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Population Genetics

by B. A. McDonald

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Knowledge Test Questions on Population Biology and Coevolution

1. What is a population and what is population genetics?

A population is a group of individuals from the same species that occupy the same geographic region and exhibit reproductive continuity from generation to generation. Populations are often defined based on geographical boundaries or evidence for genetic exchange.

Population genetics is a subdiscipline of genetics that seeks to understand and explain the processes that lead to the creation and maintenance of genetic variation within populations of organisms.

2. Why is population biology important for plant pathologists?

Pathogens exist as dynamic populations that change, or evolve, through time and space. Effective disease control requires control of a population of individuals and not simply an individual. Knowledge of population biology is needed to implement sustainable disease management practices.

3. What is coevolution?

Coevolution is a process in which two species interact in a way that determines the evolutionary path followed by each partner in the species pair. In plant pathology, we focus mainly on the coevolutionary process that occurs between pathogens and their plant hosts, often focusing on pathogen virulence and host resistance. As a result of coevolution, we expect that plant resistance genes will be most common in regions where pathogen and plant have coexisted for the longest period of time.

4. Why don't agroecosystems exhibit coevolution?

In agroecosystems, the plant population does not respond to changes in the pathogen population through a process of natural selection. Instead, humans (plant breeders) decide what plant genotypes should replace existing plant genotypes in response to an evolving pathogen population. Thus, plant breeders determine the evolutionary path followed by pathogens in agricultural ecosystems. This presents an opportunity for humans to guide the evolution of plant pathogens.

5. What are the five evolutionary factors considered by population geneticists?

The five forces are mutation, genetic drift, gene/genotype flow, mating/reproduction systems, and natural selection.


Knowledge Test Questions on Mutation

1. Why is mutation important in the population genetics of organisms?

Mutation is the ultimate source of base pair substitutions, insertions, or deletions that lead to new alleles at existing loci. These new alleles may encode unique properties that provide advantages or disadvantages to mutants within a population. Mutation provides the ultimate raw material for evolution.

2. Does mutation acting alone cause changes in allele frequencies?

Yes, but the rate of change is extremely slow compared to other evolutionary processes such as gene flow and natural selection. Thus, we do not generally consider mutation to be a major cause of changes in allele frequencies.

3. Why do large populations have more alleles than small populations?

Mutation rates are small but constant. With a typical mutation rate of 1 x 10-6, it is expected that 1 out of a million individuals in a population will carry the mutation. If the population size is small (10,000 or fewer individuals), the probability that the mutation will be present is small (~1% with 104 individuals). If population sizes are large (107 or more individuals), the probability that the mutation will be present is large (~10 mutants expected if 107 individuals are in the population). Mutations can be lost from populations through genetic drift, and large populations experience less genetic drift than small populations. Thus mutations are more likely to exist and persist in large populations than in small populations.

4. Why do plant breeders seek the center of origin to find resistant germplasm?

As a result of coevolution, the center of origin is expected to have the largest diversity of plant resistance alleles, as well as the largest diversity of pathogen virulence and avirulence alleles. The center of origin is usually the center of diversity for an organism because it has existed there for the longest period of time, and time is needed for mutations to occur and accumulate in populations. Among the mutations that will occur are those that affect resistance to pathogens. If disease pressure exists, resistant mutants are expected to increase in frequency over time. Thus we expect that the greatest diversity of resistance alleles will exist at the place where coevolution between plant and pathogen has occurred for the longest time.

5. What is a resistance gene pyramid?

A resistance gene pyramid is a set of separate resistance genes (not alleles at the same locus) that is present in a single plant genotype. The R-gene pyramid may be intentionally introgressed through a plant breeding program, or it may exist naturally as a consequence of a long coevolutionary process between plants and pathogens. The pyramid may be composed of many different genes deployed against a single pathogen (e.g. a series of different resistance genes that are effective against the wheat stem rust pathogen), or it may be composed of genes that encode resistance against many different pathogens (e.g. an R-gene for a nematode, an R-gene for a stem rust pathogen, an R-gene for a bacterium, etc).

6. How many resistance genes would a plant breeder need to introduce into a susceptible cultivar if a pathogen has a very large population size (>1012 individuals per field)?

If the pathogen has a large effective population size, then mutations from avirulence to virulence are likely to be present. Assuming a mutation rate of 10-6, the expectation is that one individual per million will be a virulent mutant. Assuming that mutations are independent events, the probability of two different mutations occurring in the same individual is the product of each event occurring individually. Thus, assuming the same mutation rate for each mutation, we expect that one double mutant will occur in a population of 1012 individuals. In this case, the plant breeder should use at least three resistance genes in a pyramid to be certain that a simultaneous mutation to virulence against the three resistance genes will not defeat the pyramid through a strictly mutational process. If recombination exists in the pathogen, the breeder may need to incorporate even more R-genes!

