1
Q
A
2
Q
- Why do we use a single strand of letters to represent the double stranded DNA molecule?a. To make it easier to visualize mutations.
b. One strand of the molecule doesn’t have any variable sequences.
c. One sequence for one strand of the molecule can’t be determined.
d. Because DNA is complementary, so if you know the sequence of one strand, you know the sequence of the second strand as well. Writing both strands would be redundant.
e
A
d. Because DNA is complementary, so if you know the sequence of one strand, you know the sequence of the second strand as well. Writing both strands would be redundant.
3
Q
- For the DNA sequence 5’-CCTTGAGTC-3’ what nucleotides (and in what order) would be found in the complementary strand?5’-CCTTGAGTC-3’
5’-GACTCAAGG-3’
5’-GGAACTCAG-3’
5’-TTCCAGACT-3’
5’-AGTCTGGAA-3’
A
5’-GACTCAAGG-3’
4
Q
- Which of the following statements is the best definition for a gene?
A gene is a section of DNA that is different from any other section and can be mapped to a specific locus.
A gene is a section of DNA that is transcribed into an RNA product.
A gene is a piece of DNA that corresponds to an amino acid sequence in a functional protein.
A gene is a portion of DNA that helps to regulate transcription and translation.
A
a gene is a section of DNA that is transcribed inot an RNA product
5
Q
- What percentage of the human genome is composed of genes and what percentage is protein coding (exons)?
Genes make up approximately 25% of the human genome and approximate 1.5% is protein coding
Genes make up approximately 80% of the human genome and approximate 25% is protein coding
Genes make up approximately 60% of the human genome and approximate 1.5% is protein coding
Genes make up approximately 95% of the human genome and approximate 25% is protein coding
A
Genes make up approximately 25% of the human genome and approximate 1.5% is protein coding
6
Q
- Which of the following is not an accurate description of the basic structure of DNA?
The outer part of the double helix is composed of a repeated sugar, phosphate chain
The inner part of the double helix is composed of paired nucleotides
Purines on one side of the double helix pair with pyrimidines on the the other side of the double helix
Nucleotide pairs (e.g., guanine on one side of the helix and cytosine on the other) are bonded together via covalent bonds
A
Nucleotide pairs (e.g., guanine on one side of the helix and cytosine on the other) are bonded together via covalent bonds
7
Q
- Which part of the DNA molecule is of interest to the study of evolution between species?
Deoxyribose molecules
Phosphate groups
The entire deoxyribose-phosphate backbone
Nucleotides
A
Nucelotides
8
Q
- Select the correct statement regarding how eukaryotic gene sequence is used to make proteins.
Double-stranded DNA is transcribed into single stranded RNA, the RNA strand is spliced to remove exons and the resulting mature mRNA is translated into amino acid sequence with every three nucleotides coding for one amino acid.Double-stranded DNA is transcribed into double stranded RNA, the RNA strands are spliced together to remove the introns and the resulting mature mRNA is translated into amino acid sequence with every three nucleotides coding for one amino acid.Double-stranded DNA is transcribed into single stranded RNA, the entire RNA strand is translated into amino acid sequence with every three nucleotides coding for one amino acid.Double-stranded DNA is transcribed into single stranded RNA, the RNA strand is spliced to remove introns and the resulting mature mRNA is translated into amino acid sequence with every three nucleotides coding for one amino acid.
A
Double-stranded DNA is transcribed into single stranded RNA, the entire RNA strand is translated into amino acid sequence with every three nucleotides coding for one amino acid.
9
Q
- Match the mutation type with its best description.When a large section of a chromosome reads in the opposite direction as compared to before the mutation.
A mutation that swaps out a single nucleotide pair for another
If this type of mutation occurs in an exon it would result in a frameshift mutation
Any type of mutation that only impacts single nucleotide pair
A
When a large section of a chromosome reads in the opposite direction as compared to before the mutation. ( c)
A mutation that swaps out a single nucleotide pair for another (b)
If this type of mutation occurs in an exon it would result in a frameshift mutation (d)
Any type of mutation that only impacts a single nucleotide pair (a)
a. Point Mutation b. Substitution c. Inversion d. in/del
10
Q
- All genes are translated into proteins.
