Evolution by gene duplication: an update

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Abstract

The importance of gene duplication in supplying raw genetic material to biological evolution has been recognized since the 1930s. Recent genomic sequence data provide substantial evidence for the abundance of duplicated genes in all organisms surveyed. But how do newly duplicated genes survive and acquire novel functions, and what role does gene duplication play in the evolution of genomes and organisms? Detailed molecular characterization of individual gene families, computational analysis of genomic sequences and population genetic modeling can all be used to help us uncover the mechanisms behind the evolution by gene duplication.

Section snippets

Prevalence of gene duplication in all three domains of life

Table 1 lists the estimated numbers of duplicated genes in completely or nearly completely sequenced genomes of representative bacteria, archaebacteria and eukaryotes. One finds that, in all three domains of life, large proportions of genes were generated by gene duplication. It is almost certain that these proportions are underestimates, because many duplicated genes have diverged so much that virtually no sequence similarity is found.

Lynch and Conery estimated that gene duplication arises

Generation of duplicate genes

Gene duplication can result from unequal crossing over (Fig. 1a), retroposition (Fig. 1b), or chromosomal (or genome) duplication, the outcomes of which are quite different. Unequal crossing over usually generates tandem gene duplication; that is, duplicated genes are linked in a chromosome (Fig. 1a). Depending on the position of crossing over, the duplicated region can contain part of a gene, an entire gene, or several genes. In the latter two cases, introns, if present in the original genes,

Evolutionary fate of duplicate genes

Duplication occurs in an individual, and can be fixed or lost in the population, similar to a point mutation. If a new allele comprising duplicate genes is selectively neutral, compared with pre-existing alleles, it only has a small probability, 1/2N, of being fixed in a diploid population [19], where N is the effective population size. This suggests that many duplicated genes will be lost. For those that do become fixed, fixation is time consuming, because it takes, on average, 4N generations

Evolutionary forces behind functional divergence of duplicate genes

In the case of division of expression, such as the engrailed-1 and engrailed-1b genes of zebrafish, it is likely that random fixations of complementary degenerate mutations under relaxed functional constraints are the main cause [37]. In other words, it is a result of neutral evolution, without the involvement of positive selection. In the case of functional specialization and neofunctionalization, two models have been widely cited. The first model is known as the Dykhuizen–Hartl effect, which

Contributions of gene duplication to genomic and organismal evolution

The most obvious contribution of gene duplication to evolution is providing new genetic material for mutation, drift and selection to act upon, the result of which is specialized or new gene functions. Without gene duplication, the plasticity of a genome or species in adapting to changing environments would be severely limited, because no more than two variants (alleles) exist at any locus within a (diploid) individual. It seems difficult to imagine, for instance, how the vertebrate adaptive

Acknowledgements

I thank Lizhi Gao, Xun Gu, David Mindell, David Webb and three anonymous reviewers for valuable comments. This work was supported by a startup fund and a Rackham research fellowship of the University of Michigan and an NIH grant (R01-GM67030) to J.Z.

Glossary

Glossary

Concerted evolution:
a mode of gene family evolution in which members of a family remain similar in sequence and function because of frequent gene conversion and/or unequal crossing over.
Gene conversion:
a recombination process that nonreciprocally homogenizes gene sequences.
Nonsynonymous (nucleotide substitution):
a nucleotide substitution in the coding region of a gene that changes the protein sequence.
Positive (darwinian) selection:
natural selection that promotes the fixation of advantageous

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