Advanced Evolution Test 2

Front 1

In Eukaryotes, the transcribed sequence of a gene consists of coding regions called ______, which in most genes are separated by noncoding regions called ________

Back 1

1. Exons

2. Introns

Front 2

What is the genetic code?

Back 2

a triplet of bases (a codon) specifies a particular amino acid in the growing polypeptide chain

Front 3

Define Point Mutation

Back 3

single base pair substitutions

* coding region

Front 4

Define Transitions Mutation

Back 4

a substitution of a purine for a purine (A<-->G) or a pyrimidine for a purine

Front 5

Define Transversions Mutation

Back 5

of eight possible kinds, are substitutions of purines for pyrimidines

Front 6

Define Synonymous Mutations

Back 6

a point mutations that does not change amino acid sequence

Front 7

Define Nonsynonymous mutation

Back 7

result in amino acid substitutions, have little or no effect on the functional properties of the polypeptide or protein and no effect on the phenotype. May have substantial consequences.

Front 8

Define Frameshift Mutations (insertion and deletion)

Back 8

1 more bp being inserted or removed from an amino acid sequence

Front 9

Define Discrete trait and Continuous Trait

Back 9

1. Discrete Trait: which can only take a finite number of values (usually integer), such as how many members in your family

2. Continuous Trait: which, IN PRINCIPLE, can take any value. In practice, the measuring instrument and recording will often result in the continuous trait being converted to a discrete one

Front 10

Gregor Mendel (1822-1884)

Back 10

- Born in Austria

- Had love for nature

-experimented with several plants including peas.

-interested in process of hybridization

Front 11

What did Mendel conclude?

Back 11

- Inheritance is not "blended", are controlled by genes

-made Law of Segregation

- Dominant (dominant one is always expressed)and recessive, genes and alleles (2 alleles, only 1 is passed)

Front 12

Mendel's Law of Independent Assortment

Back 12

- each pair of allele segregates independently

Front 13

Define Mendelians

* Population Genetics

Back 13

traits evolve with large mutational jumps

Front 14

Define Biometricians

* Population Genetics

Back 14

evolution by gradual change in continuous traits

Front 15

IBD

Back 15

identity by descent

Front 16

Algorithm of Natural Selection

Back 16

- More individuals produced that can survive and reproduce

-Inheritance

Front 17

Define Variation

* Upload chart from lecture

Back 17

Variation in survival and reproduction

- Evolution is the combination of random (variation) and non random (sorting in the variance mutation)

Front 18

Define Blending Inheritance

Back 18

* offspring= mean of parents

- in next generation, the most abundant trait will fall right in the middle between the large and small

- if you get a favorite variation, under selection it will go under the original

Front 19

First Hypothesis

* put picture from slides

Back 19

In the f2 you get the same ratio aka the 3:1 ratio

Front 20

Second Hypothesis

*put picture from slides

Back 20

The traits are seperated

Front 21

Inversion Mutation

Back 21

the connection between genes break and the sequence of these gees are reveresed

Front 22

Duplication Mutation

Back 22

a chromosome is duplicated or replicated, resulting of multiple copies of that region

Front 23

Define Translocation

Back 23

when chromosomes rearrange

Front 24

The 6 conditions for Hardy Weinberg Equilibrium

Back 24

1. Sexual Reproduction

2. Random Mating

3. Non-overlapping Generation

4. No mutation

5. No migration

6. No Genetic Drift

Front 25

What is Allele Frequency? What is Genotype frequency?

Back 25

1. Allele Frequency: the frequency of an allele relative to that of other alleles in the same gene in a population

2. Genotype Frequency: is how often a gene or chromosome determines a specific characteristic or trait that shows up in a group

Front 26

Allele Frequency example

Back 26

Find A ex) PA=0.4

Find a ex) Pa=0.6

Front 27

Genotype Frequency example

Back 27

PAA= p^2

PAa= 2pq

Paa=q^2

Front 28

What does F mean in the HWE?

Back 28

It is the proportion of inbreeding

- the probability of IBD

- 0<-F<-1

Inbreeding coefficient

Front 29

Expected/Observed equation under HWE

Back 29

Obs: 2pq(1-F)=Hobserved

Front 30

Imbreeding Depression

Back 30

reduction in fitness, mutation may occur such as deleterious recessive alleles

Front 31

Wright Fisher Model

Back 31

the random sampling of AA and Aa

- losing little a, making it have an allele frequency of (p:1 to q:0 from original p:0.5 and q: 0.5)

Front 32

smaller populations and Genetic Drift

Back 32

smaller populations lead to faster genetic drift.....faster fixcation in the alleles

Front 33

Loss of alleles in Gene Drift

Back 33

if you have small population of drift

Front 34

The probability of fixation

Back 34

starting allele frequency

Front 35

How is Effective population size abbreviated?

