Biol 415: Lecture 11 (10/6/15)

Front 1

Define: Neutral Theory

Back 1

Neutral mutations rise and fall in frequency as a result of genetic drift. Many are lost, but some are fixed and most of these mutations exist on a molecular level and are fixed by drift. Also, alleles that are vital are less likely to be mutated

Front 2

Which position of the codon would you likely see a mutaton?

A. 1st

B. 2nd

C. 3rd

Back 2

C. 3rd

Front 3

What is Ds?

Back 3

The number of silent substitutions that encode the same codon. Often these changes are assumed to be neutral. Given ac onstant rate of point mutations, ds can be used to date a sequence

Front 4

What is Dn?

Back 4

number of substitutions encoding a nonsynonymous codon.

Front 5

T/F: The number of differences should correlate with the number of divergences

Back 5

True

Front 6

What does it mean to have Dn/Ds=1?

Back 6

The rate of amino acid changes is the same as the rate of silent changes which would mean that there's no contraint on gene sequence that there is no selection

Front 7

What does it mean to have Dn/Ds<1

Back 7

The rate of amino acid changes is less than the rate of neutral change. This implies deleterious codon changes were removed by purifying selection (negative selection) and therefore implies constaint on gene sequence. So there are less Nonsynonymous mutations than synonymous mutations

Front 8

What does it mean to have Dn/Ds>1

Back 8

The rate of amino acid change is greater than the rate of the silent change implying that amino acid change have been selected for positive selection. There are less synonymous mutations than non synonymous mutations.

Front 9

Which of the following most likely represents deleterious mutations and thus negative selection?

A. Dn/Ds=1

B. Dn/Ds<1

C. Dn/Ds>1

Back 9

B. Dn/Ds<1

Front 10

How does neutral theory explain the faster sequence evolution in non-functional sites?

Back 10

Because they're neutral and don't affect fitness they are less likely to be removed by purifying selection.

Front 11

T/F: Neutral theory serves as the null hypothesis tot est against the alternative hypothesis of positive selection.

Back 11

True

Front 12

T/F: Wright believed that selection, random drit, and mutation were important and were prominant in small populations while Fisher believed that selection and mutation were in prominant in large populations

Back 12

True

Front 13

What is the fundamental difference between Fisher and Wrights hypothesis on neutral theory

Back 13

Fisher believed that even a small amount of alele will have an impact on a large population as the favored allele increases in frequency over time. Wright believed that even in a small population there is no guarantee that an allele will be fixed.

Front 14

T/F: Depending on your selection coefficient, the allele frequency is governed by natural selection or genetic drift

Back 14

True

Front 15

Non-random mating is otherwise known as

Back 15

Inbreeding

Front 16

Certain snails are able to inbreed through the process of selfing. What happens to their allele frequency as generations progress

Back 16

Their allele frequencies remain the same however, they progressively lose their heterozygosity thus only the genotype frequency changes.

Front 17

T/F: Nonrandom mating changes allele frequencies not genotype frequencies

Back 17

False. nonrandom mating changes genotype frquencies not allele frequencies.

Front 18

What does Inbreeding and Random genetic drift have in common?

Back 18

Both process cause a decline in heterozygosity and thus an increase in homozygosity

Front 19

T/F: Random genetic drift leads to a change in genotype frequencies but not allele frequencies

Back 19

False. Random genetic drift leads to a change in both genotype and allele frequencies

Front 20

Define: Continuous drift

Back 20

Populations that are always small in size (n)

Front 21

Provide examples of continuous drift

Back 21

1. Endangered species

2. Insular species (small islands, fragmented habitats)

3. Polygynous or polyandrous mating systems - many individuals but few breeders.

Front 22

Define: Intermittent drift

Back 22

Large fluctuations in population size (N) from one generation to the next. It is the generation with low population size that causes the most drift

Front 23

Provide an example of intermittent drift

Back 23

plants that experience cycles of drought and rainy seasons.

Front 24

Define: Bottle neck effect

Back 24

When populations are reduced to near extinction but then expand to large numbers. Similar to Intermittent drift, but only occurs once, not in cycles.

Front 25

Define: Founder Effects

Back 25

Colonization by a small group of individuals and becomes isolated from the remainder of the species.

