DOI: 10.5061/dryad.sqv9s4nc2
title: The genetic consequences of range expansion and its influence on diploidization in polyploids

description: Despite newly formed polyploids being subjected to myriad fitness
 consequences, the relative prevalence of polyploidy both contemporarily
 and in ancestral branches of the tree of life suggests alternative
 advantages that outweigh these consequences. One proposed advantage is
 that polyploids may more easily colonize novel habitats such as
 deglaciated areas. However, previous research conducted in diploids
 suggests that range expansion comes with a fitness cost as deleterious
 mutations may fix rapidly on the expansion front. Here, we interrogate the
 potential consequences of expansion in polyploids by conducting spatially
 explicit forward-in-time simulations to investigate how ploidy and
 inheritance patterns impact the relative ability of polyploids to expand
 their range. We show that under realistic dominance models, autopolyploids
 suffer greater fitness reductions than diploids as a result of range
 expansion due to the fixation of increased mutational load that is masked
 in the range core. Alternatively, the disomic inheritance of
 allopolyploids provides a shield to this fixation resulting in minimal
 fitness consequences. In light of this advantage provided by disomy, we
 investigate how range expansion may influence cytogenetic diploidization
 through the reversion to disomy in autotetraploids. We show that under a
 wide range of parameters investigated for two models of diploidization,
 disomy frequently evolves more rapidly on the expansion front than in the
 range core, and that this dynamic inheritance model has additional effects
 on fitness. Together our results point to a complex interaction between
 dominance, ploidy, inheritance, and recombination on fitness as a
 population spreads across a geographic range.
description: All data were generated using simulations in SLiM version 4.0.1
 using the scripts in this repository
description: # The genetic consequences of expansion and its influence on
 diploidization in polyploids This repository contains the necessary
 scripts and files to run all simulations in the manuscript and plot all
 figures unzip PPEL_scripts_plotting_data.zip to get access to all files
 described below To plot figures, use Polyploid_expansion_load.Rproj which
 will allow the use of all plotting scripts in plotting_expansion_load.r
 using relative paths to the Rproject folder without needing to change
 locally Data for plotting are stored in **sim*data/**** folder. Within
 ***sim_data/**, the **basic/** folder contains simulations for generating
 Figures 1-4 which are simulations that don't include diploidization
 in the main text. **burnin/** contains the data generated for testing the
 burnin period. **low_mig/** contains simulation data for lower migration
 rates where m is set to 0.005. **dip/** contains all of the main
 diploidization simulation data and can be used to generate Figures 5-6.
 **no_PAFC/** contains diploidization simulation data where pairing
 associated fitness costs are removed. The **SLiM_scripts/** folder
 contains each script and supporting files to run the simulations. the
 **src/** folder contains necessary model functions for processing
 simulation data and running the simulations in **model_functions.slim**.
 **output_reg.slim** contains the processing code to create the output
 files for the basic, non-diploidization simulations.
 **output_dip_dom.slim** contains the processing code to create the output
 files for the diploidization meiotic gene model scripts.
