* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Genetic Drift
Genetic studies on Bulgarians wikipedia , lookup
Genetic code wikipedia , lookup
Viral phylodynamics wikipedia , lookup
Pharmacogenomics wikipedia , lookup
Designer baby wikipedia , lookup
Quantitative trait locus wikipedia , lookup
Dual inheritance theory wikipedia , lookup
Genetics and archaeogenetics of South Asia wikipedia , lookup
History of genetic engineering wikipedia , lookup
Genetic engineering wikipedia , lookup
Polymorphism (biology) wikipedia , lookup
Public health genomics wikipedia , lookup
Behavioural genetics wikipedia , lookup
Genetic testing wikipedia , lookup
Genome (book) wikipedia , lookup
Heritability of IQ wikipedia , lookup
Koinophilia wikipedia , lookup
Medical genetics wikipedia , lookup
Human genetic variation wikipedia , lookup
Genetic drift wikipedia , lookup
Evolutionary Genetics LV 25600-01 | Lecture with exercises | 6KP Genetic Drift HS2016 Population Genetics ▷ Hardy-Weinberg Principle A Primer of Ecological Genetics Chapter 3 - Genetic Drift - Page 52-55 2 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift Population tn Population tn+1 In each generation, some individuals may, just by chance, leave behind a few more descendants (and genes) than other individuals. The genes of the next generation will be the genes of the “lucky” individuals, not necessarily the healthier or “better” individuals. That, in a nutshell, is genetic drift. It happens to ALL populations—there’s no avoiding the vagaries of chance. 3 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift Genetic drift, also called genetic sampling error or Sewall Wright effect, a change in the gene pool of a small population that takes place strictly by chance. Genetic drift can result in genetic traits being lost from a population or becoming widespread in a population without respect to the survival or reproductive value of the alleles involved. Results of computer simulations of changes in allele frequency by genetic drift for each of three population sizes (N) with an initial allele frequency of 0.5. 4 Allendorf, Luikart, and Aitken (2013) HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift PopG genetic simulation program http://evolution.gs.washington.edu/popgen/popg.html 5 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift {AB} 6 {B} HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift Genetic drift has several important effects on evolution: 1.Drift reduces genetic variation in populations, potentially reducing a population’s ability to evolve in response to new selective pressures. 7 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift Allele frequencies for 107 D. melanogaster populations where 16 individuals (eight of each sex) were randomly chosen to start each new generation. Initially, all 107 populations had equal numbers of the wildtype and bw75 alleles. adopted from: Buri (1956) Gene frequency in small population of mutant Drosophila. 8 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift What is the rate at which genetic variation is lost from populations? t0 t1 H H′ ΔH = H ′ − H 1 0.5 0.25 0.0 0.25 0.375 0.0 A1 A1 A1 A2 A2 A2 9 0.25 0.375 A1 A1 A1 A2 A2 A2 A1 A1 A1 A2 A2 A2 0.4375 0.4375 0.125 A1 A1 A1 A2 A2 A2 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift t+1 t t+1 t allele probability = 1 2N probability = 1 − Heterozygosity after one generation: H 1 = (1 − Heterozygosity after t generations: H t = (1 − 1 2N 1 2N )H 0 )H 1 t 2N 0 ➥ The equation indicates that the heterozygosity declines each generation at a rate inversely dependent on the population size. 10 HS16 | UniBas | JCW Expected heterozygosity Population Genetics ▷ Genetic Drift Generation Expected heterozygosity (2pq) in populations undergoing genetic drift. The line shows the expected change in heterozygosity. Genetic drift increases homozygosity and decreases heterozygosity. 11 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift Genetic drift has several important effects on evolution: 1.Drift reduces genetic variation in populations, potentially reducing a population’s ability to evolve in response to new selective pressures. 2.Genetic drift acts faster and has more drastic results in smaller populations. This effect is particularly important in rare and endangered species. 