7. How many resistance genes would a plant breeder need to introduce into a susceptible cultivar if a pathogen has a relatively small population size (<105 individuals per field)?

Under the assumption of a mutation rate of 10-6, the expectation is that the mutation from avirulence to virulence is not likely to be present in a population of less than 100,000 individuals. Thus a single resistance gene has a good chance of maintaining its effectiveness for an extended period of time (number of generations) under these conditions and the breeder may be successful with deployment of only one resistance gene at a time (no need to make an R-gene pyramid).


Knowledge Test Questions on Genetic Drift

1. What is genetic drift? Name three processes that cause genetic drift.

Genetic drift is a random change in allele frequencies caused by a small number of reproducing individuals in a population (small effective population size). Small Ne can result from:
   a. recurring small effective size (eg due to a small carrying capacity in the local environment)
   b. a bottleneck where the population undergoes a sudden, large reduction in size
   c. a founder event where a small number of individuals start a new population that is isolated from other populations.

2. What is a genetic bottleneck and what is a founder effect?

A genetic bottleneck occurs when a population experiences a sudden, severe reduction in the number of reproducing or surviving individuals. For example, we expect that populations of obligate parasites will experience a bottleneck after the host population has been harvested. Bottlenecks also occur when a sensitive fungal population is treated with a fungicide.

A founder effect is a reduction in genetic diversity that occurs when a restricted subsample of a source population starts a new population that is isolated from other populations. The result is often a significant difference in allele frequencies in the founder population compared to the source population. Australian populations of plant pathogens often exhibit a founder effect because of effective quarantine measures that restrict the number of individuals that enter the Australian continent.

3. How does genetic drift affect the distribution of genetic diversity among populations?

Genetic drift is a diversifying force that tends to make populations different. Genetic drift can lead to the fixation of alleles or genotypes in populations. Population subdivision and population differentiation are expected to increase if genetic drift is operating, thus more of the genetic diversity will tend to be distributed among populations instead of within populations. Drift also increases the inbreeding coefficient and increases expected homozygosity in populations as a result of removing alleles.

4. Why is genetic drift important in agroecosystems?

Pathogen populations tend to be very large (as with many microbes), but pathogen population sizes can fluctuate widely due to changes in climate (e.g. dry versus wet years), and agricultural practices such as spraying of fungicides, deployment of resistance genes, or harvesting of the crop. Thus genetic drift can explain rapid shifts in allele frequencies from year-to-year or large differences in allele frequencies among pathogen populations for both neutral and selected characters. Genetic drift can explain some of the observed differences in frequencies of virulence alleles that occur in founder populations such as Australia.

5. How can you calculate the predicted effect of genetic drift?

The expected fluctuation in allele frequencies between generations is calculated using the formula:

Var (p) = after one generation of genetic drift for diploid organisms.

Where Ne is the effective population size, and p and q are the frequencies of two alleles at a locus. For haploid organisms, multiply by two, as only half as many copies of each genes exist in populations of haploid organisms, and the expected variance should be twice as great.


Knowledge Test Questions on Gene Flow

1. What is gene flow and how does it differ from genetic drift?

Gene flow is the movement of genes between populations, usually through the process of migration of individuals among populations. Gene flow tends to make populations genetically similar, and thus is a unifying force in evolution, while genetic drift tends to make populations genetically different, and thus is a diversifying force in evolution.

2. How does gene flow differ from genotype flow?

Both gene and genotype flow require the movement of individuals or gametes (e.g. pollen) among populations. In the case of gene flow, specific genes or DNA sequences carried in the migrant become integrated into many different genetic backgrounds in the recipient, or native, population. Genotype flow refers to the movement of entire multilocus genotypes where the association among alleles in the genotype is maintained after arriving in the recipient population. Genotype flow occurs only for asexual organisms or for organisms that undergo extreme inbreeding.

As an example of gene flow, consider the movement of a fungicide resistance allele between two different countries through the movement of a wind-dispersed ascospore. After arriving, the resistance allele can be recombined into many different genetic backgrounds through sexual reproduction with the native population. In this case, the same allele encoding the fungicide resistance is present in different populations, but in different genetic background, and the fungicide resistance allele can become associated with many different combinations of alleles in the genome (leading to gametic equilibrium). As an example of genotype flow, consider the movement of a fungicide resistant mutant between different countries through wind-dispersal of an asexual spore (conidium). In the absence of any recombination (e.g. an asexual pathogen such as Fusarium oxysporum), the resistance allele will be present in the same genetic background in both populations. In this case, the fungicide resistance allele will be associated with all other alleles in the genome (leading to gametic disequilibrium).

