Prof. Kelsey's

Question 1

Population structure?

Answer 1

= spatial structure divided into smaller local populations.

Question 2

F(IS) = (Hs - Hi)/Hs ?

Answer 2

= measures the reduction of heterozygosity within a subpopulation.

Question 3

R = h²S ?

Answer 3

= determines the amount of selection due to evolutionary change.

R = response to selection.
h² = heritability.
S = selection differential.

Question 4

Inbreeding coefficient?

Answer 4

= determines how much of inbreeding is occurring in populations.

● F = (Ho - H)/Ho

Ho = expected heterozygosity = 2pq.
H = actual observed heterozygotes.

Question 5

F 0 —> 1 for inbreeding coefficient?

Answer 5

Suggests inbreeding.

Question 6

Selective agent?

Answer 6

= environmental cause of fitness differences among organisms with different phenotypes.

Eg. Seeds eaten by Darwin’s finches.

Question 7

w = fitness of individual/average fitness

Answer 7

= relative fitness of individual in the population in terms of selection.

Question 8

F(ST) = Ht - Hs (with dash on top) / Hs (with dash on top) ?

Answer 8

• measures differentiation among subpopulations.
- gives you a # 0<x<1
- close to or = to zero, little difference.
- close to one, more differentiated.

• tells you how different the subpopulations are from one another.

Question 9

F(IT) = Ht - Hi (dash) / Ht

Answer 9

• reduction in individual hetero relative to metapopulation.

Hi (dash) = average reduction of heteroz in one individual.

Ht = reduction heteroz in total metapopulation.

Question 10

Absolute fitness

Relative fitness

Answer 10

• average number of offspring produced by a genotype over its lifetime.

          0 < w < 1
   will die       most fit

• (w) relative difference between genotypes.

w = absolute fit of interest/ absolute fit of most fit genotype

Question 11

Indirect selection?

Answer 11

• takes place on correlated traits
- one trait target of selection, 2nd is not target, but may appear to be due to correlation with target.

• changes in correlated trait not affecting fitness.

Question 12

Beta?

Answer 12

= selection gradient.
• measure of direct selection.
• partial regression of slopes.

• when positive: direct selection active.
• + or - depicts + or - slxn.

Question 13

Ne = 4NmNf / Nm+Nf

Nm + Nf = Na

Answer 13

• determines magnitude of genetic drift when or more assumptions are violated (¹ #sexes; ² no sex/nat slxn; ³ subpop same in next generation).

Nm = males.
Nf = females.

Question 14

Population genetics?

Answer 14

= study of naturally occurring genetic differences between organisms and populations.

Question 15

Migration

m

Answer 15

• homogenizes the population.
• increases allelic variation.

• movement of individuals between populations.
• proportion of individuals that move between populations in a generation.

Question 16

Mutation?

Answer 16

• ultimate source of genetic variation.
• changes allele frequency because it can change actual allele.
• 4 kinds of mutation.

Question 17

How do you identify selection agent based on selection gradients?

Answer 17

• partition fitness into various fitness components.
• look at fitness components & see what selection is acting on.

Question 18

Adaptive radiation?

Answer 18

= evolution of ecological diversity within ecological habitats.

• closely related species evolving to live in varying habitats.

Question 19

Selection vs Migration?

Answer 19

• local adaptation from local selection; variation among subpopulations.

• relative activity of each can mean the difference of homogenizing a population or adaptation.

Question 20

Frequency of alleles?

Answer 20

= proportion of alleles present in a population.

Question 21

Target of selection?

Answer 21

= trait that helps the organism deal with challenge in the environment, i.e., selective agent.

• phenotypic traits that selection acts directly upon.

Question 22

Genetic drift?

Answer 22

= fluctuations in allele frequency that are due to random chance.

• important in small populations.

Increases variance among subpopulations.

Decreases variation within subpopulations.

Question 23

Evolution requirements of natural selection?

Answer 23

1. Phenotypic variation for a trait.
2. Consistent relationship between phenotypic variation & variation in fitness.
3. Must be heritable trait.

Question 24

Directional selection?

Answer 24

= selection acting in positive or negative direction.
• moves mean left or right.
• width of curve decreases.
• changes the diversity, i.e., homogenizes.

Question 25

Non random mating Negative assortment mating

Answer 25

- dissimilar phenotype mating. Result : High heterozygosity.

Question 26

Five factors that effect/criteria of Hardy-Weinberg?

Answer 26

1. Random mating. 2. No slxn. 3. Large population size (no drift). 4. No migration. 5. No mutation.

Question 27

Molecular clocks?

Answer 27

• main assumption: sub. rate constant across lineages. • allows use of molecules to date species events (i.e., divergence).

Question 28

Migration vs Drift?

Answer 28

• migration can balance drift according to: FsubST = 1/(1+4NeM) • can use to calculate migration with allele frequency...but does have problems.

Question 29

Hardy-Weinberg Principle?

Answer 29

= non changing population (equilibrium) • allele frequency should be constant over time.

