Topic 8 Flashcards
(25 cards)
1
Q
genetic drift
A
- Genetic drift refers to chance fluctuations in allele frequencies as a result of randomly sampling gametes each generation.
- Gametes unite to form zygotes. To conceptualize drift, think of each generation as a random sample of the gametes produced by the previous generation. Think of drift as sampling error spread across generations.
- Adults produce a pool of gametes, and allele frequencies among the gametes are the same
as in the adults. However, not all the gametes will unite to form zygotes. Zygotes are
produced from a RANDOM SAMPLE of gametes taken from the initial pool, and allele
frequencies can stochastically change because of sampling error. So long as mating
is random, this new pool of gametes will randomly unite to form zygotes according to the
Hardy-Weinberg principle. As a result, the zygotes will be in perfect HW equilibrium, but
based on the NEW allele frequencies after sampling error has occurred. Hence, genetic
drift DOES NOT cause HW disequilibrium, but it does change allele frequencies, which is
why it violates the assumptions of the HW principle. This process of sampling error will
repeat itself over generations, stochastically changing allele frequencies as it does so.
2
Q
important points about genetic drift
A
- The direction of genetic drift is random, and hence cannot be predicted. In any generation, allele frequencies could increase or decrease, or by chance stay the same.
- The magnitude of genetic drift depends on population size. The smaller the population size, the larger the potential change from one generation to the next (e.g., the sampling error)
- Genetic Drift causes populations to genetically diverge from each other (on average)
- Genetic drift will reduce genetic (allelic) variability within a population over time, in the absence of anything else. It reduces heterozygosity and causes alleles to randomly go to fixation
3
Q
genetic drift reduces allelic variability and heterozygosity
A
- Given that Genetic Drift will eventually move a population to fixation (in the absence of anything else), it will reduce the heterozygosity over time (once a population becomes fixed for an allele, the heterozygosity will be zero).
- This will occur in a completely random and unpredictable way. In any generation, drift can randomly increase or decrease the heterozygosity (or potentially leave it unchanged), but over time it will become equal to zero once an allele becomes fixed
4
Q
genetic drift causes populations to diverge
A
- Drift changes allele frequencies among a group of populations such that the variance of their mean allele frequencies will increase over time.
- We do not expect the actual mean allele frequency to change among a very large group of populations.
5
Q
genetic drift and Fi
A
- Over time, drift increases the probability that two randomly chosen alleles in a population will be identical by descent (or autozygous) as well.
- The smaller the population, the greater the increase in Fi. We refer to Fi as the FIXATION INDEX (Fi)
6
Q
genetic drift does not result in deviations from HW equilibrium
A
- Drift increases Fi because of reductions in Heterozygosity. However, heterozygosity is reduced because population allelic variability is reduced (remember, heterozygosity is highest when alleles are equal frequent in a randomly mating population), not because of non-random mating.
- Hence, the reduction in heterozygosity will not result in HW deviations. Don’t confuse Fi with the inbreeding coefficient F
- As a result, we use Fi to describe the population autozygosity instead of F. The inbreeding coefficient F gives us the fractional reduction in heterozygosity in comparison to a panmictic population.
- Fi gives us the probability that two randomly chosen alleles will be identical by descent (or autozygous).
7
Q
why is large or infinite population size an assumption of HW Principle
A
- Even though drift does not cause deviations from Hardy-Weinberg equilibrium, it profoundly affects an important attribute of the HW principle.
- In the absence of violations of the HW principle’s assumptions, both allele and genotype frequencies will be stable from one generation to the next. This will not be the case when population size is not large, and drift comes into play
8
Q
population size
A
- N refers to the census population size, or the population size that has been estimated by an enumeration method
- However, from a genetic point of view, the census size (N) is rarely (if ever) equivalent to the effective population size Ne
9
Q
effective population size
A
- The size of a population with equal numbers of breeding males and females, panmictic, and constant population size over time, with no variation in the numbers of progeny contributed to the next generation that will undergo reductions in heterozygosity at the same rate as our census population size due to drift alone.
- Stated differently, Ne is the size of a population that will undergo the same rate of increase in Fi over time as our census population (Fi = the fixation index, or the probability that two randomly chosen alleles are IBD).
10
Q
effective and census sizes
A
- Usually, the effective population size is much smaller than the census size.
- A convenient way to look at this is by examining the Ne/N ratio. These are often less than 0.2
11
Q
What contributes to the reduction of the effective population size in comparison to the census size?
A
- The number of breeding individuals
- Unequal numbers of males and females
- Variation in contributions to the next generation in terms of numbers of individuals among mating pairs.
- Fluctuations in population size over time
12
Q
breeding population size
A
- When the census size of a population is enumerated, non reproducing juveniles and individuals of very old age (e.g., no longer reproducing) are typically included in the estimate. However, such individuals do not contribute to the reduction in heterozygosity over time by drift. Only breeding individuals contribute to heterozygosity and allele frequency changes in the next generation.
- The breeding population size can be enumerated by counting the number of individuals on nests, mating grounds, spawning beds etc. In the context of genetic drift, we will from now on assume that the census size (N) is the actual breeding size.
