Data from: Coexistence of sexual and asexual reproduction in facultatively parthenogenetic populations under sexual conflict: an agent-based simulation
Data files
Jun 08, 2026 version files 4.50 GB
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25_ab_behav_1of2.csv
377.10 MB
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25_ab_behav_2of2.csv
391.09 MB
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25_ab_struc_1of2.csv
507.58 MB
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25_ab_struc_2of2.csv
508.58 MB
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25_out_rela_behav_1of1.csv
522.89 MB
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25_out_rela_struc_1of1.csv
650.52 MB
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4_ab_behav_1of1.csv
271.98 MB
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4_ab_struc_1of1.csv
286.92 MB
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4_out_rela_behav_1of1.csv
184.04 MB
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4_out_rela_struc_1of1.csv
194.71 MB
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con_ab_behav_1of1.csv
96.98 MB
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con_ab_struc_1of1.csv
104.25 MB
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con_out_rela_behav_1of1.csv
62.60 MB
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con_out_rela_struc_1of1.csv
65.95 MB
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README.md
13.86 KB
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v6_con_ab_behav_lifeex.csv
132.45 MB
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v6_con_ab_struc_lifeex.csv
139.39 MB
Abstract
Facultative parthenogenesis is rare in animals, even though its benefits could allow facultatively sexual individuals to outcompete those with obligate reproductive modes. One potential reason for this rarity might be that a facultative strategy is unstable. Previous studies have investigated the evolution of facultative strategies in obligately sexual populations, but the reverse evolution of obligate sex in an asexual population has rarely been investigated. This process could occur in facultative parthenogens, which often form populations consisting solely of parthenogenetically reproducing females, via invasion by males dispersing from mixed-sex populations. However, the chance of successful male invasion might be reduced by (1) female resistance against sexual reproduction, which could suppress the production of sons; (2) the lack of partially isolated demes that could serve as refugia for males, as patchy populations could buffer against local male extinction and thereby increase the chance of male persistence within a metapopulation; and (3) inbreeding, because inbreeding depression could reduce the fitness of sexually produced individuals. Using agent-based models, we investigated the outcome of simulated male invasions into all-female populations. We found that male invasion success was highly dependent on the presence of female resistance: the lower the resistance cost, the more likely resistance was to spread, and the less likely males were to invade, suggesting that sexual conflict might play a role in the persistence of all-female populations. Relative to a fully connected population (single patch), moderate patchiness (four patches) increased the chance for successful male invasion, but high patchiness (25 patches) reduced invasion success due to edge effects favouring the spread of female resistance. Inbreeding slightly reduced the chance for successful male invasion. Overall, populations in which females utilised both sex and parthenogenesis could persist only within a narrow parameter range where the cost of sex balanced the cost of resistance, supporting the hypothesis that facultative parthenogenesis is demographically unstable.
Dataset DOI: 10.5061/dryad.fn2z34v6q
Description of the data and file structure
The data was collected from BehaviourSpace in NetLogo. There are three NetLogo code files, including version5_connected.nlogo, version5_4sub.nlogo, and version5_25sub.nlogo, which are the codes for simulations of connected populations, populations with four sub-populations, and populations with 25 sub-populations, respectively. The only differences between the three files are the parts that implement different spatial structures. Data collected is divided into 14 files (files 1-14), and the R files contains the codes used to analyse the data. Stat_analysis_sim.R contains the codes for statistical analyses, including the sensitivity analyses and the overall GLMMs. It also contains the codes for Figures 3, A1 to A4. All the other R files contain the code for the figures indicated by their file names, including Figure_4_sim.R, Figure_5_8_9b_sim.R, Figure_6_sim.R, Figure_7_A7_sim.R, Figure_A5_sim.R, and Figure_A8_sim.R.
There are four experiments in BehaviourSpace: out_rela_struc; ab_struc; out_rela_behav, and ab_behav. out_rela_struc includes scenarios where female resistance is structural, and the cost of inbreeding is either relative or absent. ab_struc includes scenarios where female resistance is structural and the cost of inbreeding is absolute. out_rela_behav includes scenarios where female resistance is behavioural, and the cost of inbreeding is either relative or absent. ab_behav contains scenarios where female resistance is behavioural and the cost of inbreeding is absolute.
There is another NetLogo code file, v6_connected_lifeex.nlogo, which is just the same as version5_connected.nlogo but with additional reporters for the calculation of turtle life expectancies (Data included in files 15 and 16). The BehaviourSpace in this file has two experiments: ab_behav_lifeex and ab_struc_lifeex, which contain scenarios where female resistance is behavioural and structural, respectively.
Files and variables
File 1: con_out_rela_struc_1of1.csv
- This file contains the output of 40 simulation replicates from each parameter combinations in scenarios where the simulated population is connected, inbreeding depression does not occur or has a relative cost, and female resistance is structural.
