population genetics

The branch of science that deals with the statistical analysis of the inheritance and prevalence of genes in populations.

The study of both experimental and theoretical consequences of mendelian heredity on the population level, in contradistinction to classical genetics which deals with the offspring of specified parents on the familial level. The genetics of populations studies the frequencies of genes, genotypes, and phenotypes, and the mating systems. It also studies the forces that may alter the genetic composition of a population in time, such as recurrent mutation, migration, and intermixture between groups, selection resulting from genotypic differential fertility, and the random changes incurred by the sampling process in reproduction from generation to generation. This type of study contributes to an understanding of the elementary step in biological evolution. The principles of population genetics may be applied to plants and to other animals as well as humans. See also Genetics; Mendelism.

Population genetics is the study of the genetic structure of populations, the frequencies of alleles and genotypes. A population is a local group of organisms of the same species that normally interbreed. Defining the limits of a population can be somewhat arbitrary if neighboring populations regularly interbreed. All the humans in a small town in the rural United States could be defined as a population, but what about the humans in a suburb of Los Angeles? They can interbreed directly with nearby populations, and, indirectly, with populations extending continuously north and south for a hundred or more miles. In addition, a large human population often consists of subpopulations that do not readily interbreed because of differences in education, income, and ethnicity. Despite these complexities, one can make some simple definitions.

Gene Pool and Genetic Structure

All of the alleles shared by all of the individuals in a population make up the population's gene pool. In diploid organisms such as humans, every gene is represented by two alleles. The pair of alleles may differ from one another, in which case it is said that the individual is "heterozygous" for that gene. If the two alleles are identical, it is said that the individual is "homozygous" for that gene. If every member of a population is homozygous for the same allele, the allele is said to be fixed. Most human genes are fixed and help define humans as a species.

The most interesting genes to geneticists are those represented by more than one allele. Population genetics looks at how common an allele is in the whole population and how it is distributed. Imagine, for example, an allele "b" that when homozygous, "bb," produces blue-eyed individuals. Allele b might have an overall frequency in the population of 20 percent; that is, 20 percent of all the eye-color alleles are b.

However, not everyone who has the b allele will be homozygous for b. Some people will have b combined with another allele, "B," which gives them brown eyes (because B is dominant and b is recessive). Others won't have the b allele at all and instead will be homozygous for B.

The frequency of each genotype—whether bb, Bb, or BB—in the population is also of interest to population geneticists. The frequency of alleles and genotypes is called a population's genetic structure. Populations vary in their genetic structure. For example, the same allele may have a frequency of 3 percent among Europeans, 10 percent among Asians, and 94 percent among Africans. Blood types vary across different ethnic groups in this way. The frequency of genotypes depends partly on the overall allele frequencies, but also on other factors.

Hardy-Weinberg Theorem

Large, isolated populations whose members mate randomly and do not experience any selection pressure will tend to maintain a frequency of genotypes predicted by a simple equation called the Hardy-Weinberg Theorem. For example, if b has a frequency of 20 percent and B has a frequency of 80 percent, we can predict the frequency of the three genotypes (bb, Bb, and BB). The total of all the genotype frequencies is 100 percent (b + B), and the frequencies of each are given by (b + B)² 100 percent. This can be restated as the following equation: 100% = b² + 2(bB + B²).

And we can calculate the genotype frequencies as: 100% = (20%)² + 2(20% × 80%) + (80%)² = 4% + 32% + 64%.

So even though 20 percent of all the genes in this imaginary population are b alleles, only 4 percent of the population is homozygous for b and actually has blue eyes. Furthermore, this same distribution will be maintained over time, as long as the conditions of the Hardy-Weinberg Theorem are met.

However, few, if any, natural populations (including human ones) actually conform to the assumptions of Hardy-Weinberg, so both genotype frequencies and allele frequencies can and do change from generation to generation. For example, humans do not mate randomly. Instead, they tend to take partners of similar height and intelligence. And even in modern human populations, genetic diseases such as Tay-Sachs kill children long before they grow up and reproduce. A difference in survival and reproduction due to differences in genotype is called selection. Even subtle selection can change gene frequencies over long periods of time.

