DOI: 10.5061/dryad.v15dv422v
title: Modelling the carbon balance in bryophytes and lichens: Presentation of PoiCarb 1.0, a new model for explaining distribution patterns and predicting climate-change effects

description: Premise  Bryophytes and lichens have important functional roles
 in many ecosystems. Insight into how their CO2 exchange responds to
 climatic conditions is essential for understanding current and predicting
 future productivity and biomass patterns, but responses are hard to
 quantify at time-scales beyond instantaneous measurements. We present
 PoiCarb 1.0, a model to study how CO2 exchange rates of these
 poikilohydric organisms change through time as a function of weather
 conditions. Methods PoiCarb simulates diel fluctuations of CO2 exchange
 and estimates long-term carbon balances, identifying optimal and limiting
 climatic patterns. Modelled processes are net photosynthesis, dark
 respiration, evaporation and water uptake. Measured CO2-exchange responses
 to light, temperature, atmospheric CO2 concentration, and thallus water
 content (calculated in a separate module) are used to parameterise the
 model's carbon module. We validated the model by comparing modelled
 diel courses of net CO2 exchange to such courses from field measurements
 on the tropical lichen Crocodia aurata. To demonstrate the model's
 usefulness, we simulated potential climate-change effects. Results Diel
 patterns were reproduced well and modelled and observed diel carbon
 balances were strongly positively correlated. Simulated warming effects
 via changes in metabolic rates were consistently negative, while effects
 via faster drying were variable, depending on the timing of hydration.
 Conclusions Being able to reproduce the weather-dependent variation in
 diel carbon balances is a clear improvement compared to simple
 extrapolations of short-term measurements or potential photosynthetic
 rates. Apart from predicting climate-change effects, future uses of
 PoiCarb include testing hypotheses about distribution patterns of
 poikilohydric organisms and guiding species' conservation.
description: Usage Notes We here present the data and code
 used in this paper. The list of data files together with their detailed
 explanations can be found in the README.PDF
description: # Data and code for: Modelling the carbon balance in bryophytes and
 lichens: presentation of PoiCarb 1.0, a new model for explaining
 distribution patterns and predicting climate-change effects
 ## Description of the data
 and file structure ### **File list** ·      
 Nikolic_et_al_2023_CO2_curve_data_Lange_2002.csv ·      
 Nikolic_et_al_2023_Light_curve_data_Lange_2004.csv ·      
 Nikolic_et_al_2023_Tempetarure_curve_data_Lange_2004.csv ·      
 Nikolic_et_al_2023_Tempetarure_dark_respiration_curve_data_Lange_2004.csv
 ·       Nikolic_et_al_2023_Water_curve_data_Lange_2004.csv ·      
 Nikolic_et_al_2023_Water_dark_respiration_curves_data_Lange_2002.csv
 ·      
 Nikolic_et_al_2023_Microclimatic_input_data_17-Sept-01-Oct-1993_Lange_2004.csv ·       Nikolic_et_al_2023_Parameters_for_the_model_P_aurata_and_L_muralis.csv ·       Nikolic_et_al_2023_Microclimatic_input_data_17-24-Sep-93.csv ·       Nikolic_et_al_2023\_ Microclimatic_input_data_24-Sep-1-Oct-93.csv  ·       Nikolic_et_al_2023_Getting_parameters_from_response_curves.R ·       Nikolic_et_al_2023_PoiCarb_model.R ### **File descriptions** **Nikolic_et_al_2023_CO2_curve_data_Lange_2002.csv** Data of measured responses of CO2-exchange rates to different CO2 levels. Gas-exchange measurements were made on the lichen *Protoparmeliopsis muralis (Lange, 2002).* We did not have access to the original data, so we used WebPlotDigitizer to extract data points from the published data visualizations. Explanation for each column in the file: CO2abs – CO2 concentration in ppm A – The instantaneous gas-exchange rate in nmolg-1s-1 **Nikolic_et_al_2023_Light_curve_data_Lange_2004.csv** Data of measured responses of CO2-exchange rates (net photosynthesis and dark respiration) to different light (PAR) levels. Gas-exchange measurements were made on the broad-lobed lichen *Crocodia aurata *from a montane rainforest (at ca 1200 m a.s.l) in Panama (Lange et al., 2004). We did not have access to original data, so we used WebPlotDigitizer to extract data points from the published data visualizations. Explanation for each column in the file:       PAR - Photosynthetic Active Radiation expressed in µmol m-2 s-1 A – The instantaneous gas-exchange rate in nmolg-1s-1 **Nikolic_et_al_2023_Tempetarure_curve_data_Lange_2004.csv** Data of measured responses of CO2-exchange rates (net photosynthesis and dark respiration) to different temperature levels. Gas-exchange measurements were made on the broad-lobed lichen *Crocodia aurata *from a montane rainforest (at ca 1200 m a.s.l) in Panama (Lange et al., 2004). We did not have access to the original data, so we used WebPlotDigitizer to extract data points from the published data visualizations. Explanation for each column in the file: Tcuv - Temperature in Celsius degrees measured A – The instantaneous gas-exchange rate in nmolg-1s-1 **Nikolic_et_al_2023_Tempetarure_dark_respiration_curve_data_Lange_2004.csv** Data of measured responses of CO2-exchange rates (dark respiration) to different temperature levels. Gas-exchange measurements were made on the broad-lobed lichen *Crocodia aurata *from a montane rainforest (at ca 1200 m a.s.l) in Panama (Lange et al., 2004). We did not have access to the original data, so we used WebPlotDigitizer to extract data points from the published data visualizations. Explanation for each column in the file: Tcuv - Temperature in Celsius degrees measured A – The instantaneous gas-exchange rate in nmolg-1s-1 **Nikolic_et_al_2023_Water_curve_data_Lange_2004.csv** Data of measured responses of CO2-exchange rates to changes in lichen water content. Gas-exchange measurements were made on the broad-lobed lichen *Crocodia aurata *from a montane rainforest (at ca 1200 m a.s.l) in Panama (Lange et al., 2004). We did not have access to the original data, so we used WebPlotDigitizer to extract data points from the published data visualizations. Explanation for each column in the file: WC - Relative Water content expressed in % of the dry mass A – The instantaneous gas-exchange rate in nmolg-1s-1 **Nikolic_et_al_2023_Water_dark_respiration_curves_data_Lange_2002.csv** Data of measured responses of CO2-exchange rates (dark respiration) to changes in lichen water content. Gas-exchange measurements were made on the lichen *Protoparmeliopsis muralis (Lange, 2002).