| File(s) | Type | Description | Action |
|---|---|---|---|
Viability.csv (40.41 KB) | Comma Separated Values (.csv) | Contains the data from experiments measuring the impact of different EZ55 strains or axenic culture on mortality of Prochlorococcus strains. These data were used to make Figure 4A Lu, et al. (2024). Column headings are as follows: LTPE: LTPE Strain designation of the Prochlorococcus strain in the experiment. Pro: Whether the Prochlorococcus strain was ancestral (Anc), evolved at 400 ppm pCO2 (400ppm), or evolved at 800 ppm pCO2 (800ppm) Het: Whether the culture was axenic (X), grown in co-culture with ancestral Alteromonas EZ55 (A), or with an Alteromonas strain evolved at the pCO2 condition the culture was grown at (E) CO2: The pCO2 condition under which the culture was grown ViaRes: Whether or not the culture survived (s) or failed (f). Failure was considered to occur if the culture did not attain the cutoff cell density for transfer of 2,600,000 cells per milliliter within 30 days. | |
MixnMatch.csv (53.83 KB) | Comma Separated Values (.csv) | Contains the data from experiments where ancestral and evolved Prochlorococcus were grown with different strains of Alteromonas EZ55 (or axenically). These data were used to generate main text Figure 4B of Lu, et al. (2024). Column headings are as follows: LTPE: LTPE strain designation of the Prochlorococcus strain in the experiment. Pro: Whether the Prochlorococcus strain was ancestral (Anc), evolved at 400 ppm pCO2 (Evo400), or evolved at 800 ppm pCO2 (Evo800) Het: Whether the culture was axenic (X), grown in co-culture with ancestral Alteromonas EZ55 (A), or with an Alteromonas strain evolved at the pCO2 condition the culture was grown at in co-culture with Prochlorococcus (P), Thalassiosira oceanica (TO), or Emiliania huxleyi (EH) t: Elapsed time between culture inoculation and final measurement IniDens: Initial cell density of the culture FinDens: Final cell density of the culture EGR: Exponential growth rate as calculated in the Methods R^2: r-squared value of the regression used to calculate the EGR; cultures with r-squared values less than 0.95 were removed from the analysis MGR: Malthusian growth rate as calculated in the Methods | |
LTPE_Transfers.csv (424.63 KB) | Comma Separated Values (.csv) | Contains the day-by-day flow cytometry data collected during the evolution phase of the Long Term Phytoplankton Evolution experiment that forms the basis of the manuscript. Each row represents the results of a single transfer cycle of a single evolving lineage; i.e., the beginning and ending cell densities, dates, and so forth. These data were used to generate main text Figure 1 Lu, et al. (2024). Column heading explanations are: Strain: which phytoplankton strain was measured -- Prochlorococcus MIT9312, Synechococcus CC9311, Synechocystis PCC6803, Thalassiosira oceanica CCMP1005, or Emiliania huxleyi CCMP371. Replicate: which replicate lineage each measured sample was taken from. Each lineage has a unique designation. Treatment: whether the lineage was grown at 400 ppm (CO2-) or 800 ppm (CO2+) pCO2. Method: how the phytoplankton biomass was measured. Most samples were assessed for cell density using a Guava flow cytometer, but some early samples were assessed by in vivo chlorophyll-a fluorescence with a Turner Designs Trilogy fluorometer. Restart: Rarely, a lineage would crash or become contaminated and would have to be restarted. Measurements applying to the first culture transfer after a restart and indicated here. Cultures that would eventually crash are not depicted in main text Figure 1. Transfer: the sequential number of each transfer, representing the evolutionary distance between the culture and its ancestor. Each transfer represents log(2) 26 = 4.7 generations. T0: date of culture inoculation Tend: date of culture transfer deltaT: days elapsed between T0 and Tend InitDens: initial cell density (or chl-a fluorescence) FinalDens: final cell density (or chl-a fluorescence) MGR: Malthusian growth rate, calculated as described in the Methods Notes: special notes pertaining to certain transfers corresponding to reasons for breaks in transfer number or dates (e.g., crash, contamination, cryopreservation prior to moving labs) | |
