Founder effect

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Founder effect: The original population (left) could give rise to different founder populations (right). Founder effect.svg
Founder effect: The original population (left) could give rise to different founder populations (right).

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, [1] using existing theoretical work by those such as Sewall Wright. [2] As a result of the loss of genetic variation, the new population may be distinctively different, both genotypically 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. [3]

Contents

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, though it is not strictly a new population.

The founder effect occurs when a small group of migrants—not genetically representative of the population from which they came—establish in a new area. [4] [5] In addition to founder effects, the new population is often very small, so it shows increased sensitivity to genetic drift, an increase in inbreeding, and relatively low genetic variation.

Founder mutation

In genetics, a founder mutation is a mutation that appears in the DNA of one or more individuals which are founders of a distinct population. Founder mutations initiate with changes that occur in the DNA and can be passed down to other generations. [6] [7] Any organism—from a simple virus to something complex like a mammal—whose progeny carry its mutation has the potential to express the founder effect, [8] for instance a goat [9] [10] or a human. [11]

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. [12]

General

The founder effect is a type 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. The homozygosity increase can be calculated as , where equals inbreeding coefficient and equals population size. [13] This consequence of inbreeding makes the colony more vulnerable to extinction. [14]

The small founding population experiences a loss of heterozygosity after multiple generations. ("Genetic Drift" by Boundless, 2015. ) Founder effect Illustration.jpg
The small founding population experiences a loss of heterozygosity after multiple generations. (“Genetic Drift” by Boundless, 2015. )

The per generation loss of heterozygosity can be calculated as , where equals heterozygosity. [13] The population of the founders of the colony can also be calculated if the loss of heterozygosity from the bottleneck is known using the same equation. [13]

When a newly formed colony is small, its founders can strongly affect the population's genetic makeup far into the future. In humans, who 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. The post-bottleneck population growth rate can be calculated as , where equals the number of generations, is the growth rate, is the population equilibrium size, is the natural logarithm base, and is the constant , where is the original size of the founding colony. [13]

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. [13] The equation to calculate reccessive allele frequencies is based on Hardy-Wienberg assumptions. [13]

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 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. [16] 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. [17] However, much less support for this view is shown 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. [18] 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 longer compatible with the original population. [ further explanation needed ] [19]

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. [20] The migration of humans out of Africa is characterized by serial founder effects. [21] Africa has the highest degree of human genetic diversity of any continent, which is consistent with an African origin of modern humans. [22]

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 was done following the catastrophic 1883 eruption of Krakatoa, which erased all life on the island. [23] [24] 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 about 73,000 years ago, covered some parts of India with 3–6 m (10–20 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. [25]

However, not all founder effect studies are initiated after a natural disaster; some scientists study the reinstatement of a species that became locally extinct or hadn't existed there before. A study has been in place since 1958 studying the wolf/moose interaction on Isle Royale in Lake Superior after those animals naturally migrated there, perhaps on winter ice. Hajji and others, and Hundertmark & Van Daele, studied the current population statuses of past founder effects in Corsican red deer and Alaskan elk, respectively. Corsican red deer are still listed as an endangered species, decades after a severe bottleneck. They inhabit the Tyrrhenian islands and surrounding mainlands currently, and before the bottleneck, but Hajji and others wanted to know how the deer originally got to the islands, and from what parent population or species they were derived. Through molecular analysis, they were able to determine a possible lineage, with red deer from the islands of Corsica and Sardinia being the most related to one another. These results are promising, as the island of Corsica was repopulated with red deer from the Sardinian island after the original Corsican red deer population became extinct, and the deer now inhabiting the island of Corsica are diverging from those inhabiting Sardinia. [26] [27]

Kolbe and others set up a pair of genetically sequenced and morphologically examined lizards on seven small islands to watch each new population's growth and adaptation to its new environment. Specifically, they were looking at the effects on limb length and perch width, both widely varying phenotypic ranges in the parent population. Unfortunately, immigration did occur, but the founder effect and adaptive differentiation, which could eventually lead to peripatric speciation, were statistically and biologically significant between the island populations after a few years. The authors also point out that although adaptive differentiation is significant, the differences between island populations best reflect the differences between founders and their genetic diversity that has been passed down through the generations. [28]

