Pseudogenes and Their Evolution

Abstract Pseudogenes are relics of former genes that no longer possess biological functions. They are abundant in the genomes of complex organisms such as vertebrates and flowering plants and provide a useful resource for studying mutation rates and neutral evolutionary patterns. Processed pseudogenes can be regarded as fossilised footprints of past gene expression, permitting a peek into ancient transcriptomes. Occasionally adaptive, pseudogenisation is usually a neutral process. Yet, it can have a substantial impact on future evolution by limiting or opening certain evolutionary possibilities. Studies of pseudogenisation may help date key phenotypic changes in evolution and understand the genetic basis of phenotypic evolution. Recent studies found some pseudogenes to possess apparent functions in gene regulation, creating a difficulty in defining pseudogenes. Key Concepts: Pseudogenes are relatives of functional genes that have lost their functions. Most pseudogenes arise from degenerated replicates of functional genes produced by either DNA‐mediated gene duplication or RNA‐mediated retroposition. Processed pseudogenes arise from retroposition and their copy numbers are positively correlated with the germline expression levels of their parent genes. Thus, they may be regarded as fossilised footprints of past gene expression for studying ancient transcriptomes. Most pseudogenes evolve neutrally and thus have been used to study the rates and patterns of mutations. The human and mouse genomes contain nearly as many pseudogenes as functional genes. The number of pseudogenes in a genome, compared to that of functional genes, varies substantially among organisms. Pseudogenisation is usually a neutral process; yet, it can have significant impacts on future evolution by either limiting or opening certain evolutionary possibilities. Pseudogenisation may occasionally be adaptive when the expression of a gene becomes deleterious, due to changes of the genetic background or environment. Some apparent pseudogenes have been found to possess regulatory functions, causing a difficulty in defining pseudogenes.