Evolution Exam 3

Front 1

The genetic variation that natural selection and other evolutionary forces act on originates in?

Back 1

Mutations

Front 2

What is the only evolutionary force that creates new alleles and genes?

Back 2

Mutations

Front 3

The instructions for making and maintaining an organism are enclosed where?

Back 3

In the DNA

Front 4

Which strand of the DNA is transcribed, the coding or non-coding strand?

Back 4

Anticoding

Front 5

What is the result of a mutation in the hemoglobin?

Back 5

The mutation is a result of a mutation in position 6 of the nucleotide sequence, altering in nucleotide 2(A) to 2(T).

Wild Type-GAG,GAA-Glutamate
Mutant- GTG, GTA-Valine

Front 6

How are point mutations created?

Back 6

Either by random errors in DNA synthesis or random errors in the repair of sites damaged by chemical mutagens or high energy radiation.

Front 7

Why are transitions said to occur more often than transversions?

Back 7

Because transitions cause much less disruption in the DNA helix so they are less likely to be recognized as errors and therefore less likely to be immediately corrected by DNA polymerase or later by mismatch repair enzymes.

Front 8

What type of point mutation leads to sickle cell disease?

Back 8

A transversion leading for A going to T.

Front 9

Point mutations that results in an amino acid chage are called __________ ________.

Back 9

Replcaement sibstituions (nonsynonymous)

Front 10

Point mutations that result in no change are called ___ ___ ______

Back 10

Silent site substitutions (synonymous)

Front 11

Do the synonymous or nonsynonymous substituions create new alleles?

Back 11

They both do.

Front 12

Why was the traditional method of estimating mutation rates revamped?

Back 12

Because the old method simply took large populations and counted the number of offspring that had observable mutant phenotypes in each generation. But all this simply did was count the observablemutant phenotypes due to loss of function mutations (change in DNA that inactivate a gene or lead to a complete loss of gene product).

The silent type mutations would go un detected and the new alleles created by these types of mutations go completely uncounted in traditional surveys.

Front 13

What was a result of the traditional method in which mutation rates were obtained?

Back 13

Mutation rate were scaled for generation time and reported on a per-genome, per cell-division basis, and all organisms seemed to have a roughly equal mutation rate. It seemed Natural Selection had led to a single, common mutation rate.

Front 14

When Denver et al was obtaining a direct estimate of mutation rates using C. elegans, what was done to minimize the amount of natural selection and mutations that may occur in each line?

Back 14

They made possible:
optimal temperature and humidity, minimal crowding, abundant food and no predators or parasites

Front 15

How did Denver et Al get an estimate for mutation rates when the C. elegans had reproduced?

Back 15

They sequenced tens of thousands of base pairs of DNA from the founding individual and from each of the 50 lines derived from that individual at generations 280,353, and 396.

Front 16

Does nuclear DNA or Ribosomal DNA have a higher mutation rate?

Back 16

Mitochondrial, because there are less DNA repair enzymes found in the nucleus.

Front 17

When Denver et Al were studying the mutation rates in C, elegans, what mutations made up more than half of the 30 mutations detected?

Back 17

More than half consisted of indels, small numbers of bases inserted into or removed from the genome

Front 18

Understanding that DNA replication and repairing rarely make mistakes, one can assume what concerning selection?

Back 18

The enzymes involved with DNA repair and replication are under intense selection

Front 19

What example given in lecture presents an opportunity where a type of mutation, decreases the mutation rate of a DNA poly?

Back 19

This is seen in T4. The single base substitution will decrease the rate at which the polymerase makes errors during DNA replication, thus reducing the overal mutation rate.

Front 20

Mutants that increased _______ are slower than more error prone _______. This is discussion on how DNA polymerases have been seen to vary in accuracy.

Back 20

Accuracy; mutants

Front 21

When might having a higher mutation rate be a positive effect on an organism?

Back 21

When organisms are colonized in new environments to which they are poorly adapted or when rapid copying of genes is advantageous.

Front 22

If mutations accumlate what usually is affected?

Back 22

The organisms fitness will decline, as well as, longevity and production of offspring.

Front 23

wHAT IS THE SELECTION COEFFIIENT?

Back 23

The difference in fitness between each experimental population and the control.