True
False
A
FALSE
11
Q
- What does an interior branch of a phylogram represent? (see diagram below)
An extant species
An estimate of relative amount of evolution between nodes
An ancestral population only
The common ancestor of all species included in the phylogram
A
An estimate of relative amount of evolution between nodes
12
Q
- Both _________ and ___________ are forms of homoplasy. (select both correct answers)
symplesiomorphy
convergence
autapomorphy
mutation
xenology
A
symplesiomorphy
convergence
13
Q
- The image below is a cladogram that is a summary of the relationships between members of the group Dictyoptera which includes mantises (Mantodea), roaches (Blattodea) and termites (Isoptera). Based only on this phylogeny select all the correct statements.Blattodea and Isoptera are more closely related to each other than they are to the MantodeaMantodea species have evolve more than the other two groups since divergence from their common ancestor.Mantodea and Isoptera are valid classifications, however Blattodea is invalid.Eusocial behavior in termites evolved prior to the transition to wood as a food source.
A
**Blattodea and Isoptera are more closely related to each other than they are to the Mantodea
Mantodea and Isoptera are valid classifications, however Blattodea is invalid.**
14
Q
- By reference to the phylogeny below, which of the following is an accurate statement of relationships?
A human is a member of the Hominidae, but not a member of the Simiiformes
Orangutans are equally related to humans and gorillas
New world monkeys are more closely related to old world monkeys than to gibbons
Humans are related to a chimpanzees but not gibbons.
A
Orangutans are equally related to humans and gorillas
15
Q
- Which of the five marks in the tree below corresponds to the most recent common ancestor of a mushroom and a sponge?
a
b
c
d
e
A
D. common ancesotr of sponge,mouse, and mushroom
16
Q
- Which of the four trees below depicts a different pattern of relationships than the others?c
b
d
a
A
c
17
Q
- In the tree below, assume that the ancestor was a herb (not a tree) without leaves or seeds. Based on the tree and assuming that all evolutionary changes in these traits are shown, which of the tips has a tree habit and lacks true leaves?Psilotum
Lepidodendron
Fern
Oak
Clubmoss
A
Lepidodendron
18
Q
- Using the diagram below select all the gene pairs that would be considered paralogous.
Gene 2 and 4
Gene 1 and 5
Gene 1 and 4
Gene 4 and 5
Gene 3 and 4
A
1 and 5
1 and 4
3 and 4
19
Q
- Which of the following statements is the most correct regarding the homology of a bird wing and a bat wing?
They are not homologous
They are homologous as both a forelimb and as a wing (flying structure).
They are homologous as a forelimb, but the ability to fly is convergent and therefore not homologous.
They have the some of the same developmental genetic networks, but otherwise are not homologous.
A
They are homologous as a forelimb, but the ability to fly is convergent and therefore not homologous.
20
Q
They are homologous as a forelimb, but the ability to fly is convergent and therefore not homologous.
A
True
21
Q
- Genes copies that can trace their homology to a horizontal gene transfer event are said to be ________.
orthologous
paralogous
xenologous
analogous
A
xenologous
22
Q
- If I wanted to trace the history of a species it would be best to choose _________ genes.
xenologous
paralogous
orthologous
invariable
A
orthologous
23
Q
- Which of the numbered characters in the DNA alignment is a potential synapomorphy for the species D, E and F?
Character 1Character 3
Character 5
Character 7
Character 9
A
character 3
24
Q
- Mark all cladograms that are equivalent.
A
b,d,and e
25
26. Although there is no explicit model used for a strict parsimony analysis; because all mutations are treated equally the closest implied model of evolution would be _____.
HKY 85
Kimura 2 Parameter (K2P)
Jukes and Cantor (JC)
General Time Reversible (GTR)
Jukes and Cantor (JC)
26
27. What is the main drawback of optimality methods for phylogenetic inference?
They cannot use genetic data
They can only be performed if all of the species included are still living
They have to evaluate an incredibly large number of phylogenies and so aren't very efficient
They have to estimate pairwise differences
They have to evaluate an incredibly large number of phylogenies and so aren't very efficient
27
28. The BLAST algorithm is a relativly fast method of doing local DNA alignments and can be used to search an online database of deposited DNA sequences. Which of the following would be the most productive use of BLAST?
