Although variation in the DNA molecule at single sites (e.g., individual SNPs) is generally well known, the discovery of a novel set of variation namely copy number variation (CNVs) four years ago become popular among human geneticists. These have been implicated in many human disorders, including mental disorders such as schizophrenia and autism. Evolutionary change is often narrowly defined as change in allele frequencies. But, genetic variation at the molecular level is also caused by sequence length variations, involving alterations of large scale chromosomal differences, such as deletions, duplications, insertions inversions and translocations. Copy number variation includes all of these processes.

The concept of CNVs is embraced with enthusiasm by the human genetics community, and has quickly emerged as hot area of research. But is it new?  No – it is not. The role of duplication in genetic diversity and as a potential evolutionary force has long been recognized by evolutionary biologists such as Haldane (1933), Bridges (1936) and Ohno (1970) to name a few.   Duplications also called paralogous sequences often arise due to unequal crossing over and also via capture of DNA inserts. They provide novel functions for the ancestral genes, the new ones assume new functions, and could even generate novel gene families (Lynch 2007). Nearly 30% of all duplications in the human genome are in tandem (Kent et al 2002).  Examples of tandemly duplicated sequences in the human genome include the Hox, the ubiquitin and the ribosomal gene clusters (Li 1997).  The duplicated genome may often confer beneficial effect to the organism as they produce additional amount of gene products. Numerous examples of gene and genome duplications (auto- and allo -polyploidy) are available on plants (Otto and Whitton 2000). Such examples are infrequent in animals, and more so in humans. Certain duplications may be seen across divergent species and genera, called arthologous sequences. An example of arthologous duplication for amylase gene in response to changing starch diet was recently demonstrated by Perry et al (2007).  What does duplication do in the genome? It provides plasticity and redundancy to the genome, and concomitant buffering capacity to organisms in the face of environmental uncertainty (de Visser et al 2003).
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Duplications cannot continue forever, however. Accumulation of paralagous sequences may be compared to genetic load, which could affect genome size and also have deleterious effects on the population that carries them. The same processes that fix or selectively remove single nucleotide polymorphisms also govern the maintenance of genome size. Newly arisen mutations with lethal effects are lost, and mildly deleterious and neutral mutations would take a longer time to get eliminated from populations. These processes obviously affect both viability and reproductive fitness of individuals, indicating evolutionary forces acting on the genome.  Most new mutations are slightly deleterious and these are eliminated due to selection and drift.  In small populations genetic drift eliminates newly arisen mutations due to chance alone, but selection operates in large populations. Large deletions will be quickly removed relative to smaller ones (Petrov 2002). Although many investigators have demonstrated selection using the SNP data (Nielsen 2005), selection for CNVs has been recently demonstrated in Drosophila (Emerson et al 2008).
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While symmetric division and inheritance is desirable in heredity, it is the asymmetry of the genome, due to structural variation, may lead to many pathological conditions in humans, and also propel evolutionary changes.  These new findings indicate that understanding of the distribution and maintenance of structural variants would be helpful to understand genome architecture and its health and evolution (Conrad and Hurles 2007) and bolster the importance of evolutionary process in the maintenance of genome architecture. Hence, these processes are aptly called “Evolution’s cauldron” (Kent et al 2003). It is difficult to interpret and make sense of the origin, maintenance and the role of CNVs without evolutionary insights.
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References

Bridges CB (1936). The Bar ‘Gene’ a duplication. Science 83: 210-211.

Conrad DF and Hurles ME (2007). The population genetics of structural variation. Nature Genet. 39: S30-S36.

de Visser JA, Hermisson J, Wagner GP, Meyers LA, Bagheri-Chaichian H et al (2003). Perspective: Evolution and detection of genetic robustness. Evolution 57: 1959-1972.

Emerson JJ, Cardoso-Moreira M, Borevitz, JO, and Long M. (2008). Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster. Science 320: 1629-1631.

Haldane JBS (1933). The Causes of Evolution. Longwood Green, London.

Kent WJ, Baertsch R, Hinrichs A, Miller W and Haussler D (2003). Evolution’s Cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl. Acad. Sci. USA. 100: 11484-11489.

Li WH (1997). Molecular Evolution. Sinauer Associates, Sunderland, MA.

Lynch M (2007). The Origins of Genome Architecture. Sinauer Associates, Sunderlans, MA.

Nielsen R. (2005). Molecular signatures of natural selection. Ann. Rev. Genet. 39: 197-218.

Ohno S (1970). Evolution by Gene Duplication. Springer, Berlin

Otto SP and Whitton J (2000). Polyploid incidence and evolution. Ann. Rev. Genet. 34: 401-437.

Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H et al (2007). Diet and the evolution of human amylase gene copy number variation. Nat. Genet.

Petrov DA (2002). DNA loss and evolution of genome size in Drosophila, Genetics 115: 81-91.