There’s strong empirical evidence that gene duplication is a major driver of innovations in evolution. However it has received only scant modeling and theoretical analysis, especially compared to the amount of work in population genetics. Moreover most of the efforts were on modeling duplication at the sequence level rather than on the functions.

Basic numbers of gene duplication. In yeast 10^{-6} per gene per generation. In worm 10^{-7} per gene per generation. The rate at which duplicated genes are fixed in eukaryotes is 0.01 per gene per million years, suggesting that the vast majority of duplications do not reach fixation. Human and chimps gain and lose genes (0.004 gain and lose/gene/my) faster than other primates (0.0024 gene/my), and almost 3X faster than non-primate mammals (0.0014 gene/my).

Mechanisms of gene duplication. There are three main mechanisms: unequal cross-over, retroposition, and chromosomal/genome duplication. Unequal cross-over is often caused by similar stretches of DNA sequences, including transposable elements, that accidentally recombine.

Effects of gene duplication. The majority of duplicated genes quickly decay into pseudogenes. Of the functional ones, there are four types of functions:

  1. Amplification. More expression the better.
  2. Neofunctionalization. One copy retains the original function and one copy diverge to a new function through drift and selection.
  3. Subfunctionalization. The original gene might be performing multiple jobs (pleiotropy), and the new copies each performs a subset of the jobs better than before.

It seems that subfunctionalization is particularly (maybe is the most) common. Duplicate gene expression patterns tend to diverge quickly after the duplication event. OR genes is a good example of this. However, many duplicate genes (even very old ones) are functionally redundant to some extent, as observed from deletion studies.

Other genomic innovations. Micro-RNA have expanded and functionally diversified via gene duplication. RNA-based duplications involve retroposition of mRNA back into the genome and results in “stripped-down” genes devoid of introns. Thousands of retrocopies and >100 functional retrogenes have been identified in the human genome. De novo emergence of genes is rare but has been observed in open reading frames. New genes may also arise from domesticated genomic parasites such as retroviruses and transposons. Many news formed genes tends to be specifically expressed in the testis. The testis constitutes the most rapidly evolving organ, hence may have especially large selection for new genes.

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