Coop

Question 1

Def. Evolution

Answer 1

Descent with modification; changes in allele freq over time in populations

Question 2

If mutation rates per base are low what causes large #’s of mutations?

Answer 2

Large # of individuals in population or large genome size

Question 3

Pairwise diversity

Answer 3

Fraction of sites that differ between two sequences chosen at random

Question 4

Heterozygosity

Answer 4

Fraction of sites where 1 individual is heterozygous

Question 5

Hardy-Weinberg assumes

Answer 5

At least 1 generation random mating

Question 6

Linkage Disequilibrium & equation for D

Answer 6

The non-random association (covariance) of alleles at different sites in the genome in a population.
Dab=Pab-Pa*Pb

Question 7

What creates LD?

Answer 7

Genetic drift and Hitchhiking
Epistatic selection*
Assortative Mating: Inbreeding –  Population structure and admixture –  Assortative mating by phenotype*

Question 8

Example types of neutral alleles (4)

Answer 8

1) A synonymous change in a codon. •  2) A non-‐synonymous change that replaces one amino-‐acid with a funconally similar one.
3) A non-‐synonymous change which produces a large change in a phenotype on which selecon no longer acts
4) not protein coding or important to regulation

Question 9

Effective pop size Ne

Answer 9

size of an idealized population in which pop size is constant, variance in reproductive success is low, anddriftoccurs at the same rate as that in the actual population of interest

Question 10

Molecular clock & evidence

Answer 10

The expected number of neutral substitutions = 2T µ i.e. substitutions occur at a linear rate; evidence comes from linear rates of protein evolution across species with different generation times but similar mutation rates

Question 11

Neutral theory expectation for dN/dS

subst./site nonsynonymous/synonymous:

Answer 11

dN/dS = 1

Question 12

Expected dN/dS for a gene coding for an important protein (constrained)

Question 13

Expected dN/dS for a gene Under directional selection; natural example

Answer 13

> 1; vertebrate immune system

Question 14

Why do you get incomplete lineage sorting?

Answer 14

2 alleles don’t coalesce before the next earliest species divergence… So the gene has a different tree than the species..even when species B and C are more related, A coalesces with B first (less distant past), then C.

Question 15

What does the Frequency spectrum of alleles look like in a recently expanded population?

Answer 15

Excess of singletons

Question 16

What does the Frequency spectrum of alleles look like in a recently bottleneckedpopulation?

Answer 16

excess of intermediate frequencies (from mutations in pre-bottleneck branches)

Question 17

What does the Frequency spectrum of alleles look like in constant size pop evolving neutrally?

Answer 17

Theta/i, eg theta/2 doubles, theta singletons

Question 18

What is the nearly neutral theory and some evidence to support ?

Answer 18

Levels of constraint aren’t absolute but determined in part by Ne; rodents have larger Ne than primates and so evolve slower

Question 19

To power studies of demographics through time you want more individuals or loci?

Answer 19

Loci bc they’re inherited independently and most individuals will coalesce rapidly

Question 20

What was the flaw of the mitochondrial analysis paper stating we were no more than 1/1000 Neanderthal bc 1000 subjects nine had Neanderthal mitochondria

Answer 20

Low power bc modern subjects mitochondrial Dna coalesce quickly in recent past so very small ancient sample. Need more loci to get bigger ancient sample (2%eurasian genome is Neanderthal)

Question 21

3 components necessary for evolution

Answer 21

1) variation in phenotype
2) fitness differences between phenotypes
3) variation is heritable

Question 22

Low heritability comes from

Answer 22

Low genetic variance or high environmental variance in phenotype

Question 23

Natural selection

Answer 23

Nonrandom variation in fitness across individuals with diff. phenotypes

Question 24

Beta, selection coefficient

Answer 24

Slope of regression between phenotype and fitness, i.e. Covariance of phenotype and fitness over total phenotypic variance

Question 25

Antagonistic pleiotropy w example

Answer 25

1 gene controls multiple traits where at least one has fitness benefit and another fitness decrease. Derwin’s finches beak length under neg selection but increases due to pleiotropy and positive selection for beak depth

Question 26

What are three reasons for sexual selection/choosy females?

Answer 26

1) more fit mates = more fit offspring
2) more sexy mates = more sexy offspring ‘sexy sons hypothesis’
3) increase female or offsprings fitness directly, eg by providing resources

Question 27

How does co-evolution of fisher’s proposed male sexy but ther wise useless signal and female preference?

