Meeting with Jason (23/03/05)

Today we talked about the basic outline of the simulation and worked through some of the decisions involved in defining the more detailed points.


This form of the simulation is going to be simplistic and easy.



All mutations will be assumed to be:

• deleterious


• recessive


• non-reversible (because each locus is supposed to represent something akin to a gene)




• As locus complexity goes up the probability of exact reverse goes down
  
  
  


• Each locus can only exist in two states, wild-type and mutant.
  
  
  

The population

• The population will be of a fixed size of 1000 individuals (number will vary in later versions)


• The population will NOT be spatially distributed

The individuals

• Each individual will have an explicitly represented genome

The Genome

• The genome will be diploid


• The genome will have 1000 loci (number will vary in later versions)


• The order of loci is irrelevant




•  The loci are therefore unlinked






• There will be no epistatic interactions




• Each locus will have a state denoted by 1(normal/wild-type) or
  0(mutant)




• There will therefore be only two states for each locus




• Each genome will begin in a heterogenous state




• The genome will start as mostly 1's with some 0's




• Each locus will have two real numbers associated with it to
  denote




• The fitness of homozygous recessive






• The fitness of heterozygous




• 10% of the genome will be devoted to female preference




• These loci will not influence males

The Simulation lifecycle

• The population will be simulated for 1000 generations


• Each generation will contain 3 stages




• Assessment of individuals (do they live or die)


• Breeding of individuals (if still alive) 


• Formation of the new generation
  
  

Assessment stage

• The assessment stage will determine an additive fitness value based on the number of wild-type alleles present


• Females will have an additional fitness cost defined by their preference loci


• Survival to sexual maturity will be determined by the additive fitness value with any recessive homozygous or heterozygous modifiers

Breeding stage

• A randomly chosen female will be presented with 2 randomly chosen males and she will then choose one of the two to mate with.


• Subsequent females will also be chosen at random (each with an equal chance of selection and reselection).


• Each mating pair will produce a single offspring with a genome generated by uniform crossover.




• Each locus of the genome will have a 50% chance of coming from either the mother or the father






• The genome will be subjected to mutation at a rate of 0.01 mutations per locus/per individual/per generation (avg. 10 mutations per genome per individual per generation).




• Offspring will be kept separate from the breeding population until this stage terminates. 


• Breeding will continue until an offspring population of 1000 is reached (fixed population size) 


• All previous breeding individuals will be replaced by the new generation of offspring to form the new generation