Topic 9: Individual Differentiation

Question 1

What is a metapopulation? What is genetic differentiation?

Answer 1

Metapopulation: a group of spatially separated populations of the same species which interact at some level
Genetic differentiation: difference in allele frequencies among subpopulations, it is a prerequisite for speciation

Question 2

How can subpopulations become genetically differentiated?

Answer 2

Genetic drift, as they are isolated from each other, and thus have little gene flow
Selection and mutation also contribute to differentiation genetically due to this little gene flow

Question 3

What is gene flow?

Answer 3

Movement of individuals between subpopulations (genetic exchange), it is a force that prevents differentiation and speciation.

Question 4

What is population structure?

Answer 4

Pattern of genetic differentiation observed in a network of subpopulations.
Arises when individuals breed mostly within subpopulations and not between them.
This is inbreeding-like because there is not random mating within the total population, because subpopulations preferentially breed within themselves.
This results in loss of heterozygosity relative to expected (under random mating for population)

Question 5

What is an F-statistic?

Answer 5

A way to measure genetic differentiation over subpopulations based on deviations from HWE.
It is an approach to partition the genetic variation in a subdivided population into components relating to inbreeding, at the levels of total population, subpopulation, and individuals

Question 6

What are the different F-stats? Which can be negative?

Answer 6

Fst : measure of differentiations over subpopulations and is always positive
Fit and Fis are measures of differentiation from HWE for individuals relative to subpopulations (Fis) and individuals to the total population (Fit). These can be positive or negative

Question 7

What is the panmictic index? What is the fixation index?

Answer 7

Panmictic index: measure of relative heterozygosity and is equal to Hobs/Hex
If the P=1, this means that there is random mating and no inbreeding
Fixation index: 1-P, therefore if P=1 then F=0 and if P=0, then F=1

Question 8

How many levels can variation within subpopulations be considered at?
How are their panmictic indices related?

Answer 8

3 Levels:
Individuals (I)
Subpopulations (S)
Total population (T)
Pit = PstPis
And this can be expanded to 1-Fit = (1-Fst)(1-Fis)

Question 9

What are the F-stats (fixation indices)?

Answer 9

Describes the reduction in heterozygosity from what is expected with random mating at one level of hierarchy relative to what is expected at a higher level of hierarchy.
FST= subpopulation relative to total pop
FIT= individual relative to total pop
FIS= individual relative to subpopulation
We are most interested in FST

Question 10

What is HT and HS and HI?

Answer 10

HT: expected heterozygosity of the total population based on the average allele frequencies (during random mating)
HS: expected heterozygosity across N subpopulations (with random mating)
HI: average observed heterozygosity among individuals across N subpopulations

Question 11

What is the range of FST? What does it mean at each end of the range?

Answer 11

It can range from 0-1
0 = complete panmixia or NO genetic differentiation, complete random mating therefore technically no subpopulations)
1 = populations do not share variation, differential fixation of alleles

Question 12

What are the rules of thumb for FST?

Answer 12

0-0.05 = little genetic differentiation
0.05-0.15 = moderate genetic differentiation
0.15-0.25 = great genetic differentiation
>0.25 = very great genetic differentiation
The higher the FST value is, the more different the subpopulations are, and therefore less random mating, there is positive assortative mating for others in their subpopulation and not those outside of the subpopulation

Question 13

What do FIS and FIT mean?

Answer 13

Positive values for these mean there is less heterozygosity observed (inbreeding), and negative means there is more heterozygosity than expected (outbreeding)
If they are both greater than 0, this means mating is non-random within populations due to inbreeding or cryptic population structure
If FIT is greater than 0, and FIS is 0, this means that there is random mating between individuals within subpopulation, and there is inbreeding/non-random mating between individuals within the total population (subpopulations are differentiated)

Question 14

What is the second way of measuring FST that is not the heterozygosity method? What is one condition of this method?

Answer 14

Using the variance in allele frequencies across subpopulations when there are ONLY 2 ALLELES

Question 15

What is the Wahlund effect/principle?

Answer 15

The phenomenon where average homozygosity decreases and heterozygosity increases temporarily when genetically isolated populations are fused and interbreed. This indicated the coming together of alleles that are different between populations initially, and then it will eventually decrease again

Question 16

What do we expect to see if we assume an area we sample is a random mating population, but it actually is composed of multiple random mating subpopulations that are isolated from each other?

Answer 16

According to the Wahlund principle, we should see excess homozygosity when we pool data collected from sub-populations that are genetically differentiated.

Question 17

If we sample a population and genotype them at one microsat locus, and observe an excess of homozygosity OR high FIS value, what are three explanations for this?

Answer 17

1. Selective advantage for homozygosity
2. Non-random mating in population (Wahlund principle)
3. Null alleles at this locus
   If one locus of many shows excess homo, than it is likely due to null alleles or selection
   If all loci have increased homo then there may be non-random mating resulting in the Wahlund effect

Question 18

How do we test whether allele frequencies are significantly different between populations?

Answer 18

Chi-square test
DF= (m-1)(n-1)
M is number of populations
n is number of alleles

Question 19

What does the result of the chi-square test tell us?

Answer 19

The significant difference in allele frequencies means that there has been genetic differentiation between the two subpopulations at this locus (NON-RANDOM MATING)
Sometimes a significant result comes from small number of founders, rapid genetic drift

Question 20

How do you combine results from different loci into the same Chi-square stat?

Answer 20

You use the equation on the sheet, that uses the p-values, and 2k df (2 times the number of loci)

Question 21

TRUE OR FALSE:
Microsatellites are powerful at detecting whether there are statistically significant differences (because of large numbers of alleles) BUT they do not tell us how different they are, or anything about biological significance

Answer 21

TRUE

Question 22

TRUE OR FALSE:
You can use drift/gene flow to determine the FST and the differentiation between subpopulations

Answer 22

TRUE

Question 23

What is NeM?

Answer 23

Number of effective migrants

Question 24

What are some assumptions when relating FST to NeM?

Answer 24

Long term equilibrium
Even exchange of migrants between all subpopulations
All subpopulations are of equal size
Assumes the island model

Question 25

What are the 4 models of gene flow?

Answer 25

Island model: symmetrical gene flow
Continent island: one large population emits migrants to islands
Stepping-stone: migrants exchanged between adjacent subpopulations that are linearly ordered
2D stepping stone: migrants exchanged between adjacent subpopulations in two dimensions

Question 26

What is a rule of thumb in conservation genetics?

Answer 26

1 effective migrant (NeM) per generation is sufficient to prevent populations differentiating through drift, which equated to an FST of 0.2, which is great genetic differentiation
This relationship only holds under equilibrium conditions and often times 1 migrant per generation is insufficient to maintain population connectivity