3. Why is gene flow important in agricultural ecosystems?

Gene flow is the process that moves newly emerged mutations (such as fungicide resistance alleles or virulence alleles) among farmers' fields and different geographical regions. Thus, a fungicide resistance (or new virulence) that emerges only one time in a farmer's field in France may become widely disseminated across Germany, Switzerland, and Poland through a combination of gene flow and selection. Gene flow is also an important consideration for risk assessment of genetically engineered crops, as it would be undesirable for the transgene to become incorporated into wild related species or neighboring fields planted to non-transgenic cultivars.

4. How does Nem relate genetic drift to gene flow?

Nem is a measure of the actual number of migrants that are shared among populations. Ne is the effective population size, and thus affects the likelihood that populations will diverge by genetic drift, while m is the fraction of that population composed of migrants, and thus affects the likelihood that populations will become similar due to exchange of the same genes. The product of these two parameters represents the number of migrants exchanged between populations each generation. The calculated Nem is a measure of the number of migrant individuals needed to account for the observed level of population differentiation under an equilibrium between gene flow and genetic drift. When one individual is exchanged between populations each generation (Nem = 1), the effects of genetic drift and gene flow exactly counterbalance each other. If Nem < 1, then populations will eventually diverge by genetic drift, and if Nem > 1, then populations will not diverge due to genetic drift.

5. What is a metapopulation and how is it relevant to agroecosystems?

A metapopulation is a population of populations, with individual populations connected by gene flow. In agricultural systems, each farmer's field can be considered as a separate population, and it is likely that a series of farmer's fields is connected by different degrees of gene flow, depending on the distance between fields and the dispersal distance of pathogen propagules.


Knowledge Test on Reproduction/Mating Systems

1. What is the difference between genetic assortative and genetic disassortative mating?

Organisms with assortative mating systems tend to mate with individuals that share alleles, such as close relatives, so they are likely to have recent common ancestors. Organisms with disassortative mating systems tend to mate with individuals that do not share alleles, meaning that they are less likely to have recent common ancestors.

2. What is the difference between gene and genotype diversity? How do you measure them?

Gene diversity refers to the diversity existing for individual loci in the genome, e.g. the number of alleles at an RFLP locus. Genotype diversity refers to diversity for the number of genetically distinct individuals in a population, e.g. the number of different DNA fingerprints in a sample of individuals. Genotype diversity is meaningless for species such as humans that are obligate outcrossers and where every individual in a population has a unique genotype.

Quantitative measures of gene diversity are based on the number of alleles per locus and the frequencies of alleles at each locus. Diversity increases as the number of alleles increases, and as the frequency of alleles becomes more evenly distributed. Quantitative measures of genotypic diversity are based on the number of genotypes and the frequencies of genotypes found in a population. Diversity increases as the number of genotypes increases and as the frequencies of genotypes become more evenly distributed.

3. Is gene diversity affected by mating system? How?

Gene diversity is not expected to be affected by mating system because recombination mainly shuffles existing alleles into new combinations without creating new alleles or changing allele frequencies. However, intragenic recombination can create new alleles (and thus increase gene diversity) following many cycles of recombination.

4. Is genotype diversity affected by mating system? How?

Genotype diversity is strongly affected by mating and reproductive system. Organisms that are strictly asexual or that undergo regular self-fertilization or extreme inbreeding will not put together new combinations of alleles on a regular basis, and are thus expected to exhibit limited genotypic diversity. Organisms that undergo regular sexual recombination will shuffle together new combinations of alleles every sexual generation as a result of independent assortment, and are thus expected to exhibit high genotype diversity.

5. Why is a mating/reproduction system relevant to plant pathology?

Mating and reproduction systems may have a significant effect on the rate at which pathogens evolve to overcome control strategies deployed against them. Sexual pathogens can recombine different, independent mutations affecting virulence and/or fungicide resistance with much greater efficiency than asexual or inbreeding pathogens. This can affect resistance gene deployment strategies or strategies for alternating fungicide applications. Pathogens with mixed reproduction systems can gain advantages from both the sexual and asexual phases.


Knowledge Test on Natural Selection

1. What is the difference between the balance model and the neutral mutation model for explaining genetic variation in populations?

According to the balance model, the gene pool contains a large number of different alleles that occur at various frequencies for each locus, and these alleles may have very similar effects on fitness. The heterozygotes in a population often have a fitness advantage over the homozygotes (overdominance). The prediction of the balance model is that populations will have a high degree of genetic variation, and most individuals will be heterozygous at a large number of loci. Evolution in these populations occurs by gradual changes in allele frequencies as different alleles or allele combinations are favored by different environments.

