Diversification or collapse of selfincompatibility haplotypes as a rescue process
Data files
Aug 20, 2020 version files 65.18 MB

analytic_survival.R

calculate_rescue.sh

calculate_survival.sh

check_sim.R

conversion_sim.R

convert_nb.R

distribution_plot.R

equilibration.R

equilibria.txt

expected_survival.csv

explicit_haplotyes.R

haplotype_iteration.R

L=2_U=10_split_traj.csv

L=2_U=10_survive_A.csv

L=2_U=10_survive.csv

L=2_U=2_initial.csv

L=2_U=2_lumped_traj.csv

L=2_U=2_split_traj.csv

L=2_U=2_survive_A.csv

L=2_U=2_survive.csv

L=2_U=2_traj.csv

L=3_U=10_split_traj.csv

L=3_U=10_survive_A.csv

L=3_U=10_survive.csv

L=4_U=10_split_traj.csv

L=4_U=10_survive_A.csv

L=4_U=10_survive.csv

L=5_U=10_split_traj.csv

L=5_U=10_survive_A.csv

L=5_U=10_survive.csv

longterm.R

lumped_to_split.R

make_expected_trajectory.R

make_initial.sh

make_lumped_trajectory.R

make_outcomes.sh

make_rescue_barplot.R

make_rescue_curves.R

make_rescue_table.R

make_trajectories.sh

migration.R

outcome_distribution.R

pollen_limitation.R

preconversion.R

README.txt

rescue_from_trajectory.R

rescue_prob.R

rescue.csv

rnase_functions.R

sc_longterm.R

scbalance.nb

sc.R

sim_survival.csv

simulate_survival.sh

split_trajectories.sh

stochastic_survival.R

survival_sim.R

test.pdf

transition_L=2_R=0.01.csv

transition_L=2_R=0.1.csv

transition_L=2_R=0.2.csv

transition_L=2_R=0.3.csv

transition_L=2_R=0.4.csv

transition_L=2_R=1.csv

transition_probs.R

view_trajectories.R
Abstract
In angiosperm selfincompatibility systems, pollen with an allele matching the pollen recipient at the selfincompatibility locus is rejected. Extreme allelic polymorphism is maintained by frequencydependent selection favoring rare alleles. However, two challenges result in a "chickenegg"problem for the spread of a new allele (a tightly linked haplotype in this case) under the widespread "collaborative nonself recognition" mechanism. A novel pollenfunction mutation alone would merely grant compatibility with a nonexistent stylefunction allele: a neutral change at best. A novel pistilfunction mutation alone could only be fertilized by pollen with a nonexistent pollenfunction allele: a deleterious change that would eliminate all seed set. However, a pistilfunction mutation complementary to a previously neutral pollen mutation may spread if it restores selfincompatibility to a selfcompatible intermediate. We show that novel haplotypes can also drive elimination of
existing ones with fewer siring opportunities. We calculate relative probabilities of increase and collapse in haplotype number given the initial collection of incompatibility haplotypes and the population gene conversion rate. Expansion in haplotype number is possible when population gene conversion rate is large, but large contractions are likely otherwise. A Markov chain model derived from these expansion and collapse probabilities generates a stable haplotype number distribution in the realistic range of 1040 under plausible parameters. However, smaller populations might lose many haplotypes beyond those lost by chance during bottlenecks.
Methods
The file equilibria.txt, which contains the equilibrium frequencies of selfcompatible intermediates, was created by numerically solving genotype frequency recursions in Mathematica using the uploaded notebook scbalance.nb. All other data were generated by simulation or deterministic iteration using custom R scripts. Data were used either to calculate derived values or as starting points for further simulations, as described in the readme.
Usage notes
The transition matrices contain NA values, which are the result of a reflecting lower boundary: the state at the lower boundary is never reached, so transitions out from it were never calculated. See the README.txt for the workflow for generating the data.