Front 24

Most mutations are only midly deleterious- each mutation reduces fitness by only about 2% when _____.

Back 24

Heterozygous

Front 25

Most of the new alleles created by mutation are quickly eliminated from the population by natural selection. This is because?

Back 25

Mutation accumulation.

Front 26

When can silent mutations be subject to natural selection?

Back 26

Codon bias

Front 27

What is gene duplication?

Back 27

Gene duplication (or chromosomal duplication or gene amplification) is any duplication of a region of DNA that contains a gene; it may occur as an error in homologous recombination, a retrotransposition event, or duplication of an entire chromosome

Front 28

How are DNA double helixes stabilized?

Back 28

Hydrophobic interations and hydrogen bonds

Front 29

What is the result of a mutation in the hemoglobin?

Back 29

The mutation is a result of a mutation in position 6 of the nucleotide sequence, altering nucleotide 2(A) to nucleotide 2(T)

Front 30

With hemoglobin the alpha like clusters are on chromosome __ and the beta like clusters are on chromosome __.

Back 30

16;11

Front 31

Why is hemoglobin thought to be a product of gene duplications?

Back 31

Due to the length and position of the exons and introns among the globin genes. Also due to the high sequence similarity among globin genes and their similar function.

Front 32

It is believed that an ancestral gene was duplicated several times during evolution. IN several of the new genes, mutation changed the function of the _______ ______ in a way that was favored by natural selection, leading to the formation of a gene family

Back 32

Protein Product

Front 33

Do all gene duplications result in sequences that evolve different functions or no function?

Back 33

No, for example in rRNA genes, multiple copies of the same gene have an identical or nearly identical base sequence and produce a product with the same function as the ancestral sequence.

Front 34

Duplicated genes are homologous to the same common ancestral sequence. True or false?

Back 34

True

Front 35

What are paralogous genes?

Back 35

They are duplcated and then diverge in sequence within a species, like alpha and beta hemo in humans

Front 36

What are orthologus genes?

Back 36

They diverge after speciation, like the a and b genes in horses and humans.

Front 37

_______ are homologous genes found in different species and can be used to estimate the degree and timing of divergence among species.

Back 37

Orthologs

Front 38

________ form gene familes and are an important aspect of genome structure and function.

Back 38

Paralogs

Front 39

Where did the neutral theory see its original problem?

Back 39

There was a high rate of molecular evolution and it was constant through time. This did not match natural selection since natural selection isn't based time but is rather episodic and correlated with changes in the environment. Allso under natural selection mutation rates shouldn't be high. This showed natural selection could not be responsible for most evolutionary change.

Front 40

Explain the neutral theory of molecular evolution?

Back 40

At the heart of the theory is molecular evolution is equal to the mutation rate.

N-population size
2N-alleles of the locus of interest
v-rate of selectively neutral mutations per allele, per generation.
Also you must assume that each mutation creates an allele that has not existed previously in the population.

There will be 2Nv new alleles created by mutation each generation.

Each new allele has same chance of drifitng to fixation, frequency of new allele=1/2N

Therefore, each generation the number of new alleles that are created by mutation and are destined to drift to fixation is:
2Nv * 1/2N=v
v is then the rate of evolution at the locus of interest

Front 41

Why is it ok to say genetic drift is the process at work in the neutral theory of evolution?

Back 41

Because we assume that all new alleles are selectively neutral

Front 42

Why was Kimura's theory alarming?

Back 42

Because size of population had no role

Positive natural selection is excluded

Front 43

What proved the neutral selection theory?

Back 43

The evolution of pseudogenes, since these are neutral, they should have a high level and go to fixation.

Front 44

2Nv equals what

Back 44

2Nv equals the new alleles created by mutation each generation.

Front 45

In the neutral theory, since we assume that new alleles are selectively neutral, what is at work here?

Back 45

Genetic drift

Front 46

Each new allele has the same chance of drifting to fixation and the chance is equal to the frequency of a new allele, equation=?

Back 46

1/2N

Front 47

What is v?

Back 47

The rate of selectively neutral alleles per allele per generation.

Front 48

Besides the pseudogenes what else proves the neutral theory of evolution?