I have a DNA sequence recovered as evidence at a crime scene and I want to see if it matches a suspect's DNA
I have a gene sequence and want to find all other genes of a similar size.
I have a gene sequences recovered from the stomach contents of a study organism and want to determine what species the organism was eating.
I have a gene sequence and want to determine the three dimensional shape of the gene once it is translated into amino acids.
I have a gene sequences recovered from the stomach contents of a study organism and want to determine what species the organism was eating.
28
29. Maximum Likelihood is a method of phylogenetic inference that uses __________ data and __________ .
distance, an optimality criterion
discrete, an optimality criterion
discrete, clustering algorithm
distance, clustering algorithm
discrete, an optimality criterion
29
30. Neighbor Joining trees are not widely used in modern phylogenetic analyses because they are too inefficient.
True
False
False
30
31. Match the vocabulary word on the left with its description on the right.
a. When three or more descendant branches diverge from a single node
b. A representation of a recent common ancestor of two or more species
c. A phylogeny that shows both relationships between organisms and estimates rates of evolution
d. There are four different codons for the amino acid proline
Polytomy a
Phylogram c
Node b
Degeneracy of DNA Code d
31
32. What is an "NP-Complete" problem?
A problem with an infinite number of possible solutions
A problem that has so many potential solutions that even the fastest super computers cannot evaluate them all in a reasonable amount of time
A problem for which different approaches will yield different optimal solutions
A problem without an overall best solution
A problem that has so many potential solutions that even the fastest super computers cannot evaluate them all in a reasonable amount of time
32
33. What is long branch attraction?
The tendency of parsimony to group distantly related species if they have elevated mutation rates.
Loss of power when too many species are included in a phylogenetic analysis.
The tendency for phylograms to be more accurate than cladograms.
The ability to calculate a probability of a data set given a particular phylogenetic hypothesis.
The tendency of parsimony to group distantly related species if they have elevated mutation rates.
33
34. What are the two ways that researchers use to test whether or not a phylogenetic method is good at reconstructing evolutionary relationships? (mark both correct answers)
Generate known phylogenies using rapidly reproducing species such as bacteria.
Simulate data representing DNA sequences with known relationships using a computer algorithim.
Use a previously published data set with well supported nodes, then anonymize the species and see if a method is still able to recover the correct relationships.
Only use nuclear genes as the mitochondrial genes evolve under different evolutionary pressures.
Only use protein coding regions of the genome as the non-protein coding regions evolve under different evolutionary pressures.
Generate known phylogenies using rapidly reproducing species such as bacteria.
Simulate data representing DNA sequences with known relationships using a computer algorithim.
34
35. The main impetus behind the development of Bayesian analysis was to find a more efficient method of phylogenetic analysis that could implement models of evolution and statistical approaches.
True
False
True
35
36. Which of the following is an accurate statement regarding Bayesian and Maximum likelihood analyses?
Bayesian analyses are statistical methods of inferring phylogenetic relationships, but maximum likelihood approaches do not use statistics.
Maximum likelihood is a clustering algorithm, but Bayesian analyses use an optimality criterion.
Maximum likelihood analyses are statistical methods of inferring phylogenetic relationships, but Bayesian approaches do not use statistics.
Bayesian analyses are more efficient than maximum likelihood analyses.
Bayesian analyses are more efficient than maximum likelihood analyses.
36
37. Weighted parsimony assumes _________.
that only molecular data are valid
that some mutations occur less frequently than others and should therefore be given more consideration
that more recent mutations might obscure mutations that happened anciently.
that both molecular and morphological data are valid
that some mutations occur less frequently than others and should therefore be given more consideration
37
38. The scala naturae is a more accurate way to depict the evolutionary relationships between species than a phylogenetic tree.