 **output_dip.slim** contains the processing code to create the output
 files for the diploidization by pairing efficiency. For using the main
 SLiM scripts in **SLiM_scripts/** : **polyploid_expansion.slim**,
 **polyploid_diploidization_dominant_meiotic.slim**, and
 **polyploid_diploidization_pairing_efficiency.slim**, follow the
 instructions below: SLiM simulator for polyploid expansion load study. All
 sims were run using SLiM v 4.0.1
 [https://messerlab.org/slim/](https://messerlab.org/slim/) For keyword
 parameters, the following are accepted: | inheritance | | | :---------- |
 :------------- | | **auto** | autotetraploid | | **allo** | allotetraploid
 | | **diploid** | diploid | | dom\_pattern | h\_vector | | :------------ |
 :---------------------------------------------------------------------------------------- | | **additive** | beneficial: (0.0, 0.25, 0.5, 0.75, 1.0), deleterious: (0.0, 0.25, 0.5, 0.75, 1.0) | | **recessive** | beneficial: (0.0, 0.0, 0.0, 0.0, 1.0), deleterious: beneficial: (0.0, 0.0, 0.0, 0.0, 1.0) | | **bd\_dr** | beneficial: (0.0, 1.0, 1.0, 1.0, 1.0), deleterious (0.0, 0.0, 0.0, 0.0, 1.0) | | **br\_dd** | beneficial: (0.0, 0.0, 0.0, 0.0, 1.0), deleterious (0.0, 1.0, 1.0, 1.0, 1.0) | | **duplex** | beneficial: (0.0, 1.0, 1.0, 1.0, 1.0), deleterious (0.0, 0.0, 0.0, 1.0, 1.0) | | **DFE** | beneficial: (0.0, 1.0, 1.0, 1.0, 1.0), deleterious (estimated h-s relationship) | NOTE: for the paper, bd_dr is used for the recessive model as deleterious are recessive and beneficial are dominant | s\_dist | | | :-------- | :------------------------------------------------------------------------------------------ | | **fixed** | both beneficial and deleterious set to b\_s and d\_s, respectively | | **exp** | deleterious drawn from an exponential distribution with mean d\_s, beneficial fixed at b\_s | | **gamma** | deleterious drawn from a gamma distribution at mean -0.001472, beneficial fixed at b\_s | Diploidization only: | dip\_model | | | :--------- | :----------------------- | | **dom** | meiotic gene model | | **diff** | pairing efficiency model | To run each of the scripts, the following will work as examples ``` slim -d "out_dir='out'" -d g_size=999999 -d K=100 -d "r=log(2)" -d mig_rate=0.05 -d u_del=2.5e-8 -d u_ben=2.5e-9 -d b_s=0.005 -d d_s=-0.005 -d rho=2.5e-8 -d "inheritance='auto'" -d "dom_pattern='bd_dr'" -d "s_dist='gamma'" polyploid_expansion.slim ``` For the diploidization scripts, if using the meiotic gene model run the following script: ``` slim -d "out_dir='out'" -d g_size=999999 -d K=100 -d "r=log(2)" -d dip_lambda=2 -d rho=2.5e-8 -d remove_dip_muts=1 -d mig_rate=0.05 -d u_del=2.5e-8 -d u_ben=2.5e-9 -d u_dip=2.5e-10 -d b_s=0.05 -d d_s=-0.005 -d "dom_pattern='auto'" -d "dip_model='dom'" polyploid_diploidization_dominant_meiotic.slim ``` and for the pairing efficiency model: ``` slim -d "out_dir='out'" -d g_size=999999 -d K=100 -d "r=log(2)" -d dip_lambda=100 -d rho=2.5e-8 -d remove_dip_muts=1 -d meiotic_fitness=1 -d mig_rate=0.05 -d u_del=2.5e-8 -d u_ben=2.5e-9 -d u_dip=2e-3 -d b_s=0.005 -d d_s=-0.005 -d "dom_pattern='bd_dr'" -d "dip_model='diff'" -d pe_inflection=85 -d pe_slope=1 -d "s_dist='gamma'" polyploid_diploidization_pairing_efficiency.slim ``` for diploidization, the extra parameter 'remove_dip_muts' governs whether diploidization mutations are removed prior to expansion (1 is yes, 0 no), and for the pairing efficiency model, 'meiotic fitness' regulates if pairing associate fitness effects are included (PAFCs; 1 for yes, 0 for no), pe_inflection is the inflection point of the model (𝛽), and pe_slope is the slope parameter of the model (𝛿). For a single population, an example script has been added to the slim_extras repository [https://github.com/MesserLab/SLiM-Extras/blob/master/models/autotetraploid.slim](https://github.com/MesserLab/SLiM-Extras/blob/master/models/autotetraploid.slim)