Founder effects can affect complex traits, such as song diversity. In the Common Myna (Acridotheres tristis), the percentage of unique songs within a repertoire and within‐song complexity were significantly lower in birds from founder populations. [29]

It was found by Tarr et al. (1998) that the loss of heterozygosity of the Laysan finch (Telespiza cantans) after founding events on small islands in the Pacific Ocean closely matched theoretical calculations upon examination of microsatellite loci. [30]

Among human populations

Genetic studies of founder effect have concentrated on discovering ancestral and novel genetic diseases caused by founder effect and, to a lesser degree, on ancestry-related founder effects on populations, races, and ancient migrations, as well other aspects. The founder population could be the common ancestry of race or ethnicity or the forced localizations caused by artificial countries inside the larger group of ancestry, hence causing an original founder effect.[ clarification needed ] Race and specific founder effect mutation diseases are found in all races or ethnicities,[ citation needed ] and country-specific mutation diseases are caused by increasing homozygosity (the existence of same gene on both chromosomes pairs, hence a recessive disease may increase in just few generations). The genetic abnormality will increase incrementally with the decrease of number of isolated populations making tribe-specific diseases (such as Ashkenazis, Amish, and Bedouins) and novel genetic defects. [31] In recessive diseases, founder populations where underlying levels of genome-wide homozygosity are high due to shared common ancestry, but also for consanguineous populations that will have large genome-wide homozygous regions due to inbreeding. Having a catalog of disease-associated variation in these populations enables rapid, early, and accurate diagnoses that may improve patient outcomes due to informed clinical management and early interventions. Enclosed communities such as Amish communities, Ashkenazi communities, and relatively isolated islands allow scientists to better understand and further discover the mutated genes that cause these rare diseases and allow them to also discover protective genes as well. [32]

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, an estimated 8,500 pioneers married and left at least one descendant on the territory. [33] Following the takeover of the colony by the British crown in 1760, immigration from France effectively stopped, but descendants of French settlers continued to grow in number mainly due to their 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. While the French Canadians of Quebec today may be partly of other ancestries, the genetic contribution of the original French founders is predominant, explaining about 90% of regional gene pools, while Acadian (descended from other French settlers in eastern Canada) admixtures contributing 4% British and 2% Native American and other groups contributing less. [34]

In humans, founder effects can arise from cultural isolation, and inevitably, endogamy. For example, the Amish populations in the United States exhibit founder effects 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 a condition such as [35] [36] Weyers acrodental dysostosis [35] or Ellis–Van Creveld syndrome [36] ) are more common in Amish communities than in the American population at large. [37] Maple syrup urine disease affects about one out of 180,000 infants in the general population.[ citation needed ] Due in part to the founder effect, [38] however, the disease has a much higher prevalence in children of Amish, Mennonite, and Jewish descent. [39] [40] Similarly, a high frequency of fumarase deficiency exists 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 an estimated 75-80% of the community are blood relatives of just two men—founders John Y. Barlow and Joseph Smith Jessop. [41] In South Asia, castes like the Gujjars, the Baniyas and the Pattapu Kapu have estimated founder effects about 10 times as strong as those of Finns and Ashkenazi Jews. [42]

The island of Pingelap also suffered a population bottleneck in 1775 following a typhoon that had reduced the population to only 20 people. As a result, complete achromatopsia has a current rate of occurrence of roughly 10%, with an additional 30% being carriers of this recessive condition.

Around 1814, a small group of 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 rare, recessive allele for retinitis pigmentosa, a progressive form of blindness that afflicts homozygous individuals. As late as 1961, the majority of the genes in the gene pool on Tristan were still derived from 15 original ancestors; as a consequence of the inbreeding, of 232 people tested in 1961, four were suffering from retinitis pigmentosa. This represents a prevalence of 1 in 58, compared with a worldwide prevalence of around 1 in 4,000. [43]

The abnormally high rate of twin births in Cândido Godói could be explained by the founder effect. [44]

On 31 August 2023, researchers reported, based on genetic studies, that a human ancestor population bottleneck (from a possible 100,000 to 1000 individuals) occurred "around 930,000 and 813,000 years ago ... lasted for about 117,000 years and brought human ancestors close to extinction." [45] [46]

See also

Related Research Articles

<span class="mw-page-title-main">Inbreeding</span> Reproduction by closely related organisms

Inbreeding is the production of offspring from the mating or breeding of individuals or organisms that are closely related genetically. By analogy, the term is used in human reproduction, but more commonly refers to the genetic disorders and other consequences that may arise from expression of deleterious recessive traits resulting from incestuous sexual relationships and consanguinity. Animals avoid incest only rarely.

