Abstract
Gene conversion is one of the major mutational mechanisms involved in the DNA sequence evolution of duplicated genes. It contributes to create unique patters of DNA polymorphism within species and divergence between species. A typical pattern is so-called concerted evolution, in which the divergence between duplicates is maintained low for a long time because of frequent exchanges of DNA fragments. In addition, gene conversion affects the DNA evolution of duplicates in various ways especially when selection operates. Here, we review theoretical models to understand the evolution of duplicates in both neutral and non-neutral cases. We also explain how these theories contribute to interpreting real polymorphism and divergence data by using some intriguing examples.
Highlights
Gene conversion is one of the major mutational mechanisms involved in the DNA sequence evolution of duplicated genes
We have described how gene conversion allows the evolution of DNA sequences of duplicated genes in a way that is not possible by independent evolution, which can be observed in the patterns of sequence divergence and polymorphism
As we illustrated using the examples of the rice duplicated region and the RNase genes in colobine monkeys, ignoring the possible effect of gene conversion can potentially result in misinterpreting molecular data, especially because regions subject to gene conversion will appear much younger than based on a molecular clock assumption
Summary
The outcome of a single gene conversion event between a pair of paralogous sequences is that the fragment of the sequences that was subject to the conversion event (conversion tract) becomes identical. If the duplicates have been evolving independently, the divergence between whichever paralogous gene pair would correspond to the time since the duplication event Gene conversion occurs between duplicated sequences until the pairing is disrupted due to the accumulation of multiple substitutions or the insertion of transposable elements (TEs) and other large indels This is one of the major factors which determines the trajectory of molecular divergence between paralogs. The orthologous divergence follows a molecular clock, and theoretically the rate of neutral nucleotide substitution (evolutionary rate) is identical to that of single-copy genes (see below for the cases with selection) Another outcome of gene conversion is manifested as a pattern of polymorphism referred to as “shared polymorphism” (Figure 4). When concerted evolution is terminated, d starts increasing roughly linearly
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