According to the neutral model, most genetic variation has no effect on fitness, and therefore is maintained for no particular purpose. The majority of mutations are deleterious, and are quickly removed by selection. The remaining mutations are neutral, or nearly neutral and persist in the population, leading to the observed levels of variation in DNA and proteins.

2. What is the difference between directional selection and stabilizing selection?

Directional selection leads to an increase or decrease in allele frequency depending on whether an allele is favored or selected against in a particular environment. The result is a linear change in allele frequency that tends to reduce gene diversity in a selected population. Stabilizing selection removes from a population phenotypes that deviate in either direction from the optimum value for a character. If the optimum phenotype results from additive or other interactions (such as overdominance) among several loci, the result is to maintain genetic diversity in a selected population.

3. Define pathogen fitness. Name as many fitness parameters as you can imagine for a pathogen in an agricultural ecosystem.

Fitness is an especially complicated concept for pathogens. Fitness is often based on the total output of viable progeny by an individual in its lifetime. But pathogen fitness must also take into account transmissiveness of the progeny because a pathogen that does not propagate by infecting another host eventually will not be able to sustain an epidemic. Fitness increases with increasing life span (also called viability) and the number of progeny produced (also called fecundity). As an example in plant pathology, the most fit pathogen genotype is the one that infects the most host plants in the shortest period of time and that produces the most infective spores (for asexual pathogens).

Fitness parameters:
Latent period, total spore production per plant, total number of viable spores produced, total pathogen biomass per host unit, effectiveness of spore dispersal (how many new plants infected per propagule produced or per host plant infected), spore/propagule longevity, many other possibilities that students and instructors should be able to dream up!

4. What is Fisher's Fundamental Theorem of Natural Selection?

According to Fisher's Theorem, the mean fitness of a population always increases in a fluctuating environment. The change in fitness will be proportional to the additive genetic variation for genes affecting fitness. As the amount of genetic variation in populations increases, the rate of change in fitness of the population increases proportionally. As a result, populations with the greatest genetic diversity have the greatest potential for evolution.

5. What happens to the frequency of pathogen virulence alleles if there is no fitness cost associated with having unneeded virulence?

If there is no fitness cost associated with the mutation from avirulence to virulence, then we expect that all pathogen populations will become fixed for the virulence allele soon after the plant resistance gene is introduced into the host population.

6. Have plant pathologists found evidence of selection against unneeded virulence genes?

The evidence is mixed. Some experiments detect selection; others do not.


Knowledge Test on Genetic Structure

1. What is a "boom-and-bust cycle"? How do they develop and why do they persist?

Boom-and-bust is a colorful term used to describe the frequency dependent phase-lagged oscillation that occurs between plant host resistance alleles and corresponding pathogen virulence alleles following introduction of a new resistance gene into a naïve pathogen population.

2. Why did the Puccinia graminis f. sp. tritici population stabilize in North America?

It appears likely that disrupting the pathogen sexual cycle by eliminating the barberry alternate host led to a reduction in overall genetic diversity for the wheat stem rust pathogen. The consequence of eliminating sexual reproduction was to take away the possibility of creating virulence allele pyramids through recombination, forcing the pathogen to accumulate a sequence of mutations in the same genetic background via asexual reproduction in order to overcome resistance gene pyramids.

3. What is genetic structure?

Genetic structure refers to the amount and distribution of genetic variation within and among populations. The observed genetic structure is due to the summed effect of all evolutionary forces that have acted on a population over time.

4. Does gene flow make populations more genetically similar or more different?

Recurring gene flow will make populations more genetically similar over time. Exchange of at least one individual each generation is sufficient to prevent populations from diverging by genetic drift.

5. How does sexual reproduction affect the genetic structure of populations?

Sexual reproduction maintains genotype diversity because of recombination, which shuffles together new combinations of alleles every sexual generation. In general, sexual populations have more genotype diversity than asexual populations, though gene diversity can be identical in sexual and asexual populations.

6. Describe the evolutionary forces that affected Phytophthora infestans populations in Europe before 1960. Now describe the evolutionary forces that affect P. infestans populations in Europe in 2000. Which population poses a greater threat to potato production and why is the threat greater?

Before 1960, the European population of P. infestans was composed of a single genotype, which was strictly asexual because the opposite mating type was absent. This old European population evolved by accumulation of mutations within a single genetic background, and hence the evolutionary potential was limited by the effects of mutation and selection. Following introduction of the opposite mating type, thought to have occurred in the 1970s, the population began sexually recombining and many new genotypes were created. These new genotypes had higher fitness than the original clone and eventually replaced the original clone. The threat to potato production in the new population is greater because the new population undergoes regular recombination and can new genotypes with greater fitness can evolve more quickly than in the old populations.