Genetic drift, also known as random genetic drift, allelic drift or the Wright effect, is the change in the frequency of an existing gene variant (allele) in a population due to random chance.

Small populations can behave differently from larger populations. They are often the result of population bottlenecks from larger populations, leading to loss of heterozygosity and reduced genetic diversity and loss or fixation of alleles and shifts in allele frequencies. A small population is then more susceptible to demographic and genetic stochastic events, which can impact the long-term survival of the population. Therefore, small populations are often considered at risk of endangerment or extinction, and are often of conservation concern.

<span class="mw-page-title-main">Population bottleneck</span> Effects of a sharp reduction in numbers on the diversity and robustness of a population

A population bottleneck or genetic bottleneck is a sharp reduction in the size of a population due to environmental events such as famines, earthquakes, floods, fires, disease, and droughts; or human activities such as genocide, specicide, widespread violence or intentional culling. Such events can reduce the variation in the gene pool of a population; thereafter, a smaller population, with a smaller genetic diversity, remains to pass on genes to future generations of offspring. Genetic diversity remains lower, increasing only when gene flow from another population occurs or very slowly increasing with time as random mutations occur. This results in a reduction in the robustness of the population and in its ability to adapt to and survive selecting environmental changes, such as climate change or a shift in available resources. Alternatively, if survivors of the bottleneck are the individuals with the greatest genetic fitness, the frequency of the fitter genes within the gene pool is increased, while the pool itself is reduced.

Population genetics is a subfield of genetics that deals with genetic differences within and among populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and population structure.

<span class="mw-page-title-main">Gene flow</span> Transfer of genetic variation from one population to another

In population genetics, gene flow is the transfer of genetic material from one population to another. If the rate of gene flow is high enough, then two populations will have equivalent allele frequencies and therefore can be considered a single effective population. It has been shown that it takes only "one migrant per generation" to prevent populations from diverging due to drift. Populations can diverge due to selection even when they are exchanging alleles, if the selection pressure is strong enough. Gene flow is an important mechanism for transferring genetic diversity among populations. Migrants change the distribution of genetic diversity among populations, by modifying allele frequencies. High rates of gene flow can reduce the genetic differentiation between the two groups, increasing homogeneity. For this reason, gene flow has been thought to constrain speciation and prevent range expansion by combining the gene pools of the groups, thus preventing the development of differences in genetic variation that would have led to differentiation and adaptation. In some cases dispersal resulting in gene flow may also result in the addition of novel genetic variants under positive selection to the gene pool of a species or population

<span class="mw-page-title-main">Genetic diversity</span> Total number of genetic characteristics in a species

Genetic diversity is the total number of genetic characteristics in the genetic makeup of a species, it ranges widely from the number of species to differences within species and can be attributed to the span of survival for a species. It is distinguished from genetic variability, which describes the tendency of genetic characteristics to vary.

Heterosis, hybrid vigor, or outbreeding enhancement is the improved or increased function of any biological quality in a hybrid offspring. An offspring is heterotic if its traits are enhanced as a result of mixing the genetic contributions of its parents. The heterotic offspring often has traits that are more than the simple addition of the parents' traits, and can be explained by Mendelian or non-Mendelian inheritance. Typical heterotic/hybrid traits of interest in agriculture are higher yield, quicker maturity, stability, drought tolerance etc.

A heterozygote advantage describes the case in which the heterozygous genotype has a higher relative fitness than either the homozygous dominant or homozygous recessive genotype. Loci exhibiting heterozygote advantage are a small minority of loci. The specific case of heterozygote advantage due to a single locus is known as overdominance. Overdominance is a rare condition in genetics where the phenotype of the heterozygote lies outside of the phenotypical range of both homozygote parents, and heterozygous individuals have a higher fitness than homozygous individuals.