Answer 27

Males have more offspring because they get additional boost from rare female preference then females who prefer those males assortativelu mate with them, creating genetic covariance between the two traits and female preference rises with increasing male success (sexy sons)

Question 28

Which reaches fixatin 1st and which rises more quickly? Additive, recessive or dominant beneficial alleles?

Answer 28

Additive has same selection independent of allele frequency and so rises and fixes pretty fast. Dominant rises faster but is slow to fix at the end due to diminishing returns in homozygous context. Recessive alleles are very slow to rise since their neutral when rare/heterozygous

Question 29

What is overdominance?

Answer 29

Heterozygous advantage.. Results in balanced polymorphism

Question 30

Balancing selection eg.s

Answer 30

Heterozygous advantage, beneficial when rare (selfing incompatible id allele or plant color morph for flowers offering no rewards to be pollinators)

Question 31

Additive effect of an allele

Answer 31

effect of an allele averaged across the possible genotypes it could occur in

Question 32

Evidence against molecular clock

Answer 32

Neutral theory of molecular evolution can not explain a molecular clock measured in years. It predicts a molecular clock measured in generations, which is exactly what we see for changes to synonymous/non-‐coding sites but not what we see for changes to the protein.

Question 33

How do explain a molecular clock measured in years for protein divergence?

Answer 33

Species with shorter generation time tend to have larger populations and therefore can select on what would be effectively neutral sites in smaller populations (which tend to have longer generation times). This leads to efficient background selection of weakly deleterious alleles in large pops, reducing substitution rates per generation.

Question 34

What does nearly neutral mean?

Answer 34

Selection acts on same order as drift, effectively neutral if
s ~ 1/(2Ne)

Question 35

3 reasons there’s so much polymorphism

Answer 35

1) balancing selection (mutation-selection balance is spatially balancing)
2) mutation-selection balance
3) mutation-drift balance (neutral theory)

Question 36

Def fitness

Answer 36

Expected number of offspring in a specific ecology and environment

Question 37

T/F: An allele with additive effects has an avg fitness benefit that doesn’t depend on frequency

Answer 37

True! Because it’s additive, it’s fitness effect is the same no matter what it’s paired with

Question 38

What are all the components contributing to total phenotypic variance?

Answer 38

Environmental, additive genetic, dominance, epistasis (Interactions between loci, Vi)

Question 39

Do we expect to find more Neanderthal alleles in the human genome at places with higher or lower recombination?

Answer 39

Higher recombination. Neutral Neanderthal alleles that don’t recombine off their mildly deleterious background will get purged from human pop

Question 40

What is one reason a recent string selection would show a typical sweep signature?

Answer 40

If it starts at 5% or more frequency, not a new mutation, when it’s selected for it will carry multiple hitchhiking backgrounds

Question 41

Def background selection

Answer 41

Purging of deleterious alleles.. Can also reduce diversity of linked neutral loci

Question 42

Why do asexual lineages accumulate deleterious mutations and what is the name of that phenomenon?

Answer 42

Muller’s ratchet, can’t recombine off weakly deleterious mutations that hitchhike up in frequency with beneficial mutations

Question 43

2 advantages and disadvantages to sex:

Answer 43

Advantages: new haplotypes through recombination; can evolve novel solutions in parallel
Disadvantages: cost of raising offspring only 1/2 similar; cost of finding a mate/allee effects; could break up winning combo haplotypes

Question 44

On avg how many generations does it take a neutral allele to fix?

Answer 44

4Ne

Question 45

Def species from pop gen

Answer 45

A species is a set of alleles/traits held in linkage disequilibrium through evolution of biological barriers to gene flow

Question 46

Dobzhansky-‐Muller Incompabilies (DMIs) are examples of

Answer 46

Epistasis. AA and aa both ok but Aa has low fitness - they affect each other’s fitness

Question 47

What is character displacement and how can it maintain reinforce speciation?

Answer 47

In sympathy one species changes to a phenotype more distinct from the other species even though they’re similar in allopatry. Eg color of flowers or mating rituals, flower timing can reinforce sexual isolation in sympatry

Question 48

How can inversions be adaptive?

Answer 48

Inversions can lock together successful phenotypes for local adaptation in the face of high migration ; eg butterfly mimicry, mimulus local adaptation,