Front 26

What kind of problems may endangered animals face in regards to allele frequencies

Back 26

Endangered animals are more likely to conduct inbreeding, not because they are asexually reproducing, but because the population size is so small, allelic diversity has decreased making the possibility that their mate has similar if not identical genotypes highly possible. One example of this is the california otters.

Front 27

What aer the expected heterozygosity under HWE and what are the actual heterozygosity using the following:

AA: 16

Aa: 7

aa: 10

Back 27

A= (2*16+7)/66=0.6

a=(7+2*10)/66=0.4

AA=0.6^2

AA=0.36

Aa=2*0.6*0.4

Aa=0.48

aa=0.4^2

aa=0.16

AA=16/33

AA=0.485

Aa=7/33

Aa=0.212

aa=10/33

aa=0.303

Front 28

What is the formula used to determine the heterozygosity of an inbred population (Hf)

Back 28

Hf=H0(1-F)

H0=heterozygosity of a random mating population

F=# of how much inbreeding is happening

Front 29

What are the southern california otter suffering from

Back 29

Severe genetic bottleneck, loss of allelic variation, small popualtion leading to sibling mating.

Front 30

Define: Coefficient of Inbreeding (F)

Back 30

The probability that two alleles in an individual are identical by descent, meaning that came from the same ancestor.

Front 31

Using the image calculate the coeficient of inbreeding

Back 31

Since the image depicts a full sibling there will be two loops of descent, one moving around the grandmother and one moving around the grandfather remember that each movement is 1/2 because there is a likelihood of getting 1/2 of the chromosome during reproduction:

Grandmother:

1/2*1/2*1/2=1/8

(mom*grandma*dad)

Grandfather:

1/2*1/2*1/2=1/8

(mom*grandpa*dad)

1/8+1/8=2/8->1/4

Front 32

What is the formula to determine the heterozygosity of an inbreeding population

Back 32

Hf=H0(1-F)

H0=Heterozygosity of a random mating population

F= Coefficient of inbreeding

Front 33

Anytime F is ____________ 0, the frequency of heterozygotes is lower in an inbreeding population than it is in a random mating population

Back 33

Greater than

Front 34

Which of the following is NOT true in regards to Inbreeding depression?

A. Reduced survival and fertility of offspring of related individuals

B. Inbreeding depression si caused by increased homozygosity of individuals

C. Higher homozygote frequencie for recessive deleterious mutant alleles among inbred individuals lower fitness.

D. Does not directlychange allele frequency

E. None of the above

Back 34

E. None of the above

Front 35

What does the image represent

Back 35

A comparison of mortality rates among children of unrelated parents and the mortality rate among children of first cousin. The graph shows that the mortality rate of children of first cousins are greater because the plot is above the line.

Front 36

T/F: Darwin married his first cousin which he used to explain the unhealthy nature of his own children.

Back 36

True

Front 37

Describe the image

Back 37

A graph representing the effects of inbreeding on failed egg hatchings to explain how inbreeding results in lower reproductive fitness.

Front 38

The Florida Panthers have been hunted to near-extinction 50 years ago and are left with about 50-80 panthers. Even though they have placed on the endangered species list, they still face great difficulty in terms of repopulating. Explain why this is

Back 38

1. Little genetic variation in the species as a result of being hunted to near extinction.

2. Inbreeding has resulted due to the low genetic variation and this has caused a reduction in reproductive fitness. 80% males have low sperm count. 93% have abnormal sperm. Congenitive heart defects

3. Inreeding results in a larg epercent of sperm with acrosomal defects.

Front 39

Because of their small size, Florida Panthers are at greater risk of genetic drift and decreasing their heterogeneity even more. How do you counter act genetic drift?

Back 39

1. Artificial migration or gene flow: bring in genetically different panthers from a subspecies and outbreed creating heterozygous cubs.

Front 40

Explain how the Amish are suffering the effects of the founder effect

Back 40

The amish were founded in the 1720-1770 by fewer than 200 people. Now there are over 18,000 Amish in Lancaster and they tend to mary within the religion with fe convert to the religion after 1800. Converts into the religion are like migrants into the population, they represent gene flow. This creates a lack in variation in histocompatibility and so the amish are at greater risk of genetic diseases as well as contracting diseases due to their suppressed immune system.