In population genetics and population ecology, population size is a countable quantity representing the number of individual organisms in a population. Population size is directly associated with amount of genetic drift, and is the underlying cause of effects like population bottlenecks and the founder effect. Genetic drift is the major source of decrease of genetic diversity within populations which drives fixation and can potentially lead to speciation events.

Genetic load is the difference between the fitness of an average genotype in a population and the fitness of some reference genotype, which may be either the best present in a population, or may be the theoretically optimal genotype. The average individual taken from a population with a low genetic load will generally, when grown in the same conditions, have more surviving offspring than the average individual from a population with a high genetic load. Genetic load can also be seen as reduced fitness at the population level compared to what the population would have if all individuals had the reference high-fitness genotype. High genetic load may put a population in danger of extinction.

Inbreeding depression is the reduced biological fitness that has the potential to result from inbreeding. Biological fitness refers to an organism's ability to survive and perpetuate its genetic material. Inbreeding depression is often the result of a population bottleneck. In general, the higher the genetic variation or gene pool within a breeding population, the less likely it is to suffer from inbreeding depression, though inbreeding and outbreeding depression can simultaneously occur.

Genetic divergence is the process in which two or more populations of an ancestral species accumulate independent genetic changes (mutations) through time, often leading to reproductive isolation and continued mutation even after the populations have become reproductively isolated for some period of time, as there is not any genetic exchange anymore. In some cases, subpopulations cover living in ecologically distinct peripheral environments can exhibit genetic divergence from the remainder of a population, especially where the range of a population is very large. The genetic differences among divergent populations can involve silent mutations or give rise to significant morphological and/or physiological changes. Genetic divergence will always accompany reproductive isolation, either due to novel adaptations via selection and/or due to genetic drift, and is the principal mechanism underlying speciation.

In natural selection, negative selection or purifying selection is the selective removal of alleles that are deleterious. This can result in stabilising selection through the purging of deleterious genetic polymorphisms that arise through random mutations.

<span class="mw-page-title-main">Fixed allele</span> Allele with a frequency of 1

In population genetics, a fixed allele is an allele that is the only variant that exists for that gene in a population. A fixed allele is homozygous for all members of the population. The process by which alleles become fixed is called fixation.

<span class="mw-page-title-main">Zygosity</span> Degree of similarity of the alleles in an organism

Zygosity is the degree to which both copies of a chromosome or gene have the same genetic sequence. In other words, it is the degree of similarity of the alleles in an organism.

The medical genetics of Jews have been studied to identify and prevent some rare genetic diseases that, while still rare, are more common than average among people of Jewish descent. There are several autosomal recessive genetic disorders that are more common than average in ethnically Jewish populations, particularly Ashkenazi Jews, because of relatively recent population bottlenecks and because of consanguineous marriage. These two phenomena reduce genetic diversity and raise the chance that two parents will carry a mutation in the same gene and pass on both mutations to a child.

<span class="mw-page-title-main">Popular sire effect</span>

The popular sire effect occurs when an animal with desirable attributes is bred repeatedly. In dog breeding, a male dog that wins respected competitions becomes highly sought after, as breeders believe the sire possesses the genes necessary to produce champions. However, the popular sire effect is not just down to wanting to produce a champion. For example, in Staffordshire Bull Terriers there are several popular sires who are used by breeders to produce specific colours that are not favoured in the show ring. The popular sire is often bred extensively with many females. This can cause undetected, undesirable genetic traits in the stud to spread rapidly within the gene pool. It can also reduce genetic diversity by the exclusion of other males.

Genetic purging is the reduction of the frequency of a deleterious allele, caused by an increased efficiency of natural selection prompted by inbreeding.

This glossary of genetics and evolutionary biology is a list of definitions of terms and concepts used in the study of genetics and evolutionary biology, as well as sub-disciplines and related fields, with an emphasis on classical genetics, quantitative genetics, population biology, phylogenetics, speciation, and systematics. Overlapping and related terms can be found in Glossary of cellular and molecular biology, Glossary of ecology, and Glossary of biology.