Back 48

Silent sites change faster than replacement sites; showing neutral mutations have a higher rate of molecular evolution.

Front 49

What was the nearly neutral theory of evolution trying to address?

Back 49

The fact that v should be very reflective of generation size, but it was not. It is expected with shorter generation size, there should be more neutral mutations. This wasn't seen as some protein sequences were seen to undergo some clocklike evolution, independent of generation size.

Front 50

Given the problems with the neutral theory of evolution, not corresponding with generation size, what was postulated?

Back 50

That nearly neutral mutations must effect phenotypes and with this these mutations can depend on either selection or drift, depending on population size.

Front 51

Species with long generation times, usually have a _____ population size.

Back 51

Small

Front 52

What does the nearly neutral model of evolution state?

Back 52

That drift fixes a larger percentage of mutations in organisms with small pop sizes. Hence an increase in evolutionary rate due to the fixation of nearly nuetral mutations in small-population, long generation species offsets the higher mutation rate in short generation species and results in the molecular clock.

Front 53

Where are the more mutations, short generation time or long generation time?

Back 53

Short, few are effectively neutral because population size is large.

Long generation time, there are few mutations on a per year basis. Many are effectively neutral, because pop size is small.

Front 54

Using the rate of nonsynonymous substitutions (dn) and rate of synonymous substitutions (ds). Give the ratios when replacements are neutral, adv, and deleterious?

Back 54

dn/ds =1
dn/ds>1
dn/ds<1

Front 55

When sequences evolve by drift and negative selection, _______ ______ will outnumber _______ _____

Back 55

synonymous substituions
replacement substituions

Front 56

What test is more sensitive method for detecting positive selection?

Back 56

The McDonald-Kreitman test

Front 57

What is at the heart of the MK test?

Back 57

The ratio of replacement to silent mutations between species should be the same as the ratio of nonsynonymous to synonymous polymorphisms in within-species comparisions.

Front 58

What explains why synonymous mutations may not accumulate as quickly as pseudogenes?

Back 58

Codon bias and other synonymous mutations may experience selection as a result of their effects on mRNA stability or exon splicing.

Also hitchhiking

Front 59

What is hitchhiking?

Back 59

Strong positive selection acts on a particular amino acid change.Neutral or even slightly deleterious mutations closely linked to favarable site will increase in frequency along with the beneficial locus.

This only occurs when recombination fails to break up the linkage between hitchhiking sites and the site that is under selection.

Hitchhiking usually results in reductions in polymorphism.

Front 60

What is the difference of microevolution and macroevolution?

Back 60

Microevolution is bio evolution that occurs within individual species, such as change in beak shape, form of an enzyme, selection for a flower color.

While macroevolution is refered to changes in organisms which are significant enough that, over time, the newer organisms would be considered an entirely new species. Macroevolution includes:
Speciation
Classification and phylogenetic reconstruction
Uses phylogenies to understand coevolution
Fossil record

Front 61

What is the difference between strong and weak inference?

Back 61

Strong inference: testing hypothesis under carefully constructed control factors.
Causation can be inferred wwith a high degree of confidence.


Weak inference:
Testing a hypothesis when experiments are not fully controlled.
Can lead to false inferences due to correlation.

Front 62

True or False?
Saturated fats are less energetically expensive and produce and yield less energy than unsaturated

Back 62

False, yield more

Front 63

Unsaturated fats have much ______ mp than saturated fats

Back 63

Lower

Front 64

Germination temp are ______ at ____ latitudes and altitudes

Back 64

Lower;
Higher

Front 65

The morphospecies concept is the careful analysis of phenotypic differences. What are the benefits of this?

Back 65

Define species that are extinct, living, or species that reproduce sexually or asexually

Front 66

What is the difficulties of the morphospecies concept?

Back 66

Small organisms
Fossils that differed in characters that aren't preserved
Populations that are similar in morphology but differ in other characteristics (habitat use, courtship display,drought tolerace)-cryptic species

Front 67

Under the biological species concept the criterion for identifying evolutionary independence is reproductive isolation.

Back 67

JK

Front 68

What is the strength of the biological species concept?

Back 68

Reproductive isolation is a meaningful criterion for identifying species because it confirms a lack of gene flow

Front 69

What are negative to bio species?

