Haploid genomes

This section builds on the information found in Mutations.

A haploid genome is the information inherited from a single parent. For example, a diploid individual contains two haploid genomes. In the case of obligate outcrossers, one genome may be labelled “maternal” and the other “paternal”.

The type fwdpp::haploid_genome represents a haploid genome in fwdpp. This type is itself a typedef of fwdpp::haploid_genome_base.

The key data members are:

• fwdpp::haploid_genome_base::n is the number of times this genome is present in the simulation.

• fwdpp::haploid_genome_base::mutations contains the indexes of mutations that do not affect genetic values and/or fitness.

• fwdpp::haploid_genome_base::smutations contains the indexes of mutations that do affect genetic values and/or fitness.

The two classes of mutation keys are stored in different containers so that we can skip “neutral” mutations when calculating genetic values.

The type of the index containers is fwdpp::haploid_genome_base::mutation_container. The value_type of this container is fwdpp::uint_t.

Note

The field fwdpp::haploid_genome_base::n is not equivalent to the frequency of a genome. Rather, it is the number of occurrences of a specific genome object.

Containers of genomes

In a simulation, genome objects must be stored in random-access containers of objects.

In other words, the value_type of your container must equal a genome type;

For example:

using genome_container = std::vector<fwdpp::haploid_genome>;