True
False
False
38
39. What is the best way to be 100% sure we have the true phylogeny?
Check for congruence among different methods
Increase taxon sampling
Use orthologous genes
None of the above, because phylogenetics attempts to reconstruct historical relationships we can never be 100% sure we have the "true" phylogeny
None of the above, because phylogenetics attempts to reconstruct historical relationships we can never be 100% sure we have the "true" phylogeny
39
1. I complete a phylogeny of reptiles and want to be 100% sure it’s completely accurate. Which of the following statements is most correct about my process of ensuring 100% accuracy?
If I use multiple analytic approaches (eg., Bayesian, Maximum Likelihood, Parsimony) and they all agree then I can be certain the result is accurate.
If there is an insignificant level of conflict between all the phylogenies that are saved after the "burn-in" period of my Bayesian analysis, then I can be certain that the result is accurate.
If my bootstrap support measures are high on each node in the analysis, then I can be sure that the phylogeny is accurate.
Although congruence among methods might increase my confidence that my results are accurate, because I am trying to reconstruct historical relationships, I can never know with 100% certainty that my results are accurate.
Although congruence among methods might increase my confidence that my results are accurate, because I am trying to reconstruct historical relationships, I can never know with 100% certainty that my results are accurate.
40
2. What do the numbers above nodes represent in a Bayesian analysis?
These are posterior probability scores estimated via a majority rule consensus tree of all the phylogenies generated after the "burn-in" period.
These are congruence estimates that are used to represent the amount of conflict between different partitions in the data set.
They are consistency indices that are automatically generated during the analysis.
These are Bremer support values that are estimated by comparing the Bayesian topology to a parsimony analysis of the same data.
These are posterior probability scores estimated via a majority rule consensus tree of all the phylogenies generated after the "burn-in" period.
41
3. Dense taxon sampling tends to generate better estimates of phylogenetic relationships, but increases the computational time needed to complete an analysis.
True
False
True
42
4. Which of the following is not a valid criticism of supertree methods?
They can support novel clades that are not present in any of the constituent phylogenies.
They do not rely on the primary data, and therefore are a form of meta-analysis.
Models of evolution cannot be incorporated in any of the components of a supertree analysis.
There can be inadvertent replication of data if there is overlap between the data present in any of the constituent matrices.
They do not allow for signal enhancement because each data set is treated independently.
Models of evolution cannot be incorporated in any of the components of a supertree analysis.
43
5. Which of the following supertree methods is the most efficient?
6.
Agreement
Optimization
Informal
informal
44
6. Some modern supertree analyses have an a priori design to optimize the compatibility of separate analyses and then join them together using a supertree (meta-analysis) approach. Which are the two methods that use this approach? (select both)
Disk covering method
MEGA tree method
Biclique method
Parsimonious method
disk covering method and biclique method
45
7. Select all of the answers below that accurately describes a pattern of characters mapped onto the phylogeny below.
Character X is best categorized as convergence
Character Z is a synapomorphy for the group consisting of species D, E, F and G
Character Z is a symplesiomorphy for the group consisting of species D, E, F and G
Character Y provides no evidence for relationships between these species
Character X and character Y exhibit homoplasy on this phylogeny
Character X is best categorized as convergence
Character Z is a symplesiomorphy for the group consisting of species D, E, F and G
Character Y provides no evidence for relationships between these species
46
8. Which of the following is not a method that would be useful in testing alternative phylogenetic hypotheses?
Likelihod Ratio Test (LRT)
Shimodaira Hasegawa Test (SH)
Posterior Branch Support
posterior branch support
47
9. Which of the following best describes the mapping of character states on to ancestral nodes in a maximum likelihood analysis?
It is accomplished in the same way as a parsimony mapping.
Log likelihood scores are given to each character prior to the phylogenetic analysis based on their relative frequency in the data set, these scores then determine the model of evolution which unambiguously assigns ancestral states to each node for each character.
Branch lengths are converted into a distance matrix, a neighbor-joining analysis then uses this distance matrix to estimate relationships without a model of evolution.
Character states are represented by probabilities at each node, these probabilities are calculated using the model of evolution and the relative branch lengths.
Character states are represented by probabilities at each node, these probabilities are calculated using the model of evolution and the relative branch lengths.