Back 69

If populations don't overlap, there is no way to know they are reproductively isolated.

Inability to test fossil forms

No meaning in asexual population

Hard in many plant groups where hybridization between strongly divergent populations is routine.

Front 70

How do phylogenetic species concept and monophyly intertwine?

Back 70

The phylogenetic species concept uses monophyletic groups, groups defined as lineages that contain all of the known descendants of a single common ancestor.

The species are then defined by using the closely related populations and finding the smallest monophyletic groups.

Front 71

What species concept can be allied to any type of organism, sexual, asexual, fossil?

Back 71

Phylogenetic species concept

Front 72

What is a negative of the phy species concept?

Back 72

It takes a lot of time, money and careful anaylsis

Front 73

What is good and wrong with the recognition species concept?

Back 73

Good-provides a role for sexual selection in speciation (its like bio spec concept, the emphaseis is on what causes the species to chose each other as mates rather than what isolates them from other orgnaisms)

Bad-
Organisms that release their gametes into the air or water
Use vectors to move their gametes

Front 74

Where is the cohesion mechanism seen?

Back 74

Recognition species concept

Front 75

What are usually the three steps that lead to speciation?

Back 75

1. An isolation in populations
2. Divergence in traits such as mating system or habitat use
3. A step that produces reproductive isolation

Front 76

The first two steps of speciation was thought to occur over extended time while the populations were located in different geo area AND the third happens when they come back together, but what happens?

Back 76

The first two steps can occur together in the same place and the third may never happen.

Front 77

Gene flow tends to homogenize gene ________ and reduce differentiation of populations

Back 77

frequencies

Front 78

Geographic isolation can be made by what?

Back 78

Vicariance
Dispersal and Colonization

Front 79

Besides physcial isolation, how else might there be a barrier to gene flow?

Back 79

Sympatric speciation, polyploidization.
Also this polyploid may lead to other characteristics such as flower shape and the timing of flowering will be different.

There also, besides polyploidy, might be an increase in chromosome number.

Genetic drift and natural selection

Sexual selection

Front 80

What are the two evolutionary forces that play a part in divergence?

Back 80

Genetic drift and natural selection.

Front 81

Genetic drift is powerful because?

Back 81

Random fixation and random loss of alleles

Front 82

What has been the problem with saying genetic drift is a major cause of divergence

Back 82

It has been shown that in bottleneck only very rare alleles are lost.

GD must work in extremely small populations and the population must remain small for a sig time.

Lots of small pop have been introduced but few dramatic changes in genotype and no speciation events have resulted.

Front 83

What is the result of secondary contact, or what can occur?

Back 83

The diverged species that hybiridze can now have a lower fitness than the parental species

Develop new characteristics and create a new population

May thrive and interbreed with parental erasing the previous divergence

Front 84

If a hybrid species occupies a new habitat than either of the parents, is there a chance that they will have a higher fitness than both of them?

Back 84

Yes, and they may make new species

Front 85

What is a hybrid zone?

Back 85

The hybrid zone is a region where interbreeding between diverged pop occurs and hybrid offspring are frequent.

Front 86

When are hybrid zones usually produced?

Back 86

When secondary contact occurs between species that diverged while allopatric.

Front 87

What determines the type of hybrid zones that are formed and eventual outcome of the populations that hybridize?

Back 87

The fitness of hybrid individuals

Front 88

When the fitness of hybrids equals to parental species, hybrid zones are:
Hybrid zone is _____
Allele frequency change are dominated by ____
Individuals with hybrid traits are found at high frequency at the ________ of the zone.

The width of the zone depends on how far indv.from each pop are disperesed each generation and how long the zone has existed.

Back 88

Wide
Drift
Center

Front 89

When the fitness of hybrids lower to parental species, hybrid zones are:

Hybrid zone depends on the strength of selection against ______; if selection strong and reinforcement, hybrid zone is ______ and short lived.

Back 89

Hybrids
Narrow

Front 90

When the fitness of hybrids higher to parental species, hybrid zones are:

The fate of the hybrid zone depends on the extent of ________ in which hybrids have an advantage.

If hybrids achieve higher fitness in eviro outside the ranges of parental species, then a new species may form in the new habitat.

Back 90

Environment