12 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift Nindividuals=20 fixed:1 lost:0 13 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift Nindividuals=5 fixed:2 lost:8 14 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift Population size: 5 Generation time: 20 Number of populations: 10 Initial allele freq: q=p=0.5 15 fixed (p=1) lost (p=0) 1 6 4 2 5 3 Population size: 20 Generation time: 20 Number of populations: 10 Initial allele freq: q=p=0.5 fixed (p=1) lost (p=0) 1 0 1 4 2 0 0 6 3 3 0 1 4 3 6 4 1 0 5 3 5 5 2 0 6 4 2 6 0 0 7 2 6 7 1 0 8 4 4 8 2 0 9 3 6 9 3 0 10 3 5 10 0 2 m 3.9 4.5 m 0.9 0.4 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift Large changes in allele frequency from one generation to the next are likely in small populations due to chance. This effect may cause an increase in frequency of alleles that have harmful effects (e.g. inbreeding depression). Such deleterious alleles are continually introduced by mutation but are kept at low frequencies by natural selection. Moreover, most of these harmful alleles are recessive, so their harmful effects on the phenotype are only expressed in homozygotes. It is estimated that every individual in a population harbours several of these harmful recessive alleles in a heterozygous condition without any phenotypic effects. (Cruz et al. 2008, vonHoldt et al. 2010) 16 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift Genetic drift has several important effects on evolution: 1.Drift reduces genetic variation in populations, potentially reducing a population’s ability to evolve in response to new selective pressures. 2.Genetic drift acts faster and has more drastic results in smaller populations. This effect is particularly important in rare and endangered species. 3.Genetic drift tend to make different populations different from each other. It can contribute to speciation. 17 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift Genetic drift tend to make different populations different from each other. – 18 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift A population bottleneck is a significant reduction in the size of a population that causes the extinction of many genetic lineages within that population, thus decreasing genetic diversity. Population bottlenecks have occurred in the evolutionary history of many species, including humans. The probability of an allele being lost after a bottleneck is: (1 − p) 19 2N HS16 | UniBas | JCW (1 − p)2 N Probability of an allele being lost Population Genetics ▷ Genetic Drift N=2 N=5 N=25 p plot(p,(1-p)^(2*N1),xlab="p",type="l",col="blue",ylab="") points(p,(1-p)^(2*N2),col="green",type="l") points(p,(1-p)^(2*N3),col="red",type="l") 20 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift If a population is reduced to N individuals for one generation then the expected total number of alleles (A’) remaining is: A E( A′ ) = A − ∑ (1 − p) 2N j =1 A : initial number of alleles pj :the frequency of the jth allele 21 HS16 | UniBas | JCW j =1 A E( A′ ) = A − ∑ (1 − p)2 N Population Genetics ▷ Genetic Drift Probability of retaining a rare allele (p = 0.01, 0.05, or 0.10) after a bottleneck of size N for a single generation. Allendorf, Luikart, and Aitken (2013) 22 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift The founder effect is a particular example of the influence of random sampling. It was defined by Ernst Mayr: "The establishment of a new population by a few original founders (in an extreme case, by a single fertilised female) which carry only a small fraction of the total genetic variation of the parental population." The founding of a new population by a small number of individuals could cause abrupt changes in allele frequency and loss of genetic variation. 23 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift Species with lower population growth rates may persist at small population sizes for many generations, during which heterozygosity is further eroded. Therefore, bottlenecks and founder events have a more long-lasting effect on the loss of genetic variation in species with smaller growth rate. 24 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift Simulated loss of heterozygosity and allelic diversity at eight microsatellite loci during a bottleneck of two individuals for five generations. The initial allele frequencies are from a population of brown bears from the Western Brooks Range of Alaska. Redrawn from Luikart and Cornuet (1998). Bottlenecks and founder events have a greater effect on the allele diversity (number of alleles) in a population than on heterozygosity. 25 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift A1A2 A3A4 A3A4 A5A6 A7A8 Nallele = 8 f(AxAy) = 100% 26 Nallele = 2 f(AxAy) = 100% HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift 27 HS16 | UniBas | JCW Population Genetics ▹ Exercises Population Genetics ▷ Genetic Drift 28 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift A founder effect occurs when a new colony is started by a few members of the original population. This small population size means that the colony may have: • _________ genetic variation from the original population. • a _______________ of the genes in the original population. 