Adaptive phenotypic evolution of Skeletonema costatum to ocean acidification and warming with trade-offs from a multi-year outdoor experiment
Data files
Jul 02, 2025 version files 614.88 KB
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all.csv
3.70 KB
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Code_growth_dynamics_and_gen.R
7.66 KB
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Code_other_figures.R
5.66 KB
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Data_combined_Growth_long-term.csv
175.64 KB
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Data_HTHC_assay.csv
1.90 KB
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Data_LTLC_assay.csv
1.88 KB
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Data_PAR_record_long-term.csv
118.95 KB
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Data_temperature_record_long-term.csv
54.14 KB
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gen.csv
15.33 KB
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growth_summary.csv
40 KB
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README.md
8.24 KB
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Result_GAMM_model_selection.csv
6.12 KB
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ZGrowth_Data.csv
175.64 KB
Abstract
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.
Dataset DOI: 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.