In population genetics, the founder effect is the loss of genetic variation that occurs when a new population is established by a very small number of individuals from a larger population. It was first fully outlined by Ernst Mayr in 1942, using existing theoretical work by those such as Sewall Wright. As a result of the loss of genetic variation, the new population may be distinctively different, both genetically and phenotypically, from the parent population from which it is derived. In extreme cases, the founder effect is thought to lead to the speciation and subsequent evolution of new species.
In the figure shown, the original population has nearly equal numbers of blue and red individuals. The three smaller founder populations show that one or the other color may predominate (founder effect), due to random sampling of the original population. A population bottleneck may also cause a founder effect even though it is not strictly a new population.
The founder effect occurs when a small number of migrants that are not genetically representative of the population from which they came establish in a new area. In addition to founder effects, the new population is often a very small population and so shows increased sensitivity to genetic drift, an increase in inbreeding, and relatively low genetic variation. This can be observed in the limited gene pool of Iceland, Faroe Islands, Easter Islanders and those native to Pitcairn Island. Another example is the legendarily high deaf population of Martha's Vineyard, which resulted in the development of Martha's Vineyard Sign Language.
In genetics, a 'founder mutation' is a mutation that appears in the DNA of one or more individuals who are founders of a distinct population. Founder mutations initiate with changes that occur in the DNA and can get passed down to other generations. 
Founder mutations originate in long stretches of DNA on a single chromosome—indeed, the original haplotype is the whole chromosome. As the generations progress, the proportion of the haplotype that is common to all carriers of the mutation is shortened (due to genetic recombination). This shortening allows scientists to roughly estimate the age of the mutation.
The founder effect is a special case of genetic drift, occurring when a small group in a population splinters off from the original population and forms a new one. The new colony may have less genetic variation than the original population, and through the random sampling of alleles during reproduction of subsequent generations, continue rapidly towards fixation. This consequence of inbreeding makes the colony more vulnerable to extinction.
When a newly formed colony is small, its founders can strongly affect the population's genetic makeup far into the future. In humans, which have a slow reproduction rate, the population will remain small for many generations, effectively amplifying the drift effect generation after generation until the population reaches a certain size. Alleles which were present but relatively rare in the original population can move to one of two extremes. The most common one is that the allele is soon lost altogether, but the other possibility is that the allele survives and within a few generations has become much more dispersed throughout the population. The new colony can experience an increase in the frequency of recessive alleles as well, and as a result, an increased number who are homozygous for certain recessive traits.
The variation in gene frequency between the original population and colony may also trigger the two groups to diverge significantly over the course of many generations. As the variance, or genetic distance, increases, the two separated populations may become distinctively different, both genetically and phenotypically, although not only genetic drift but also natural selection, gene flow and mutation will all contribute to this divergence. This potential for relatively rapid changes in the colony's gene frequency led most scientists to consider the founder effect (and by extension, genetic drift) a significant driving force in the evolution of new species. Sewall Wright was the first to attach this significance to random drift and small, newly isolated populations with his shifting balance theory of speciation. Following behind Wright, Ernst Mayr created many persuasive models to show that the decline in genetic variation and small population size accompanying the founder effect were critically important for new species to develop. However there is much less support for this view today since the hypothesis has been tested repeatedly through experimental research, and the results have been equivocal at best.[further explanation needed] Speciation by genetic drift is a specific case of peripatric speciation which in itself occurs in rare instances. It takes place when a random change in genetic frequency of population favours the survival of a few organisms of the species with rare genes which cause reproductive mutation. These surviving organisms then breed among themselves over a long period of time to create a whole new species whose reproductive systems or behaviors are no more compatible with the original population.[further explanation needed]
Serial founder effect
Serial founder effects have occurred when populations migrate over long distances. Such long distance migrations typically involve relatively rapid movements followed by periods of settlement. The populations in each migration carry only a subset of the genetic diversity carried from previous migrations. As a result, genetic differentiation tends to increase with geographic distance as described by the "Isolation by distance" model. The migration of humans out of Africa is characterized by serial founder effects. Africa has the highest degree of genetic diversity, which is consistent with an African origin of modern humans. After the initial migration from Africa, the Indian subcontinent was the first major settling point for modern humans. Consequently, India has the second highest genetic diversity in the world. In general, the genetic diversity of the Indian continent is a subset of Africa, and the genetic diversity outside Africa is a subset of India.