29 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift [1] Exercise Huntington Disease 30 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift Huntington’s chorea is a devastating but rare (30-70 cases per million people in most Western countries) human genetic disease. People who inherit this genetic disease have an abnormal dominant allele that disrupts the function of their nerve cells, slowly eroding their control over their bodies and minds and ultimately leading to death. In 1993, a collaborative research group discovered the culprit responsible for Huntington’s: a stretch of DNA that repeats itself over and over again: HTT at chr4:3046206-3215485 1 matleklmka feslksfqqq qqqqqqqqqq qqqqqqqqqq pppppppppp pqlpqpppqa 61 qpllpqpqpp ppppppppgp avaeeplhrp kkelsatkkd rvnhcltice nivaqsvrns 121 pefqkllgia melfllcsdd aesdvrmvad eclnkvikal mdsnlprlql elykeik... CAG is the genetic code for the amino acid glutamine (Gln or Q), so a series of them results in the production of a chain of glutamine known as a polyglutamine tract (or polyQ tract), and the repeated part of the gene, the PolyQ region. 31 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift In the fishing villages located near Lake Maracaibo in Venezuela (see map at right), there are more people with Huntington’s disease than anywhere else in the world. In some villages, more than half the people may develop the disease. (Q1) How is it possible that such a devastating genetic disease is so common in some populations? (Q2) Shouldn’t natural selection remove genetic defects from human populations? 32 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift MORE THINGS CONSIDERED 39 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift Population genetics theory predicts that severe population bottlenecks result in a loss of genetic variation (Nei et al. 1975, Lacy 1997, Frankham 1995). This loss increases the likelihood of inbreeding, reducing individual fitness and overall population viability (Lande 1988). Inbreeding can reduce fitness through the production of homozygotes. Homozygotes result in reduced fitness when (i) heterozygotes for rare lethal or nearly lethal alleles interbreed (Lande 1988), or (ii) when homozygotes are produced at loci where over-dominance (heterozygote advantage) is acting. In addition to these well known inbreeding effects, theory also predicts that smaller populations are more likely to respond to genetic drift than to selection even when selection is acting (Barton and Charlesworth 1984, Ohta 1995). Overall, a loss of genetic diversity reduces individual fitness and mean population fitness, and results in less evolution through natural selection and more evolution via genetic drift. The empirical effects of a genetic bottleneck include a loss of heterozygosity (Nei 1987, Frankham et al. 1999), a decrease in allele frequency, a loss of alleles (Bouzat et al. 1998, Glenn et al. 1999), and an increase in frequency or fixation of alleles that may be deleterious (Lacy 1997, Ralls et al. 2000). However since these measures are only meaningful if they can be used to demonstrate a loss or change, they are best interpreted through comparisons with a pre-bottleneck sample from the same population (Bouzat et al. 1998, Matocq and Villablanca 2000). Otherwise, we may erroneously attribute low genetic diversity to a demographic bottleneck (change) when in fact it reflects historically low levels of diversity (no change). 40 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift Effect of bottleneck size (smallest number of individuals recorded in the population) and percentage hatching failure in 51 bird species. Hatching failure is plotted on a linear scale and bottleneck size is plotted on a logarithmic scale, although both were log transformed in analyses (Heber and Briskie, 2010). 41 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift Northern elephant seals (Mirounga angustirostris) have reduced genetic variation probably because of a population bottleneck humans inflicted on them in the 1890s. Hunting reduced their population size to as few as 20 individuals at the end of the 19th century. Their population has since rebounded to over 30,000—but their genes still carry the marks of this bottleneck: they have much less genetic variation than a population of southern elephant seals that was not so intensely hunted. The California Condor (Gymnogyps californianus) has recently survived a severe population bottleneck. The entire population was reduced to 27 individuals in 1982. The number of genetic founders was even smaller. Of the 169 fertile California Condor eggs laid in captivity through 1998, five resulted in severely deformed embryos. These birth defects were diagnosed as chondrodystrophy, a lethal form of dwarfism. 