Isolation by distance

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The patterns of isolation by distance as shown among human genetic data representing 346 microsatellite loci taken from 1484 individuals in 78 human populations. The horizontal axis of both charts is geographic distance as measured along likely routes of human migration. The upper graph illustrates that as populations are further from East Africa (represented by the city of Addis Ababa), they have declining genetic diversity as measured in average number of microsatellite repeats at each of the loci. The bottom chart measures the genetic distance between all pairs of populations according to the Fst statistic. Populations separated by greater distance are more dissimilar than those that are geographically close. Human genetic isolation by distance in Kanitz 2018.png
The patterns of isolation by distance as shown among human genetic data representing 346 microsatellite loci taken from 1484 individuals in 78 human populations. The horizontal axis of both charts is geographic distance as measured along likely routes of human migration. The upper graph illustrates that as populations are further from East Africa (represented by the city of Addis Ababa), they have declining genetic diversity as measured in average number of microsatellite repeats at each of the loci. The bottom chart measures the genetic distance between all pairs of populations according to the Fst statistic. Populations separated by greater distance are more dissimilar than those that are geographically close.

Isolation by distance (IBD) is a term used to refer to the accrual of local genetic variation under geographically limited dispersal. [1] The IBD model is useful for determining the distribution of gene frequencies over a geographic region. [2] Both dispersal variance and migration probabilities are variables in this model and both contribute to local genetic differentiation. [3] Isolation by distance is usually the simplest model for the cause of genetic isolation between populations. Evolutionary biologists and population geneticists have been exploring varying theories and models for explaining population structure. Yoichi Ishida compares two important theories of isolation by distance and clarifies the relationship between the two. [3] According to Ishida, Sewall Wright's isolation by distance theory is termed ecological isolation by distance while Gustave Malécot's theory is called genetic isolation by distance. Isolation by distance is distantly related to speciation. Multiple types of isolating barriers, namely prezygotic isolating barriers, including isolation by distance, are considered the key factor in keeping populations apart, limiting gene flow. [4]

Contents

Sewall Wright- Ecological Isolation By Distance

Wright introduced two different models of population structure, one not taking short-distance dispersal into account and one model incorporating short-distance dispersal. The "island model" [5] is quite artificial and proposes the idea that a population is divided into two geographically, unique subpopulations (islands) with random mating occurring with exchange of individuals occurring when a migrant is drawn randomly from the total population. In a more realistic model, where short-distance dispersal is taken into account, [6] a population is compiled of continuously distributed individuals over a region of space. Populations in remote locations may become differentiated simply by isolation by distance, restricting the probability of individuals mating with one another. Local populations are small in comparison to the total population and reproduction occurs solely within the local population. This ecological isolation by distance, according to Wright, can create genetic differentiation among subpopulations, leading to evolutionary change. Individuals within the subpopulation are neighbors in the sense that their gametes may come together and inbreeding within the subpopulation increases homozygosity. Wright's statistical theory for isolation by distance looks at population genetic consequences measured by F-statistics where the correlation of randomly uniting gametes within a subpopulation relative to those of the total population is the FST value.

The equation takes into account the variance in the distribution (var), the allele frequency within the total population (qT), and the allele frequency within the subpopulation (qST). Neighborhood size affects the local genetic differentiation (FST). Higher FST values indicate greater local genetic differentiation [3]

Gustave Malécot- Genetic Isolation By Distance

Malécot's theory refers to a population genetic pattern where genetic differentiation among individuals increases as geographical distances increases. [3] Dispersal is normally localized in space, lending to the expectation that individuals from closer subpopulations will be more genetically similar. [7] Malécot argues that neighborhood size is not important because a decrease in the kinship coefficient does not depend on neighborhood size. This probabilistic theory solely depends on distances between that of offspring and their parents. A population, at equilibrium, displays genetic isolation by distance with stochastic processes producing genetic isolation. This genetic isolation by distance theory involves concepts of gametic kinship chains, identity by descent, and migration probabilities. The kinship coefficient (φ) is the probability that two homologous loci are identical by descent.

The equation takes into account distance (r), mutation rate (k), and the standard deviation of migration (σ). The kinship coefficient decreases as a function of distance and if a mutation occurs in either locus or if the gamete kinship chain is zero, the kinship coefficient will be zero. Yoichi Ishida interprets alteration in neighborhood size as alteration in dispersal variance linking both Wright's statistical theory and Malécot's probabilistic theory explaining why they both invite similar conclusions. [3] Alteration in neighborhood size is alteration in dispersal variance and alteration corresponds to alteration in the variance of the probability of distribution associated with migration probabilities. Both dispersal variance and migration probabilities contribute to local genetic differentiation.