LTPE_RCode_Cultures.R (20.39 KB) | R Script | Contains the code necessary to run the statistical analyses described in the text (Lu, et al., 2024). | |
FinalGR.csv (86.07 KB) | Comma Separated Values (.csv) | Contains growth rates for experiments done at the end of the experiment comparing the ancestral and evolve phytoplankton organisms. Each row represents a single transfer cycle as in the above description. These data were used to generate main text Figure 2 Lu, et al. (2024). Column headings are: Strain: which phytoplankton strain was measured -- Prochlorococcus MIT9312, Synechococcus CC9311, Thalassiosira oceanica CCMP1005, or Emiliania huxleyi CCMP371. EvolTreat: Whether the culture represents an ancestor (Anc), 400 ppm pCO2 evolved population (CO2-), or 800 ppm pCO2 evolved population (CO2+) AssayTreat: Whether the culture was assessed at 400 ppm (CO2-) or 800 ppm (CO2+) pCO2 t: the number of days between culture inoculation and final reading N0: initial cell density Nt: final cell density EGR: exponential growth rate, calculated as described in the Methods rsq: r-squared value of the regression used to calculate the EGR; cultures with r-squared values less than 0.95 were removed from the analysis MGR: Malthusian growth rate, calculated as described in the METHODS | |
| Supplemental File(s) | Type | Description | Action |
ReadMe.cultures.txt (5.61 KB) | Plain Text | Explanation of the files in this dataset, how the data files are organized, and how to run the code to replicate the analyses we used in our manuscript (Lu, et al., 2024). |
Files
Filename: Viability.csv (40.41 KB)
Type: Comma Separated Values (.csv)
Description: Contains the data from experiments measuring the impact of different EZ55 strains or axenic culture on mortality of Prochlorococcus strains. These data were used to make Figure 4A Lu, et al. (2024). Column headings are as follows: LTPE: LTPE Strain designation of the Prochlorococcus strain in the experiment. Pro: Whether the Prochlorococcus strain was ancestral (Anc), evolved at 400 ppm pCO2 (400ppm), or evolved at 800 ppm pCO2 (800ppm) Het: Whether the culture was axenic (X), grown in co-culture with ancestral Alteromonas EZ55 (A), or with an Alteromonas strain evolved at the pCO2 condition the culture was grown at (E) CO2: The pCO2 condition under which the culture was grown ViaRes: Whether or not the culture survived (s) or failed (f). Failure was considered to occur if the culture did not attain the cutoff cell density for transfer of 2,600,000 cells per milliliter within 30 days.
Type: Comma Separated Values (.csv)
Description: Contains the data from experiments measuring the impact of different EZ55 strains or axenic culture on mortality of Prochlorococcus strains. These data were used to make Figure 4A Lu, et al. (2024). Column headings are as follows: LTPE: LTPE Strain designation of the Prochlorococcus strain in the experiment. Pro: Whether the Prochlorococcus strain was ancestral (Anc), evolved at 400 ppm pCO2 (400ppm), or evolved at 800 ppm pCO2 (800ppm) Het: Whether the culture was axenic (X), grown in co-culture with ancestral Alteromonas EZ55 (A), or with an Alteromonas strain evolved at the pCO2 condition the culture was grown at (E) CO2: The pCO2 condition under which the culture was grown ViaRes: Whether or not the culture survived (s) or failed (f). Failure was considered to occur if the culture did not attain the cutoff cell density for transfer of 2,600,000 cells per milliliter within 30 days.
