Genetics and modeling

Question 1

What can cause low levels of genetic diversity?

Answer 1

Low levels of genetic diversity may be as a result of either high ongoing migration or historic high migration but no current, ongoing migration

Question 2

Can you use genetic inference methods when genetic divergence is low?

Answer 2

Issues arise with most current population genetic inference methods when the genetic divergence is low among putative populations

Question 3

What are the two groups of methods that can be used to infer population genetic structure?

Answer 3

Population-based methods and kinship-based methods

Question 4

What are common population-based methods for inferring population genetic structure?

Answer 4

Moment-based statistics such as Wright’s Fst and coalescent methods, assignment methods, spatial methods that assign the individual multilocus genotypes to a population of samples

Question 5

Which method (kinship-based or population-based) is best suited for populations with low genetic diversity, and why?

Answer 5

Kinship-based approaches complement more traditional population-based genetic inference methods by providing a means to detect population structure and estimate current migration rates when genetic divergence is low. But in order for kinship-based methods to become widely adopted, formal estimation procedures applicable to a range of species life histories are needed

Question 6

Why detect population structure? Why is this of interest for researchers?

Answer 6

Interests in detecting population structure are many, including understanding processes of local adaptation, effects of habitat fragmentation and delineating management units

Question 7

What are the most commonly used population genetic inference methods, and what are the drawbacks of using these?

Answer 7

Wrights Fst

Assignment tests

Coalescent-based inference methods

These perform well when the degree of genetic structure is high because the interpretation is relatively straight-forward. It is another matter when the degree of genetic divergence among putative populations is low because current low genetic divergence has two possible causes - ongoing migration or recent historic migration but no (or low) current migration

But low genetic divergence does not necessarily imply ongoing migration among populations!

Question 8

What are the major assumptions of population-based genetic methods?

Answer 8

1. the population size and migration rates remain constant through time
2. an ideal Wright-Fisher population - each population is panmictic with no reproductive skew amongst individuals
3. discrete generations

For most natural populations, these assumptions are not realistic and will be violated in the model.

When these assumptions are valid, then low genetic divergence (Fst < 0.05-0.02) implies high migration rates, and high genetic divergence implies low migration rates. However, most natural populations undergo changes in population size and migration rates fluctuate - in which case the correlation between current genetic diversity and current migration rates is less straightforward - but this is not an issue for inferring population structure when the degree of genetic divergence is high.

Low genetic divergence among populations does not necessarily imply that current migration rates are high, because such low genetic divergence structure could be because of high historical migration rates among populations that are now isolated

Question 9

How do assignment-based methods work?

Answer 9

Individual multilocus genotypes are assigned to putative populations based upon the relative likelihoods of multilocus genotypes given the population allele frequencies and assuming panmictic populations

The proportion of individuals assigned to other populations than that from which they were sampled is positively correlated with the immigration rate and reflects migration during the last generation(s). Identifying descendants of immigrants can extend the time frame over which migration rates are estimated beyond a single generation (implemented in BayesAss+ and BIMr)

Question 10

What are some advantages and disadvantages of assignment-based methods?

Answer 10

Advantages:
1. Assignment tests have been promoted as a means to obtain ‘real-time’ estimates of migration rates

Disadvantages:

1. Successful implementation of assignment tests require individuals to be assigned to their source population with statistical rigour, which is correlated to the degree of genetic divergence among source populations
2. The confidence in assignments increases with the degree of genetic divergence among populations. However, high levels of genetic divergence also imply low migration rates, and consequently a large proportion of each population needs to be sampled for immigrants to be among the collected samples or the result will be a zero rate of migration rates
3. At low levels of genetic divergence, confidence in assignments is low because the likelihood of a given genotype is similar across populations
4. These methods work best at intermediate levels of genetic divergence (Fst > 0.05)

Question 11

How do kinship-based methods work? What are some advantages and disadvantages to using these methods?