Question 30

Selection vs Drift?

Answer 30

• selection will have an effect on genotype frequencies. S > 1/2Ne if not true, drift has greater effect

Question 31

Consequences of genetic drift in a subpopulation

Answer 31

• decrease allelic variation. • increase homozygotes.

Question 32

Negative frequency dependent selection

Answer 32

• more common. • genotype fitness decreases as frequency decreases. - fitness of rare genotypes is higher (fewer individuals there are, higher the fitness). - maintains a balance between alternative phenotypes in a population.

Question 33

Inbreeding Non-random mating

Answer 33

• mating among individuals closely related. Result: • more likely to share genes. • affect multiple loci. • increase homozygosity. • offspring similar with multiple characters.

Question 34

Consequences of genetic drift in a metapopulation?

Answer 34

• average allele frequency does not change. • increase homozygosity.

Question 35

Test for equilibrium

Answer 35

• determine if genotypes in a population differ significantly from expected with HW. • if it does differ, can lead to what is causing evolutionary change.

Question 36

Disruptive selection

Answer 36

• intermediate trait is minimum for fitness. • non linear fitness function. • means stays same. • increase in # of individuals with trait values are decreased. • can lead to speciation.

Question 37

Positive frequency dependent selection

Answer 37

• genotype fitness increases as frequency increases. I.e., Mimicry - often leads to fixation of the increasing genotype frequency.

Question 38

Direct selection

Answer 38

• causal relationship of genotype & phenotype. • trait (target of slxn) interacts with selective agent which directly influences fitness.

Question 39

Selection

Answer 39

• leads to differential reproductive success of certain phenotypes. • acts on phenotypes.

Question 40

Non random mating Positive assortative mating

Answer 40

• mating among similar phenotype. Result: • Increases homozygosity (only for trait looking at). • Decreases heterozygosity by 1/2 each generation.

Question 41

Polymorphic

Answer 41

= population has multiple genes present in population for a given gene.

Question 42

Stabilizing selection

Answer 42

• intermediate is optimum for fitness, i.e., intermediate trait increases fitness. • non linear function. • decreases variance of individuals. • does not move mean.

Question 43

Chi squared

Answer 43

• determines if HW holds or not. chi² = (obs - exp)² / exp. obs = observed allele frequency. exp = expected allele frequency.

Question 44

Codon usage bias

Answer 44

• if a gene is highly expressed; one codon over another may be chosen and if that gene frequency is selected for, that codon will increase in #.

Question 45

Mutation rate (μ)

Answer 45

• chance of a mutation happening at any given gene. 10⁴ - 10⁶ per generation.

Question 46

Selection coefficient (s)

Answer 46

• measures strength of selection against a genotype. s = 1 - w when: s = 1 selected against. s = 0 is normal.

Question 47

Correlation selection

Answer 47

• occurs when 2 traits interact to determine fitness. - certain combinations of traits have a higher fitness. • similar to epistasis.

Question 48

Fitness function

Answer 48

• describes the relationship of phenotype and fitness based on slope. • indicative of directional selection. • slope = strength of selection.

Question 49

4-fold degenerate codon

Answer 49

• can change to any of the 4 nucleotides, the amino acid stays the same. I.e., Proline, Leucine, Ala, Val.

Question 50

Codominance

Answer 50

• equal effect on fitness. A1A1 = 1 A2A2 = 0.5 A1A2 = 0.75 (= .5/2 + ½ = 0.25+0.5 = 0.75) All arbitrary.

Question 51

Overdominance

Answer 51

• fitness of heterozygote is higher than homozygous. • balancing selection occurs to lead to 50-50 allele frequency. A1A1 = 1-s A1A2 = 1 A2A2 = 1-s All arbitrary.

Question 52

dS

Answer 52

# synonymous sites/ #sites * * = # 4 fold degenerate sites + ⅓ of 2 fold deg. • gives you rate of sub type/site/sequence.

Question 53

dN

Answer 53

# nonsynonymous sites/ # sites ° • only relative to # of sites where you could have a nonsyn. sub. ° # sites that could have occurred at (# nonden. + ⅔ of 2 fold deg.) • rate of variation basically due to slxn.

Question 54

What can cause rate variation among lineages?

Answer 54

• positive selection on one lineage. • purifying selection on one lineage. • if using a coding region, you could get around this by just using synonymous sites.

Question 55

Mutation-selection balance

Answer 55

• slxn removes deleterious alleles. • mutation introduces deleterious alleles. • balance between this is that deleterious alleles are maintained through mutation.

Question 56

Relative Selective Codon Usage (RSCU) RSCU <1 RSCU> 1

Answer 56

# of occurrences of codon / # of expected to occur (at random) • more frequent than expected at random (RSCU <1) • less frequent than expected at random (RSCU >1)

Question 57

Experimental manipulation

Answer 57

• determine experimentally what is causing correlation or what traits affect fitness. * tests if your target of selection hypothesis holds true or not.