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In peppered moths, the allele for dark-bodied moths is dominant, while the allele for light-bodied moths is recessive, meaning that the typica moths have a phenotype (visible or detectable characteristic) that is only seen in a homozygous genotype (an organism that has two copies of the same allele), and never in a heterozygous one. This helps explain how dramatically quickly the population changed when being selected for dark colouration.

The peppered moth Biston betularia is also a model of parallel evolution in the incidence of melanism in the British form (f. carbonaria) and the American form (f. swettaria) as they are indistinguishable in appearance. Genetic analysis indicates that both phenotypes are inherited as autosomal dominants. Cross hybridizations indicate the phenotypes are produced by isoalleles at a single locus.

The gene for carbonaria in B. betularia was thought to be in a region of chromosome 17, but it was later concluded that it could not contain it because none of the genes in the chromosome coded for either wing pattern or melaninization. The region that was used to find it was the first intron of the orthologue of the cortex gene in Drosophila. Through elimination of candidates within the region based on rarity, a 21,925 base pair insert remained.

The insert, labeled carb-TE, is a class II transposable element that has an approximately 9-kb non-repetitive sequence that is tandemly repeated two and a third times. There are 6 base pairs of inverted repeats and duplicated 4 base pairs at the target site that is not present in typica moths. Carb-TE has higher expression during the stage of rapid wing disc morphogenesis. The mechanism of how it increases expression or if it is the only gene involved is still not known.

Pseudogenes are be found in bacteria. Most are in bacteria that are not free-living; that is, they are either symbionts or obligate intracellular parasites. Thus, they do not require many genes that are needed by bacteria living in changeable environments such as metabolism and DNA repair. However, there is not an order to which functional genes are lost first. For example, the oldest pseudogenes in Mycobacterium laprae are in RNA polymerases and the biosynthesis of secondary metabolities while the oldest ones in Shigella flexneri and Shigella typhi are in DNA replication, recombination, and repair.

Since most bacteria that carry pseudogenes are either symbionts or obligate intracellular parasites, genome size eventually reduces. An extreme example is the genome of Mycobacterium leprae, an obligate parasite and the causative agent of leprosy. It has been reported to have 1,133 pseudogenes which give rise to approximately 50% of its transcriptome. The effect of pseudogenes and genome reduction can be further seen when compared to Mycobacterium marinum, a pathogen from the same family. Mycobacteirum marinum has a larger genome compared to Mycobacterium laprae because it can survive outside the host, therefore, the genome must contain the genes needed to do so.

Although genome reduction focuses on what genes are not needed by getting rid of pseudogenes, selective pressures from the host can sway what is kept. In the case of a symbiont from the Verrucomicrobia phylum, there are seven additional copies of the gene coding the mandelalide pathway. The host, species from Lissoclinum, use mandelalides as part of its defense mechanism.

The relationship between epistasis and the domino theory of gene loss was observed in Buchnera aphidicola. The domino theory suggests that if one gene of a cellular process becomes inactivated, then selection in other genes involved relaxes, leading to gene loss. When comparing Buchnera aphidicola and Escherichia coli, it was found that positive epistasis furthers gene loss while negative epistasis hinders it. An additional study in 2018 further quantified survivability by looking at color and luminance camouflauge and avian artificial predation models. For color camouflage, typica moths blended better under lichen bark than carbonaria, but when placed under plain bark, there was no significant difference. However, in luminance camouflauge, carbonaria moths blended better compared to typica on a plain bark tree. When both variants were placed on an unpolluted lichen covered tree, typica moths had a 21% better survival rate.