Founder effects in island ecology
Founder populations are essential to the study of island biogeography and island ecology. A natural "blank slate" is not easily found, but a classic series of studies on founder population effects were done following the catastrophic 1883 eruption of Krakatoa, which erased all life on the island. Another continuing study has been following the biocolonization of Surtsey, Iceland, a new volcanic island that erupted offshore between 1963 and 1967. An earlier event, the Toba eruption in Sumatra of about 73,000 YBP, covered some parts of India with 3–6 metres (9.8–20 ft) of ash, and must have coated the Nicobar Islands and Andaman Islands, much nearer in the ash fallout cone, with life-smothering layers, forcing the restart of their biodiversity from zero.
Founder effects in human populations
Due to various migrations throughout human history, founder effects are somewhat common among humans in different times and places. The French Canadians of Quebec are a classical example of founder population. Over 150 years of French colonization, between 1608 and 1760, it was estimated that 8,500 pioneers married and left at least one descendent on the territory.  Following the takeover of the colony by the British crown in 1760, descendents of French settlers continued to grow in number mainly because of high fertility rate. Intermarriage occurred mostly with the deported Acadians and migrants coming from the British Isles. Since the 20th century, immigration in Quebec and mixing of French Canadians involve people from all over the world. It was estimated that French Canadians of Quebec have ancestors of 6.75 different origins on average. However, the genetic contribution of the original French founders is predominant, explaining ~90% of regional gene pools, while Acadians (descended from other French settlers in eastern Canada) explain 4%, British 2% and Native American and other groups contributed less. [clarification needed]
Founder effects can also occur naturally as competing genetic lines die out. This means that an effective founder population consists only of those whose genetic print is identifiable in subsequent populations. Because in sexual reproduction, genetic recombination ensures that with each generation, only half the genetic material of a parent is represented in the offspring, some genetic lines may die out entirely, even though there are numerous progeny. A recent study concluded that of the people migrating across the Bering land bridge at the close of the ice age, only 70 left their genetic print in modern descendants, a minute effective founder population—this can be easily misread as though implying that only 70 people crossed to North America. The misinterpretations of "Mitochondrial Eve" are a case in point: it may be hard to explain that a "mitochondrial Eve" was not the only woman of her time.
In humans, founder effects can arise from cultural isolation, and inevitably, endogamy. For example, the Amish populations in the United States exhibit founder effects. This is because they have grown from a very few founders, have not recruited newcomers, and tend to marry within the community. Though still rare, phenomena such as polydactyly (extra fingers and toes, a symptom of Ellis-van Creveld syndrome) are more common in Amish communities than in the American population at large. Maple syrup urine disease affects approximately 1 out of 180,000 infants in the general population. Due in part to the founder effect, however, the disease has a much higher prevalence in children of Amish, Mennonite, and Jewish descent. Similarly, there is a high frequency of fumarase deficiency among the 10,000 members of the Fundamentalist Church of Jesus Christ of Latter Day Saints, a community which practices both endogamy and polygyny, where it is estimated 75 to 80 percent of the community are blood relatives of just two men—founders John Y. Barlow and Joseph Smith Jessop.
In 1814, 15 British colonists founded a settlement on Tristan da Cunha, a group of small islands in the Atlantic Ocean, midway between Africa and South America. One of the early colonists apparently carried a recessive allele for retinitis pigmentosa, a progressive form of blindness that afflicts homozygous individuals. Of the founding colonists' 240 descendants on the island in the late 1960s, 4 had retinitis pigmentosa. The frequency of the allele that causes this disease is ten times higher on Tristan da Cunha than in the populations from which the founders came.
More severe illnesses exist among certain Jewish groups. Ashkenazi Jews, for example, have a particularly high chance of suffering from Tay-Sachs disease, a fatal condition in young children (see Medical genetics of Ashkenazi Jews).
- Provine WB (July 2004). "Ernst Mayr: Genetics and speciation". Genetics 167 (3): 1041–6. PMC 1470966. PMID 15280221.
- Templeton AR (April 1980). "The Theory of Speciation VIA the Founder Principle". Genetics 94 (4): 1011–38. PMC 1214177. PMID 6777243.
