DOI: 10.5061/dryad.866t1g1tf
title: Data from: Shifting precipitation regimes influence optimal germination strategies and population dynamics in bet-hedging desert annuals

description: This submission contains all that is necessary to generate Figures 1-6 and
 Appendices A-D of the paper entitled "Shifting Precipitation Regimes
 Influence Optimal Germination Strategies and Population Dynamics in
 Bet-hedging Desert Annuals". A readme.txt file is incorporated and
 describes all csv and R-script files. It also includes a roadmap for
 running the scripts on one's own if one wants to re-generate their
 own data files. However, data files have been included so that one can
 instantly generate the figures.
description: The data collection was supported by NSF: DEB-9107324,
 DEB-9419905 (LTREB), DEB-0212782 (LTREB), DEB-0717466 (LTREB), DEB-0817121
 (LTREB), DEB-1256792 (LTREB) and DEB- 0844780. See the paper entitled
 "Shifting Precipitation Regimes Influence Optimal Germination
 Strategies and Population Dynamics in Bet-hedging Desert Annuals" for
 more details. See also Gremer, Jennifer R., and D. Lawrence Venable.
 "Bet hedging in desert winter annual plants: optimal germination
 strategies in a variable environment." <em>Ecology
 letters</em> 17.3 (2014): 380-387; Venable, D. Lawrence. "Bet
 hedging in a guild of desert annuals." <em>Ecology</em>
 88.5 (2007): 1086-1090.; see also the website for the LTREB Data Sets for
 desert annual field data: http://www.eebweb.arizona.edu/faculty/venable/LTREB/LTREB%20data.htm.
description: Any text editor will open the readme.txt file. All other scripts
 should be visible with any typical editor; scripts may be more readable in
 Rstudio. 
description: # Data from: Shifting precipitation regimes influence optimal germination
 strategies and population dynamics in bet-hedging desert annuals Climate
 change will affect both the mean and variability in environmental
 conditions and may have major, negative impacts on population densities in
 the future. For annual plants that already live in an extreme environment
 like the Sonoran Desert, keeping a fraction of their seeds dormant
 underground (for possibly years at a time) is critical to survive. Here,
 we consider how this form of bet-hedging (i.e., delayed germination) for
 ten Sonoran Desert annuals mediates responses to precipitation shifts. We
 use a demographic model parameterized with long-term field and
 precipitation data to explore how forecasted changes in precipitation
 impact annual plant species’ population densities. We then examine how
 instantaneous adaptation to optimal germination fractions in the shifted
 precipitation regimes bolsters population densities. Our results indicate
 that overall less rainfall and, to a lesser extent, increased variance in
 rainfall drive population levels down. Instantaneous adaptation to optimal
 germination fractions in new regimes only benefited species'
 populations marginally and only for small-to-moderate shifts in
 precipitation. Thus, even rapid adaptation is unlikely to save populations
 experiencing larger shifts in precipitation. Finally, species exhibiting
 both higher dormant seed survivorships and abilities to capitalize on
 wet-year bonanzas were the most resilient to precipitation shifts and
 benefited relatively the most from instantaneous adaptation to optimal
 germination fractions. --- ## CORRESPONDING AUTHOR INFORMATION NAME:
 William S. Cuello CORRESPONDING AUTHOR EMAIL (Los Alamos National
 Laboratory email; current institution of employment):
 [wscuello@lanl.gov](mailto:wscuello@lanl.gov), ALTERNATE EMAIL (if not
 reachable via above email):
 [wscuello@gmail.com](mailto:wscuello@gmail.com) --- ## R INFO VERSION:
 2022.07.1+554 PACKAGES: leaps, viridis, gridExtra, ggplot2 --- ## ORDERING
 OF THE FOLLOWING SECTIONS SECTION 1: R SCRIPT CALL FILES SECTION SECTION
 2: R SCRIPT FIGURE FILES SECTION SECTION 3: CSV FILES Work Flow: If
 starting from scratch: 1. Run master_flag_caller_HIREC_mean_only.R to have
 specified number of runs (see within script: variable name --
 num_of_source_retrials; type -- integer). This will generate a data file
 similar to "mean_only flag= 1 init_run_size= 5000 time_forward= 5000
 N_amount= 2". Here, variables init_run_size and time_forward can be
 changed in master_flag_caller_HIREC_mean_only.R. This file allows you to
 call figures_HIREC_v2.R, which generates Figures 1-4 and Appendices B and
 F. 2. Obtaining all other files for Figures 5-7 and Appendices A and C
 require modification of master_flag_caller_HIREC_mean_only.R. In
 particular, to perform the sensitivity analyses, one has to go to
 use_table within pre_processing_HIREC_mean_only.R and manually subtract or
 add 10% to the point-value listed under the correct category: survs -&gt;
 dormant seed survivorships survs_new -&gt; fresh seed survivorships a_comp
 -&gt; intraspecific competition alphas -&gt; dry-year seed yield betas
 -&gt; sensitivity of seed yield to precipitation LH_b0s -&gt; dry-year
 chance of reproduction LH_b1s -&gt; sensitivity of chance of reproduction
 to precipitation You will have to change the save.image(...) file name or
 change the file directory, so that it does not overwrite your previous
 save. With these files saved, you can now run
 HIREC_amnat_post_processing_and_figures_positive.R for all 10% increases
 in life-history traits and functional responses to precipitation; you can
 run HIREC_amnat_post_processing_and_figures_negative.R for reductions in
 these parameters. These two files are similar but require both data files
 generated for increases in standard deviation in precipitation and mean
 reductions in precipitation. In particular, one will have to repeat
 process 1), 2) and onward with master_flag_caller_HIREC_SD_only.R. Then to
 generate the rest of the figures (in Appendix C) one must run
 quasi_extinction_probabilities_experiment_QEP_mean.R for quasi-extinction
 probability pdfs;
 quasi_extinction_probabilities_experiment_PTB_type_1_mean.R for percent
 time below the historical threshold pdfs; and
 quasi_extinction_probabilities_experiment_PTB_type_2_mean_scenario.R for
 percent time below a fraction of the original density pdfs. NOTE: CREATION
 OF THE DATA (USING CLUSTERS) IS CURRENTLY ONLY COMPATIBLE WITH UBUNTU AND
 LINUX-BASED SYSTEMS.
