[1] This is mostly achieved through the mathematical discipline of population genetics, along with evolutionary game theory.
Most population genetics considers changes in the frequencies of alleles at a small number of gene loci.
When infinitesimal effects at a large number of gene loci are considered, one derives quantitative genetics.
Traditional population genetic models deal with alleles and genotypes, and are frequently stochastic.
Many variants on these models have been developed, which incorporate weak selection, mutual population structure, stochasticity, etc.