42 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift The main cause of the catastrophic decline of the population of Mauritius kestrels (Falco punctatus) was the destruction of a huge amount of the native forest habitat. Introduced predators such as black rats (Rattus rattus), feral cats (Felis catus), and mongooses (Herpestes auropunctatus), also took their toll. In the mid 20th Century, pesticides such as DDT were widely used on the island and this further decimated the population; predators such as the kestrel that are at the top of the food chain are particularly susceptible to the build up of these chemicals. By 1974, only four birds remained in the wild, and this minute population was incredibly vulnerable. Today there are more than 800 mature birds, with numbers rising; it is estimated that the remaining habitat allows for a carrying capacity of maybe 50-150 more. The Golden Toad (Bufo periglenes) was once abundant in a small region of highaltitude cloud-covered tropical forests, about 30 square kilometers in area, above the city of Monteverde, Costa Rica. It was first described in 1966 and since 1989, not a single B. periglenes is reported to have been seen. It is classified by the IUCN as an extinct species 43 The Passenger Pigeon (Ectopistes migratorius) was a species of pigeon that lived in enormous migratory flocks sometimes containing more than two billion birds. The Bali Tiger (Panthera tigris balica) was a subspecies of tiger which was found solely on the small Indonesian island of Bali. This was one of three sub-species of tiger found in Indonesia along with the Javan tiger (also possibly extinct) and Sumatran tiger (critically endangered). HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift Genetic drift—one of the basic mechanisms of evolution—is simply the evolutionary equivalent of a sampling error. Imagine a game in which you have a bag holding 100 marbles, 50 of which are brown and 50 green. You are allowed to draw 10 marbles out of the bag. Now imagine that the bag is restocked with 100 marbles, with the same proportion of brown and green marbles as you have just drawn out. The game might play out like this: The ratio of brown to green marbles “drifts” around (5:5, 6:4, 7:3, 4:6 . . .) This drifting happens in populations of organisms. Due to many random factors, the genes in one generation do not wind up in identical ratios in the next generation, and this is evolution. It is possible for the frequency of a certain gene to increase in a population without the help of natural selection. While this is evolution, it is evolution due to chance, not selection. 44 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift Imagine that our random draws from the marble bag produced the following pattern: 5:5, 6:4, 7:3, 4:6, 8:2, 10:0, 10:0, 10:0, 10:0, 10:0... Why did we keep drawing 10:0? Because if the green marbles fail to be represented in just one draw, we can’t get them back—we are “stuck” with only brown marbles. The same thing can happen to populations. If the gene for green coloration drifts out of the population, the gene is gone for good—unless, of course, a mutation or gene flow reintroduces the green gene again. The 10:0 situation illustrates one of the most important effects of genetic drift: it reduces the amount of genetic variation in a population. And with less genetic variation, there is less for natural selection to work with. If the green gene drifts out of the population, and the population ends up in a situation where it would be advantageous to be green, the population is out of luck. Selection cannot increase the frequency of the green gene, because it’s not there for selection to act on. Selection can only act on what variation is already in a population; it cannot create variation. 45 HS16 | UniBas | JCW Population Genetics ▷ Genetic Drift t+1 t t+1 t allele probability = 1 2N probability = 1 − Heterozygosity after one generation: H 1 = (1 − Heterozygosity after t generations: H t = (1 − 1 2N 1 2N )H 0 )H 1 t 2N 0 ➥ The equation indicates that the heterozygosity declines each generation at a rate inversely dependent on the population size. 46 UniBas HS2015 HS16 | UniBas | JCW