Another assumption of the Hardy-Weinberg theorem is that individuals from different populations do not mate, so that gene flow, the passage of new genetic information from one gene pool into another, is zero. Such isolation does characterize many animal and plant populations, but almost no modern human populations are isolated from all other populations. Instead, humans travel to different countries, intermarrying and producing children who reflect the novel intermingling of unusual alleles.

Genetic Drift

In very small populations, rare alleles can become common or disappear because of genetic drift—random changes in gene frequency that are not due to selection, gene mutation, or immigration. We can explain this as follows. When flipping a coin 1,000 times, it is likely to get 50 percent heads and 50 percent tails (if it's a fair coin). But flip it only five or ten times, and it is unlikely to get exactly half heads and half tails. Chances are good that the results will be something quite different. In the same way, if 10,000 people mate and produce children, the bb genotype will pretty much conform to the Hardy-Weinberg equation described above (provided the other assumptions are approximately true). For example, in a sample of just twenty people, instead of getting a group of children of whom 4 percent have blue eyes, the result could end up none with blue eyes, or maybe half having blue eyes. It all depends on how the alleles happen to combine when eggs meet sperm.

Because of genetic drift, small, isolated populations often have unusual frequencies of a few alleles. Although similar to other people in most important respects, such isolated populations may harbor high frequencies of one or more alleles that are rare in most other populations. For example, in 1814, fifteen people founded a British colony on a group of small islands in the mid-Atlantic, called Tristan de Cunha. They brought with them a rare recessive allele that causes progressive blindness, and the disease, extraordinarily rare in most places, is common on Tristan de Cunha. Such "inbreeding" produces more homozygotes than usual and increases the probability of children born with genetic diseases. The Old Order Amish have a high frequency of Ellis-van Creveld syndrome, and Ashkenazi Jews were, until a few years ago, susceptible to Tay-Sachs disease. Fortunately, genetic testing has greatly reduced the incidence of Tay-Sachs and many other such genetic diseases.

Population genetics also provides information about evolution. It is known, for example, that populations that have unusual allele frequencies must have been isolated from other populations. And we can surmise that populations that share similar frequencies of certain rare alleles may have interbred at some point in the past. Human populations in sub-Sarahan Africa show the greatest diversity of all human populations. On the basis, in part, of this diversity, one theory of human evolution suggests that all humans originated in Africa, and then emigrated to Asia, Europe, and the rest of the world.

Bibliography

Jones, J. S. "How Different Are Human Races?" Nature 293 (1981): 188-190.

Klug, W. S., and M. R. Cummings. Concepts of Genetics, 6th ed. Upper Saddle River, NJ: Prentice Hall, 2000.

Lewontin, R. Human Diversity. Redding, CT: W. H. Freeman, 1982.

—Jennie Dusheck

The study of the genetic composition of populations in order to understand the evolutionary forces that select for a particular gene.

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Population genetics is the study of the allele frequency distribution and change under the influence of the four evolutionary processes: natural selection, genetic drift, mutation and gene flow. It also takes account of population subdivision and population structure in space. As such, it attempts to explain such phenomena as adaptation and speciation. Population genetics was a vital ingredient in the modern evolutionary synthesis, its primary founders were Sewall Wright, J. B. S. Haldane and R. A. Fisher, who also laid the foundations for the related discipline of quantitative genetics.

Contents 1 Scope and theoretical considerations 2 Genetic structure 3 Microbial population genetics 4 Population geneticists 5 See also 6 References 7 External links

Scope and theoretical considerations

The framework of mathematical population genetics is an important achievement of the modern evolutionary synthesis. According to Beatty (1986), for example, it defines the core of the modern synthesis.

