Genome Multi

A Multi-Genome is a genome with one or more non-circular chromosomes. Multi genomes can be multi ploidy by setting chromosome_ploidy to a value greater than one. The total number of chromosomes in multi-genome is chromosome_sets times chromosome_ploidy. For example, chromosome_sets = 3 and chromosome_ploidy = 2 would define a genome with 6 chromosomes.

Reproduction - Sexual vs Asexual and Crossover vs. Recombination

Parents must have the same values for chromosome_sets and chromosome_ploidy.

Asexual (and any value for chromosome_ploidy)

offspring are copies of their parent with mutation

Sexual and chromosome_ploidy = 1

offspring are generated by performing crossover between the parents' chromosome sets (which each contain only one chromosome). The resulting genome is then subjected to mutations.

Sexual and chromosome_ploidy > 1

each parent performs crossover between all of the chromosomes in each of their chromosome sets, in order to generate one new chromosome per set. Then each parent contributes those new chromosomes to the corresponding chromosome set in the offspring. The resulting genome is then subjected to mutations.

Incomplete Features (what happens at the end of a chromosome!)

If the end of a chromosome is reached while a gene is being read, the genome handler will stop reading and report that the end of the chromosome was reached. Generally (in the case of Markov Brains) this will stop gene translation, and the resulting element will no be constructed. This behavior was chosen as it appears to be analogous to biology and may be useful in studying telomere shortening.

for more details and parameters, see settings_organisms.cfg