Molecular Ecology

Question 1

What is “coalescent theory”?

Answer 1

Coalescent theory concerns the tracing of allelic ancestries back to their point of coalescence, that is to the time of their most recent common ancestor

Question 2

Which factors determine the time to common ancestry?

Answer 2

1. The size of the population
2. Rates of migration
3. Change in population size

Question 3

Which factors interact to cause non-uniform nucleotide substitutions rates among lineages?

Answer 3

1. Body size
2. Generation times
3. Population size
4. Metabolic rate

Question 4

What is the “effective population size”?

Answer 4

Effective population size is the number of individuals in an idealized, randomly mating population with an equal sex ratio that would exhibit the same rate of heterozygosity loss over time as an actual population with a particular census (total adult number) size.

Question 5

How can one estimate the effective population size?

Answer 5

1. One such approach is to compare the change en allele frequencies within a population between generations.
2. Ne can can be estimated by using models based on coalescent theory when the divergence times of populations are known.
3. Ne is proportional to the rate at which genetic diversity is lost or gained.

Question 6

Why is an excess of heterozigosity an indicator of a possible bottleneck?

Answer 6

Rare alleles are lost more rapidly than heterozigosity during bottlenecks, generating heterozygosity excess because most heterozygosity is contributed by common alleles, whereas the converse is true during rapid population growth.

Question 7

What is a bottleneck?

Answer 7

Bottlenecks are significant declines in effective population size and may be temporary or permanent.

Question 8

Considering a bottleneck, why is there a more serious consequence after a rapid fall than from a gradual one in the long-term?

Answer 8

This is because slow changes allow natural selection to continue purging deleterious alleles, whereas a sudden loss of individuals can result in the subsequent fixation of damaging alleles by chance

Question 9

What is the relation between effective population size and genetic diversity?

Answer 9

The effective size of a real biological population is proportional to the rate at which genetic diversity is lost or gained - if one obtains a measure of this rate in a real biological population, the effective size of that population is equal to the size of an ideal Fisher-Wright population that losses or gains genetic diversity at exactly that rate.

Question 10

Does the effective size of a population correlate with the expected intervals between coalescent events?

Answer 10

YES! (Large city vs. small town example)

Question 11

How can one expect a genealogy from a growing population to be? And from a declining population?

Answer 11

One can expect a tree with long terminal branches and shorter internal branches from a growing population, compared to a genealogy from a constant-sized population.
In a declining population, coalescent events tend to occur with greater rapidity, but as one moves past a series of coalescence backwards in time, population sizes grow ever larger and, concomitantly, coalescence intervals get longer.

Question 12

What is the “island model” of migration?

Answer 12

The island model of migration breaks the population into subpopulations or ‘demes’, with migration of individuals between demes.

Question 13

What is the stepping-stone model of migration?

Answer 13

The stepping-stone model of migration, is a type of island model, where demes are arrange linearly or in a two-dimensional grid, and migration only takes place between neighboring demes.

Question 14

What is “gene flow”?

Answer 14

Gene flow means the movement of genes, mediated by individual organisms or their gametes, between subpopulations.

Question 15

How can one detect gene flow between populations?

Answer 15

By using Allele frequency data, which permit inferences of gene flow between populations, ultimately based on the level of disturbance migration causes to Hardy Weinberg equilibrium expectations.

Question 16

What is “Nm”?

Answer 16

The average number of successfully reproducing migrants per generation moving between subpopulations, and it is calculated by:

Nm = 1/4 (1/Fst-1) (in diploid organisms)

Question 17

What is isolation by distance?

Answer 17

Is the correlation between migration rate and geographical distance between pairs of subpopulations, and is a useful method fir assessing whether subpopulations are in equilibrium or have recently become fully isolated.

Question 18

What can one expect if there exists isolation by distance?

Answer 18

One can expect a correlation between Fst value and geographical distance. Fst value increases with geographical distances.

Question 19

How can one identify a immigrant in a population?

Answer 19

Assignment tests begin by determining the expected frequency of a potentials migrant’s genotype in each possible source population, based on the allele frequencies in those populations.

Question 20

What is phylogeography?

Answer 20

Phylogeography is the field of study concerned with the principles and processes governing the geographical distribution of genealogical lineages, especially those at the intraspecific level.

Question 21

What are the effects of genetic drift and gene flow in a population?

Answer 21

Genetic drift promotes genetic differentiation among populations whereas gene flow has the opposite effect.

Question 22

Which are the most useful measures of genetic diversity?

Answer 22

1. Mean # of alleles per locus
2. % of polymorphic loci
3. Mean heterozygosity (most widely used)

Question 23

What is the “observed heterozygosity” (Ho)?

Answer 23

Ho is the mean proportion of loci for which an individual is heterozygous.

Question 24

What is the “expected heterozygosity” (He)?

Answer 24

He is the proportion of expected from allele frequencies in the sample and assuming the population is in H-W equilibrium
(2pq)

Question 25

What types of F-statistics exist?

Answer 25

1. Fis, relates individuals to populations
2. Fit, relates individuals to to the total population
3. Fst, relates subpopulations to the total population

Question 26

To what can be the loss of heterozygosity attributed?

Answer 26

1. Genetic drift

2. Inbreeding

Question 27

By Which processes genetic variation is created?

Answer 27

1. Mutation

2. Recombination

Question 28

Errors in DNA replication can lead to nucleotide substitutions if one nucleotide is replace by another. These can be of two types:

Answer 28

1. Transitions, which involve changes between either purines (A,C) or pyramidines (T,G)
2. Transversions, in which a purine is change by a pyramidine or vice versa

Question 29

Which demographic influences exist on Effective Population Size?

Answer 29

1. Sex Ratios: uneven sex ratios cause Ne to be 36% lower than census population sizes
2. Variation on reproductive success: even if sex ratios are 1:1, not all individuals will produce the same numbers of viable offspring, and this variation in reproductive success (VRS) will also decrease Ne relative to Nc.
3. Fluctuating population size: fluctuating population sizes have reduced the Ne of wild populations by an average of 65%, making this the most important driver of low Ne/Nc ratios. This is because long-term effective population size is determined not by the Ne averaged across multiple years, but by the harmonic mean of the Ne (Wright, 1969). The harmonic mean is the reciprocal of the average of the reciprocals, which means that low values have a lasting and disproportionate effect on the long-term Ne. A population crash in one year may therefore leave a lasting genetic legacy even if a population subsequently recovers its former abundance. A population crash of this sort is known as a bottleneck, and it may result from a number of different factors including environmental disasters, over-hunting or disease.