,
 HTLC, and HTHC). #### File: growth_summary.csv
 **Description:** Statistical sunnary of the growth rate. ##### Variables *
 treatment: Selection treatments (LTLC, LTHC, HTLC, and HTHC); * time.real:
 Time recorded from the experiment started (day); * mean_growth: ; *
 se_growth: Standard error of the mean, unitless. #### File:
 Result_GAMM_model_selection.csv **Description:** Results of the model
 selection. ##### Variables * model: Reduced models that were used for the
 selection (model. number); * Intercept: Intercept of the GAMM model (μ); *
 CO2: Effect of the dependent variable CO2 (+ means significant); * s(time,
 by = interaction(temperature, CO2), bs = "cr"): Smoother (time,
 day); * CO2:temperature: Interaction effects of the dependent variables
 CO2 and temperature (+ means significant); * temperature: Effect of the
 dependent variable temperature (+ means significant); * df: Degree of
 freedom, unitless; * logLik: Log transformed likelyhood constant,
 unitless; * AICc: Corrected Akaike Information Criterion, unitless; *
 delta: Relative difference between the AICc value and the minimum AICc
 value, unitless; * weight: The relative probability that a model is the
 best among the candidate set, given the data, unitless. #### File:
 Data_PAR_record_long-term.csv **Description:** The recorded light
 intensity from the long-term experiment. ##### Variables * day: Days from
 the beginning of the experiment (day); * light: Ambient light intensity
 (μmol photons/m2/s); * group: Group of the temperature treatment (LT and
 HT); * year: Years from the beginning of the experiment (year); *
 season: Seasons that the time belongs to (S1 represents autum when the
 experiment started and the coming seasons are recorded as S2, S3, S4, and
 so on). #### File: ZGrowth_Data.csv **Description:** Growth rate recorded
 during the long-term experiment. ##### Variables * time: Dilution cycle
 (number); * time.real: Time recorded from the experiment started (day); *
 temperature: Temperature treatments (LT and HT); * CO2: CO2 treatments (LC
 and HC); * temp.real: Ambient temperature (℃); * treatment: Selestion
 treatments (LTLC, LTHC, HTLC, and HTHC); * growth: Relative growth rate
 (μ); * replicate: Replicates (number); * id: Sample ID (number); * season:
 Seasons that the time belongs to (S1 represents autum when the experiment
 started and the coming seasons are recorded as S2, S3, S4, and so on); *
 PAR: Ambient light intensity (μmol photons/m2/s). ## Code/software
 Microsoft Excel or other software that can open .csv files is required for
 reviewing the .csv files in the uploaded data. For the R files, the R code
 can be run within the R environment (version 4.2.2). R packages that are
 used in the code scripts are: ggplot2, dplyr, readr, mgcv, ggnewscale,
 grid, broom, and cowplot.