evobiR (version 1.0)

GenomeSym: Genome Simulation

Description

THIS FUNCTION IS STILL IN THE DEVELOPMENT PHASE AND RESULTS FROM IT SHOULD NOT BE TRUSTED WITHOUT CONTACTING ME FIRST!!!

This function is designed to simulate the evolution of a diploid organism with chromosomal sex determination. It allows for the evolution of sexual antagonism, recombination supression, anneuploidy, haplosufficiency.

Usage

GenomeSym(model = "fragileY", generations = 100, census = 50,  gametes = 4,
          loci.a  = 100, loci.s = 50, prob.point.mut = .0010, 
          DFE = (c(rnorm(1000, mean = 0.9, sd = 0.06), rgamma(1000, rate = 2,
          shape = 0.4))), sex.bias.mut = .85, haplosuff.mut = 1, crossovers = 2, 
          recom.mu = 10, anneuploi.mut = c(0, .0002), distance.mut = c(0, .000002),
          achiasmat.mut = c(0, .00002), sex.ant = c(.5, .3, .2), 
          fragile.fact = 20, reporting = "None")

Arguments

model

the type of simulation to be run

generations

integer indicating the number of generations that the simulation should be run

census

integer indicating total census size

gametes

integer indicating number of gametes drawn from each individual

loci.a

integer indicating loci on autsomes

loci.s

integer indicating loci on sex chromosomes

prob.point.mut

probability that an new allele will arrise

DFE

a vector of fitness effect for mutations

sex.bias.mut

propotion of mutations to arrise in males

haplosuff.mut

a value of less than 1 from which mutations in haplosufficiency will be drawn from a uniform distribution between 0 and the specified value.

crossovers

the average number of crossovers per chromosome per meiosis in autosomes

recom.mu

maximum number of loci N that can quit recombining in a single mutational step

anneuploi.mut

probability of a Y aneuploidy mutation drawn from a uniform dist between X and Y

distance.mut

prob of evolving dist pairing uniform dist from X to Y

achiasmat.mut

prob of evolving achiasmatic meiosis in males unirom from X to Y

sex.ant

numerical vector must sum to 1 indicating the probability of unbiased, male biased, female biased mutations

fragile.fact

this is the factor by which we increase aneuploidy based on par reduction

reporting

a character string indicating the desired type of insimulation reporting: 'PAR', 'XY.fitness', 'all.loci'.

Details

This function simulates a genome as a series of numerical vectors each chromosome in a genome has vectors to represent those genes fitness when in a female or when in a male additionally if they are sex chromosomes they have vectors describing the recombination characteristics and haplosufficiency data. All of these genome characteristics are allowed to evolve during the simulation through a variety of mutational mechanisms. The genomes perform in silico gametogenesis with recombination. The probability of gametes being used to create the next generation is in proportion to their parents relative fitness.

default values for the function are as follows: model = "fragileY"

generations = 100

census = 50

gametes = 4

loci.a = 100

loci.s = 50

prob.point.mut = .3

DFE = (c(rnorm(1000,mean=.9,sd=.06),rgamma(1000, rate=2, shape=.4)))

sex.bias.mut = .85

haplosuff.mut = 1

crossovers = 2

recom.mu = 10

anneuploi.mut = c(0, .0002)

distance.mut = c(0, .000002)

achiasmat.mut = c(0, .00002)

sex.ant = c(.5, .3, .2)

fragile.fact = 20

reporting ="None"

References

http://www.uta.edu/karyodb/evobiR/

Examples

## just a small simulated genome
Genome <- GenomeSym(census = 20, generations = 10, reporting = 'all.loci')