Alternate Models to Isolation by Distance

Both adaptive and nonadaptive processes play a part, individually or acting together, and create variation in populations and species. Understanding the roles of both processes has been a central goal in biology. As previously described, gradual genetic drift across populations (isolation by distance) and limited gene dispersal can account for some of the genetic and phenotypic divergence across populations, but there are alternative models besides isolation by distance that can contribute to these differences as well. Two of these alternate models include isolation by colonization and isolation by adaptation. The former is a product of colonization history and founder effects while the latter is a product of adaption to varying environments inhibiting migration between populations. [8] A recent scientific article (Spurgin et al., 2014) tried to differentiate between these processes by utilizing island populations of Anthus berthelotii (Berthelot's pipit) native to three Atlantic archipelagos. Microsatellite markers and approximate Bayesian computation revealed that the northward colonization of the species produced genetic bottlenecks. High levels of genetic structure occurring across the archipelagos indicate an isolation by colonization pattern. Significant morphological divergence was present that is highly consistent with trends of bottleneck and genetic structure history, not with geographic distance or environmental variation.

Applications in Genetic/Evolutionary Research

Understanding genetic and phenotypic divergence across populations of varying species is important in elucidating ecological and evolutionary differences among populations. One such study where genetic structure among human individuals is investigated is by Relethford and Brennan, (1982) where pedigree and marriage data from Sanday, Orkney Islands in Scotland were used to evaluate temporal patterns in isolation by distance. The data considered were for three time periods, 1855-1884, 1885-1924, and 1925-1964. These time periods were categorized by birth year for married males. Average inbreeding coefficient of all potential spouses (chosen within the known demographic and genealogical limits of the population's structure) of each married male was calculated to determine random kinship values. Over time, the isolation by distance model reveals a decline in local isolation and a rise in short and long range migration and the Sandy population experienced an isolate breakdown over time. Distance plays a role in determining kinship, but becomes less significant over time as the measures of the fit of the model decline. Overall inbreeding decreased and mean marital distance increased. Additionally consanguinity avoidance occurred over all distances, but avoidance was more prominent at closer distances. [9]

The genetic structure, dynamics, and evolution of populations and species are also important from an ecological point of view when considering the probability of colonization and extinction. One of the key processes influencing these dynamics is dispersal. When localized, populations that are geographically closer are expected to exchange more migrants and should tend to share neutral genetic markers. [10] One such study investigated the direct and indirect measures of dispersal in Branchipodopsis wolfi (fairy shrimp), located in spatially fragmented, ephemeral rock pools located in southeastern Botswana. Dispersal trends and rates were compared by using both spatial genetic structure and direct measures of dispersal. A total of 29 populations from three spatially different rock pools were subjected to allozyme analysis for four loci to access genetic variation and estimates of gene flow between populations were generated using population genetic software. Direct measures of dispersal were determined by quantifying the number of viable floating dormant eggs and larvae that circulated intro overflow traps during flooding events. Genetic differentiation among sites was highly significant (with neighboring sites being more similar). FST ratios for all populations increased with geographical distance in all three rock pool sites, indicating a small-scale isolation-by-distance pattern. Research shows that a distance of 50 meters is an important constraint on the effective dispersal and gene flow for fairy shrimp. [11] Isolation by distance also occurs a result of competition between species: spatial segregation may be due to the negative impact of a species' activity on another one. [12]

See also

Related Research Articles

Genetic drift The change in the frequency of an existing gene variant in a population

Genetic drift is the change in the frequency of an existing gene variant (allele) in a population due to random sampling of organisms. The alleles in the offspring are a sample of those in the parents, and chance has a role in determining whether a given individual survives and reproduces. A population's allele frequency is the fraction of the copies of one gene that share a particular form.

Population genetics Study of genetic differences within and between populations including the study of adaptation, speciation, and population structure

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

Quantitative genetics The study of the inheritance of continuously variable traits

Quantitative genetics deals with phenotypes that vary continuously —as opposed to discretely identifiable phenotypes and gene-products.

Gene flow The 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 adaption. 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

Allopatric speciation Speciation that occurs between geographically isolated populations

Allopatric speciation, also referred to as geographic speciation, vicariant speciation, or its earlier name, the dumbbell model, is a mode of speciation that occurs when biological populations become geographically isolated from each other to an extent that prevents or interferes with gene flow.

