DOI: 10.5061/dryad.6m905qg92
title: Population genetic recursions to model-biased X chromosome inactivation

description: In eutherians, one of the X chromosomes in each cell of the early female
 embryo is rendered transcriptionally silent through X chromosome
 inactivation. The choice of which X chromosome to inactivate takes place
 independently in each cell and is stably inherited through development,
 leading to a roughly 50:50 ratio of cells in the adult body expressing one
 or the other X chromosome. However, X chromosome inactivation can be
 skewed, with certain X chromosomes showing a heritable tendency to avoid
 inactivation. Using population genetic models, we test whether genetic
 variation for this trait can be maintained by linked sexually antagonistic
 selection. In favor of this hypothesis, we find that a neutral modifier
 that affects the chances of its chromosome’s inactivation—e.g., a variant
 of the X controlling element (Xce)—can spread when linked to a sexually
 antagonistic gene. We explore the logic of this modifier’s spread, which
 we find to be similar in many respects to that of a modifier of dominance.
 We also test for the presence of a “drift barrier”—i.e., a population size
 below which the indirect selective force favoring the modifier becomes too
 weak to overcome drift. On balance, we find that sexual antagonism may
 encourage the spread of skewed X chromosome inactivation, but only under
 favorable conditions. 
description: # Population genetic recursions to model-biased X chromosome inactivation
 Dataset DOI: [10.5061/dryad.6m905qg92](10.5061/dryad.6m905qg92)
 **Manuscript information** Naomi L Greenberg, Manus M Patten, Skewed X
 chromosome inactivation as a response to sexually antagonistic
 selection, *Journal of Evolutionary Biology*, Volume 38, Issue 7, July
 2025, Pages
 1023–1030, [https://doi.org/10.1093/jeb/voae157](https://doi.org/10.1093/jeb/voae157) ## Description of the data and file structure This data archive is structured in a way that it is clear how the various files are used to generate specific elements from the manuscript. The data and analysis scripts are labeled according to the figure from the main text or supplementary material to which they correspond. ### Files and variables #### File: Figure_1_Graphs_.R #### File: Figure_1_Invasion_Function.R #### File: Figure_1_LinkageFunction.R **Description:** Contains the code “Figure 1 Invasion Function.R” and “Figure 1 LinkageFunction.R”. The first outputs the allele frequency of the modifier, while the second outputs the linkage values. Both must be run prior to running “Figure 1 Graphs”, which calls both the invasion function and linkage function and produces the plot used in Figure 1.  #### File: Figure_2._Female_Fitness_Function.R #### File: Figure_2._Female_Fitness_Trumpet.R #### File: Figure_2._Male_Fitness_Function.R #### File: Figure_2._Male_Fitness_Trumpet.R **Description:** Contains the code “Figure 2 Female Fitness Function.R” which outputs female fitness for a given input of parameter values. “Figure 2 Female Fitness Trumpet.R” calls this function by running through combinations of sexually antagonistic male and female fitness costs, and plots the outputs in a figure. “Figure 2 Male Fitness Function.R” and “Figure 2 Male Fitness Trumpet.R” operate analogously.  #### File: Figure_3_Function.R #### File: Figure_3_Plot.R **Description:** Contains the code “Figure 3 Function.R” which outputs the effective dominance coefficient for a given set of parameter values. “Figure 3 Plot.R” calls the function, runs through a combination of sexually antagonistic male and female fitness costs, and plots the outputs in a figure.  #### File: Figure_4._Drift_Barrier_Graphs__3.R #### File: Figure_4._Drift_Barrier_Graphs.R **Description:** Contains the code “Figure 4 Drift Barrier Graphs.R” which simply plots the drift barrier values given from the numerical analysis in a line plot.  #### File: Figure_S1_Invasion_Function.R #### File: Figure_S1_Graphs_.R **Description:** Contains the code “Figure S1 Invasion Function.R” and “Figure S1 Graphs.R”. “Figure S1 Invasion Function.R” returns the allele frequencies for a given set of inputs, while “Figure S1 Graphs.R” plots the output from six different input sets that vary the h (dominance) and r (recombination) parameters.  #### File: Figure_S2._Female_Fitness_Function.R #### File: Figure_S2._Female_Fitness_Trumpet.R #### File: Figure_S2._Male_Fitness_Function.R #### File: Figure_S2._Male_Fitness_Trumpet.R **Description:** Analogous to Figure 2. Contains the code “Figure S2 Female Fitness Function.R” which outputs female fitness for a given input of parameter values. “Figure S2 Female Fitness Trumpet.R” calls this function by running through combinations of sexually antagonistic male and female fitness costs, this time also running through different dominance parameters, and plots the outputs in a composite figure. #### File: S3_plot.R #### File: S3_function.R **Description:** Analogous to Figure 3. Contains the code “Figure S3 Function.R” which outputs the effective dominance coefficient for a given set of parameter values. “Figure S3 Plot.R” calls the function and runs through a combination of sexually antagonistic male and female fitness costs, creating a trumpet for each of three different dominance parameters in a composite plot.