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Speciation is the evolutionary process by which new biological species arise. There are four modes of natural speciation, based on the extent to which speciating populations are geographically isolated from one another: allopatric, peripatric, parapatric, and sympatric. Speciation may also be induced artificially, through animal husbandry or laboratory experiments. Observed examples of each kind of speciation are provided throughout.
All forms of natural speciation have taken place over the course of evolution, though it still remains a subject of debate as to the relative importance of each mechanism in driving biodiversity. 
There is debate as to the rate at which speciation events occur over geologic time. While some evolutionary biologists claim that speciation events have remained relatively constant over time, some palaeontologists such as Niles Eldredge and Stephen Jay Gould have argued that species usually remain unchanged over long stretches of time, and that speciation occurs only over relatively brief intervals, a view known as punctuated equilibrium.
During allopatric speciation, a population splits into two geographically isolated allopatric populations (for example, by habitat fragmentation due to geographical change such as mountain building or social change such as emigration). The isolated populations then undergo genotypic and/or phenotypic divergence as they (a) become subjected to dissimilar selective pressures or (b) they independently undergo genetic drift. When the populations come back into contact, they have evolved such that they are reproductively isolated and are no longer capable of exchanging genes.
- Observed instances
Island genetics, the tendency of small, isolated genetic pools to produce unusual traits, has been observed in many circumstances, including insular dwarfism and the radical changes among certain famous island chains, like Komodo and Galápagos, the latter having given rise to the modern expression of evolutionary theory, after being observed by Charles Darwin. Perhaps the most famous example of allopatric speciation is Darwin's Galápagos Finches.
In peripatric speciation, new species are formed in isolated, small peripheral populations which are prevented from exchanging genes with the main population. It is related to the concept of a founder effect, since small populations often undergo bottlenecks. Genetic drift is often proposed to play a significant role in peripatric speciation.
- Observed instances
- Mayr bird fauna
- The Australian bird Petroica multicolor
- Reproductive isolation occurs in populations of Drosophila subject to population bottlenecking
The London Underground mosquito is a variant of the mosquito Culex pipiens which entered in the London Underground in the nineteenth century. Evidence for its speciation include genetic divergence, behavioral differences, and difficulty in mating.
In parapatric speciation, the zones of two diverging populations are separate but do overlap. There is only partial separation afforded by geography, so individuals of each species may come in contact or cross the barrier from time to time, but reduced fitness of the heterozygote leads to selection for behaviours or mechanisms which prevent breeding between the two species.
Ecologists refer to parapatric and peripatric speciation in terms of ecological niches. A niche must be available in order for a new species to be successful.
- Observed instances
- Ring species
- the grass Anthoxanthum has been known to undergo parapatric speciation in such cases as mine contamination of an area.
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In sympatric speciation, species diverge while inhabiting the same place. Often cited examples of sympatric speciation are found in insects which become dependent on different host plants in the same area. However, the existence of sympatric speciation as a mechanism of speciation is still hotly contested. People have argued that the evidences of sympatric speciation are in fact examples of micro-allopatric, or heteropatric speciation. The most widely accepted example of sympatric speciation is that of the cichlids of Lake Nabugabo in East Africa, which is thought to be due to sexual selection.
Speciation via polyploidization
Polyploidy is a mechanism often attributed to causing some speciation events in sympatry. Not all polyploids are reproductively isolated from their parental plants, so an increase in chromosome number may not result in the complete cessation of gene flow between the incipient polyploids and their parental diploids (see also hybrid speciation).
Polyploidy is observed in many species of both plants and animals. In fact, it has been proposed that all of the existing plants and most of the animals are polyploids or have undergone an event of polyploidization in their evolutionary history.
Speciation via hybrid formation
Hybridization between two different species sometimes leads to a distinct phenotype. This phenotype can also be fitter than the parental lineage and as such natural selection may then favor these individuals. Eventually, if reproductive isolation is achieved, it may lead to a separate species. However, reproductive isolation between hybrids and their parents is particularly difficult to achieve and thus hybrid speciation is considered an extremely rare event.