Founder effect Loss of genetic variation resulting from a few individuals establishing a new population

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 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.

The coefficient of relationship is a measure of the degree of consanguinity between two individuals. The term coefficient of relationship was defined by Sewall Wright in 1922, and was derived from his definition of the coefficient of inbreeding of 1921. The measure is most commonly used in genetics and genealogy. A coefficient of inbreeding can be calculated for an individual, and is typically one-half the coefficient of relationship between the parents.

Motoo Kimura Japanese biologist

Motoo Kimura was a Japanese biologist best known for introducing the neutral theory of molecular evolution in 1968. He became one of the most influential theoretical population geneticists. He is remembered in genetics for his innovative use of diffusion equations to calculate the probability of fixation of beneficial, deleterious, or neutral alleles. Combining theoretical population genetics with molecular evolution data, he also developed the neutral theory of molecular evolution in which genetic drift is the main force changing allele frequencies. James F. Crow, himself a renowned population geneticist, considered Kimura to be one of the two greatest evolutionary geneticists, along with Gustave Malécot, after the great trio of the modern synthesis, Ronald Fisher, J. B. S. Haldane and Sewall Wright.

In population genetics, F-statistics describe the statistically expected level of heterozygosity in a population; more specifically the expected degree of (usually) a reduction in heterozygosity when compared to Hardy–Weinberg expectation.

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The effective population size is the number of individuals that an idealised population would need to have in order for some specified quantity of interest to be the same in the idealised population as in the real population. Idealised populations are based on unrealistic but convenient simplifications such as random mating, simultaneous birth of each new generation, constant population size, and equal numbers of children per parent. In some simple scenarios, the effective population size is the number of breeding individuals in the population. However, for most quantities of interest and most real populations, the census population size N of a real population is usually larger than the effective population size Ne. The same population may have multiple effective population sizes, for different properties of interest, including for different genetic loci.

Sewall Wright American geneticist

Sewall Green Wright FRS(For) HFRSE was an American geneticist known for his influential work on evolutionary theory and also for his work on path analysis. He was a founder of population genetics alongside Ronald Fisher and J. B. S. Haldane, which was a major step in the development of the modern synthesis combining genetics with evolution. He discovered the inbreeding coefficient and methods of computing it in pedigree animals. He extended this work to populations, computing the amount of inbreeding between members of populations as a result of random genetic drift, and along with Fisher he pioneered methods for computing the distribution of gene frequencies among populations as a result of the interaction of natural selection, mutation, migration and genetic drift. Wright also made major contributions to mammalian and biochemical genetics.

Molecular ecology A field of evolutionary biology that applies molecular population genetics, molecular phylogenetics, and genomics to traditional ecological questions

Molecular ecology is a field of evolutionary biology that is concerned with applying molecular population genetics, molecular phylogenetics, and more recently genomics to traditional ecological questions. It is virtually synonymous with the field of "Ecological Genetics" as pioneered by Theodosius Dobzhansky, E. B. Ford, Godfrey M. Hewitt, and others. These fields are united in their attempt to study genetic-based questions "out in the field" as opposed to the laboratory. Molecular ecology is related to the field of conservation genetics.

Parapatric speciation Speciation within a population where subpopulations are reproductively isolated

In parapatric speciation, two subpopulations of a species evolve reproductive isolation from one another while continuing to exchange genes. This mode of speciation has three distinguishing characteristics: 1) mating occurs non-randomly, 2) gene flow occurs unequally, and 3) populations exist in either continuous or discontinuous geographic ranges. This distribution pattern may be the result of unequal dispersal, incomplete geographical barriers, or divergent expressions of behavior, among other things. Parapatric speciation predicts that hybrid zones will often exist at the junction between the two populations.

Genetic distance

Genetic distance is a measure of the genetic divergence between species or between populations within a species, whether the distance measures time from common ancestor or degree of differentiation. Populations with many similar alleles have small genetic distances. This indicates that they are closely related and have a recent common ancestor.

Coalescent theory is a model of how gene variants sampled from a population may have originated from a common ancestor. In the simplest case, coalescent theory assumes no recombination, no natural selection, and no gene flow or population structure, meaning that each variant is equally likely to have been passed from one generation to the next. The model looks backward in time, merging alleles into a single ancestral copy according to a random process in coalescence events. Under this model, the expected time between successive coalescence events increases almost exponentially back in time. Variance in the model comes from both the random passing of alleles from one generation to the next, and the random occurrence of mutations in these alleles.

