Model organisms

A model organism is a species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms. This is possible because fundamental biological principles such as metabolic, regulatory, and developmental pathways, and the genes that code for them, are conserved through evolution.

Often, model organisms are chosen on the basis that they are amenable to experimental manipulation. This usually will include characteristics such as; short life-cycle, techniques for genetic manipulation (inbred strains, stem cell lines, and transfection systems), 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.

There are many model organisms. The first model organism for molecular biology was probably the bacterium Escherichia coli which is common in the human digestive system (and usually beneficial -- the dangerous E. coli O157:H7 is a rare strain). This also led to a study of many bacteriophages, particularly phage lambda.

In eukaryotes, several yeasts, particularly Saccharomyces cerevisiae ("baker's" or "budding" yeast), have been widely studied, largely because they are quick and easy to grow. The cell cycle in a simple yeast is very similar to the cell cycle in humans, and regulated by homologous proteins. The fruit fly Drosophila melanogaster was studied, again because it was easy to grow for a multicellular organism. The roundworm Caenorhabditis elegans is studied because it has very defined development patterns and can be rapidly assayed for abnormalities.

When researchers look for an organism to use in their studies, they look for several traits. Common 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 that represent assorted lineages of life.

Viruses

 * lambda phage

Prokaryotes

 * Escherichia coli (E. coli)
 * Bacillus subtilis
 * Mycoplasma genitalium - a minimal organism
 * Vibrio fischeri - quorum sensing, bioluminescence and animal-bacterial symbiosis with Hawaiian bobtail squid
 * Synechocystis, a photosynthetic cyanobacteria widely used in photosynthesis research.
 * Pseudomonas fluorescens, a soil bacterium that readily diversifies into different strains in the lab.

Protozoa

 * Chlamydomonas reinhardtii - a unicellular green alga used in photosynthesis research.
 * Tetrahymena thermophila - a free living freshwater ciliate protozoan

Fungi

 * Aspergillus nidulans, subject of genetics studies
 * Neurospora crassa - red bread mold
 * Saccharomyces cerevisiae, baker's yeast or budding yeast (used in brewing and baking)
 * Schizosaccharomyces pombe, fission yeast, subject of genetic studies

Plants

 * Arabidopsis thaliana, a plant, usually called Arabidopsis. A considerable amount of new knowledge today is being generated from studying this plant model. This to mustard related, quickly growing weed was the first plant to have its genome sequenced. Perhaps the most important model in plant sciences. (Plant physiology, Developmental biology, Molecular genetics, Population genetics, Cytology, Molecular biology)
 * Tobacco BY-2 cells is suspension cell line from tobacco (Nicotiana tabaccum). Useful for general plant physiology studies on cell level. Genome of this particular cultivar will be not sequenced (at least in near future), but seqencing of its wild species Nicotiana tabaccum is presently under progres. (Cytology, Plant physiology, Biotechnology)
 * Lotus japonicus a model legume plant. (Agronomy, Molecular biology)
 * Medicago truncatula is a model legume, closely related to the common alfalfa. It's rather small genome is currently being sequenced. (Agronomy, Molecular biology)
 * Rice (Oryza sativa) is used as a model for cereal biology. Sequencing of its genome is under progres. (Agronomy, Molecular biology)
 * Brachypodium distachyon is an emerging experimental model grass that has many attributes that make it an excellent model for temperate cereals. (Agronomy, Molecular biology, Genetics)
 * Maize (Zea mays ssp. mays) is a cereal grain. Its genetic features helped to create transposon theory of "jumping genes. Its genome is being sequenced. (Genetics,  Molecular biology, Agronomy)

Invertebrates

 * Arbacia punctulata, the purple-spined sea urchin, classical subject of embryological studies
 * Caenorhabditis elegans, a nematode, usually called C. elegans - an excellent model for understanding the genetic control of development and physiology. C. elegans was the first multicellular organism whose genome was completely sequenced
 * Drosophila, usually the species Drosophila melanogaster - a kind of fruit fly, famous as the subject of genetics experiments by Thomas Hunt Morgan and others. Easily raised in lab, rapid generations, mutations easily induced, many observable mutations. Recently, Drosophila has been used for neuropharmacological research . (Molecular genetics, Population genetics, Developmental biology).
 * Euprymna scolopes, the Hawaiian bobtail squid, model for animal-bacterial symbiosis, bioluminescent vibrios.
 * Hydra, a Cnidaria, is the model organism to understand the evolution of bilaterian body plans.
 * Loligo pealei, a squid, subject of studies of nerve function because of its giant axon (nearly 1 mm diameter, roughly a thousand times larger than typical mammalian axons)
 * Stomatogastric ganglion, arthropods digestive systems are a model for motor pattern generation seen in all repetitive motions
 * Tribolium castaneum, the flour beetle - a small, easily kept darkling beetle used especially in behavioural ecology experiments.

Vertebrates

 * Cavius porcellus, the guinea pig, used by Robert Koch and other early bacteriologists as a host for bacterial infections, hence a byword for "laboratory animal" even though rarely used today.
 * Rat (Rattus norvegicus) - particularly useful as a toxicology model; also particularly useful as a neurological model and source of primary cell cultures, owing to the larger size of organs and suborganellar structures relative to the mouse. (Molecular evolution, Genomics)
 * Mouse (Mus musculus) - the classic model vertebrate. Many inbred strains exist, as well as lines selected for particular traits, often of medical interest, e.g. body size, obesity, muscularity. (Quantitative genetics, Molecular evolution, Genomics)
 * Zebrafish (Brachydanio rerio), a freshwater fish, has a nearly transparent body which provides unique visual access to the animal's internal anatomy throughout its life. Zebrafish are used to study development, toxicology and toxicopathology, specific gene function and roles of signaling pathways.
 * Xenopus laevis, the African clawed toad, also used in development because of its large cells, esp. egg cells.
 * Takifugu rubipres, a pufferfish - has a small genome with little junk DNA
 * Dog (Canis lupus familiaris) - an important respiratory and cardiovascular model
 * Oryzias latipes, Medaka (the Japanese ricefish) is an important model in developmental biology, and has the advantage of being much sturdier than the traditional Zebrafish.

Sexual selection and sexual conflict

 * Callusobruchus maculatus, the bruchid beetle
 * Chorthippus parallelus, the meadow grasshopper
 * Coelopidae - seaweed flies
 * Diopsidae - stalk-eyed flies
 * Drosophila spp. - fruit flies
 * Gryllus bimaculatus, the field cricket
 * Scathofaga stercoraria, the yellow dung fly

Hybrid zones

 * Bombina bombina and variegata
 * Podisma spp. in the Alps