13
Q
variation in family size (contribution to the next generation)
A
- Even when a population remains constant in size, each mating pair will not leave exactly two offspring. If we set the number of offspring left by a mating pair as K, when population size is stable, the mean and variance of K are equal to 2 (under a Poisson model).
- The assumption here is that all individuals (mating pairs) have an equal probability of contributing to the next generation, but many factors such as fertility, gamete quality etc. can violate this assumption, making the variance of K greater than 2.
14
Q
fluctuating population size and Ne
A
- Population size fluctuates over time because of many ecological factors such as predation, competition, disease, environmental factors and so on.
- As a result, it is important to consider the impact these fluctuations have on effective population size over time
15
Q
population bottlenecks
A
- The previous example illustrates what is referred to as a population bottleneck. In the 4rth generation, the population was reduced to 18 individuals, which had a major impact on the effective population size.
- Population bottlenecks are important in nature. As a result of genetic drift, they will have the impact of reducing genetic variability (heterozygosity) and increasing Fi.
16
Q
conservation implications of bottleneck and drift
A
- Conservation biologists are interested in maintaining genetic variation in threatened populations. If genetic variation can be maintained, so can a populations capacity to adapt, or undergo adaptive evolution in response to new environmental variables.
- Hence, conservation biologists seek to maintain a populations ability to evolve. Bottlenecks and small population sizes are a concern for these reasons.
17
Q
molecular markers and effective population size
A
- Given that there are two copies of diploid biparentally inherited markers (e.g., allozymes, nuclear genes, SNPs, microsatellites) in an organism, and one copy of haploid markers such as mitochondrial and Chloroplast DNA, biparentally inherited diploid markers have a larger effective population size than uniparentally inherited haploid markers.
- In fact, because mitochondria and chloroplasts are uniparentally inherited, they have half the effective population size of biparentally inherited markers.
- However, because they are also haploid, we half the effective size again
- Hence, all else being equal, these markers will diverge at ≈4X the rate of biparentally inherited markers due to effective population size and drift. As a result, they are also more sensitive to bottlenecks and founder events
18
Q
founder effect
A
- A reduction in genetic variation as a result of a population being founded (started) from a small number of colonizing individuals from a parent population.
- It is sampling error from the parent population and will typically result in reduced variability and different allele frequencies in the new population
19
Q
founder effects and bottlenecks
A
- Founder effects are the name given to bottlenecks that occur because of the formation of a new population, but they are really the same thing and have identical effects.
- We could have used the previous formula to calculate the probability of loosing an allele during a bottleneck
20
Q
binomial probability
A
- We are often interested in the probability that a sample contains a certain number of alleles.
- The sample can be a group of founders, survivors of a bottleneck, or number of individuals that we may use in a genetic rescue operation etc
21
Q
sampling error and the binomial probability
A
- The binomial probability formula can also be used to estimate the probability of obtaining a certain number of alleles from one generation to the next, with random mating.
- In this case, N is equal to the number of offspring in generation t+1, and p and q are the allele frequencies in the parental generation (generation t).
22
Q
genetic drift and mutation
A
- We will consider an ‘infinite alleles’ model of mutation, which simply means that every mutation creates a new unique allele.
- Although this assumption isn’t always realistic, it simplifies the math and provides a quite reasonable approximation
- What is the probability that a new selectively neutral mutation will go to fixation?
- When such a mutation is first introduced, it will have a frequency of 1/2N (where N is the population size), and the probability that it will be fixed is 1/2N
- At what point will the introduction of new mutations be exactly balanced by their loss due to genetic drift. In other words, what are the equilibrium values of Fi and H (heterozygosity)?
23
Q
drift and selection
A
- Drift and Selection can interact with each other. Drift is most powerful when population sizes are small.
- Under these circumstances, drift can overpower natural selection such that a new advantageous mutation can be lost by drift, and a new deleterious mutation can be fixed by drift
- The previous relationships indicate that most advantageous mutations, even when population sizes are large, will be lost.
- Most advantageous mutations only slightly increase fitness (s is small, e.g., 0.001), and 2s will also be small (0.002). As a result, advantageous mutations often require ‘luck’ to go to fixation
24
Q
more conservation implications
A
- When population sizes are small, drift can fix slightly deleterious mutations with the same probability as neutral mutations.
- At a population size of 20, the probability that a slightly deleterious mutation with s= -0.001 will be fixed is 1/2N, or 1/40.
- That is to say that 1 out of 40 of such deleterious mutations will be fixed. This is a concern for conservation biologists working with small, threatened populations.
- In addition to fixing deleterious alleles, drift reduces allelic variability, which provides the raw material for natural selection. In doing so, it reduces adaptive potential.
- When population size is quite small, most individuals will also be related to each other, resulting in inbreeding and inbreeding depression, in addition to the effects of drift
25
drift and gametic disequilibrium
- What is the relationship between Genetic Drift and (D), the disequilibrium coefficient?:
- Genetic Drift is stochastic sampling error of gametes (AB, ab, Ab, aB) across generations. It can increase or decrease the value of D in any generation in an unpredictable way and affect the rate at which D breaks down in an unpredictable way.
- The smaller our population size, the greater our sampling error and impact on the value of D.
- Among a very large group of populations of the same size, the smaller our population size, the larger the variance of the mean value of D