Filename: MixnMatch.csv (53.83 KB)
Type: Comma Separated Values (.csv)
Description: Contains the data from experiments where ancestral and evolved Prochlorococcus were grown with different strains of Alteromonas EZ55 (or axenically). These data were used to generate main text Figure 4B of Lu, et al. (2024). Column headings are as follows: LTPE: LTPE strain designation of the Prochlorococcus strain in the experiment. Pro: Whether the Prochlorococcus strain was ancestral (Anc), evolved at 400 ppm pCO2 (Evo400), or evolved at 800 ppm pCO2 (Evo800) Het: Whether the culture was axenic (X), grown in co-culture with ancestral Alteromonas EZ55 (A), or with an Alteromonas strain evolved at the pCO2 condition the culture was grown at in co-culture with Prochlorococcus (P), Thalassiosira oceanica (TO), or Emiliania huxleyi (EH) t: Elapsed time between culture inoculation and final measurement IniDens: Initial cell density of the culture FinDens: Final cell density of the culture EGR: Exponential growth rate as calculated in the Methods R^2: r-squared value of the regression used to calculate the EGR; cultures with r-squared values less than 0.95 were removed from the analysis MGR: Malthusian growth rate as calculated in the Methods
Type: Comma Separated Values (.csv)
Description: Contains the data from experiments where ancestral and evolved Prochlorococcus were grown with different strains of Alteromonas EZ55 (or axenically). These data were used to generate main text Figure 4B of Lu, et al. (2024). Column headings are as follows: LTPE: LTPE strain designation of the Prochlorococcus strain in the experiment. Pro: Whether the Prochlorococcus strain was ancestral (Anc), evolved at 400 ppm pCO2 (Evo400), or evolved at 800 ppm pCO2 (Evo800) Het: Whether the culture was axenic (X), grown in co-culture with ancestral Alteromonas EZ55 (A), or with an Alteromonas strain evolved at the pCO2 condition the culture was grown at in co-culture with Prochlorococcus (P), Thalassiosira oceanica (TO), or Emiliania huxleyi (EH) t: Elapsed time between culture inoculation and final measurement IniDens: Initial cell density of the culture FinDens: Final cell density of the culture EGR: Exponential growth rate as calculated in the Methods R^2: r-squared value of the regression used to calculate the EGR; cultures with r-squared values less than 0.95 were removed from the analysis MGR: Malthusian growth rate as calculated in the Methods
Filename: LTPE_Transfers.csv (424.63 KB)
Type: Comma Separated Values (.csv)
Description: Contains the day-by-day flow cytometry data collected during the evolution phase of the Long Term Phytoplankton Evolution experiment that forms the basis of the manuscript. Each row represents the results of a single transfer cycle of a single evolving lineage; i.e., the beginning and ending cell densities, dates, and so forth. These data were used to generate main text Figure 1 Lu, et al. (2024). Column heading explanations are: Strain: which phytoplankton strain was measured -- Prochlorococcus MIT9312, Synechococcus CC9311, Synechocystis PCC6803, Thalassiosira oceanica CCMP1005, or Emiliania huxleyi CCMP371. Replicate: which replicate lineage each measured sample was taken from. Each lineage has a unique designation. Treatment: whether the lineage was grown at 400 ppm (CO2-) or 800 ppm (CO2+) pCO2. Method: how the phytoplankton biomass was measured. Most samples were assessed for cell density using a Guava flow cytometer, but some early samples were assessed by in vivo chlorophyll-a fluorescence with a Turner Designs Trilogy fluorometer. Restart: Rarely, a lineage would crash or become contaminated and would have to be restarted. Measurements applying to the first culture transfer after a restart and indicated here. Cultures that would eventually crash are not depicted in main text Figure 1. Transfer: the sequential number of each transfer, representing the evolutionary distance between the culture and its ancestor. Each transfer represents log(2) 26 = 4.7 generations. T0: date of culture inoculation Tend: date of culture transfer deltaT: days elapsed between T0 and Tend InitDens: initial cell density (or chl-a fluorescence) FinalDens: final cell density (or chl-a fluorescence) MGR: Malthusian growth rate, calculated as described in the Methods Notes: special notes pertaining to certain transfers corresponding to reasons for breaks in transfer number or dates (e.g., crash, contamination, cryopreservation prior to moving labs)
Type: Comma Separated Values (.csv)