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  35. 1 2 "Weyers acrofacial dysostosis / "Genetics Home Reference" ("Your Guide to Understanding Genetic Conditions"), from the "US National Library of Medicine"". National Library of Medicine (NLM), which is part of the National Institutes of Health, an agency of the U.S. Department of Health and Human Services ... ((Note: archived from an earlier version of the original.)). July 18, 2017. Archived from the original on June 27, 2017. Retrieved July 24, 2017. People with Weyers acrofacial dysostosis have abnormally small or malformed fingernails and toenails. Most people with the condition are relatively short, and they may have extra fingers or toes (polydactyly). [...] The features of Weyers acrofacial dysostosis overlap with those of another, more severe condition called Ellis–Van Creveld syndrome. In addition to tooth and nail abnormalities, people with Ellis-van Creveld syndrome have very short stature and are often born with heart defects. The two conditions are caused by mutations in the same genes.
  36. 1 2 "How are genetic conditions and genes named? / "Genetics Home Reference" ("Your Guide to Understanding Genetic Conditions"), from the "US National Library of Medicine"". National Library of Medicine (NLM), which is part of the National Institutes of Health, an agency of the U.S. Department of Health and Human Services ... ((Note: archived from an earlier version of the original.)). July 18, 2017. Archived from the original on July 9, 2017. Retrieved July 24, 2017.
  37. ↑ McKusick, V. A.; Egeland, J. A.; Eldridge, R; Krusen, D. E. (1964). "Dwarfism in the Amish I. The Ellis-Van Creveld Syndrome". Bulletin of the Johns Hopkins Hospital. 115: 306–36. PMID   14217223.
  38. ↑ Jaworski, M. A.; Severini, A; Mansour, G; Konrad, H. M.; Slater, J; Hennig, K; Schlaut, J; Yoon, J. W.; Pak, C. Y.; MacLaren, N (1989). "Genetic conditions among Canadian Mennonites: Evidence for a founder effect among the old colony (Chortitza) Mennonites". Clinical and Investigative Medicine. 12 (2): 127–41. PMID   2706837.
  39. ↑ Puffenberger, E.G. (2003). "Genetic heritage of the Old Order Mennonites of southeastern Pennsylvania". American Journal of Medical Genetics. 121C (1): 18–31. doi: 10.1002/ajmg.c.20003 . PMID   12888983. S2CID   25317649.
  40. ↑ "Maple Syrup Urine Disease (MSUD) - Jewish Genetic Disease".
  41. ↑ 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.
  42. ↑ Yin, Steph (2017-07-17). "In South Asian Social Castes, a Living Lab for Genetic Disease". The New York Times. ISSN   0362-4331 . Retrieved 2020-03-13.
  43. ↑ Berry, RJ (1967). "Genetical changes in mice and men". Eugen Rev. 59 (2): 78–96. PMC   2906351 . PMID   4864588.
  44. ↑ De Oliveira, Marcelo Zagonel; Schüler-Faccini, Lavínia; Demarchi, Dario A.; Alfaro, Emma L.; Dipierri, José E.; Veronez, Mauricio R.; Colling Cassel, Marlise; Tagliani-Ribeiro, Alice; Silveira Matte, Ursula; Ramallo, Virginia (2013). "So Close, So Far Away: Analysis of Surnames in a Town of Twins (Cândido Godói, Brazil)". Annals of Human Genetics. 77 (2): 125–36. doi:10.1111/ahg.12001. hdl: 11336/11007 . PMID   23369099. S2CID   206980257.
  45. ↑ Zimmer, Carl (31 August 2023). "Humanity's Ancestors Nearly Died Out, Genetic Study Suggests - The population crashed following climate change about 930,000 years ago, scientists concluded. Other experts aren't convinced by the analysis". the New York Times . Archived from the original on 31 August 2023. Retrieved 2 September 2023.
  46. ↑ Hu, Wangjie; et al. (31 August 2023). "Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition". Science . 381 (6661): 979–984. doi:10.1126/science.abq7487. Archived from the original on 1 September 2023. Retrieved 2 September 2023.

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