Quest 4

Question 1

The Law of Large Numbers

Answer 1

Actual frequencies mirror expected frequencies when samples sizes are very large

Question 2

The Wright-Fisher model

Answer 2

Just like HW but relaxes the infinite population size assumption.

Question 3

Genetic drift

Answer 3

The process of random fluctuation in allele frequencies due to sampling effects in finite populations

Question 4

3 consequences of genetic drift

Answer 4

1. In finite pops, all allele freqs fluctuate over time, even in the absence of natural selection
2. Some alleles are fixed others are lost n fractions of heterozygotes in the pop decreases over time
3. Separate populations diverge in their allele freqs, and in terms of which alleles are present

Question 5

What is Ne?

Answer 5

Effective population size. The population size that is reproducing and contributing to population.

Question 6

Population bottleneck

Answer 6

Cuts the population size dramatically leading to shifts in allele frequency simply by chance.

Question 7

What is He?

Answer 7

Heterozygote population

Question 8

Kimura (Selection or drift)

Answer 8

When pop size is large and selection is strong, selection determines allele frequencies.
When pop size is small and/or selection is weak, drift determines allele frequencies

Question 9

If s> 1/2Ne

Answer 9

selection coefficient is greater than 1/2 effective population
Selection wins

Question 10

If s< 1/2Ne

Answer 10

selection coefficient is less than 1/2 effective population
Drift wins

Question 11

Leading edge expansion

Answer 11

a form of drift via founder effects leading to reduced genetic diversity in a newly colonized area

Question 12

Neutral Theory of Molecular Evolution

Answer 12

Looks at the genotype, not phenotype.
Fine scale view to nucleotide changes over time, which push phenotypic changes.

Question 13

2 points of the variation in population

Answer 13

1. Most variation in a population is selectively neutral
2. Most changes in the DNA are selectively neutral

Question 14

Substitution

Answer 14

When a base changes due to mutation and is subsequently fixed in the population
Usually measured by substitutions/generation.

Question 15

Substitutions vs mutations

Answer 15

Substitutions are not mutations.
Sub. are neutral
Most mutations are deleterious

Question 16

Synonymous substitutions

Answer 16

Change in base pairs that encodes same protein

Question 17

Purifying selection

Answer 17

A type of natural selection that removes harmful mutations from a population, preserving the function of essential genes over generations.

Question 18

Positive selection

Answer 18

A type of natural selection that favors beneficial mutations, increasing their frequency in a population and driving adaptive evolution.

Question 19

Ka =

Answer 19

number of nonsynonymous subs / nonsynonymous sites

Question 20

Ks =

Answer 20

number of synonymous subs / synonymous sites

Question 21

Ka/Ks <1

Answer 21

Purifying selection

Question 22

Ka/Ks >1

Answer 22

Positive selection

Question 23

Pseudogenes

Answer 23

Non-functional DNA sequences that resemble functional genes but have lost their ability to code for proteins due to mutations. They arise from gene duplication or retro-transposition and accumulate mutations without selective pressure.

Question 24

Neutralist vs selectionist

Answer 24

Neutralists - drift is most important for evo
Selectionist - selection is most important for evo

Question 25

Molecular clocks

Answer 25

can look at mutations and estimate how old a clade is

Question 26

The genetic equidistance principle

Answer 26

suggests that if molecular changes occur at a constant rate across lineages the members of any given clade should be equidistant from the members of an outgroup

Question 27

Founders effect

Answer 27

a type of genetic drift that occurs when a small group of individuals becomes isolated from a larger population, leading to reduced genetic diversity and a gene pool that may not be representative of the original population.

Question 28

Are molecular clocks useful?

Answer 28

They are when comparing a single locus over a short time for closely related organisms. As time passes saturation becomes and issue.

Question 29

The Nearly Neutral Theory of molecular evolution

Answer 29

Smaller populations have longer generations, smaller pops have higher sub rates due to drift

Question 30

Coalescent Theory

Answer 30

How gene copies spread through finite pops over time

Question 31

Gene tree

Answer 31

Species tree H0w is the gene tracked without selection it is a random process

Question 32

Coalescent time

Answer 32

The number of generations that we must go back for a population to be reduced to 2 parental lineages. (~ 2N generations)

Question 33

What is the largest factor of coalescent time?

Answer 33

population size

Question 34

polygenic traits

Answer 34

traits that are influenced by multiple genes, often along with environmental factors, resulting in a continuous range of variation, such as height, skin color, and eye color in humans

Question 35

Additive gene effects

Answer 35

Occur when multiple genes contribute to a trait, and each allele's effect is cumulative, meaning their combined influence determines the phenotype in a predictable way

Question 36

Latent variation

Answer 36

Not new variation but a new assortment of previously occurring Mendelian variation when multiple genes control "one" trait Revealed by selection

Question 37

Epistasis

Answer 37

Two or more alleles interact in non-additive ways

Question 38

Haplotype

Answer 38

A set of alleles inherited together on the same chromosome

Question 39

Genotype

Answer 39

The allele identity whole organism

Question 40

Physical linkage

Answer 40

When loci are close together on the same chromosome and thus are segregated together In absence of recom, a double heterozygote produces only two gamete types

Question 41

Linkage disequilibrium

Answer 41

The non-random association of alleles at different loci in a given population. The frequency of association of their different alleles is higher or lower than expected

Question 42

Influences of linkage disequilibrium

Answer 42

1. selection 2. rate of recombination 3. mutation rate 4. genetic drift 5. system of mating 6. pop structure 7. genetic linkage

Question 43

Linkage equilibrium

Answer 43

When the genotype of a chromosome at one locus is independent of its genotype at another locus.

Question 44

What does a D = 0 mean?

Answer 44

Linkage equilibrium

Question 45

What does a nonzero D mean?

Answer 45

Linkage disequilibrium

Question 46

4 causes of LD

Answer 46

1. new mutation 2. selection 3. migration 4. drift in a small pop

Question 47

How is LD lost in a population?

Answer 47

meiosis with crossing over and outbreeding (sexual repro)

Question 48

Genetic hitchhiking

Answer 48

Occurs when a neutral or even slightly deleterious allele increases in frequency because it is linked to a beneficial allele undergoing positive selection.

Question 49

Background selection

Answer 49

A process in which negative (purifying) selection against deleterious mutations in a genome region leads to a reduction in genetic variation at nearby neutral sites.

Question 50

Selective Sweeps

Answer 50

The process where a beneficial genetic mutation rapidly increases in frequency within a population, reducing genetic variation near the mutation due to strong natural selection.

Question 51

Why is selective sweeps more consequential in haploid oganisms

Answer 51

They have no crossing over

Question 52

Genetic draft

Answer 52

neutral alleles follow strong selection on a close allele

Question 53

What causes genetic draft?

Answer 53

Hitchhiking

Question 54

Genetic drift vs genetic draft

Answer 54

Both reduce overall diversity drIft is more powerful in small populations drAft is independent of population size

Question 55

Big take away of Drift and Draft

Answer 55

drIft - pos alleles are more likely fixed and neg are more likely lost AS POP SIZE INCREASES drAft- opposite, mildly beneficial more likely lost and mildly deleterious more likely fixed AS N INCREASES

Question 56

Two main points on Linkage and Selection

Answer 56

1. Alleles can increase in frequency due to selection because they code for good traits, or because they are linked to genes that code for good traits 2. Natural selection (good or bad) decreases genetic variation at loci to the selected allele

Question 57

What are the 2 hallmarks for genetic drift?

Answer 57

1. Low genetic diversity within populations 2. High genetic diversity between populations