Answer 11

Rely upon individual multilocus genotypes to other individual multilocus genotypes (as opposed to a population of multilocus genotypes). They are essentially assignment methods but assigned to other multilocus genotypes rather than populations

Advantages:

1. the statistical rigour and power of each assignment (and thus any inferred population structure or estimated migration rates) depends upon overall level of genetic variation but not the degree of genetic divergence among populations
2. yield estimates of current population structure or migration rates

Main obstacles:

1. the necessary ‘scaling-up’ in terms of samples and loci
2. The integration of demographic and genetic theory and modeling to develop suitable estimation procedures

Question 12

In what situations are population-based methods or kinship-based methods best?

Answer 12

Population-based methods are best for strongly structured populations (displaying a high degree of genetic divergence) are readily detected with high statistical power with modest amounts of data

Kinship-based methods are well suited when the degree of genetic divergence is low, such as when current migration rates are high or when populations have undergone a recent reduction in migration rates, which is when population-based methods tend to be uninformative

Question 13

What is effective population size?

Answer 13

The effective population size is proportional to the loss of genetic diversity through gene drift and the rate of inbreeding - the rate at which genetic diversity is lost in an ideal population due to (nearly) neutral genetic variation

It is essential for describing the rate of evolution and understanding extinction processes

Directly linked to demography, especially juvenile and adult survival and thus generational overlap, reproductive success and its variation among sexes or individuals and sex ratios

Question 14

What are the assumptions of effective population size? What are the issues with these assumptions?

Answer 14

Assumes an ideal population with diploid genotype, monoecious individuals reproducing through random mating (which leads to census and effective population size being identical)

Issues:

1. In order to use Ne on species with overlapping generations, it requires sampling of populations across generations (suggested 4 generations) which is not feasible in long-lived species (leads to highly biased estimates due to migration or environmental stochasticity)
2. Issues with these assumptions are that real population differ from ideal populations, and these deviations influence the rate at which genetic diversity is lost

Question 15

What are some of the methods used for estimating effective population size?

Answer 15

1. Temporal method - genetic approach for estimating Ne by sampling allele frequencies at two different points in time and assume that the differences in allele frequencies are due to random genetic drift
2. Single sample method - refers to the inbreeding effective size, which often, but not always, results in the same number as the variance effective size
3. Close-kin method - developed for fish spawning stock sizes

Question 16

What two types of effective sizes can be estimated?

Answer 16

Variance effective size - focuses on changes in genetic variance, on consequences for the offspring generation, and hence naturally leads to consideration of interpopulation divergence. Estimated through the temporal method

Inbreeding effective size - focuses on changes in heterozygosity, on consequences for the parental generation, and hence naturally leads to consideration of the level of inbreeding within populations. Estimated through the single sample method

Question 17

What is the difference between effective population size and effective number of breeders?

Answer 17

Effective number of a breeders is the effective size of a breeding population in a given year. It is usually smaller than Ne. Used often in studies of populations with overlapping generations

Question 18

What impact does overlapping generations have on estimates of effective population size?

Answer 18

Nunney 1993 found that different mating systems, and thus different reproductive success, have less impact on the effective population size than expected. Proposed that the impact of reproductive success is higher with lower generational overlap but becomes negligible with increasing generational overlap

Question 19

What methods can be used to accurately estimate effective population size for species with generational overlap?

Answer 19

Grimm et al. 2016 proposed an individual-based model that allows calculation of Ne based on demographic parameters that can be obtained in a time period much shorter than a generation, and can be adapted to every life history parameter combination

Uses heterozygosity as a measure for Ne, as Ne is proportional to the loss of genetic diversity and heterozygosity provides a good indicator of genetic diversity

Question 20

What is the impact of increased generational overlap on effective population size?

Answer 20

Increased generational overlap leads to overall increased heterozygosity per year, but decreased heterozygosity per generation.

