Evolution of daily temporal niches model

## OverviewThis dataset contain the code and data necessary to simulate a stochastic, individual-based birth-and-death process (e.g. Méléard, 2016; Otto and Day, 2011), to study the evolution of daily periods of sexual activity timings within species, and its potential effect on population divergence and speciation.This dataset contains the data and code required to replicate analyses. ## How to Use This code is made to be run using the multiprocessing feature. A linux build is recommended, or a cluster as it is ressource intensive. To test the effet of one parameter, you must comment it at the start of the script, and modify the parameter later as explained at the start of the script. This code will return text based results, made to be outputted by a cluster. The results will only be displayed on the console if run locally ! ## Layout The repository is split into 4 directories : Python Code, R code, Data, and Supplementary Data ### **`Python Code`** All code to reproduce the simulation of the manuscript * **`Daily_niche_model.py`**: Base simulation code, evolution of the activity timing on the same trait for males and females, emergence timing fixed. * **`Independant_MF_evolution.py`**: Considers that male and female activity timing traits are independant and evolve separately. * **`Coevo_Emergence.py`**: Considers that the emergence timing trait can also evolve along the activity timing trait, although independently. ### **`Data`** All raw data collected from simulation, necessary to output the graphs of the main manuscript. The main file are "Data.xlsx" and "LD_values.xlsx", but a ziped file "Data_csv.zip" containing all the sheets as csv files can also be found here.Here is a description of each sheet: * **`Emergence_NG`**: Emergence: emergence timing tested; Percentage: percentage of simulations displaying this type of sub-population; Type: type of sub-population detected; sd: standard deviation of the percentage. * **`Var_Emerg_NG`**: ve: variance in the emergence timing tested; Percentage: percentage of simulations displaying this type of sub-population; Type: type of sub-population detected. * **`Competition_Females`**: p: maximum number of mating events per female; bimodality: percentage of simulation displaying bimodal activity timings; sd: standard deviation of the percentage. * **`G_Fst`**: G: incompatibility threshold value tested; Fst_G: Fst value measured; Fst_sd: standard deviation of the Fst; Early_popsize: delayed-dawn sub-population size measured; early_sd: delayed-dawn sub-population size standard deviation; Late_popsize: immediate sub-population size measured; late_sd: immediate sub-population size standard deviation * **`Competition_Bimodal`**: dltc: male-male competition value tested; Percentage: percentage of simulation displaying bimodal activity timings; sd: standard deviation of the percentage. * **`Competition_Fst`**: dltc: male-male competition value tested; Fst_dltc: mean Fst measured; sd: standard deviation of the mean Fst. * **`LD_values`**: G: incompatibility threshold value tested; LD_neutral_together_raw: record of all linkage disequilibrium values between ecologically neutral loci; LD_timing_together_raw: record of all linkage disequilibrium values between activity timing loci; LD_timing_neutral_together_raw: record of all linkage disequilibrium values between activity timing loci and ecologically neutral loci. ### **`Supplementary Data`** All raw supplementary data collected from simulation, necessary to output the graphs of the Supplementary Material. The main file is "Supplementary_data.xlsx", but a ziped file "Supplementary_data_csv.zip" containing all the sheets as csv file can also be found here.Here is a description of each sheet: * **`Uni_vs_Bimodal`**: E: emergence timing tested; Uni: percentage of simulations displaying unimodal activity timing trait distribution; uni_sd: standard deviation of the percentage of unimodel distributions; Bi_Late: percentage of immediate subpopulations in simulations displaying bimodal activity timing trait distribution; sd_late: standard deviation the percentage of immediate subpopulations in simulations displaying bimodal activity timing trait distribution; Bi_Early: percentage of delayed-dawn subpopulations in simulations displaying bimodal activity timing trait distribution; sd_late: standard deviation the percentage of delayed-dawn subpopulations in simulations displaying bimodal activity timing trait distribution. * **`MF_inde`**: G: : incompatibility threshold value tested; bimo: percentage of simulation displaying bimodal activity timings; sd: standard deviation of the percentage. * **`G_histogram`**: G: : incompatibility threshold value tested; BM_G: percentage of simulation displaying bimodal activity timings; sd: standard deviation of the percentage; * **`Base_G`**: G: incompatibility threshold value tested; Extinction: Percentage of simulations where populations went extinct; Type: type of sub-population detected; Percentage: percentage of simulations displaying this type of sub-population; sd_percent: standard deviation of the percentage; Fst: mean Fst measured; sd_fst: standard deviation of the mean Fst; distance_peaks: average distance between peaks in the activity timing trait distribution; sd_dist: standard deviation of the distance between peaks in the activity timing trait distribution; width_peaks: average width of peaks in the activity timing trait distribution; sd_width: standard deviation of the width of peaks in the activity timing trait distribution; peak_type: "double" if the distribution is bimodal, "single" if unimodal; Average_divergence: average time before the first divergence into two sub-populations is detected; sd_divergence: standard deviation of the time before the first divergence into two sub-populations is detected * **`Sex_G`**: G: incompatibility threshold value tested; Percentage: percentage of simulations displaying this type of sub-population; Type: type of sub-population detected; std_percent: standard deviation of the percentage; width: average width of peaks in the activity timing trait distribution; sd_w: standard deviation of the width of peaks in the activity timing trait distribution; width_type: "bimo" if the distribution is bimodal, "solo" if unimodal; peaks: average time of day where a peak in the activity timing trait was detected; std_peaks: standard deviation of the average time of day where a peak was detected; peak_type: "first" for a delayed-dawn peak, "second" for an immediate peak; peaks_dist: average distance between peaks; p_std: standard deviation of the distance between peaks. * **`G_Coexistence`**: G: incompatibility threshold value tested; Elength: coexistence time between sub-populations; sd: standard deviation of the coexistence time; number_coex: average number of distinct coexistence over 2000 days; sd_nb: standard deviation of the number of distinct coexistence events. * **`Competition_Coexistence`**: dltc: male-male competition value tested; Elength: coexistence time between sub-populations; sd: standard deviation of the coexistence time. * **`Coevolution`**: G: incompatibility threshold value tested; Bimo: percentage of simulations displaying this type of sub-population; sd: standard deviation of the percentage; peak_type: "early" for a delayed-dawn sub-population, "late" for an immediate sub-population; pos_peaks: average time of day of the activity timing peak; sd_pos: standard deviation of the time of day of the activity timing peak; emerg_pos: average time of day of the emergence timing peak; sd_emerg: standard deviation of the time of day of the emergence timing peak; * **`Effect_size`**: Effect_size: Mutational effect size for the activity timing trait; bimo: percentage of simulations displaying bimodal distribution of the activity timing trait; sd: standard deviation of the percentage; ratio_male: ratio between male dawn-shifted and immediate population sizes; sd_male: standard deviation of the ratio. * **`Competition_Variance`**: dltc: male-male competition value tested; variance_single: average variance of activity timing distribution; std_single: standard deviation of the measured variance; width_single: average measured width of the activity timing distribution; std_w_single: standard deviation of the measured width. * **`Width_activity`**: wa: activity timing window tested; Type: type of sub-population detected; Percentage: percentage of simulations displaying this type of sub-population; std_percent: standard deviation of the percentage; wa_width: activity timing window tested; width: average width of activity timing peaks; sd: standard deviation of the measured width; width_type: "bimo" if the distribution is bimodal, "solo" if unimodal. ### **` R code`** R code necessary to reproduce the figures of the main manuscript ("Main_figures.R"), and Supplementary Material ("Supplementary_figures.R").