- Hartwell, Hood, Goldberg, Reynolds, Silver, Veres, 2004, Genetics – from genes to genomes, page 688, McGraw Hill Higher Education
- Raven, Evert, Eichhorn, 1999, Biology of plants, page 241, W H Freeman and Company
- "Bioinformatics Glossary". bscs.org. Retrieved 2009-03-23.
- "Colorectal Cancer Research Definitions". www.mshri.on.ca. Retrieved 2009-03-23.
- "Founder Mutations: Scientific American". www.sciam.com. Retrieved 2009-03-23.
- Wade, Michael S.; Wolf, Jason; Brodie, Edmund D. (2000). Epistasis and the evolutionary process. Oxford [Oxfordshire]: Oxford University Press. p. 330. ISBN 0-19-512806-0.
- Mayr, Ernst, Jody Hey, Walter M. Fitch, Francisco José Ayala (2005). Systematics and the Origin of Species: on Ernst Mayr's 100th anniversary (Illustrated ed.). National Academies Press. p. 367. ISBN 978-0-309-09536-5.
- Howard, Daniel J.; Berlocher, Steward H. (1998). Endless Forms (Illustrated ed.). United States: Oxford University Press. p. 470. ISBN 978-0-19-510901-6.
- Ramachandran S, Deshpande O, Roseman CC, Rosenberg NA, Feldman MW, Cavalli-Sforza LL (November 2005). "Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa". Proc. Natl. Acad. Sci. U.S.A. 102 (44): 15942–7. doi:10.1073/pnas.0507611102. PMC 1276087. PMID 16243969.
- DeGiorgio M, Jakobsson M, Rosenberg NA (September 2009). "Explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa". Proc. Natl. Acad. Sci. U.S.A. 106 (38): 16057–62. doi:10.1073/pnas.0903341106. PMC 2752555. PMID 19706453.
- Maji S, Krithika S, Vasulu TS (April 2009). "Phylogeographic distribution of mitochondrial DNA macrohaplogroup M in India". J. Genet. 88 (1): 127–39. doi:10.1007/s12041-009-0020-3. PMID 19417557.
- Thangaraj K, Chaubey G, Singh VK, et al. (2006). "In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup 'M' in India". BMC Genomics 7: 151. doi:10.1186/1471-2164-7-151. PMC 1534032. PMID 16776823.
- "H. Charbonneau, B. Desjardins, J. Légaré, H. Denis, in A Population History of North America, M. R. Haines, Steckel, R.H., Ed. (Cambridge Univ. Press, 2000), pp. 99–142.
- "C. Bhérer et al., Am. J. Phys. Anthropol. 144, 432 (2011).
- Hey J (June 2005). "On the Number of New World Founders: A Population Genetic Portrait of the Peopling of the Americas". PLoS Biol. 3 (6): e193. doi:10.1371/journal.pbio.0030193. PMC 1131883. PMID 15898833.
- McKusick VA, Egeland JA, Eldridge R, Krusen DE (October 1964). "Dwarfism in the Amish I. The Ellis-van Creveld syndrome". Bull Johns Hopkins Hosp 115: 306–36. PMID 14217223.
About.com: Rare diseases - June 2004. Maple syrup urine disease by Mary Kugler, R.N.
Article describes MSUD prevalence among Amish and Mennonite children.
- Jaworski MA, Severini A, Mansour G, Konrad HM, Slater J, Henning K, Schlaut J, Yoon JW, Pak CY, Maclaren N, et al. (1989). "Genetic conditions among Canadian Mennonites: evidence for a founder effect among the old country (Chortitza) Mennonites". Clin Invest Med 12 (2): 127–141. PMID 2706837.
- Puffenberger EG (2003). "Genetic heritage of Old Order Mennonites in southeastern Pennsylvania". Am J Med Genet C Semin Med Genet. 121 (1): 18–31. doi:10.1002/ajmg.c.20003. PMID 12888983.
- Forbidden Fruit:Inbreeding among polygamists along the Arizona-Utah border is producing a caste of severely retarded and deformed children, by John Dougherty, The Phoenix New Times News, December 29, 2005, page 2.
- Founder effect
- Mayr, Ernst (1954). "Change of genetic environment and evolution". In Julian Huxley. Evolution as a Process. London: George Allen & Unwin. OCLC 974739.
- Mayr, Ernst (1963). Animal Species and Evolution. Cambridge: Belknap Press of Harvard University Press. ISBN 0-674-03750-2.