Observations per generation showed a decreasing heterozygosity loss every time generation length increased by 1. Consequently, the process of losing heterozygosity involves an additional year and Ne decreases. Leads to lower Ne per generation with increasing generation length

Recruitment rates had an effect at lower adult survival rates (decreased generational overlap) with lower recruitment rates reducing the loss of heterozygosity. Recruitment rates had little effect on heterozygosity loss at higher adult survival rates. Small changes in survival rates can considerably change the growth rate of the population and in turn affect effective sizes

Question 21

How much effect does changing demographic parameters have on effective population size?

Answer 21

Grimm et al. 2016 found remarkable changes of Ne with changing demographic parameters:

1. Ignoring increase in generational overlap increased Ne
2. Actual Ne decreased with increasing generation length
3. At low overlapping degrees, lower recruitment rates increased Ne
4. Small changes in demographic parameters can have strong effects on population trajectories and consequently Ne
5. Variability in mate pairing may reduce Ne
6. Different mating systems resulting in reproductive skew as well as different sex ratios may have large effects on Ne

Question 22

What is the general idea behind Close-Kin Mark-Recapture?

Answer 22

Using modern genetics, one can generalize from “recapture of self” to “recapture of closely-related kin”. An individual is marked by its presence in the sample, and “recaptured” if the sample contains one or more close relatives. This is less likely to happen in bigger populations, so the number of “recaptures” provides information on adult abundance

Question 23

What makes close-kin mark-recapture difficult to use in open populations?

Answer 23

Adult mortality in the interval between birth and sampling
Non-random sampling
Reproductive variability
Different types of kinship (P-O vs. half-sibs)
Uncertainty in genotyping
Time-of-marking is unknown unless age is measured

Question 24

What are the main challenges with extending mark-recapture to close-kin mark-recapture?

Answer 24

1. Different demographic equations and extra parameters (e.g. Fecundity-at-age) needed to describe recapture probabilities
2. A more complicated likelihood because the latent space of possible histories is much more intricate (in effect, the genealogy of the entire population)
3. Quantifying to reliability of kinship-determination from genotype data (loosely analogous to misidentification in photo-ID studies)

Question 25

What is gene flow?

Answer 25

In population genetics, gene flow (also known as gene migration or allele flow) is the transfer of genetic variation from one population to another. If the rate of gene flow is high enough, then two populations are considered to have equivalent allele frequencies and therefore effectively be a single population.

Question 26

Why is effective population size useful to estimate?

Answer 26

It quantifies the magnitude of genetic drift and inbreeding in real-world populations The effective size of a real population is then defined as the size of an idealised population, which would give rise to the rate of inbreeding and the rate of change in variance of gene frequencies actually observed in the population under consideration, which correspond to the so-called inbreeding and variance effective sizes, respectively

Question 27

Is Ne a useful parameter or still limited in its applications?

Answer 27

Minimizing the loss of genetic variation should be of great concern for conservation and management, so Ne is a useful parameter as it quantifies the magnitude of genetic drift and inbreeding in real populations. Minimizing the loss of genetic variation is achieved through minimizing genetic drift and maximizing Ne Ne is still a useful parameter even with limitations that come from assuming an idealised population. In populations with overlapping generations, you can obtain yearly estimated of Nb, the effective number of breeders, which summarises the effects of variation in reproductive success between age classes, between sexes and between individuals within an age–sex class on genetic drift in a single breeding season, instead of in a lifetime.

Question 28

What is genetic drift?

Answer 28

Variation in the relative frequency of different genotypes in a small population, owing to the chance disappearance of particular genes as individuals die or do not reproduce

Question 29

What is linkage disequilibrium?

Answer 29

linkage disequilibrium is the non-random association of alleles at different loci in a given population. Loci are said to be in linkage disequilibrium when the frequency of association of their different alleles is higher or lower than what would be expected if the loci were independent and associated randomly