Back 35

Ne

Front 36

FSI and FST

Back 36

1. FIS: is individuals and subpopulation

2. FST: is subpopulation and total

Front 37

What happens to allele size if you have imbreeding?

Back 37

You will have an excessive amount of alleles

Front 38

What happens to drift if you have a large population size?

Back 38

much slower drift

Front 39

What happens to drift if you have a small population size?

Back 39

much dramatic and faster drift

Front 40

Why did Darwin write so much in Origin of Species?

Back 40

1. It provides an analogy for natural election

2. direct evidence of natural selection

Front 41

Neutral Theory holds that most allele fixation events are the result of:

Back 41

genetic drift

Front 42

_______ typically reduces genetic variation, while ______ maintains it.

Back 42

1. Genetic Drift

2. heterozygote advantage

Front 43

At equilibrium in an island model, Fst at neutral loci:

Back 43

depends only on Nm, the product of population size and migration rate

Front 44

Which of the following can be used to detect selection from molecular data?

Back 44

1. proportion of admixture across loci

2. ratio of synonymous to non-synonymous substitutions

3. extent of linkage disequlibrium around loci

4. relative values of Fst across loci

Front 45

______ typically increases LD around a locus, and ______reduces it

Back 45

1. selective sweep

2. recombination

Front 46

Define Effective Population Size

Back 46

Effective # of individuals contributing to next generation

Front 47

Define Frequency Dependent selection

Back 47

natural selection in which Fitness of a trait varies as a function of the frequency of that trait in the population

Front 48

Define Sexual selection

Back 48

differential reproductive success as a result of a variation in the ability to successfully mate

Front 49

How does hidden population structure lead Fis>0?

*Short answer

Back 49

With hidden population structure, mating is more likely within subpopulations than between. If allele frequencies differ among subpopulations, this non-random mating will produce an excess of homozygotes relative to the overall expectation, leading to Fis>0

Front 50

Why is the substitution rate of neutral mutations equal to the mutation rate, independent of population size?


*short answer

Back 50

1. New mutation rates each generation is: 2Nemu
2. The probability of any of these mutations reaching fixation by drift is its starting allele frequency: 1/2Ne
3. Rate of substitution: mu

*If you times them by eachother, only mu will be left

Front 51

In some mice, individuals with genotype tt do not survive yet heterozygotes (Tt) exhibit segregation distortion so that most of their gametes carry that t allele. Use the concept of levels of selection to explain how this maintains both the T and t alleles in the population

*short answer

Back 51

Segregation distortion in heterozygotes produces selection for t at the genocide level. The conflict between these two levels f selection leads to a balanced polymorphism at this locus

Front 52

What was the first type of molecular data?

Back 52

allozyme aviation ➡ protein alleles

Front 53

if you look at any gene....

Back 53

they found lots of genetic variation

Front 54

What is non selection forces? (neutral forces)

Back 54

1. mutation
2. drift

Front 55

Natural Selection

Back 55

predicts low level of genetic drift

Front 56

what did Lewiston discover?

Back 56

Allozyme variation into he 1970s

Front 57

Substitution

Back 57

New mutation reaches fixation

Front 58

Probability of fixation = initial frequency

Back 58

if it is a new mutation, frequency is 1/2N

Front 59

what is mutation rate number?

Back 59

10 ^-9 is rate of nucleotides sequence

Front 60

2Np*1/2N = mutation rate

Back 60

at population level, 2NP
-what's probability of it reaching fixation is 1/2N
-substitution rate is equal to mutation rate (under neutral Theory, you would expect the molecular clock)

Front 61

what is the mutations rate equations and what does it mean?

Back 61

2NP = # of new mutations per generation
1/2N= probability that one will fixate

Front 62

Molecular Clock

Back 62

*Substitution rate = mutation rate
rate of change constant
- amount of change is same over stretch of time

Front 63

Neutral theory

Back 63

most evolution of molecular/genetic level is the result of neutral forces. ex. genetic drifts and mutation

Front 64

is allele fixation events the result of genetic drift?

Back 64

yes

Front 65

Neutral theory holds that most allele fixation events are the result of:

Back 65

generic drift

Front 66

______ and_ ________ are 2 types of selection that maintain genetic diversity?

Back 66

1. Negative frequency
2. heterozygous advantage

Front 67

At equilibrium in an island model, Fst at neutral loci:

Back 67

depends only on nm, the product of population size and migration rate

Front 68

Hardy-weinberg equilibrium:

Back 68

is reached in just one generation of random mating

Front 69

define Coalescent theory?

Back 69

1. lineage of alleles backward in time
2. relates population size to the timing of coalescence
3. is based on a Wright- Fisher model

Front 70

According to Gregory Mendel, the 3:1 ratio of phenotypes in an F2 cross?