The fixation index (FST) is a measure of population differentiation due to genetic structure. It is frequently estimated from genetic polymorphism data, such as single-nucleotide polymorphisms (SNP) or microsatellites. Developed as a special case of Wright's F-statistics, it is one of the most commonly used statistics in population genetics.

This glossary of evolutionary biology is a list of definitions of terms and concepts used in the study of evolutionary biology, population biology, speciation, and phylogenetics, as well as sub-disciplines and related fields. For additional terms from related glossaries, see Glossary of genetics, Glossary of ecology, and Glossary of biology.

In quantitative genetics, QST is a statistic intended to measure the degree of genetic differentiation among populations with regard to a quantitative trait. It was developed by Ken Spitze in 1993. Its name reflects the fact that it was intended to be analogous to the fixation index for a single genetic locus, which is denoted FST. QST is often compared with FST to test the hypothesis that a given quantitative trait has been the subject of divergent selection between the populations being studied. Generally, if QST is found to exceed FST, this is interpreted as evidence of such divergent selection, because it indicates that there is more differentiation in the trait than could be produced solely by genetic drift. By contrast, if the values of QST and FST in the same study are approximately equal, it is considered to reflect that the observed trait differentiation could be entirely due to genetic drift. However, the assumptions on which studies using this methodology are based have been questioned.

References

  1. ↑ Slatkin, Montgomery (1993). "Isolation by Distance in Equilibrium and Non-Equilibrium Populations". Evolution. 47 (1): 264–279. doi:10.2307/2410134. JSTOR   2410134. PMID   28568097.
  2. ↑ Rohlf, F. James; Schnell, Gary D. (1971). "An Investigation of the Isolation-By-Distance Model". The American Naturalist. 105 (944): 295–324. doi:10.1086/282727.
  3. 1 2 3 4 5 Ishida, Yoichi (2009). "Sewall Wright and Gustave Malecot on Isolation by Distance". Philosophy of Science. 76 (5): 784–796. doi:10.1086/605802.
  4. ↑ Coyne, JA; Orr, HA (2004). Speciation. Massachusetts: Sinauer Associates, Inc.
  5. ↑ Wright, Sewall (1931). "Evolution in Mendelian Populations". Genetics. 16 (2): 97–159. PMC   1201091 . PMID   17246615.
  6. ↑ Wright, Sewall (1943). "Isolation by Distance". Genetics. 28 (2): 114–138. PMC   1209196 . PMID   17247074.
  7. ↑ Rousset, Francois (2004). Genetic Structure and Selection in Subdivided Populations. New Jersey: Princeton University Press.
  8. ↑ Spurgin, Lewis G.; Illera, Juan Carlos; Jorgensen, Tove H.; Dawson, Deborah A.; Richardson, David S. (2014). "Genetic and phenotypic divergence in an island bird: isolation by distance, by colonization or by adaptation?" (PDF). Molecular Ecology. 23 (5): 1028–1039. doi: 10.1111/mec.12672 . PMID   24447303.
  9. ↑ Relethford, John H.; Brennan, Ellen R. (1982). "Temporal Trends in Isolation by Distance on Sanday, Orkney Islands". Human Biology. 54 (2): 315–327. PMID   7095798.
  10. ↑ Puebla, Oscar; Bermingham, Eldredge; Guichard, Frederic (2009). "Estimating Dispersal from Genetic Isolation by Distance in a Coral Reef Fish (Hypoplectrus puella)". Ecology. 90 (11): 3087–3098. doi:10.1890/08-0859.1. PMID   19967864.
  11. ↑ Hulsmans, Ann; Moreau, Kelle; Meester, Luc De; Riddoch, Bruce J.; Brendonck, Luc (2007). "Direct and Indirect Measures of Dispersal in the Fairy Shrimp "Branchipodopsis wolfi" Indicate a Small-Scale Isolation-by-Distance Pattern". Limnology and Oceanography. 52 (2): 676–684. doi: 10.4319/lo.2007.52.2.0676 .
  12. ↑ Borzée, Amaël; Kim, Jun Young; Jang, Yikweon (7 Sep 2016). "Asymmetric competition over calling sites in two closely related treefrog species". Scientific Reports. 6: 32569. doi:10.1038/srep32569. PMC   5013533 . PMID   27599461.
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