Topic 13: Assignment Tests and Population Structure

Question 1

What are assignment tests based on?

Answer 1

Likelihood of individuals genotype being found in either population

Question 2

What is involved in the assignment test principle and use?

Answer 2

Assign each individual genotype to the subpopulation in which it has the highest likelihood of occuring.
When subpopulations have very different allele frequencies, individuals should be assigned to the subpopulation in which they were born (natal population) where their genotype has higher probability
Immigrants should be assigned to their natal population and not the subpopulation they were sampled in after dispersal

Question 3

What two things can assignment tests do? What can they not do?

Answer 3

They can measure population structure and they can quantify contemporary dispersal
CANNOT quantify effective migration

Question 4

Which F stat is applicable to assignment tests?

Answer 4

FST

Question 5

What are strongly differentiated populations?

Answer 5

LARGE FST VALUES therefore large genetic distances and very different allele frequencies, they are both far from the middle line on the graph and have all their shapes in seperate places

Question 6

What are weakly differentiated populations?

Answer 6

Not much population structure and genetic distance, similar allele frequencies, small FST values, both close to middle line

Question 7

What are non-differentiated populations?

Answer 7

Pretty much one population, no clear pattern, populations grouped together on center line and exchange over line between them

Question 8

What does shape and location on graph mean in an assignment plot?

Answer 8

Shape: where they were sampled
Location: population where the individual is assigned due to genes

Question 9

What is a measure of genetic divergence on an assignment plot?

Answer 9

The number of cross assigned individuals. They can either arise by chance or indicate it is a migrant into the population it was found, from its original population

Question 10

What are the three major uses of assignment plots?

Answer 10

Population structure (genetic differentiation), wildlife forensics (matching specimens to source populations), measuring contemporary gene flow (identifying recent immigrants or dispersers)

Question 11

What is the traditional approach to determine the differentiation between subpopulations?

Answer 11

Consider geographic sample locations as subpopulations and then estimate genetic structure, genetic distance, test for differentiation between the designated subpopulations

Question 12

When do we use Bayesian methods? What is it?

Answer 12

When population structure is cryptic and we do not know how many randomly mating subpopulations there really is.
You use genetic information first to cluster individuals in such a way as to maximize the differences between groups (FsT) and minimize differentiation within groups (FIS) for any given number of groups.
The likelihood of observing the actual genotype data given K groups
The k that gives the highest probability of the data is the best way of designating the subpopulations

Question 13

What do Bayesian methods also allow for?

Answer 13

They also allow for admixture (interbreeding) between genetic groups and resulting in mixed individual ancestry

Question 14

What is an admixture or Structure plot?

Answer 14

A graph that visualizes each individual’s genetic assignment
Each individual is a column, and each genetically distinct cluster (corresponding to a genetic background) plotted in a different colour.
The genetic composition of each individual column shows how much of their genetic background can be assigned to each of the K clusters.
If there is complete population structure and every subpopulation is genetically distinct, then all the individuals within each subpopulations will have the same solid color bar

Question 15

What does underestimating structure lead to?

Answer 15

Management actions at the wrong spatial scale, inflating population size estimates and preventing protection under legislation such as Species at Risk Act,

Question 16

What can overestimating structure lead to?

Answer 16

Costly conservation actions for “rare taxa” such as translocations or habitat restoration to unnecessarily promote gene flow.

Question 17

How can you tell on a graph which K is best?

Answer 17

Where the plateau on the graph is the best K value, if there is a big jump then take the lower K value

Question 18

What is principal component analysis?

Answer 18

A statistical procedure that uses an orthogonal transformation to convert a set of observations into a set of values linearly uncorrelated variables called principal components
For n observations of p variables the number of principal components will be (n-1,p).
In all cases the first principal component accounts for as much of the variability in the data as possible, and each succeeding component explains the highest amount of variation remaining from the preceding components

Question 19

What is the goal of Principal Component Analysis?

Answer 19

Goal is to reduce complexity of the dataset to ease visualization, attempt to show as much genetic variability as possible in a few axes. Individuals close to each other on the axes are more genetically similar

Question 20

What are pros and cons to Bayesian methods?

Answer 20

PROS: can be used to find K and can identify admixed individuals
CONS: assumes HWE within populations, assumes linkage equilibrium between loci, computationally intensive.

Question 21

What are pros and cons of PCA?

Answer 21

PROS: no assumptions made about underlying genetic model, computationally quick, can handle large data sets
CONS: inherently explorative, generally cannot be used to find k, cannot be used to identify admixed individuals