According to Lewontin (1974) the theoretical task for population genetics is a process in two spaces: a "genotypic space" and a "phenotypic space". The challenge of a complete theory of population genetics is to provide a set of laws that predictably map a population of genotypes (G₁) to a phenotype space (P₁), where selection takes place, and another set of laws that map the resulting population (P₂) back to genotype space (G₂) where Mendelian genetics can predict the next generation of genotypes, thus completing the cycle. Even leaving aside for the moment the non-Mendelian aspects of molecular genetics, this is clearly a gargantuan task. Visualizing this transformation schematically:

(adapted from Lewontin 1974, p. 12). XD

T₁ represents the genetic and epigenetic laws, the aspects of functional biology, or development, that transform a genotype into phenotype. We will refer to this as the "genotype-phenotype map". T₂ is the transformation due to natural selection, T₃ are epigenetic relations that predict genotypes based on the selected phenotypes and finally T₄ the rules of Mendelian genetics.

In practice, there are two bodies of evolutionary theory that exist in parallel, traditional population genetics operating in the genotype space and the biometric theory used in plant and animal breeding, operating in phenotype space. The missing part is the mapping between the genotype and phenotype space. This leads to a "sleight of hand" (as Lewontin terms it) whereby variables in the equations of one domain, are considered parameters or constants, where, in a full-treatment they would be transformed themselves by the evolutionary process and are in reality functions of the state variables in the other domain. The "sleight of hand" is assuming that we know this mapping. Proceeding as if we do understand it is enough to analyze many cases of interest. For example, if the phenotype is almost one-to-one with genotype (sickle-cell disease) or the time-scale is sufficiently short, the "constants" can be treated as such; however, there are many situations where it is inaccurate.

Genetic structure

Because of physical barriers to migration, along with limited vagility, and natal philopatry, natural populations are rarely panmictic (Buston et al., 2007). There is usually a geographic range within which individuals are more closely related to one another than those randomly selected from the general population. This is described as the extent to which a population is genetically structured (Repaci et al., 2007).

Microbial population genetics

Microbial population genetics is a rapidly advancing field of investigation with relevance to many other theoretical and applied areas of scientific investigations. The population genetics of microorganisms lays the foundations for tracking the origin and evolution of antibiotic resistance and deadly infectious pathogens. Population genetics of microorganisms is also an essential factor for devising strategies for the conservation and better utilization of beneficial microbes (Xu, 2010).

Population geneticists

The three founders of population genetics were the Britons R.A. Fisher and J.B.S. Haldane and the American Sewall Wright. Fisher and Wright had some fundamental disagreements and a controversy about the relative roles of selection and drift continued for much of the century between the Americans and the British. The Frenchman Gustave Malécot was also important early in the development of the discipline. John Maynard Smith was Haldane's pupil, whilst W.D. Hamilton was heavily influenced by the writings of Fisher. The American George R. Price worked with both Hamilton and Maynard Smith. American Richard Lewontin and Japanese Motoo Kimura were heavily influenced by Wright.

See also

Evolutionary biology portal

• Coalescent theory
• Dual inheritance theory
• Ecological genetics
• Evolutionarily Significant Unit
• Ewens's sampling formula
• Fitness landscape
• Founder effect
• Genetic diversity
• Genetic drift
• Genetic erosion
• Genetic pollution
• Gene pool
• Genotype-phenotype distinction
• Habitat fragmentation
• Hardy-Weinberg principle
• Microevolution
• Molecular evolution
• Muller's ratchet
• Mutational meltdown
• Neutral theory of molecular evolution
• Population bottleneck
• Quantitative genetics
• Reproductive compensation
• Selection
• Small population size
• Viral quasispecies