Back 70

1. demonstrates the principle of segregation of alleles
2. fits a model of dominant and recessive alleles

Front 71

Darwin's finches experience temporal fluctuations in selection, meaning that

Back 71

1. phenotypic diversity remained over time
2. sometimes larger beaks are more fit, sometimes smaller beaks are more fit

Front 72

A new mutation has ______ than the existing allele. it _______ in the population in a process known as a selective sweep

Back 72

1. higher. fitness
2. increases

Front 73

In white throated sparrows, white striped females mate with tan striped males., and tab striped females with white striped males is known as

Back 73

disassortative mating

Front 74

Substitution rates of synonymous (silent) mutations are often highly correlated with time. This is predicted by Neutral theory because:

Back 74

1. synonymous mutations are neutral
2. Motoo Kimura said so

Front 75

Effective population size definition?

Back 75

is the effective # of individuals that contribute to the next generation

Front 76

Indel definition?

Back 76

a mutation that involves deletion or insertion of one or more nucleotides in a sequence

Front 77

Hidden population structure definition?

Back 77

when mating more likely to occur in subpopulations than between subpopulations

ex) mice on either side of barn w/cat in middle of barn preventing migration

Front 78

SNP definition

Back 78

-Single Nucleotide Polymorphism
-occurs when. one nucleotide is substituted with another

Front 79

Inbreeding definition

Back 79

individuals of a population that are closely related mate with each otger, which can be measured by an F value (positive F value correlates to inbreeding; higher f value =more inbreeding)

Front 80

Balancing selection definition

Back 80

a form of natural selection that maintains stable frequencies of 2 or more phenotypic forms of a population.

Front 81

Directional selection

Back 81

form of natural selection in which the entire curve moves
-occurs when individuals in one end of a distribution curve have a higher fitness than individuals in the middle or at the other end of the curve

Front 82

Stabilizing selection

Back 82

a form of natural selection that favors intermediate variants by acting against extreme phenotypes

Front 83

disruptive selection

Back 83

a single curve splits into 2
-occurs when individuals at the upper and lower end of a distribution curve have higher fitness than individuals near the middle

Front 84

selective sweep

Back 84

act to reduce levels of linked silent polymorphism
-generates positive levels of neutral polymorphism and levels of recombination

Front 85

Linkage Dependent

Back 85

tendency for certain alleles at 2 linked loci to occur together more often than expected by chance

Front 86

E. coli selected to grow at 40 degrees show reduction growth rate at 37 degrees. this is result of what?

Back 86

antagonistic pleiotropy

Front 87

Define Fitness

Back 87

the lifetime reproductive success of a biological entity (allele, individual, etc)
ability to survive and reproduce

Front 88

Is evolution by natural selection a random process? non-random? both? explain?

Back 88

Both: the production of variation by mutation is random, but the selection of variants on the basis of differential fitness is non-random

Front 89

Why are p2, 2pq and q2 the expected genotype frequencies under Hardy Weinberg Equilibrium?

Back 89

Under HWE assumptions, genotype frequencies are produced by randomly sampling two alleles to form each diploid individual. The probability of randomly picking two A alleles is p x p=p2 (same for q2). For heterozygotes: pick A and a (probability p x q=pq) and it's sum 2pq

Front 90

You conduct a chi-square test for Hardy Weinberg Equilibrium and find that p<0.001. what does this mean?

Back 90

The genotype frequencies deviate significantly from HWE and one or more assumptions of HWE is violated

Front 91

Further, you estimate Fis: 0.35, What are 2 possible explanations for this result?

Back 91

1. Inbreeding
2. assortative mating
3. hidden population structure
4. natural selection

Front 92

Back 92

B

Front 93

If a neutral allele A is at a frequency of p=0.3, what is the probability that it will eventually fix by genetic drift?

Back 93

0.3

Front 94

If a selectively advantageous allele B is at a frequency of p=0.01, is it more likely to reach fixation in a small population or large population?

Back 94

Large population (bc selection overcomes drift better in a large population)

Front 95

Back 95

1. Fst =0.0
(mostly homozygous with some heterozygotes)
2. Fst=0.7
(top is homozygous recessive and bottom is homozygous dominant, minus the 3 That are heterozygotes)
3. Fst=1
(one circle s homozygous dominant and bottoms circle is homozygous recessive)

Front 96

Blending Inheritance:

Back 96

was used as a counterargument to Darwinism natural selection

Front 97

Back 97

Front 98

Back 98

Front 99

If a selectively advantageous allele R is at a frequency of p=0.01, is it more likely to reach fixation in a small population or a large population? why?

Back 99

more likely to reach fixation in a large population because selection is more effective in large populations than drift is.