Editing Comparative genomics (section)

==Evolutionary principles==
{{Main|Evolution}}
One character of biology is evolution, [[evolutionary theory]] is also the theoretical foundation of comparative genomics, and at the same time the results of comparative genomics unprecedentedly enriched and developed the theory of evolution. When two or more of the genome sequence are compared, one can deduce the evolutionary relationships of the sequences in a phylogenetic tree. Based on a variety of biological genome data and the study of vertical and horizontal evolution processes, one can understand vital parts of the gene structure and its regulatory function.

Similarity of related genomes is the basis of comparative genomics. If two creatures have a recent common ancestor, the differences between the two species genomes are evolved from the ancestors' genome. The closer the relationship between two organisms, the higher the similarities between their genomes. If there is close relationship between them, then their genome will display a linear behaviour ([[synteny]]), namely some or all of the genetic sequences are conserved. Thus, the genome sequences can be used to identify gene function, by analyzing their homology (sequence similarity) to genes of known function.
[[File:BrowserFoxp2.jpg| Human [[FOXP2]] gene and evolutionary conservation is shown in and multiple alignment (at bottom of figure) in this image from the [[UCSC Genome Browser]]. Note that conservation tends to cluster around coding regions (exons). |thumb|right]]
Orthologous sequences are related sequences in different species: a gene exists in the original species, the species divided into two species, so genes in new species are orthologous to the sequence in the original species. Paralogous sequences are separated by gene cloning (gene duplication): if a particular gene in the genome is copied, then the copy of the two sequences is paralogous to the original gene. A pair of orthologous sequences is called orthologous pairs (orthologs), a pair of paralogous sequence is called collateral pairs (paralogs). Orthologous pairs usually have the same or similar function, which is not necessarily the case for collateral pairs. In collateral pairs, the sequences tend to evolve into having different functions.

Comparative genomics exploits both similarities and differences in the [[proteins]], [[RNA]], and [[regulatory regions]] of different organisms to infer how [[Selection (biology)|selection]] has acted upon these elements. Those elements that are responsible for similarities between different [[species]] should be conserved through time ([[stabilizing selection]]), while those elements responsible for differences among species should be divergent ([[Directional selection|positive selection]]). Finally, those elements that are unimportant to the evolutionary success of the organism will be unconserved (selection is neutral).

One of the important goals of the field is the identification of the mechanisms of eukaryotic genome evolution. It is however often complicated by the multiplicity of events that have taken place throughout the history of individual lineages, leaving only distorted and superimposed traces in the genome of each living organism. For this reason comparative genomics studies of small [[model organisms]] (for example the model [[Caenorhabditis elegans]] and closely related [[Caenorhabditis briggsae]]) are of great importance to advance our understanding of general mechanisms of evolution.<ref>{{cite journal |vauthors=Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D'Eustachio P, Fitch DH, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, Waterston RH |title=The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics |journal=PLOS Biology |volume=1 |issue=2 |pages=E45 |date=November 2003 |pmid=14624247 |pmc=261899 |doi=10.1371/journal.pbio.0000045 |doi-access=free}}</ref><ref>{{Cite journal |title=Newly Sequenced Worm a Boon for Worm Biologists |journal=PLOS Biology |volume=1 |issue=2 |pages=e4 |year=2003 |doi=10.1371/journal.pbio.0000044| doi-access=free |pmc=261884}}</ref>