Reinforcement is the process by which natural selection increases reproductive isolation. It may occur after two populations of the same species are separated and then come back into contact. If their reproductive isolation was complete, then they will have already developed into two separate incompatible species. If their reproductive isolation is incomplete, then further mating between the populations will produce hybrids, which may or may not be fertile. If the hybrids are infertile, or fertile but less fit than their ancestors, then there will be no further reproductive isolation and speciation has essentially occurred (e.g., as in horses and donkeys.) The reasoning behind this is that if the parents of the hybrid offspring each have naturally selected traits for their own certain environments, the hybrid offspring will bear traits from both, therefore would not fit either ecological niche as well as the parents did. The low fitness of the hybrids would cause selection to favor assortative mating, which would control hybridization. If the hybrid offspring are more fit than their ancestors, then the populations will merge back into the same species within the area they are in contact.
Reinforcement is required for both parapatric and sympatric speciation. Without reinforcement, the geographic area of contact between different forms of the same species, called their "hybrid zone," will not develop into a boundary between the different species. Hybrid zones are regions where diverged populations meet and interbreed. Hybrid offspring are very common in these regions, which are usually created by diverged species coming into secondary contact. Without reinforcement the two species would have uncontrollable inbreeding. Reinforcement may be induced in artificial selection experiments as described below.
New species have been created by domesticated animal husbandry, but the initial dates and methods of the initiation of such species are not clear. For example, domestic sheep were created by hybridisation, and no longer produce viable offspring with Ovis orientalis, one species from which they are descended. Domestic cattle, on the other hand, can be considered the same species as several varieties of wild ox, gaur, yak, etc., as they readily produce fertile offspring with them.
The best-documented creations of new species in the laboratory were performed in the late 1980s. William Rice and G.W. Salt bred fruit flies, Drosophila melanogaster, using a maze with three different choices of habitat such as light/dark and wet/dry. Each generation was placed into the maze, and the groups of flies which came out of two of the eight exits were set apart to breed with each other in their respective groups. After thirty-five generations, the two groups and their offspring were isolated reproductively because of their strong habitat preferences: they mated only within the areas they preferred, and so did not mate with flies that preferred the other areas. 
Diane Dodd was also able to show allopatric speciation by reproductive isolation in Drosophila pseudoobscura fruit flies after only eight generations using different food types, starch and maltose. Dodd's experiment has been easy for many others to replicate, including with other kinds of fruit flies and foods.
The history of such attempts is described in Rice and Hostert (1993).
Hybridization between two different species sometimes leads to a distinct phenotype. This phenotype can also be fitter than the parental lineage and as such natural selection may then favor these individuals. Eventually, if reproductive isolation is achieved, it may lead to a separate species. However, reproductive isolation between hybrids and their parents is particularly difficult to achieve and thus hybrid speciation is considered an extremely rare event. The Mariana Mallard arose from hybrid speciation.
Hybridization without change in chromosome number is called homoploid hybrid speciation. It is considered very rare but has been shown in Heliconius butterflies  and sunflowers. Polyploid speciation, which involves changes in chromosome number, is a more common phenomena, especially in plant species.
Gene transposition as a cause
Theodosius Dobzhansky, who studied fruit flies in the early days of genetic research in 1930s, speculated that parts of chromosomes that switch from one location to another might cause a species to split into two different species. He mapped out how it might be possible for sections of chromosomes to relocate themselves in a genome. Those mobile sections can cause sterility in inter-species hybrids, which can act as a speciation pressure. In theory, his idea was sound, but scientists long debated whether it actually happened in nature. Eventually a competing theory involving the gradual accumulation of mutations was shown to occur in nature so often that geneticists largely dismissed the moving gene hypothesis.
However, recent research shows that jumping of a gene from one chromosome to another can contribute to the birth of new species. This validates the reproductive isolation mechanism, a key component of speciation.
