Midterm 2 - Diploids

Question 1

What does Fst measure?

Answer 1

It measures population structure or differentiation

Question 2

Describe a microsatellite

Answer 2

Di-nucleotide repeats

Question 3

What is an allele?

Answer 3

A unique DNA sequence at a genetic locus (region within a genome)

Question 4

What are Hardy Weinberg expectations?

Answer 4

Expected genotype frequencies with random mating

Question 5

Random Mating

Answer 5

Occurs when individuals mate independent of their genotype and their relatedness

Question 6

Inbreeding

Answer 6

When mating invloves individuals that are more closely related to each other than randomly chosen individuals from a population

Question 7

Inbreeding coefficient (f)

Answer 7

The probability two randomy chosen alleles from two individuals at a locus are identical by descent

Question 8

Indentity by descent (IBD)

Answer 8

When two alleles descend from a particular ancestral allele

Question 9

what is f for parent-offspring

Answer 9

1/4

Question 10

What is f for full-sibs

Answer 10

1/4

Question 11

What is f for uncle-nephew

Answer 11

1/8

Question 12

What os f for 1st cousins

Answer 12

1/16

Question 13

What does a high f value indicate?

Answer 13

Most matings are among close relatives

Question 14

Fis

Answer 14

Level of inbreeding within individuals relative to a randomly mating sub-population

Question 15

Fst

Answer 15

Level of inbreeding within sub-populations relative to an entire or total population that randomly mates

Question 16

Fit

Answer 16

Level of inbreeding within individuals relative to a total population that randomly mates

Question 17

H1

Answer 17

Average observed heterozygosity across subpopulations

Question 18

Hs

Answer 18

Average heterozygosity if random mating occurs within each subpopulation

Question 19

Ht

Answer 19

Expected heterozygosity if random mating across entire or total populations

Question 20

What do Fst values between 0 - 0.05 indicate in terms of population structure

Answer 20

Little population structure

Question 21

What do Fst values between 0.05 - 0.15 indicate in terms of population structure

Answer 21

Moderate structure

Question 22

What do Fst values between 0.15 - 0.25 indicate in terms of population structure

Answer 22

Great structure

Question 23

What do Fst values of 025+ indicate in terms of population structure

Answer 23

Very great structure

Question 24

Describe the two steps of “Structure” analysis

Answer 24

1. Identify subpopulations based on H-W expectations
2. Determine the proportion of an individuals genotype that has ancestry in sub-populations identified in step 1

Question 25

Marginal Fitness

Answer 25

The average fitness of an entity overall backgrounds that entity occurs.

Question 26

h = 0...

Answer 26

Fully ressesive

Question 27

h = 0.5

Answer 27

Co-dominant

Question 28

h = 1

Answer 28

fully dominant

Question 29

0 < h < 0.5

Answer 29

Partially ressesive

Question 30

0.5 < h < 1

Answer 30

Partially dominant

Question 31

True or False: Inbreeding selects out deleterious alleles more efficiently than with random mating

Answer 31

True This is purging of the deleterious alleles with inbreeding

Question 32

Heterozygote Advantage

Answer 32

Heterozygote genotypes have highest fitness

Question 33

Frequency-dependent Selection

Answer 33

Fitness of a genotype is a function of frequencies of genotypes in a population

Question 34

Density-depedent Selection

Answer 34

Fitness of a genotype is a function of the population size

Question 35

Heterogenous Selection

Answer 35

Fitness of a genotype is a function of the environment it occurs in which may vary across space and/or time

Question 36

What conditions indicate a polymorphic equilibrium?

Answer 36

0 < phat < 1 or wbarA = wbar or WbarA = wbara

Question 37

Negative Frequency dependent selection

Answer 37

Fitness of a genotype is a negative function of its frequency

Question 38

Positive frequency dependent selection

Answer 38

Fitness of a genotype is a positive function of its frequency

Question 39

Epistasis

Answer 39

When the phenotype or fitness of an allele depends on the state of another allele at another locus

Question 40

Genetic Hitch-Hiking

Answer 40

Selection at one locus indirectly affects allele frequencies at another physically limited loci

Question 41

Haplotype

Answer 41

A set of alleles inherited together from a single parent - can be at the gamete or chromosome level

Question 42

Linkage Equalibrium

Answer 42

Haplotype frequencies at frequencies that are equal to what is expected with independent inheritance of alleles between loci

Question 43

Linkage disequilibrium

Answer 43

Haplotype frequencies at frequencies that are not equal to what is expected with independent inheritance of alleles between loci

Question 44

D = 0

Answer 44

Linkage Equalibrium

Question 45

D > 0

Answer 45

AB, ab haplotypes are over-represented

Question 46

D < 0

Answer 46

Ab, aB haplotypes are over-represented

Question 47

True or False: Older populations have a longer time for linkage disequalibrium to be reduced by recombination?>

Answer 47

true

Question 48

What 4 Processes Generate Linkage Disequalibrium

Answer 48

1. Mutation 2. Random Genetic Drift 3. Selection 4. Dispersal

Question 49

What process breaks down linkage disequalibrium?

Answer 49

Recombination

Question 50

Selective Sweep and Genetic Hitch-Hiking

Answer 50

When a beneficial mutation quickly increases in frequency and simultaneously causes physically linked alleles to increase in frequency because of a lack of recombination within a short period of time

Question 51

Background selection with recombination

Answer 51

- low levels of nucleotide variation - low recombination around centromere - gene closer to centromere curved have less variation further

Question 53

Linear = (what in terms of epistasis)

Answer 53

no epistasis

Question 54

Curved = (what in terms of epistasis)

Answer 54

signs of epistasis

Question 55

Synergistic Epistasis

Answer 55

As you have beneficial alleles they positivly interact with each other and create non linear increase

Question 56

Smaller pop = (what in terms of variance)

Answer 56

larger variance

Question 57

Beneficial alleles can go extinct due to...

Answer 57

Drift

Question 58

Increased pop size =

Answer 58

Decreased varience - also vice versa

Question 59

What can maintain an equilibrium?

Answer 59

A balance between selection and recombination.