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population genetics
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{{short description|Study of genetic differences within and between populations including the study of adaptation, speciation, and population structure}}{{Evolutionary biology}}{{genetic genealogy}}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.WEB,weblink Population genetics - Latest research and news {{!, Nature|website=www.nature.com|access-date=2018-01-29}}Population genetics was a vital ingredient in the emergence of the modern evolutionary synthesis. Its primary founders were Sewall Wright, J. B. S. Haldane and Ronald Fisher, who also laid the foundations for the related discipline of quantitative genetics. Traditionally a highly mathematical discipline, modern population genetics encompasses theoretical, lab, and field work. Population genetic models are used both for statistical inference from DNA sequence data and for proof/disproof of concept.JOURNAL, Servedio, Maria R., Maria Servedio, Brandvain, Yaniv, Dhole, Sumit, Fitzpatrick, Courtney L., Goldberg, Emma E., Stern, Caitlin A., Van Cleve, Jeremy, Yeh, D. Justin, Not Just a Theory—The Utility of Mathematical Models in Evolutionary Biology, PLoS Biology, 9 December 2014, 12, 12, e1002017, 10.1371/journal.pbio.1002017, 25489940, 4260780, What sets population genetics apart today from newer, more phenotypic approaches to modelling evolution, such as evolutionary game theory and adaptive dynamics, is its emphasis on genetic phenomena as dominance, epistasis, and the degree to which genetic recombination breaks up linkage disequilibrium. This makes it appropriate for comparison to population genomics data.

History

Population genetics began as a reconciliation of Mendelian inheritance and biostatistics models. Natural selection will only cause evolution if there is enough genetic variation in a population. Before the discovery of Mendelian genetics, one common hypothesis was blending inheritance. But with blending inheritance, genetic variance would be rapidly lost, making evolution by natural or sexual selection implausible. The Hardy–Weinberg principle provides the solution to how variation is maintained in a population with Mendelian inheritance. According to this principle, the frequencies of alleles (variations in a gene) will remain constant in the absence of selection, mutation, migration and genetic drift.BOOK, Ewens W.J., 2004, Mathematical Population Genetics (2nd Edition), Springer-Verlag, New York, 978-0-387-20191-7, {{Multiple image | direction=vertical | align=right | image1=Biston.betularia.7200.jpg | image2=Biston.betularia.f.carbonaria.7209.jpg | width=200 | caption1=The typical white-bodied form of the peppered moth. | caption2=Industrial melanism: the black-bodied form of the peppered moth appeared in polluted areas.}}The next key step was the work of the British biologist and statistician Ronald Fisher. In a series of papers starting in 1918 and culminating in his 1930 book The Genetical Theory of Natural Selection, Fisher showed that the continuous variation measured by the biometricians could be produced by the combined action of many discrete genes, and that natural selection could change allele frequencies in a population, resulting in evolution. In a series of papers beginning in 1924, another British geneticist, J.B.S. Haldane, worked out the mathematics of allele frequency change at a single gene locus under a broad range of conditions. Haldane also applied statistical analysis to real-world examples of natural selection, such as peppered moth evolution and industrial melanism, and showed that selection coefficients could be larger than Fisher assumed, leading to more rapid adaptive evolution as a camouflage strategy following increased pollution.BOOK, Bowler, Peter J., Evolution : the history of an idea, 2003, University of California Press, Berkeley, 978-0-520-23693-6, 3rd, 325–339, BOOK, Larson, Edward J., Evolution : the remarkable history of a scientific theory, 2004, Modern Library, New York, 978-0-679-64288-6, Modern Library, 221–243,weblink The American biologist Sewall Wright, who had a background in animal breeding experiments, focused on combinations of interacting genes, and the effects of inbreeding on small, relatively isolated populations that exhibited genetic drift. In 1932 Wright introduced the concept of an adaptive landscape and argued that genetic drift and inbreeding could drive a small, isolated sub-population away from an adaptive peak, allowing natural selection to drive it towards different adaptive peaks.The work of Fisher, Haldane and Wright founded the discipline of population genetics. This integrated natural selection with Mendelian genetics, which was the critical first step in developing a unified theory of how evolution worked. 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.

