Population Genetics
I. Classical (Mendelian) genetics tracks patterns of in...
2. There must be no selection, natural or artificial.
3. There must be no mutation. No...
with any partner of the opposite sex they encounter when they are in the mood to mate. Though
some of these ef...
a. Another example which has turned out to be of tremendous benefit to humans
occurred ...
d. Complete selection against a recessive trait can be calculated. This calculation you
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** Population Genetics Study Guide

Published on: Mar 4, 2016

Transcripts - ** Population Genetics Study Guide

  • 1. 1 Population Genetics I. Classical (Mendelian) genetics tracks patterns of inheritance from individual parents to their offspring. These patterns fall into relatively simple statistical patterns. Geneticists are also interested in the ways that genetic traits distribute in breeding populations. A. Population geneticists study the interrelated patterns of phenotypic, genotypic and allelic frequencies within populations. These frequencies are generally expressed in relatively formal statistical notation. 1. For each genetically controlled trait, a population will show a characteristic distribution of the possible phenotypes. For example, if the gene in question is the brown/black fur color gene in gerbils, some proportion of the population will be brown and the rest will be black. The frequency of brown gerbils would be represented as f(Brown), and would be calculated as the number of brown gerbils in the population divided by the total number of gerbils in the population. The frequency of black gerbils (f(black) would be the number of black gerbils divided by the total number of gerbils. Note that if these are the only two colors of gerbils in the population, their frequencies should add up to 1.0. 2. Of course, the phenotypes of the gerbils are the result of their genotypes. Genotypic frequencies in this example would be f(BB), f(Bb) and f(bb). Again, if this gene has only these two alleles, these three frequencies should add up to 1.0. Not also that the f(black) will be equal to the f(bb), and that the f(brown) will be equal to the sum of the f(BB) and the f(Bb). 3. At the core of all of the genotypic and phenotypic variation are, of course, alleles. And the frequencies of those alleles are at the core of the calculations of population genetics. In our example, the frequencies of our two alleles would be f(B) and f(b). If there are only two alleles for this gene in the population, then f(B) and f(b) will add up to 1.0 It is very common in population genetics to use the symbols p and q to represent these allelic frequencies. If there is a dominant allele, it’s frequency will be represented as p. So f(B) = p and f(b) = q. If there is no dominance (as in incomplete or codominance) either letter may be used for either allele. If the gene has more than one allele, the frequency of the third allele would be represented as r. B. The total genetic bank of a population is its gene pool. C. Not only are population geneticists interested in calculating these frequencies, they are also interested in tracking changes in those frequencies due to influences like selection and chance. II. Given knowledge of genotypic frequencies, it is possible to calculate the allelic frequencies for any population. A. f(A) = p; f(a) = q. B. p = f(A) = #A/total # alleles = f(AA) + ½ f(Aa) C. q = f(a) = #a/total # alleles = f(aa) + ½ f(Aa) –OR- q = 1 – p. (Remember that p + q = 1.) D. This calculation makes no assumptions about the condition of the population. (In other words, it doesn’t require that the population be in any kind of equilibrium.) III. Basic population genetics begins with the concept of a “perfect” population in which all allelic frequencies are constant, and in which all mating is random. This ideal population is called a Hardy-Weinberg population, after the statisticians responsible for developing the concept. A population which simulates this ideal population is often described as being “in equilibrium.” The relationship between the allelic and genotypic frequencies in this ideal population is described by the Hardy-Weinberg equation (H-W equation). A. In order for allelic frequencies to be stable, five conditions must be met. 1. There must be completely non-random mating.