48
10. The likelihood ratio test (LRT) is a very flexible statistical test and can be used to determine if there is a significant difference between many different types of molecular analyses. Which of the following is not an application of the LRT?
Test the difference between different models of evolution.
Test the difference between different phylogenetic hypotheses.
Test whether a data set is evolving neutrally and can therefore be used as a molecular clock.
Test the difference between different competing equally parsimonious fitch optimization character mappings.
Test whether natural selection is acting on a region of the genome.
Test the difference between different competing equally parsimonious fitch optimization character mappings.
49
11. If I was doing a phylogeny of species using genes that were all part of a large gene family which of the following would give me the best chance of accurately reconstructing the species history?
Decrease the overall taxon sampling of the group so that I can include all gene copies present in each species.
Identify orthologous gene copies and represent each orthologous set of genes as a separate component of the overall matrix
Identify potential lineage sorting events based on overall heterogeneity and adjust for this via a more complex model of evolution.
Use only one randomly chosen member of the gene family for each species.
Identify orthologous gene copies and represent each orthologous set of genes as a separate component of the overall matrix
50
12. What is homology?
Similarity due to convergence
Physical features that have similar form, but different functions
Molecular markers that can help us determine geographic origins
Similarity due to a common ancestry
Similarity due to a common ancestry
51
Match the gene homology type with the process that generates it.
a. Speciation
b. Gene duplication
c. Horizontal gene transfer
Xenology c
Orthology a
Paralogy b
52
14. Lineage sorting is common when coalescence is fast and speciation is slow.
True
False
false
53
15. What is different about reconstructing the phylogenetic history of bacteria compared to eukaryotic species?
Bacteria have a more complex network like pattern of relationships
Bacteria don't have a shared genetic history
Bacteria analyses can use parsimony approaches, but not maximum likelihood approaches
Bacteria genomes can't be sequenced
16. Matching (2 pts each)
Bacteria have a more complex network like pattern of relationships
54
Match the following gene duplication terms with their definition.
a. The initial advantage provided by a gene duplication event.
b. A gene that has more than one phenotypic impact
c. When one of the products of a gene duplication event is no longer translated and transcribed into a protein product.
d. When a gene is duplicated and then one of the copies begins to do something new.
e. When a gene with more than one function is duplicated and then the two resulting copies begin to specialize on different parts of its previous functions.
Pleiotropy ( b)
Pseudogene ( c)
Subfunctionalization (e)
Neofunctionalization (d)
Redundancy (a)
55
17. What is the biological process that generates gene families?
Mitosis
Purifying selection
Meiosis
Gene duplication events
Gene duplication events
56
18. The pie chart below represents the mutations that occur in a population of eukaryotic organisms after both natural selection and genetic drift work on them. Which of the following would be the most accurate labels for each section of the pie chart?
X = beneficial, Y = deleterious, Z = neutral
X = neutral, Y = beneficial, Z = deleterious
X = deleterious, Y = beneficial, Z = neutral
X = beneficial, Y = neutral, Z = deleterious
X = beneficial, Y = deleterious, Z = neutral
57
19. What accounts for the majority of the C-value paradox?
Strong natural selection favoring sexually reproducing organisms
The streamlining of genomes during the transition to a terrestrial environment
The differing amounts of non-coding DNA in eukaryotic genomes
Frequency of recombination during meiotic cell division
The differing amounts of non-coding DNA in eukaryotic genomes
58
20. Which of the following is not a valid explanation for the G-Value paradox?
Complex gene networks can explain a significant portion of cellular and morphological complexity
Some genes can be differentially spliced into multiple protein products
All eukaryotes have mitochondria with their own genome.
Regulation of gene expression accounts for a significant portion of complexity
All eukaryotes have mitochondria with their own genome.
59
Match the following characteristics we have observed about organismal genomes features with their correct description or example.
a. Gained anciently from a symbiotic association with an early eukaryotic cell and a bacterium.
b. In eukaryotes this is because the vast majority of the genome ( > 95%) is non-protein coding.
c. An observation that the complexity of organisms doesn't correlate with the number of genes they have.
d. The process of identifying and describing the coding regions of a genome.
e. Using many small, possibly repeated sections of DNA sequence to determine the entire DNA complement of an organism.