Description: Contains the day-by-day flow cytometry data collected during the evolution phase of the Long Term Phytoplankton Evolution experiment that forms the basis of the manuscript. Each row represents the results of a single transfer cycle of a single evolving lineage; i.e., the beginning and ending cell densities, dates, and so forth. These data were used to generate main text Figure 1 Lu, et al. (2024). Column heading explanations are: Strain: which phytoplankton strain was measured -- Prochlorococcus MIT9312, Synechococcus CC9311, Synechocystis PCC6803, Thalassiosira oceanica CCMP1005, or Emiliania huxleyi CCMP371. Replicate: which replicate lineage each measured sample was taken from. Each lineage has a unique designation. Treatment: whether the lineage was grown at 400 ppm (CO2-) or 800 ppm (CO2+) pCO2. Method: how the phytoplankton biomass was measured. Most samples were assessed for cell density using a Guava flow cytometer, but some early samples were assessed by in vivo chlorophyll-a fluorescence with a Turner Designs Trilogy fluorometer. Restart: Rarely, a lineage would crash or become contaminated and would have to be restarted. Measurements applying to the first culture transfer after a restart and indicated here. Cultures that would eventually crash are not depicted in main text Figure 1. Transfer: the sequential number of each transfer, representing the evolutionary distance between the culture and its ancestor. Each transfer represents log(2) 26 = 4.7 generations. T0: date of culture inoculation Tend: date of culture transfer deltaT: days elapsed between T0 and Tend InitDens: initial cell density (or chl-a fluorescence) FinalDens: final cell density (or chl-a fluorescence) MGR: Malthusian growth rate, calculated as described in the Methods Notes: special notes pertaining to certain transfers corresponding to reasons for breaks in transfer number or dates (e.g., crash, contamination, cryopreservation prior to moving labs)
Filename: LTPE_RCode_Cultures.R (20.39 KB)
Type: R Script
Description: Contains the code necessary to run the statistical analyses described in the text (Lu, et al., 2024).
Type: R Script
Description: Contains the code necessary to run the statistical analyses described in the text (Lu, et al., 2024).
Filename: FinalGR.csv (86.07 KB)
Type: Comma Separated Values (.csv)
Description: Contains growth rates for experiments done at the end of the experiment comparing the ancestral and evolve phytoplankton organisms. Each row represents a single transfer cycle as in the above description. These data were used to generate main text Figure 2 Lu, et al. (2024). Column headings are: Strain: which phytoplankton strain was measured -- Prochlorococcus MIT9312, Synechococcus CC9311, Thalassiosira oceanica CCMP1005, or Emiliania huxleyi CCMP371. EvolTreat: Whether the culture represents an ancestor (Anc), 400 ppm pCO2 evolved population (CO2-), or 800 ppm pCO2 evolved population (CO2+) AssayTreat: Whether the culture was assessed at 400 ppm (CO2-) or 800 ppm (CO2+) pCO2 t: the number of days between culture inoculation and final reading N0: initial cell density Nt: final cell density EGR: exponential growth rate, calculated as described in the Methods rsq: r-squared value of the regression used to calculate the EGR; cultures with r-squared values less than 0.95 were removed from the analysis MGR: Malthusian growth rate, calculated as described in the METHODS
Type: Comma Separated Values (.csv)
Description: Contains growth rates for experiments done at the end of the experiment comparing the ancestral and evolve phytoplankton organisms. Each row represents a single transfer cycle as in the above description. These data were used to generate main text Figure 2 Lu, et al. (2024). Column headings are: Strain: which phytoplankton strain was measured -- Prochlorococcus MIT9312, Synechococcus CC9311, Thalassiosira oceanica CCMP1005, or Emiliania huxleyi CCMP371. EvolTreat: Whether the culture represents an ancestor (Anc), 400 ppm pCO2 evolved population (CO2-), or 800 ppm pCO2 evolved population (CO2+) AssayTreat: Whether the culture was assessed at 400 ppm (CO2-) or 800 ppm (CO2+) pCO2 t: the number of days between culture inoculation and final reading N0: initial cell density Nt: final cell density EGR: exponential growth rate, calculated as described in the Methods rsq: r-squared value of the regression used to calculate the EGR; cultures with r-squared values less than 0.95 were removed from the analysis MGR: Malthusian growth rate, calculated as described in the METHODS
Supplemental Files
Filename: ReadMe.cultures.txt (5.61 KB)
Type: Plain Text
Description: Explanation of the files in this dataset, how the data files are organized, and how to run the code to replicate the analyses we used in our manuscript (Lu, et al., 2024).
Type: Plain Text
Description: Explanation of the files in this dataset, how the data files are organized, and how to run the code to replicate the analyses we used in our manuscript (Lu, et al., 2024).