Interspersed repetitive DNA sequences function as isolating mechanisms. These repeats protect newly evolving gene sequences from being overwritten by gene conversion, due to the creation of non-homologies between otherwise homologous DNA sequences. The non-homologies create barriers to gene conversion. This barrier allows nascent novel genes to evolve without being overwritten by the progenitors of these genes. This uncoupling allows the evolution of new genes, both within gene families and also allelic forms of a gene. The importance is that this allows the splitting of a gene pool without requiring physical isolation of the organisms harboring those gene sequences.
Humans have genetic similarities with chimpanzees and gorillas, suggesting common ancestors. Analysis of genetic drift and recombination using a Markov model suggests humans and chimpanzees speciated apart 4.1 million years ago.
- Observed Instances of Speciation by Joseph Boxhorn. Retrieved 28 October 2006.
- J.M. Baker (2005). "Adaptive speciation: The role of natural selection in mechanisms of geographic and non-geographic speciation". Studies in History and Philosophy of Biological and Biomedical Sciences. 36: 303–326. available online
- Katharine Byrne and Richard A Nichols (1999) "Culex pipiens in London Underground tunnels: differentiation between surface and subterranean populations"
- Ridley, M. (2003) "Speciation - What is the role of reinforcement in speciation?" adapted from Evolution 3rd edition (Boston: Blackwell Science) tutorial online
- Hiendleder S., et al. (2002) "Molecular analysis of wild and domestic sheep questions current nomenclature and provides evidence for domestication from two different subspecies" Proceedings of the Royal Society B: Biological Sciences 269:893-904
- Nowak, R. (1999) Walker's Mammals of the World 6th ed. (Baltimore: Johns Hopkins University Press)
- Rice, W.R. and G.W. Salt (1988). "Speciation via disruptive selection on habitat preference: experimental evidence". The American Naturalist. 131: 911–917.
- Dodd, D.M.B. (1989) "Reproductive isolation as a consequence of adaptive divergence in Drosophila pseudoobscura." Evolution 43:1308–1311.
- Kirkpatrick, M. and V. Ravigné (2002) "Speciation by Natural and Sexual Selection: Models and Experiments" The American Naturalist 159:S22–S35 DOI
- W.R. Rice and E.E. Hostert (1993). "Laboratory experiments on speciation: What have we learned in forty years?". Evolution. 47: 1637–1653.
- Mavarez, J. (2006). "Speciation by hybridization in Heliconius butterflies". Nature. Unknown parameter
- University of Rochester Press Releases
- Masly, John P., Corbin D. Jones, Mohamed A. F. Noor, John Locke, and H. Allen Orr (September 2006). "Gene Transposition as a Cause of Hybrid Sterility in Drosophila". Science. 313 (5792): pp. 1448-1450. Retrieved 2007-03-18.
- Minkel, J.R. (September 8, 2006) "Wandering Fly Gene Supports New Model of Speciation" Science News
- Hobolth A, Christensen OF, Mailund T, Schierup MH (2007) "Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model." PLoS Genet 3(2): e7 (doi:10.1371/journal.pgen.0030007)
- Coyne, J. A. & Orr, H. A. (2004). Speciation. Sunderlands, Massachusetts: Sinauer Associates, Inc. ISBN 0-87893-089-2.
- Grant, V. (1981). Plant Speciation (2nd Edit. ed.). New York: Columbia University Press. ISBN 0-231-05113-1.
- Mayr, E. (1963). Animal Species and Evolution. Harvard University Press. ISBN 0-674-03750-2
- White, M. J. D. (1978). Modes of Speciation. San Francisco, California: W. H. Freeman and Company. ISBN 0-716-70284-3.
- Dedicated issue of Philosophical Transactions B on Speciation in microorganisms is freely available.
- Observed Instances of Speciation from the Talk.Origins Frequently Asked Questions
- Speciation, and
- Evidence for Speciation from Understanding Evolution by the University of California Museum of Paleontology
- Speciation from John Hawks' Anthropology Weblog - paleoanthropology, genetics, and evolution
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