C-value paradox b
Mapping and Annotation d
Mitochondrion a
Shotgun sequencing e
G-value paradox c
60
23. Which of the main types of RNA are we targeting when doing transcriptome sequencing?
mRNA
tRNA
rRNA
microRNA
mRNA
61
24. Matching (2 pts each)
You calculate the dN/dS (Ka/Ks) ratio for a number of genes across 20 species. Match the value on the left with the gene descriptions on the right.
a. Any gene that is essential for survival, but has evolved to do something unique in a subset of the 20 species.
b. A gene that's evolving neutrally and probably doesn't have much of an impact at all on fitness of the included species.
c. Hemoglobin, a gene that is critical to survival and has a conserved function across all 20 species.
Ka/Ks >> 1 a
Ka/Ks << 1 c
Ka/Ks = 1 b
62
25. What are the two issues about the classical "5 Kingdom" classification that we highlighted during our discussion of the tree of life. (select both correct answers)
26.
Protozoa is not a valid taxonomic group as some are more closely related to plants, some are more closely related to fungi, and others form distinct clades of their own.
Protista (Bacteria and Archaea) is not a valid, monophyletic group
Fungi are shown as more closely related to animals, but they should be more closely related to plants.
Genetic material can be transferred horizontally between different species of bacteria.
Protozoa is not a valid taxonomic group as some are more closely related to plants, some are more closely related to fungi, and others
form distinct clades of their own.
Protista (Bacteria and Archaea) is not a valid, monophyletic group
63
he original taxonomic designation for reptiles was paraphyletic due to the rapid morphological evolution of birds and _____________.
genome duplication amongst the crocodilians
convergent evolution with the turtles
loss of genes in the lizards
extinction of most dinosaur lineages
extinction of most dinosaur lineages
64
What is the one gene, two allele equivalent of stabilizing selection?
Directional selection
Underdominance
Negative selection
Overdominance
Overdominance
65
28. Which of the following best describes the General Time Reversible (GTR) model of evolution?
There is a different probability for each type of mutation (although direction is not important eg., A-->C = C-->A), but each nucleotide is assumed to occur at a frequency of 0.25.
All mutation probabilities are treated equally and the frequency of each nucleotide can vary.
There is a different probability of mutation transitions v. transversions and the frequency of each nucleotide can vary.
There is a different probability for each type of mutation (although direction is not important eg., A-->C = C-->A) and the frequency of each nucleotide can vary.
There is a different probability for each type of mutation (although direction is not important eg., A-->C = C-->A) and the frequency of each nucleotide can vary.
66
1. Which of the following would be the best approach to estimate the Heterozygosity of a population?
a. Genotype a randomly selected sample of the population for a number of different loci.
b. Determine the genotype for a single locus for every individual in a population.
c. Estimate the mutation rate for both the mitochondrial and nuclear genome.
d. Map and annotate the genome for a representative individual
A
67
Match each population genetics vocabulary word with its definition.
a. A genetic variant of a gene that causes a distinct phenotypic difference.
b. Any genetic variant, whether large, small, coding, non-coding or silent.
c. A genetic marker that was created by a substitution mutation.
d. A diploid individual that carries two identical copies of the same gene.
Allele a
Homozygous d
Polymorphism b
Single Nucleotide Polymorphism (SNP) c
68
6. How does a small population size create a population that is not at HW equilibrium?
a. It increases the chance that selection will be acting on a population
b. It skews the sex ratio, which causes an autosomal disequilibrium
c. It increases the amount of inbreeding
d. It causes the effects of genetic drift to be greater
e. It reduces the efficiency of DNA repair mechanisms
D
69
7. You survey a population of wild cheetahs and find the following distribution of genotypes: AA: 250 Aa: 500 aa: 250 What are the allele frequencies for this population and are there evolutionary forces acting on this gene?
