The duplication of DNA sequences occurs at many scales within genomes and contributes to genome evolution at all of these levels.

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The duplication of DNA sequences occurs at many scales within genomes and contributes to genome evolution at all of these levels. Discuss this statement providing examples and reflect on how this mechanism contributes to genome evolution.

Gene duplication has had a significant impact on all genomes. Gene duplication contributes most of the raw material for natural selection in order to shape novel genes. The importance of the raw genetic material that is supplied by gene duplication for biological evolution, has been recognised since the 1930s. The interest of gene duplication, in the context of human evolution, has been intense. This is due to the human genome being particularly rich in duplicated genomic regions. The duplicated gene therefore contribute to genomic instability which then leads to genome rearrangement and speciation. A number of recent studies have shown evidence which suggests that the duplicated genes have undergone greater diversification than any other loci in humans. It has been observed that the increase in gene numbers with increasing biological complexity involves the expansion of families of closely related genes. This observation has helped in concluding that gene duplication has been a major evolutionary process.

The high density of segments of duplicated DNA is a vital feature of the human genome. From the entire genome, a total of approximately 13.7% is believed to consist of duplicated gene sequences. While most of this duplicated material is quite small and non-functional pieces of DNA, a lot of the duplicated material is relatively large duplications that possibly contains intact functional elements.

A vital consequence of gene duplication is the production of new genes. As mentioned earlier, gene duplication is most certainly a major source of novel genes. Gene duplication can result from unequal crossing over, retroposition or chromosomal duplication, the outcomes of which are quite different. A tandem gene duplication occurs when the duplicated genes are linked in a chromosome. Tandem gene duplication is usually generated by unequal crossing. Depending on the position of crossing over, the duplicated region can contain a part of a gene, an entire gene, or several genes. Retroposition occurs once a messenger RNA is retrotranscribed to complementary DNA and then inserted into the genome. Chromosomal duplication most likely occurs by the lack of disjunction among daughter chromosomes after DNA replication. A great amount of evidence has shown that such large scale duplications can occur much more frequently in plants than compared to animals. Segmental duplication which is another type of large scale duplication has been discovered from recent analysis of the human genome. This type of duplication often involves between 1000 and >200,000 nucleotides.

One of the most obvious contribution to evolution by gene duplication is that it is being provided by new genetic material. This new material is then used for mutation, genetic drift and selection which then results in the development of new gene functions or specialised gene functions. The most common mechanism that this relies on is recombination between different parts of the genome and not just between same alleles on homologous chromosomes. DNA regions that have been duplicated can lead to homologous sequences to appear at different loci. This type of recombination is known as non-allelic homologous recombination which then leads to additional duplication, deletion of DNA, transposition of genetic material between chromosomes and inversions. Another likely contribution by gene duplication is the evolution of gene networks in which sophisticated expression regulations can be established. One such example is the eyeless (Pax6), master control gene of eye development in metazoans. This gene which was duplicated in Drosophila with its paralog now regulates in the expression of eyeless. Gene duplication can also promote the maintenance and spread of these mutations through populations. This can occur even if the duplicate loci was not involved in the mutation process of genome rearrangement. This is mainly due to the fact that translocations of genes are more likely to be neutral and less deleterious when another copy is still unaffected at the original locus that is present in the genome.

A very often stated fact is that humans and chimpanzees are very similar at the DNA level and only differ by around 1% (e.g. Mikkelsen et al 2005). Therefore it would be this very small amount of coding sequence that would express all the unique traits of humans. New evidence has been found that very few genes have experienced positive selection after the divergence of humans and chimpanzees. While an early study had suggested around 35 genes that had displayed significant positive selection, none of these were statistically significant. Hence it can be concluded that positive selection at the nucleotide level might not have any significant effect in recent human evolution. The recent availability of the macaque genome sequence have given us a deeper knowledge about the divergence from humans. It has been found that the ancestors of macaques must have diverged from the hominid lineage sometime around 25 million years ago. This has greatly helped in the identification of genes under positive selection of the human and chimp lineage, as the sequence acts as an out-group. By analysing the macaque genome, further evidence has also been provided to show that positively selected single-copy genes tend to cluster near segmental duplications. A significant amount of evidence has shown that selection is most likely to occur on duplicated genes compared to single-copy genes. From this, it was observed that single-copy genes can be less significant than variation in gene content in recent evolution of humans. Therefore, gene duplication must have been the predominant process in the development of unique human traits.

By comparing the nucleotide sequence of genomes, we have achieved a greater knowledge and understanding of how gene and genome evolution occurs. Random errors in maintaining the nucleotide sequences rarely occur due to the high fidelity of the DNA replication process and also the DNA repair process. Therefore, when comparing human and chimpanzee chromosomes, we can only observe very few changes as they have only been separated from each other by about 5 million years. When comparing the two genomes we can see that the genes in both organisms are the same and that their order on the chromosome are also nearly identical. As Lynch (2007, p.194) explains, “the gene duplication process provides fuel for both of the major engines of evolution: adaptive phenotypic change within lineages and the creation of new lineages by speciation”. While many of these duplicated genes may have become pseudogenes, it is safe to assume that some of these genes may have acquired new functions. By identifying human-specific gene duplication, it is possible to pinpoint the genetic basis of features that are unique to humans. With the advent of the Human Genome Sequencing and the whole human genome sequence being available, such studies should be feasible.

By comparing genomes to two different organisms that are distantly related, a lot more changes in the genome can be observed. For example, by comparing the genome between a human and a mouse, the effects of natural selection can be clearly seen. It is observed that essential nucleotide sequences that are present both in the regulatory regions and the coding region have both been highly conserved. By comparing this to non-essential sequence such as introns we can see that it has been altered significantly that an accurate alignment due to ancestry is almost nearly impossible. Due to purifying selection, it is often possible to construct a detailed evolutionary history of a particular gene. This is made possible by recognising homologous genes over large phylogenetic distances. We can thereby see that a great deal of the genetic complexity of present-day organisms is due to the expansion of ancient gene families. DNA duplication followed by sequence divergence has thus been a major source of genetic novelty during evolution.

REFERENCE

Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell. 4th edition. New York: Garland Science; 2002. How Genomes Evolve.Available from: http://www.ncbi.nlm.nih.gov/books/NBK26836/

Cotton, James A, Encyclopedia of Life Sciences, The impact of Gene Duplication on Human Genome Evolution, Article ID: A20841

Wagner, A. (1994) Evolution of gene networks by gene duplications: a mathematical model and its implications on genome organization. Proc. Natl. Acad. Sci. U. S. A. 91, 4387–4391

Czerny, T. et al. (1999) Twin of eyeless, a second Pax-6 gene of Drosophila, acts upstream of eyeless in the control of eye development. Mol. Cell 3, 297–307

http://content.csbs.utah.edu/~rogers/bio5410/Readings/Zhang-TRE-18-292.pdf

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