Front 41

Why are the Amish more likely to suffer from outbreaks than other american

Back 41

Amsih not only live isolated and in close quarters. They suffer a genetic disadvantage because they are likely inbred, their histocompatibility complex hs no variation making them more susceptible to avoidable diseases.

Front 42

T/F: The amish are at greater risk of having recessive genetic diseases

Back 42

True

Front 43

What three types of recessive genetic diseases do amish traditionally get?

Back 43

1. Ellis-Van Creveld Syndrom

2. Pyruvate kinase dificiency

3. Hemophilia

Front 44

Define: Ellis-van crevoid Syndrome

Back 44

(Dwarfism, heart trouble, extra digits). Only 50 observed cases in the world for the past 100 years.

Front 45

Define: Pyruvate Kinase Deficiency

Back 45

Blood disorder; all cases trace back to a strong Jaco Youger

Front 46

Define Hemophilia

Back 46

Sex-linked bleeding disorder in which it takes a long time for the blood clot;

Front 47

Which of the following statements about inbreeding is NOT correct

A. Inbreeding increases the number of loci at which an average individual is homozygous.

B. Inbreeding decreases the number of recessive homozygotes in a population

C. Inbreeiding decreases the heterozygosity of the population

E. Inbreeding doesn't chang ethe allele frequency.

Back 47

B. Inbreeding decreases the number of recessive homozygotes in a population.

Front 48

Which of the following is NOT a type of genetic drift

A. Founder's effect

B. Sampling

C. Bottleneck effect

D. Continuous Drift

E. None of the above

Back 48

E. None of the above

Front 49

Define: Bottleneck effect

Back 49

The effective population size of the parent is larger than that of the next generation despite the fact that the census size is exactly the same. As a result you begin to lose genetic variation

Front 50

What animal has been shown to be affected by the bottleneck effect?

Back 50

Cheeta

Front 51

According to this graph, the probability that the frequency of A1 will increase to 0.7 in the next generation is about

Back 51

12%

Front 52

Define: Haplotype

Back 52

A specific set of linked genes (multiple loci). Short for Haploid genotype

Front 53

Define: Linkage disequilibrium

Back 53

Non-random association among alleles in a haplotype which are inherited together generation to generation

Front 54

Describe the graph in terms of certainty, pop size, and expected allele frequency

Back 54

The graph indicates a large population which would mean that there is a small number of uncertainty. As a result, the allele will take much longer to reach fixation/loss through genetic drift

Front 55

What formula is used to serve as the null hypothesis to test against the alternativ ehypothesis of positive selection under neutral theory?

Back 55

Dn/Ds=1

Front 56

How does Neutral theory explain the clock-like evolution of nucleotide sequences

Back 56

Neutral theory shows that mutations happen often when looked on a molecular level. These can be tracked through synonymous substitutions because they are neutral and are unlikely to be lost by negative selection

Front 57

How does Neutral Theory explain the faster sequence evolution in non-functional sites

Back 57

Mutations in non-functional sites (3rd place of the codon) are likely not to be removed through purifying selection as it does not affect a functional site.

Front 58

Describe R.A. Fisher's view on Natural Selection and Genetic Drift.

Back 58

In a large population even a small amount of allele with have an impact as a favored allele will increase in frequency over time through selection

Front 59

Describe S. Wright's view on natural selection and genetic drift

Back 59

In a small population an allele is neutral but it's movement towards fixation/loss will be determined by Random Genetic Drift

Front 60

T/F: Heterozygosity is lost much faster under genetic drift than by non-random mating

Back 60

False. Heterozygosity is lost much faster under non-random mating than by genetic drift

Front 61

T/F: Under non-random mating, genotypic frequencies change while allelic frequencies don't change

Back 61

True

Front 62

What Hardy-Weinberg conclusion is violated under non-random mating?

Back 62

The second conclusion (random mating)

Front 63

You find that in a population you expect the heterogeneity to be 0.48 but the actual heterogeneity is 0.212. What can you conclude from that?

Back 63

The population must be undergoing some type of inbreeding.

Front 64

What can you assume with a coefficient of inbreeding at 1/4?

Back 64

Full sibling inbreeding

Front 65

How can heterozygosity be reclaimed if a population is undergoing non-random mating as a result of genetic drift?

Back 65

Artifical migration or gene flow resulting in outbreeding and increase in heterozygosity