* We did not have access to the original data, so we used WebPlotDigitizer to extract data points from the published data visualizations. Explanation for each column in the file: WC - Relative Water content expressed in % of the dry mass A – The instantaneous gas-exchange rate in µmol m-2 s-1      **Nikolic_et_al_2023_Microclimatic_input_data_17-Sept-01-Oct-1993_Lange_2004.csv** Microclimatic data together with gas-exchange measurements data which we used for model validation and also to run the climate change experiments examples. There are data for 15 days of in situ gas-exchange measurements on the broad-lobed lichen *Crocodia aurata *from a montane rainforest (at ca 1200 m a.s.l) in Panama (Lange et al., 2004) together with the following climatic factors: air temperature, PAR, and lichen water content, determined at the same time as the CO2-exchange measurements. We did not have access to the original data, so we used WebPlotDigitizer to extract data points from the published data visualizations. Explanation for each column in the file: Datum – date of each record in the form: 17-Sep-93 time – date and time of each record PAR - Photosynthetic Active Radiation expressed in µmol m-2 s-1 T - Temperature in Celsius degrees measured WC - Relative Water content expressed in % of the dry mass CO2 - CO2 levels expressed in ppm Ameasured – Measured gas-exchange rate in nmolg-1s-1 dWC – Difference in water content between two measurements (this we used to determine coefficient k, would not be needed if you have the water loss curve measured on different VPDs) coef_k – drying speed coefficient start – contains the date and time for the beginning of the daylight for each day, the rest of the column is filled with NAs (NA stands for not available, this is how the missing values are represented in R). This column is added to the original data to be able to plot the periods of daylight and night in different colors end – contains the date and time for the end of the daylight for each day, the rest of the column is filled with NAs (NA stands for not available, this is how the missing values are represented in R). This column is added to the original data to be able to plot the periods of daylight and night in different colors day_night - contains the string value either day, night or NA (NA stands for not available, this is how the missing values are represented in R), this column is added to the original data to be able to plot the periods of daylight and night in different colors **Nikolic_et_al_2023_Parameters_for_the_model_P_aurata_and_L_muralis.csv** Table with parameters we used for validation. To use the PoiCarb 1.0 model, you will need a table like this with parameters for your species. You can obtain the same table by running the **Nikolic_et_al_2023_Getting_parameters_from_response_curves.R** Explanation for each column in the file: LC_par_a, LC_par_b, LC_par_c are the columns containing parameters from the light-response curve; WC_par_a, WC_par_b, WC_par_c are the columns containing parameters from the water-response curve; WC_Rd_par_a, WC_Rd_par_b, WC_Rd_par_c are the columns containing parameters from the dark respiration water-response curve; CO2_par_a, CO2_par_b, CO2_par_c are the columns containing parameters from the CO2-response curve; T_par_a, T_par_b, T_par_c are the columns containing parameters from the temperature-response curve; T_Rd_par_a, T_Rd_par_b are the columns containing parameters from the dark respiration temperature-response curve. **Nikolic_et_al_2023_Microclimatic_input_data_17-24-Sep-93.csv** **Nikolic_et_al_2023\_ Microclimatic_input_data_24-Sep-1-Oct-93.csv** These two files contain microclimatic data, the same columns and data as in Nikolic_et_al_2023_Microclimatic_input_data_17-Sept-01-Oct-1993_Lange_2004.csv, just separated into two different files, it was better for plotting. **Nikolic_et_al_2023_Getting_parameters_from_response_curves.R** R script to be used to get the parameters from the environmental gas exchange response curves and drying speed curves. **Nikolic_et_al_2023_PoiCarb_model.R** PoiCarb model R script. The script is commented, in case something is not clear enough or you have questions write to the author (). ## Sharing/Access information Data was derived from the following sources: * Lange, O. L. 2002. Photosynthetic productivity of the epilithic lichen *Lecanora muralis*: Long-term field monitoring of CO2 exchange and its physiological interpretation. I. Dependence of photosynthesis on water content, light, temperature, and CO2 concentration from laboratory measurements. *Flora *197: 233–249. * Lange, O. L., B. Büdel, H. Zellner, G. Zotz, and A. Meyer. 1994. Field measurements of water relations and CO2 exchange of the tropical, cyanobacterial basidiolichen *Dictyonema glabratum* in a Panamanian rainforest*. *Botanica Acta* 107: 279–290. ## Code/Software There are two R scripts that can be downloaded together with the data. Nikolic_et_al_2023_Getting_parameters_from_response_curves.R and Nikolic_et_al_2023_PoiCarb_model.R. Both scripts are commented (have explanations and notes how to use them).