References

• J. Beatty. "The synthesis and the synthetic theory" in Integrating Scientific Disciplines, edited by W. Bechtel and Nijhoff. Dordrecht, 1986.
• Buston, PM; et al. (2007). "Are clownfish groups composed of close relatives? An analysis of microsatellite DNA vraiation in Amphiprion percula". Molecular Ecology 12: 733-742. 
• Luigi Luca Cavalli-Sforza. Genes, Peoples, and Languages. North Point Press, 2000.
• Luigi Luca Cavalli-Sforza et al. The History and Geography of Human Genes. Princeton University Press, 1994.
• James F. Crow and Motoo Kimura. Introduction to Population Genetics Theory. Harper & Row, 1972.
• Warren J Ewens. Mathematical Population Genetics. Springer-Verlag New York, Inc., 2004. ISBN 0-387-20191-2
• John H. Gillespie Population Genetics: A Concise Guide, Johns Hopkins Press, 1998. ISBN 0-8018-5755-4.
• Richard Halliburton. Introduction to Population Genetics. Prentice Hall, 2004
• Daniel Hartl. Primer of Population Genetics, 3rd edition. Sinauer, 2000. ISBN 0-87893-304-2
• Daniel Hartl and Andrew Clark. Principles of Population Genetics, 3rd edition. Sinauer, 1997. ISBN 0-87893-306-9.
• Richard C. Lewontin. The Genetic Basis of Evolutionary Change. Columbia University Press, 1974.
• William B. Provine. The Origins of Theoretical Population Genetics. University of Chicago Press. 1971. ISBN 0-226-68464-4.
• Repaci, V; Stow AJ, Briscoe DA (2007). "Fine-scale genetic structure, co-founding and multiple mating in the Australian allodapine bee (Ramphocinclus brachyurus". Journal of Zoology 270: 687-691. doi:10.1111/j.1469-7998.2006.00191.x. 
• Spencer Wells. The Journey of Man. Random House, 2002.
• Spencer Wells. Deep Ancestry: Inside the Genographic Project. National Geographic Society, 2006.
• Cheung, KH; Osier MV, Kidd JR, Pakstis AJ, Miller PL, Kidd KK (2000). "ALFRED: an allele frequency database for diverse populations and DNA polymorphisms". Nucleic Acids Research 28 (1): 361–3. doi:10.1093/nar/28.1.361. PMID 10592274. 
• Xu, J. Microbial Population Genetics. Caister Academic Press, 2010. ISBN 978-1-904455-59-2

External links

• Yale University
• EHSTRAFD.org - Earth Human STR Allele Frequencies Database
• History of population genetics
• National Geographic: Atlas of the Human Journey (Haplogroup-based human migration maps)
• Monash Virtual Laboratory - Simulations of habitat fragmentation and population genetics online at Monash University's Virtual Laboratory.
• Nordic and Celtic DNA Project (Saami & Iberian).

v • d • e Topics in population genetics Key concepts Hardy-Weinberg law · Genetic linkage · Linkage disequilibrium · Fisher's fundamental theorem · Neutral theory · Price equation Selection Natural · Sexual · Artificial · Ecological Effects of selection on genomic variation Genetic hitchhiking · Background selection Genetic drift Small population size · Population bottleneck · Founder effect · Coalescence · Balding–Nichols model Founders R. A. Fisher · J. B. S. Haldane · Sewall Wright Related topics Evolution · Microevolution · Evolutionary game theory · Fitness landscape · Genetic genealogy List of evolutionary biology topics

v • d • e Genetics Introduction · History · Related topics · List of organizations Key components Chromosome · DNA · Nucleotide · RNA · Genome Fields of genetics Classical genetics · Conservation genetics · Ecological genetics · Immunogenetics · Molecular genetics · Population genetics · Quantitative genetics Related topics Geneticist · Genomics · Genetic code · Medical genetics · Molecular evolution · Reverse genetics · Genetic engineering · Genetic diversity · Heredity

v • d • e Basic topics in evolutionary biology Evidence of common descent Processes of evolution Adaptation · Macroevolution · Microevolution · Speciation Population genetic mechanisms Natural selection · Genetic drift · Gene flow · Mutation Evolutionary developmental biology (Evo-devo) concepts Phenotypic plasticity · Canalisation · Modularity The evolution of… DNA · Sex · Aging · Human intelligence · The Ear · The Eye · Flight · Plants · Fungi · Life · Humans · Dolphins and whales · Birds · Horses · Spiders · Sirenians (sea cows) · Insects · Molluscs · Dinosaurs Modes of speciation Anagenesis · Catagenesis · Cladogenesis History History of evolutionary thought · Charles Darwin · On the Origin of Species · Modern evolutionary synthesis · Gene-centered view of evolution · Life (classification trees) Other subfields Ecological genetics · Molecular evolution · Phylogenetics · Systematics List of evolutionary biology topics · Timeline of evolution

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