  • 2. 2 2. There must be no selection, natural or artificial. 3. There must be no mutation. Note that this is an impossible condition, as mutation rates can’t be reduced to zero. 4. There must be no migration of species members from outside populations (as they might come from a population with different allelic frequencies). 5. There must be no genetic drift. Genetic drift results from chance alterations in allelic frequencies, and again cannot realistically be reduced to zero. Genetic drift can be minimized if the population is very large. The smaller the population, the more influential genetic drift will be. B. The H-W equation shows the relationship between allelic and genotypic frequencies in a population which meets these exacting standards. In a situation in which completely random mating is occurring, the relationship will be strictly statistical. 1. The H-W equation was derived by the following reasoning. a. Each individual carries two alleles for each gene b. If there are only two possible alleles for a particular gene, then the possibilities for each of the alleles that an individual has can be expressed as (p + q) (because that position must have one of the two available alleles. For instance, A or a.) c. The probabilities for the possible combination of the two alleles in two positions for alleles would be calculated as the possibilities for position 1 times the possibilities for position 2. In other words, the first allele will be A or a, and the second allele will be A or a. Recall that in statistics, or means add probabilities and and means multiply probabilities. So this all boils down to the fact that you can calculate the probabilities for all of the possible allelic combinations by multiplying (p + q) x (p + q). The result of this multiplication is p2 + 2pq + q2. d. Recall that, if there are only these two alleles in the population, p + q = 1. And of course, 1 x 1 = 1. e. So p2 + 2pq + q2 = 1. This is the H-W equation. f. So what does all of this mean? This equation describes the frequencies of the three possible genotypes in our H-W population. If a population is mating randomly, then i. F(AA) = p2 ii. F(Aa) = 2pq iii. F(aa) = q2 g. So a test of whether a population is in H-W equilibrium (ie, is mating randomly) would be to determine p and q using the method described in II above, then calculate the three components of the H-W equation. Finally compare the three frequencies calculated by H-W to the original genotypic frequencies. If the two sets of frequencies match (as in part f. above), then your population can be considered a H-W population. If they do not match, then your population is not mating randomly. C. Note that, if your population is a H-W population, q will be equal to the square root of the f(aa). But this is only true if the population is a H-W population. D. Also note that a single generation of random mating is sufficient to bring your frequencies into compliance with the H-W equation (at least for that generation). So if you are told “this population has been breeding randomly,” that is a signal to you that you may assume that it is a H-W population, and that you may apply the H-W equation. IV. There are five conditions which can disrupt the equilibrium frequencies within a population (by altering allelic frequencies). A. Non-random mating is any mate-selection pattern in which the choice of a partner is based on something other than chance. Truly random mating means that males and females essentially mate
  • 3. 3 with any partner of the opposite sex they encounter when they are in the mood to mate. Though some of these effects can be calculated, we will not be covering those calculations in this class. 1. Darwin was very interested in a phenomenon called sexual selection. In some species, one or the other gender has distinct preferences when it comes to the characteristics of a mating partner. This is most frequently observed in some bird species. The classic example is among peafowl. Everyone is familiar with the flamboyant appearance of the peacock, but few would recognize a peahen. The brilliant coloration in this species is limited to the males, and is perpetuated in the species because of the mating preferences of the females. For some reason, peahens really prefer fancy looking partners. In many other species, aspects of appearance or behavior often factor into mate selection. 2. Harem-style social structure can also disrupt random mating. In some species, not all males have equal mating access. If the species has a social structure in which each grouping is dominated by one or a few males, who do the majority of the mating for the tribe, those dominant males’ genes will be passed on in larger-than-random numbers, and the less dominant males’ genes may not be passed on to the next generation at all. 3. Assortative mating is a phenomenon in which individuals tend to select mating partners who are like themselves. For instance, in some species with color variation among members, population members will tend to select mating partners of their own color. 4. Some species mate largely through inbreeding, which not only increases homozygosity, it also disrupts relative allelic frequencies. B. Genetic drift is any changes to allelic frequencies which are simply the result of chance. These effects pretty much can’t be calculated. They can’t be eliminated either. 1. Basic genetic drift is essentially sampling error. Every mating involves a number of random events, and though overall statistical predictions for the outcomes of these events can be calculated, the events are still random. We see examples of this all the time. For instance, if a particular family has a heterozygous tongue rolling parent and a homozygous non-rolling parent, we’d predict that half of the children would be tongue rollers and half would be non- rollers. But in families of multiple children, those predictions will frequently turn out to be incorrect—among such families with six children we may find four rollers and two non- rollers, or one roller and five non-rollers, etc. What makes the statistical prediction useful is that we can predict that, among many such pairings, we will see approximately half rollers and half non-rollers. And this realization provides important insight into the genetic drift issue. The larger a population is, the less significant genetic drift will be from generation to generation, because those deviations from statistical perfection will average out over the many mating pairs in the population. But if the population is small—say, fifteen mating pairs— there is much less opportunity for compensation, and genetic drift may cause significant changes in allelic frequencies from one generation to the next. Consider two populations, each with p = 0.5 and q = 0.5 for a genetic trait for which there is no selection, etc. The first population has over a thousand mating pairs; the second has only twelve. From one generation to the next, the first population will almost certainly maintain that 0.5/0.5 set of frequencies. But while the second may also maintain those ratios, pure chance may result in a change in one generation to p = .4 and q = .6. Or to p = .8 and q = .2. And there’s no way to predict whether such a change will occur, or in which direction is will occur if it does. Welcome to the world of probability ;^) 2. Founder effect is a special case of genetic drift. It refers to a situation in which one member of the population (almost always a male, because a single male potentially has a much greater influence on the overall breeding going on in a population than a single female can have) contributes much more to the next generation than his “share.” The harem situation above is a kind of founder effect.