Modern synthesis

The mathematics of population genetics were originally developed as the beginning of the modern synthesis. Authors such as BeattyBOOK, Beatty, John, Integrating Scientific Disciplines, 2, Springer Netherlands, 9789024733422, 125–135, The Synthesis and the Synthetic Theory, 10.1007/978-94-010-9435-1_7, Science and Philosophy, 1986, have asserted that population genetics defines the core of the modern synthesis. For the first few decades of the 20th century, most field naturalists continued to believe that Lamarckism and orthogenesis provided the best explanation for the complexity they observed in the living world.BOOK, Mayr, edited by Ernst, Mayer, William B. Provine ; with a new preface by Ernst, The Evolutionary synthesis : perspectives on the unification of biology, 1998, Harvard University Press, Cambridge, Massachusetts, 9780674272262, 295–298, [New ed]., During the modern synthesis, these ideas were purged, and only evolutionary causes that could be expressed in the mathematical framework of population genetics were retained.BOOK, Provine, W. B., 1988, Evolutionary progress, Progress in evolution and meaning in life, 49–79, University of Chicago Press, Consensus was reached as to which evolutionary factors might influence evolution, but not as to the relative importance of the various factors.Theodosius Dobzhansky, a postdoctoral worker in T. H. Morgan's lab, had been influenced by the work on genetic diversity by Russian geneticists such as Sergei Chetverikov. He helped to bridge the divide between the foundations of microevolution developed by the population geneticists and the patterns of macroevolution observed by field biologists, with his 1937 book Genetics and the Origin of Species. Dobzhansky examined the genetic diversity of wild populations and showed that, contrary to the assumptions of the population geneticists, these populations had large amounts of genetic diversity, with marked differences between sub-populations. The book also took the highly mathematical work of the population geneticists and put it into a more accessible form. Many more biologists were influenced by population genetics via Dobzhansky than were able to read the highly mathematical works in the original.JOURNAL, Provine, William B., 1978, The role of mathematical population geneticists in the evolutionary synthesis of the 1930s and 1940s, Studies of the History of Biology, 2, 167–192, In Great Britain E.B. Ford, the pioneer of ecological genetics, continued throughout the 1930s and 1940s to empirically demonstrate the power of selection due to ecological factors including the ability to maintain genetic diversity through genetic polymorphisms such as human blood types. Ford's work, in collaboration with Fisher, contributed to a shift in emphasis during the course of the modern synthesis towards natural selection as the dominant force.BOOK, Mayr, Ernst, Ernst Mayr, 1988, Toward a New Philosophy of Biology: Observations of an Evolutionist, Cambridge, Massachusetts, Harvard University Press, Belknap Press of Harvard University Press, 402, 978-0-674-89665-9, harv, Toward a New Philosophy of Biology, BOOK, Mayr, edited by Ernst, Mayer, William B. Provine ; with a new preface by Ernst, The Evolutionary synthesis : perspectives on the unification of biology, 1998, Harvard University Press, Cambridge, Massachusetts, 9780674272262, 338–341, [New ed].,

Neutral theory and origin-fixation dynamics

The original, modern synthesis view of population genetics assumes that mutations provide ample raw material, and focuses only on the change in frequency of alleles within populations.JOURNAL, McCandlish, David M., Stoltzfus, Arlin, Modeling Evolution Using the Probability of Fixation: History and Implications, The Quarterly Review of Biology, September 2014, 89, 3, 225–252, 10.1086/677571, The main processes influencing allele frequencies are natural selection, genetic drift, gene flow and recurrent mutation. Fisher and Wright had some fundamental disagreements about the relative roles of selection and drift.Wright and Fisher on Inbreeding and Random Drift by James F. Crow, published in Genetics (journal)|Genetics] Published 2010]The availability of molecular data on all genetic differences led to the neutral theory of molecular evolution. In this view, many mutations are deleterious and so never observed, and most of the remainder are neutral, i.e. are not under selection. With the fate of each neutral mutation left to chance (genetic drift), the direction of evolutionary change is driven by which mutations occur, and so cannot be captured by models of change in the frequency of (existing) alleles alone.JOURNAL, Casillas, Sònia, Barbadilla, Antonio, Molecular Population Genetics, Genetics, 2017, 205, 3, 1003–1035, 10.1534/genetics.116.196493, 28270526, 5340319, The origin-fixation view of population genetics generalizes this approach beyond strictly neutral mutations, and sees the rate at which a particular change happens as the product of the mutation rate and the fixation probability.

Four processes

Selection

Natural selection, which includes sexual selection, is the fact that some traits make it more likely for an organism to survive and reproduce. Population genetics describes natural selection by defining fitness as a propensity or probability of survival and reproduction in a particular environment. The fitness is normally given by the symbol w=1-s where s is the selection coefficient. Natural selection acts on phenotypes, so population genetic models assume relatively simple relationships to predict the phenotype and hence fitness from the allele at one or a small number of loci. In this way, natural selection converts differences in the fitness of individuals with different phenotypes into changes in allele frequency in a population over successive generations.Before the advent of population genetics, many biologists doubted that small differences in fitness were sufficient to make a large difference to evolution. Population geneticists addressed this concern in part by comparing selection to genetic drift. Selection can overcome genetic drift when s is greater than 1 divided by the effective population size. When this criterion is met, the probability that a new advantageous mutant becomes fixed is approximately equal to 2s.JOURNAL, JBS Haldane, A Mathematical Theory of Natural and Artificial Selection, Part V: Selection and Mutation, Mathematical Proceedings of the Cambridge Philosophical Society, 1927, 23, 838–844, 1927PCPS...23..838H, 10.1017/S0305004100015644, 7, JOURNAL, Orr, H. A., The population genetics of beneficial mutations, 10.1098/rstb.2009.0282, Philosophical Transactions of the Royal Society B: Biological Sciences, 365, 1544, 1195–1201, 2010, 20308094, 2871816, The time until fixation of such an allele depends little on genetic drift, and is approximately proportional to log(sN)/s.JOURNAL, Hermisson J, Pennings PS, Soft sweeps: molecular population genetics of adaptation from standing genetic variation, Genetics, 2005, 169, 2335–2352, 10.1534/genetics.104.036947, 15716498, 4, 1449620, Pennings,

Dominance

Dominance means that the phenotypic and/or fitness effect of one allele at a locus depends on which allele is present in the second copy for that locus. Consider three genotypes at one locus, with the following fitness valuesBOOK, Gillespie, John, John_H._Gillespie, Population Genetics: A Concise Guide, 2nd, Johns Hopkins University Press, 2004, 978-0-8018-8008-7, {| class="wikitable"
| -
| Genotype:
| A1A1
| A1A2
| A2A2
| -
| Relative fitness:
| 1
| 1-hs
| 1-s
|}
s is the selection coefficient and h is the dominance coefficient. The value of h yields the following information:{| class="wikitable"
| -
| h=0
| A1 dominant, A2 recessive
| -
| h=1
| A2 dominant, A1 recessive
| -
| 0


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