 \______________________________________________________________________________\_ If starting from files available: One can already generate figures from figures_HIREC_v2.R but will still need to generate the Appendix figures in Appendix C using quasi_extinction_probabilities_experiment_QEP_mean.R, quasi_extinction_probabilities_experiment_PTB_type_1_mean.R, and quasi_extinction_probabilities_experiment_PTB_type_2_mean_scenario.R. %%%%%%%%%%%%%%%%%%%%%%% % R SCRIPT CALL FILES % %%%%%%%%%%%%%%%%%%%%%%% File name: post_processing_HIREC.R Description: creates all the statistics for percent time below the historical threshold, ESS germination fraction, and reduction in PTB plots that are generated in the script figures_HIREC_v2.R. \______________________________________________________________________________\_ File name: 18.10.21_paper1_calledon.R Description: All functions that are needed to iterate a population (or populations in the case of multiple lineages) forward (i.e., Eq.(1)). ESS_func and mean_drdg2 are used to obtain the ESS value (i.e., Eq.(6) and the root of the expression). \______________________________________________________________________________\_ File name: pre_processing_HIREC_SD_only.R Description: This is the main file for manipulating precipitation regimes and finding population densities in each precipitation regime, calculating percentage time below the historical threshold (PTB), evolutionarily stable strategies for germination rates, and reduction in PTB due to adaptation. In particular, we grab life-history traits (e.g., survivorships and intraspecific competition rates) taken from Gremer 2014\. We relate precipitation to yield using the hurdle model (see manuscript and Cuello 2019). We calculate evolutionarily stable strategies in from the lab-measured precipitation values (see manuscript and Cuello 2019). We run each species' population forward, drawing from a log-normal distribution fitted to the precipitation values (which we call historical precipitation regime). We calculate the per-species historical threshold from the distribution of density values generated under the historical precipitation regime. In this file, we ONLY manipulate precipitation's variance in this file and calculate the PTB, ESS values, and reduction in PTB in each regime. WARNING: Does not work in WINDOWS -- need MAC OS. --- File name: pre_processing_HIREC_mean_only.R Description: The first part of this file is exactly the same as pre_processing_HIREC_SD_only.R. The only difference between these two files: we ONLY reduce mean precipitation in this file and calculate the PTB, ESS values, and reduction in PTB in each regime. WARNING: Does not work in WINDOWS -- need MAC OS. \______________________________________________________________________________\_ File name: master_flag_caller_HIREC_amnat_SD_5k.R Description: Calls pre_processing_HIREC_SD_only.R. This file can be called once or multiple times, depending on the context. For example, if one wants to average over multiple runs, the matrices are quite large; therefore, one needs to keep calling pre_processing_HIREC_SD_only.R in order to get multiple runs (for independent draws of precipitation -&gt; different draws of seed yield per species -&gt; different PTBs if the length of the run is small enough (e.g., Tf = 50)). WARNING: Does not work in WINDOWS -- need MAC OS. \______________________________________________________________________________\_ File name: master_flag_caller_HIREC_amnat_mean_5k.R Description: Calls pre_processing_HIREC_mean_only_5k.R. This file can be called once or multiple times, depending on the context. For example, if one wants to average over multiple runs, the matrices are quite large; therefore, one needs to keep calling pre_processing_HIREC_mean_only.R in order to get multiple runs (for independent draws of precipitation -&gt; different draws of seed yield per species -&gt; different PTBs if the length of the run is small enough (e.g., Tf = 50)). WARNING: Does not work in WINDOWS -- need MAC OS. %%%%%%%%%%%%%%%%%%%%%%%%% % R SCRIPT FIGURE FILES %%%%%%%%%%%%%%%%%%%%%%%%%% File name: HIREC_amnat_post_processing_and_figures_negative.R Figures generated: Appendix A1-A3; A7-A9 Figures Description: In short, this file generates all the sensitivity analyses that are performed on the percent time below the historical threshold (PTB) curves, the evolutionarily stable strategy (ESS) for germination fraction curves, and reduction in PTB curves when seed survivorships, sensitivity of chance of reproduction to precipitation, and sensitivity of seed yield to precipitation are reduced. --- File name: HIREC_amnat_post_processing_and_figures_positive.R Figures generated: Figure 4-6; Appendix A4-A6 Description: In short, this file generates all the sensitivity analyses that are performed on the percent time below the historical threshold (PTB) curves, the evolutionarily stable strategy (ESS) for germination fraction curves, and reduction in PTB curves when life-history traits and functional responses to precipitation are increased. \______________________________________________________________________________\_ File name: figures_HIREC_v2.R Description: Quick visualization of Figures 1-4 in the main text. Also for visualizing Appendix B and Appendix D. --- File name: HIREC_appendixCstar Description: Quick visualization of Appendix C Figures. --- File name: quasi_extinction_probabilities_experiment_PTB_type_1_SD.R Description: Generates Appendix C Figure C1B/2B. Run after generating all sensitivity files by modifying master_flag_caller_HIREC_amnat_SD.R (and master_flag_caller_HIREC_amnat_SD.R). --- File name: quasi_extinction_probabilities_experiment_PTB_type_1_mean.R Description: Generates Appendix C Figure C1A/2A. Run after generating all sensitivity files by modifying master_flag_caller_HIREC_amnat_mean.R (and master_flag_caller_HIREC_amnat_mean.R). --- File name: quasi_extinction_probabilities_experiment_PTB_type_2_SD.R Description: Generates Appendix C1D/2D. Run after generating all sensitivity files by modifying master_flag_caller_HIREC_amnat_SD.R (and master_flag_caller_HIREC_amnat_SD.R). --- File name: quasi_extinction_probabilities_experiment_PTB_type_2_mean.R Description: Generates Appendix C1C/2C. Run after generating all sensitivity files by modifying master_flag_caller_HIREC_amnat_mean.R (and master_flag_caller_HIREC_amnat_mean.R). --- File name: quasi_extinction_probabilities_experiment_QEP_SD.R Description: Generates Appendix C1F/2F. Run after generating all sensitivity files by modifying master_flag_caller_HIREC_amnat_SD.R (and master_flag_caller_HIREC_amnat_SD.R). --- File name: quasi_extinction_probabilities_experiment_QEP_mean.R Description: Generates Appendix C1E/2E. Run after generating all sensitivity files by modifying master_flag_caller_HIREC_amnat_mean.R (and master_flag_caller_HIREC_amnat_mean.R). %%%%%%%%%%%%%%% %% CSV FILES %% %%%%%%%%%%%%%%% FILE NAME: DataFig2Venable2007.csv Column Name: Year Description: Year of the experiment Column Name: Jmprec Total winter precipitation (mm) -- used in the script. Column Name: Fprec Non-winter precipitation years (mm) -- not used in the script. Column Name: ln(lxbx+0.5) Per-capita yield of a species' population being tracked. Column Name: SP Name of the species name (see Table 1 of manuscript to see all species names). --- FILE NAME: LTERDATA1982_2016.csv Date: Month/Day/Year Date of the collection. ########### refer to no collection. Column Name: Precip (total mm) Total precipitation collected that day at the Tumamoc Hill Laboratory. Site/Station (CAP/1): (NOT USED) Location where the precipitation values (mm) were taken from. Flag (G): (NOT USED) Location of measurement taken (ground measurements). --- FILE NAME: SpeciesByYear.csv Column Names: 1. species 2. year 3. germ 4. survive 5. seedlings_per_m2 6. lx 7. bx 8. lxbx 9. seeds_per_m2 10. germ fraction Descriptions: This file is taken directly from: [http://www.eebweb.arizona.edu/faculty/venable/LTREB/LTREB%20data.htm#data](http://www.eebweb.arizona.edu/faculty/venable/LTREB/LTREB%20data.htm#data) Every column name is detailed at this link: [http://www.eebweb.arizona.edu/faculty/venable/LTREB/metadata.htm](http://www.eebweb.arizona.edu/faculty/venable/LTREB/metadata.htm). Note: the "." entries is synonymous to leaving the cell blank (i.e. the data is not available). These columns are unnecessary in the sense that they are not used in the models or simulations; however, the R scripts account for these two columns, so they must be kept and** not deleted** upon importing. --- FILE NAME: threshold_baseline_txt.csv Column name: threshold_values Description: the lowest decile of the species' population densities on a logarithmic scale.