  • 4. 4 a. Another example which has turned out to be of tremendous benefit to humans occurred in a small Venezuelan village. Early in the nineteenth century, a Portuguese sailor, set ashore for some reason, joined this village. He married one of the village women, and apparently produced many children. Seven generations later, the Huntington’s disease gene that he carried has spread throughout this village. More than 250 members of the village currently suffer from Huntington’s disease, all traced to this one man. This is founder effect. b. So why was this so valuable? The presence of this large number of people who all inherited this genetic disorder from the same source allowed a research group to finally achieve something no one had previously been able to do—map the location of the Huntington’s disorder on the human chromosome set. And this led to scientists finally being able to determine just what is wrong with the Huntington’s gene that caused those who possess it to have the problems they have. 3. Another special case of genetic drift is bottlenecking. This is a phenomenon related to the small-population genetic drift mentioned above, but with a twist. Population bottlenecking occurs when, for some reason, a new, small population is “founded” from a larger population. This can happen when a small portion of a population becomes geographically isolated from the main population (and thus loses breeding access to the rest of the population), or it can happen when a formerly large population becomes reduced to a much smaller population through some disaster that wipes out most of the members. In either case, we get genetic drift for two causes. First, the new population will almost certainly not be a representative sample of the original population, just due to sampling error. So allelic frequencies may be changed right from the start because of unequal sampling of the various genetic commodities of the original population. And of course, the new population is small, which means there is a high probability that drift will occur every generation until the population increase in size enough for chance alterations in allelic frequency to become unlikely. C. Mutation also changes allelic frequencies, though this effect is generally very small. Mutation effects can be estimated by calculation, but we will not be doing so in this course. 1. Forward mutations, of course, will tend to reduce p and increase q. Reversions do exactly the opposite. 2. Suppressor mutations tend to produce brand new alleles of a gene. 3. Note that most mutations are neutral or silent—they produce no change in phenotype. Of those that do cause a change in the behavior of the gene produce, most are harmful while a few are actually improvements. A significant percentage of changes are conditional—their impact on the possessor will depend upon the environmental situation. D. Selection can be either in the form of natural selection or artificial selection. Note that this is not the same thing as “mate selection,” discussed above under non-random mating. Selection is an influence which prevents certain members of the population from breeding (or interferes in the sense of reducing their breeding success). 1. Selection is against the phenotype, not the genotype, so in order to be selected against, the individual must show the trait under consideration. a. Many selection effects, especially in nature, are not absolute. There are formulas to take partial selection effects into consideration, but we will not be learning about these. b. When the selection is absolute, we call it “complete selection.” c. Complete selection against a dominant trait will wipe out that trait in one generation, as there is no way for the individual to have the dominant allele and not show it (thus no alleles escape selection).
  • 5. 5 d. Complete selection against a recessive trait can be calculated. This calculation you need to learn. 2. Allelic changes are almost always tracked through what happens to q. In the case of selection, the equation calculates the change in q (designated as “delta q” or ∆ q) due to one generation of complete selection against the homozygous recessives. The equation for complete selection against a recessive trait is: Where ∆ q = change in q qo = original q q1 = q after one generation of selection and q1 = qo + ∆ q a. Note that as q decreases, so does ∆ q. Also note that as q decreases, there will be a concomitant increase in p. b. If selection is not total, the equation can be modified by the introduction of a selection coefficient. The equation may also be altered to reflect selection effects over multiple generations. 3. For some genes, the heterozygote may actually be the most fit genotype. For example, in areas where the malarial parasite is endemic, the sickle-cell heterozygote is more fit than either the homozygous normal (who is more susceptible to malaria) or the homozygous sickle- cell (who suffers from the depredations of sickle-cell anemia). The heterozygote suffers almost no symptoms due to the possession of a single copy of the sickle-cell allele, but does benefit by a degree of protection against the malarial parasite. This situation is called heterosis or hybrid vigor. 4. Some other interesting issues to explore with respect to selection effects are different modes of selection (stabilizing, directional, disruptive), sexual selection, pliotropic effects, polygene traits, and coadapted gene complexes. E. Migration occurs when two populations of the same species are combined together to form a single new population. This is generally viewed as a smaller population joining (“migrating into”) a larger population, but the equation works no matter the respective sizes of the populations. The equation describing allelic changes due to migration is: q1 = (1-m)qo + mQ Where q1 = q after one generation of random interbreeding between the two populations qo = q of original population (usually designated as the larger) Q = q of migrant population (usually the smaller) m = proportion of final population composed of migrants Note that (1-m) will thus be equal to the proportion of the final population composed of “original” members.

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