File 2: con_out_rela_behav_1of1.csv
- This file contains the output of 40 simulation replicates from each parameter combinations in scenarios where the simulated population is connected, inbreeding depression does not occur or has a relative cost, and female resistance is behavioural.
File 3: con_ab_struc_1of1.csv
- This file contains the output of 40 simulation replicates from each parameter combinations in scenarios where the simulated population is connected, inbreeding depression has an absolute cost, and female resistance is structural.
File 4: con_ab_behav_1of1.csv
- This file contains the output of 40 simulation replicates from each parameter combinations in scenarios where the simulated population is connected, inbreeding depression has an absolute cost, and female resistance is behavioural.
File 5: 4_out_rela_struc_1of1.csv
- This file contains the output of 40 simulation replicates from each parameter combinations in scenarios where the simulated population has four sub-populations, inbreeding depression does not occur or has a relative cost, and female resistance is structural.
File 6: 4_out_rela_behav_1of1.csv
- This file contains the output of 40 simulation replicates from each parameter combinations in scenarios where the simulated population has four sub-populations, inbreeding depression does not occur or has a relative cost, and female resistance is behavioural.
File 7: 4_ab_struc_1of1.csv
- This file contains the output of 40 simulation replicates from each parameter combinations in scenarios where the simulated population has four sub-populations, inbreeding depression has an absolute cost, and female resistance is structural.
File 8: 4_ab_behav_1of1.csv
- This file contains the output of 40 simulation replicates from each parameter combinations in scenarios where the simulated population has four sub-populations, inbreeding depression has an absolute cost, and female resistance is behavioural.
File 9: 25_out_rela_struc_1of1.csv
- This file contains the output of 40 simulation replicates from each parameter combinations in scenarios where the simulated population has 25 sub-populations, inbreeding depression does not occur or has a relative cost, and female resistance is structural.
File 10: 25_out_rela_behav_1of1.csv
- This file contains the output of 40 simulation replicates from each parameter combinations in scenarios where the simulated population has 25 sub-populations, inbreeding depression does not occur or has a relative cost, and female resistance is behavioural.
File 11: 25_ab_struc_1of2.csv and File 12: 25_ab_struc_2of2.csv
- These files contain the output of simulation replicates from each parameter combinations in scenarios where the simulated population has 25 sub-populations, inbreeding depression has an absolute cost, and female resistance is structural. Each file contains 20 simulation replicates.
File 13: 25_ab_behav_1of2.csv and File 14:25_ab_behav_2of2.csv
- These files contain the output of simulation replicates from each parameter combinations in scenarios where the simulated population has 25 sub-populations, inbreeding depression has an absolute cost, and female resistance is behavioural. Each file contains 20 simulation replicates.
Files 1 to 4 share the same columns:
- [run number]: The identity assigned to each individual simulation run.
- Absolute-inbreeding-cost: The test value for the absolute cost of inbreeding.
- Inbreeding?: A binary variable that indicates where inbreeding depression occurred in the simulation run. “TRUE” when there is a cost for inbreeding, “FALSE” when there is no inbreeding depression.
- Male-resistance-mutant: A binary variable that indicates the dominance of the female resistant allele, either dominant (“dominant”) or recessive (“recessive”).
- Initial-population-size: The initial population size of the simulation run, which was always set to 1000.
- ** Carrying-capacity**: The carrying capacity of the simulated population, which was always set to 1000.
- Type-of-resistance: A binary variable that indicates whether female resistance is structural (“structural”) or behavioural (“behavioural”).
- Longevity: The maximum longevity of individuals, ,which was always set to 100.
- Cost-of-resistance: The test value for the cost of structural female resistance.
- Cost-of-inbreeding: A binary variable that indicates whether the cost of inbreeding is absolute (“absolute”) or relative (“relative”).
- [step]: The time step where data is recorded.
- Sex-ratio: The population of the sex ratio at a specific time step, calculated as the proportion of females.
- Resistance-allele-frequency: The frequency of the female resistance allele at a specific time step.
- Mean-genotypic-value: The population mean fitness at a specific time step.
- Stable-equilibrium: A whole number suggests that the population sex ratio has reached equilibrium, whereas “
” suggests that the population has not reached equilibrium at a specific time step. This measure is only used in pilot tests and is not included in formal analyses. - Count turtles: The population size in a specific time step.
- Count males: The number of males in a specific time step.
- Bbgeno-resistance-frequency: The frequency of the homozygous dominant genotype (AA) at the female resistance locus at a specific time step. This measure is only used in pilot tests and is not included in formal analyses.
