Primate Evolution: Gene Loss and Inactivation


Pseudogenes are defined as genes that have lost function. However, despite the loss of function, pseudogenes can play an important role in evolution, especially when the environment changes. Owing to some environmental changes in diet or habitat, for example, pseudogenisation may be beneficial rather than deleterious for individual fitness. The human‐specific pseudogenes are of particular interest, and more than 100 have been identified. These include olfactory receptors, immune function‐related genes and metabolic pathway genes, which seem to be sensitive to environmental conditions. In this article, examples of environment‐driven pseudogenisation are presented and the role or significance of the loss‐of‐function genes in the evolution of primates and humans is discussed.

Key Concepts:

  • Functional constraints maintain function of a protein and therefore maintain the conserved way of molecular evolution.

  • Relaxation of constraints can be achieved in two ways: gene duplication and environmental changes.

  • Gene duplication provides an extra copy of a functional gene, resulting in the relaxation of a functional constraint to on the gene.

  • The ‘less‐is‐more hypothesis’ proposed by Maynard Olson in 1999 suggests loss of function could be an advantage to organisms and also affect phenotypic or physiological changes in evolution.

Keywords: environmental changes; gene loss/inactivation; single‐copy pseudogene; human evolution

Figure 1.

Classification of pseudogenes. Pseudogenes are classified into ‘processed pseudogenes’ or ‘other pseudogenes’. A pseudogene lacking an intron sequence, in particular, is called a ‘processed pseudogene’. Processed pseudogenes are derived from mRNAs. An mRNA is reverse‐transcribed by a reverse‐transcriptase encoded by LINE elements and results in the insertion of cDNA into the genome. On the contrary, other pseudogenes are caused by acquisition of premature stop codons due to nonsense or frameshift mutations. This deterioration generally results from gene duplication. However, pseudogenisation that does not follow gene duplications is often observed (a single‐copy pseudogene). Modified from Satta .

Figure 2.

A pathway of vitamin C biosynthesis. The majority of mammals can produce vitamin C, but with the following exceptions: primates, fruit bats, guinea pigs, elephants and rabbits. In primates, before the divergence of New World from Old World monkeys (around 45–50 Mya (million years ago)), there was a loss in function for the enzyme that converts l‐gulonolactone to vitamin C, l‐gulono‐γ‐lactone oxidase (GLO).

Figure 3.

Molecular causes of UOX pseudogenes. Genetic causes for deterioration of UOX genes in hominoids and gibbons. Pseudogenisation in the two lineages occurred independently. Using changes in the functional constraint at the nonsynonymous sites after the loss‐of‐functional constraint, Oda et al. dated the inactivation event at approximately 15 Mya in the stem lineage of hominoids and approximately 10 Mya in a stem lineage of gibbons.

Figure 4.

Re‐evaluation of human‐specific pseudogenes by new criteria. The condition of human specificity would satisfy the following: (1) There is no functional compensation with other paralogues, (2) there is no pseudogene orthologue in nonhuman primates and (3) these are not processed pseudogenes.



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Satta, Yoko(Feb 2011) Primate Evolution: Gene Loss and Inactivation. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0005121.pub2]