Editing Model organism (section)

==Selection==
Models are those organisms with a wealth of biological data that make them attractive to study as examples for other [[species]] and/or natural phenomena that are more difficult to study directly. Continual research on these organisms focuses on a wide variety of experimental techniques and goals from many different levels of biology—from [[ecology]], [[behavior]] and [[biomechanics]], down to the tiny functional scale of individual [[Tissue (biology)|tissues]], [[organelle]]s and [[protein]]s. Inquiries about the DNA of organisms are classed as [[Genetics|genetic]] models (with short generation times, such as the [[Drosophila melanogaster|fruitfly]] and [[Caenorhabditis elegans|nematode]] worm), [[experimental]] models, and [[genomic]] parsimony models, investigating pivotal position in the evolutionary tree.<ref>[http://genome.wellcome.ac.uk/doc_WTD020803.html What are model organisms?<!-- Bot generated title -->] {{webarchive |url=https://web.archive.org/web/20061028072001/http://genome.wellcome.ac.uk/doc_WTD020803.html |date=October 28, 2006 }}</ref> Historically, model organisms include a handful of species with extensive genomic research data, such as the NIH model organisms.<ref>[http://www.nih.gov/science/models/ NIH model organisms] {{webarchive |url=https://web.archive.org/web/20070822041956/http://www.nih.gov/science/models/ |date=August 22, 2007 }}</ref>

Often, model organisms are chosen on the basis that they are amenable to experimental manipulation. This usually will include characteristics such as short [[Biological life cycle|life-cycle]], techniques for genetic manipulation ([[inbreeding|inbred]] strains, [[stem cell]] lines, and methods of [[Transformation (genetics)|transformation]]) and non-specialist living requirements. Sometimes, the genome arrangement facilitates the sequencing of the model organism's genome, for example, by being very compact or having a low proportion of [[junk DNA]] (e.g. [[Saccharomyces cerevisiae|yeast]], [[Arabidopsis thaliana|arabidopsis]], or [[Takifugu rubripes|pufferfish]]).<ref name="Leica">{{cite web |title=Model Organisms in Research |url=https://www.leica-microsystems.com/applications/life-science/model-organisms-in-research/#:~:text=Model%20organisms%20are%20typically%20chosen,%2C%20organ%2C%20and%20system%20level. |website=Leica Microsystems |access-date=13 October 2024}}</ref>

When researchers look for an organism to use in their studies, they look for several traits. Among these are size, [[generation time]], accessibility, manipulation, genetics, conservation of mechanisms, and potential economic benefit. As comparative [[molecular biology]] has become more common, some researchers have sought model organisms from a wider assortment of [[lineage (evolution)|lineages]] on the tree of life.

===Phylogeny and genetic relatedness===
The primary reason for the use of model organisms in research is the evolutionary principle that all organisms share some degree of relatedness and genetic similarity due to [[common ancestry]]. The study of taxonomic human relatives, then, can provide a great deal of information about mechanism and disease within the human body that can be useful in medicine.{{cn|date=December 2023}}

Various phylogenetic trees for vertebrates have been constructed using comparative [[proteomics]], genetics, genomics as well as the geochemical and fossil record.<ref>{{cite journal |last1=Hedges |first1=S. Blair |title=The origin and evolution of model organisms |journal=Nature Reviews Genetics |date=November 2002 |volume=3 |issue=11 |pages=838–849 |doi=10.1038/nrg929 |pmid=12415314 }}</ref> These estimations tell us that humans and chimpanzees last shared a common ancestor about 6&nbsp;million years ago (mya). As our closest relatives, chimpanzees have a lot of potential to tell us about mechanisms of disease (and what genes may be responsible for human intelligence). However, chimpanzees are rarely used in research and are protected from highly invasive procedures. Rodents are the most common animal models. Phylogenetic trees estimate that humans and rodents last shared a common ancestor ~80-100mya.<ref>{{cite journal |last1=Bejerano |first1=Gill |last2=Pheasant |first2=Michael |last3=Makunin |first3=Igor |last4=Stephen |first4=Stuart |last5=Kent |first5=W. James |last6=Mattick |first6=John S. |last7=Haussler |first7=David |title=Ultraconserved Elements in the Human Genome |journal=Science |date=28 May 2004 |volume=304 |issue=5675 |pages=1321–1325 |doi=10.1126/science.1098119 |pmid=15131266 |bibcode=2004Sci...304.1321B }}</ref><ref name="Chinwalla2002">{{Cite journal
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| title = Initial sequencing and comparative analysis of the mouse genome
| journal = Nature
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| year = 2002
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| doi-access = free
}}</ref> Despite this distant split, humans and rodents have far more similarities than they do differences. This is due to the relative stability of large portions of the genome, making the use of vertebrate animals particularly productive.{{cn|date=December 2023}}

Genomic data is used to make close comparisons between species and determine relatedness. Humans share about 99% of their genome with chimpanzees<ref>{{Cite journal
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| last2 = Cooper | first2 = D. N.
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| title = Understanding the recent evolution of the human genome: Insights from human-chimpanzee genome comparisons
| journal = Human Mutation
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}}</ref><ref>{{cite journal |last1=Kehrer-Sawatzki |first1=Hildegard |last2=Cooper |first2=David N. |title=Structural divergence between the human and chimpanzee genomes |journal=Human Genetics |date=18 January 2007 |volume=120 |issue=6 |pages=759–778 |doi=10.1007/s00439-006-0270-6 |pmid=17066299 }}</ref> (98.7% with bonobos)<ref>{{Cite journal
| last1 = Prüfer | first1 = K.
| last2 = Munch | first2 = K.
| last3 = Hellmann | first3 = I.
| last4 = Akagi | first4 = K.
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| title = The bonobo genome compared with the chimpanzee and human genomes
| doi = 10.1038/nature11128
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| bibcode = 2012Natur.486..527P}}</ref> and over 90% with the mouse.<ref name="Chinwalla2002" /> With so much of the genome conserved across species, it is relatively impressive that the differences between humans and mice can be accounted for in approximately six thousand genes (of ~30,000 total). Scientists have been able to take advantage of these similarities in generating experimental and predictive models of human disease.{{cn|date=December 2023}}