a. p = 0.9 q = 0.1, no sign of evolutionary forces
b. p = 0.6 q = 0.4, no sign of evolutionary forces
c. p = 0.5 q = 0.5, no sign of evolutionary forces
d. p = 0.5 q = 0.5, evidence of evolutionary forces
e. p = 0.6 q = 0.4, evidence of evolutionary forces
c. p = 0.5 q = 0.5, no sign of evolutionary forces
70
8. You survey a population of wild cheetahs and find the following distribution of genotypes: AA: 250 Aa: 500 aa: 250 Which of the following statements is most likely to be false?
a. This is a relatively large population of cheetahs.
b. Cheetahs with the AA genotype strongly prefer to mate with cheetahs with the aa genotype.
c. The a allele is a relatively recent mutation.
d. The AA genotype conveys much more fitness than the aa genotype.
B
71
9. You survey a population of wild cheetahs and find the following distribution of genotypes: AA: 400 Aa: 200 aa: 400 What are the allele frequencies for this population and are there evolutionary forces acting on this gene?
a. p = 0.9 q = 0.1, no sign of evolutionary forces
b. p = 0.6 q = 0.4, no sign of evolutionary forces
c. p = 0.5 q = 0.5, no sign of evolutionary forces
d. p = 0.5 q = 0.5, evidence of evolutionary forces
e. p = 0.6 q = 0.4, evidence of evolutionary forces
D
72
10. Most new genes are the result of ______________.
a. substitution mutations
b. gene duplication events
c. de-novo evolution from non-coding DNA
d. horizontal gene transfer
b
73
11. Which of the following observations supports the answer to the question above?
a. Most genes can be placed into gene families
b. Genes on the mitochondria are translated by different ribosomes than genes in the nuclear genome
c. All life on earth shares the same genetic code
d. Bacteria only trace a portion of their genome down the same line as their ancestral cells.
a
74
You calculate the Ka/Ks ratio for a number of genes across 20 species. Match the value on the left with the gene descriptions on the right.
a. NADH2 a gene critical for metabolism with identical function in all sampled species
b. A pigmentation gene that is expressed in the dermis, but has no impact at all on the fitness of any of the sampled species
c. A venom gene that has evolved to specifically target different prey items of the different sampled species
12. Ka/Ks > 1 C
13. Ka/Ks < 1 A
14. Ka/Ks = 1 B
75
Match the gene duplication term with the best example.
a. An ancestor of all mammals had two opsins sensitive to red and blue light, humans and some of our relatives have three opsins sensitive to red, blue and green light.
b. The venom in a new species of octopus is a protein transcribed from a gene that is paralogous to a digestive enzyme gene, phylogenetic evidence show that prior to gene duplication there was a single used as both a digestive enzyme and a venom, however today the octopus expresses one gene product in the digestive tract and the other, now more toxic gene product, in the venom gland.
c. Humans have several hemoglobin genes that make up function hemoglobin, there are also two regions of the human genome that are very similar to these duplicated genes, but are no longer transcribed.
15. Subfunctionalization b
16. Neofunctionalization a
17. Pseudogene c
76
18. Alpha helices and beta pleated sheets are examples of __________.
a. non-coding DNA regions
b. secondary structures of proteins
c. promiscuous enzyme activity
d. compensatory mutations
b
77
19. One of the fastest evolving types of genetic makers are made up of tandem repeat of DNA that mutate to have different numbers of repeats. What is this type of diversity called?
a. Microsatellite
b. Single Nucleotide Polymorphism (SNP)
c. Latent variation
d. Homozygosity
a
78
20. Which of the following two mechanisms best explain the observation that the same protein domain can be found in many different genes in the human genome? (mark both answers)
a. The maternal inheritance of the mitochondrial genome.
b. Horizontal gene transfer from distantly related species
c. Gene duplication events that initially create functional redundancy
d. Sometime proteins structures with very different primary amino acid sequence can have a similar function
e. Ectopic recombination events and domain exon shuffling can result in “franken-genes”
e
79
21. Which of the following genes in humans is least likely to be subject to recombination?
a. ALDH2, found on autosome 12
b. OPN1LW, an opsin found on the X chromosome
c. NADH2, found on the mitochondrion
d. CAT, also known as catalase found on autosome 11
c
80
22. What two values would I need to estimate theta ()? (mark both answers)
a. Population size
b. C-value
c. Mutation rate
d. Hardy-Weinberg Equilibrium
a and c
81
23. The vast majority of genetic diversity in the human population shows no correlation with geography.
a. True
b. False
a
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24. Fst is a measure of genetic structure within a population. Which of the following describes how this value is determined?