- Bsgeno-resistance-frequency: The frequency of the heterozygous genotype (Aa) at the female resistance locus at a specific time step. This measure is only used in pilot tests and is not included in formal analyses.
- Sbgeno-resistance-frequency: The frequency of the heterozygous genotype (aA) at the female resistance locus at a specific time step. This measure is only used in pilot tests and is not included in formal analyses.
- Ssgeno-resistance-frequency: The frequency of the homozygous recessive genotype (aa) at the female resistance locus at a specific time step. This measure is only used in pilot tests and is not included in formal analyses.
- Sexually-reproducing-resistants: The proportion of resistant females that are reproducing parthenogenetically at a specific time step, calculated by the number of sexually reproducing resistant females by the total number of resistant females. This measure is used only in pilot tests where the efficiency of resistance was varied and is not included in formal analyses. This can return a "divdision by 0 error" when there are no resistant females.
- Ss-fitness: The average frequency of homozygous recessive genotypes over the five viability loci of the population at a specific time step.
- Bs-sb-fitness: The average frequency of heterzygous genotypes over the five viability loci of the population at a specific time step.
Files 5 to 14 have the same columns as files 1 to 4, plus additional columns that contains the same measurements in each sub-population:
Numbers are assigned to each sub-population, and are appended to the column names to indicate the values corresponding to each sub-population. For example, sex-ratio-pop-1 is the population sex ratio at a specific time step in sub-population 1, located in the upper left corner. Sub-population numbers are denoted as n below.
- Sex-ratio-pop-n: Population sex ratio at a specific time step in sub-population n.
- Bbgeno-resistance-frequency-n: The frequency of the homozygous dominant genotype (AA) at the female resistance locus at a specific time step in sub-population n.
- Bsgeno-resistance-frequency-n: The frequency of the heterozygous genotype (Aa) at the female resistance locus at a specific time step in sub-population n.
- sbgeno-resistance-frequency-n: The frequency of the heterozygous genotype (aA) at the female resistance locus at a specific time step in sub-population n.
- ssgeno-resistance-frequency-n: The frequency of the homozygous recessive genotype (aa) at the female resistance locus at a specific time step in sub-population n.
- Resist-allele-freq-n: The frequency of the female resistance allele at a specific time step in sub-population n.
- Pop-size-n: The number of individuals at a specific time step in sub-population n.
- Sexually-reproducing-resistants-n: The proportion of resistant females that are reproducing parthenogenetically at a specific time step in sub-population n.
- Mean-genotypic-valus-n: The population mean fitness at a specific time step in sub-population n.
- Ss-fitness-n: The average frequency of homozygous recessive genotypes over the five viability loci of the population at a specific time step in sub-population n.
- Bs-sb-fitness-n: The average frequency of heterzygous genotypes over the five viability loci of the population at a specific time step in sub-population n.
File 15: v6_con_ab_behav_lifeex.csv
- This file contains 30 additional simulation replicates for each parameter combination in the scenarios where inbreeding cost is absolute, the population is connected, and female resistance is behavioural.
File 16: v6_con_ab_struc_lifeex.csv
- This file contains 30 additional simulation replicates for each parameter combination in the scenarios where inbreeding cost is absolute, the population is connected, and female resistance is structural.
Files 15 and 16 also have the same columns as files 1 to 4, and additional columns to track individual life expectancies:
- Mean-ages: The mean age (in time step) of the population at a specific time step.
- Mean-death-age: The computed mean death age of individuals whose longevity was affected only by the costs of resistance and inbreeding. This does not reflect their actual life span, and is not included in formal analyses.
- Mean-chronological-death-age: The actual life span of individuals whose longevity was affected only by the costs of resistance and inbreeding. Figures A8a and A8b are plotted with these values.
- Mean-female-chronological-death-age: The actual life span of females whose longevity was affected only by the costs of resistance. Figures A8c-A8f are plotted with these values.
- Pop-deleterious-count: The total number of deleterious homozygous genotypes across the five viability loci, across all individuals in the population. This is only used in pilot tests and is not included in formal analyses.
- Mean-deleterious-count: The mean number of deleterious homozygous genotypes across the five viability loci, across all individuals in the population. This is only used in pilot tests and is not included in formal analyses.
Code/software
NetLogo (6.4.0) and R-4.3.1 were used for running simulations and data analysis respectively.
The R packages used are as follows:
- tidyverse (2.0.0)
- ggplot2 (3.5.2)
- dplyr (1.1.4)
- performance (0.12.4)
- glmmTMB (1.1.10)
- MuMIn (1.48.4)
- car (3.1-3)
- DHARMa (0.4.7)
- janitor (2.0.0)
- strucchange (1.5-4)
Contributor
Vicky Ying,
School of Biological, Earth & Environmental Sciences,
v.ying@student.unsw.edu.au