a. It is calculated by estimating the mitochondrial diversity and comparing to the nuclear diversity.
b. It is estimated as the product of the effective population size and the mutation rate.
c. It is calculated by counting relative copy number variants (CNVs) and single nucleotide polymorphisms (SNPs).
d. It is estimated by looking for differences in heterozygosity in subpopulations when compared to the total population.
d
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25. When formulating his theory of natural selection Darwin was evaluating ________, however the majority of genetic diversity ___________.
a. neutral mutations has an impact on phenotype
b. diversity that changed phenotype reflects silent mutations
c. eukaryotes is found in prokaryotes
d. genetic drift and mutation is located in the telomeres
b
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26. If natural selection works to remove deleterious mutations, why do we still see them in populations?
a. Deleterious mutations do not have an impact on phenotype and so are masked among the neutral mutations.
b. All deleterious mutations are recessive and so can “hide” in heterozygote individuals.
c. A number of factors including genetics, environmental instability and varying strengths of selection means that the removal of some deleterious mutations is very slow.
d. Differential expression compensates for the loss of fitness incurred by most deleterious mutations
c
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27. If I was doing a phylogeny of species using genes that were all part of a large gene family which of the following would give me the best chance of accurately reconstructing the species history?
a. Use only one randomly chosen member of the gene family for each species.
b. Identify orthologous gene copies and represent each orthologous set of genes as a separate component of the overall matrix.
c. Identify potential lineage sorting events based on overall heterogeneity and adjust for this via a more complex model of evolution.
d. Decrease the overall taxon sampling of the group so that I can include all gene copies present in each species.
b
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28. Opsins are part of which superfamily of proteins?
a. G-protein coupled receptors
b. Helix-turn-helix binding domain transcription factors
c. Ras cell signaling proteins
d. Dynamin cell membrane remodelers
a
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29. What group represents all of the descedants of the first organism with opsin genes?
a. Metazoa (all animals)
b. Viridiplantae (all plants)
c. Eukaryota
d. Prokaryota
e. Mammalia
a
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89
30. All members of the opsin gene family are sensitive to light.
a. True
b. False
b
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31. Which of the following is the most widely used species concept?
a. Phylogenetic
b. Ecological
c. Morphological
d. Biological
c
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32. Some transcripts can create multiple protein products through post translational modifications and alternative splicing.
a. True
b. False
b
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33. Which of the following is the most important mechanism for the extensive protein repertoire of animal venomes?
a. Gene duplication
b. Recruitment of preadapted genes
c. Genome rearrangement
d. Point mutations in the third position of codons
e. Point mutations in the second position of codons
b
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34. The rattlesnake is a good example of the ancestral delivery system of the first venomous squamates.
a. True
b. False
b
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35. Which of the following ecological factors might increase the likelihood of convergence in the evolution the venoms of different species?
a. If they live in the same area
b. If they are both nocturnal
c. If they both have relatively short life cycle compared to close relatives
d. If they both belong to the same phylum of animals
e. If they both target the same prey species
e
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Match each vocabulary term/phrase that is most closely associated with the example discussed in class.
a. All allelic diversity in modern humans can be traced back to a single variant somewhere in our ancient ancestors.
b. Many venom genes are expressed in both the liver and the salivary glands.
c. The human immune deficiency virus (HIV) evolved rapidly after it was first identified
d. Functional human hemoglobin is composed of two different types of amino acid sequences transcribed from different genes.
e. All opsins found in Metazoa are part of the same gene family.
36. Zoonotic transmission c
37. Constraint imposed by pleiotropy b
38. Adaptive Gene Radiation e
39. Quaternary Structure d
40. Coalescence a
BIOL 4330
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