Methods to determine the amino acid sequence of a protein were developed in the
In the male germline of Drosophila melanogaster:
Which of the following requires an “outgroup” sequence
Which of the following requires a protein-coding sequence?
Which of the following would suggest positive selection?
A positive value of Tajima’s D suggests an excess of:
What type of variation in the Amylase gene is associated with starch digestion in humans?
The mutations responsible for lactase persistence in European and African pastoralist populations occurred:
A deletion in which gene is associated with HIV/AIDS resistance in humans?
Which of the following can explain the observed positive correlation between DNA polymorphism and recombination rate?
Which model of human evolution involves extensive gene flow among populations?
The vertebrate homolog of the Drosophila eyeless gene is known as:
The key genes that control flower development in plants are:
Which method can be used for PTGS (post-transcriptional gene silencing)?
. What is the difference between a non-degenerate site, a 2-fold degenerate site, and a 4-fold degenerate site? (6 pts)
Non-degenerate site: every base change leads to a change in the amino acid
2-fold degenerate site: 2 of the 3 possible base changes lead to a change in the amino acid
4-fold degenerate site: non of the possible base changes leads to a change in the amino acid
Regarding sex chromosome evolution, what is the difference between the “fast-X effect” and the “large-X effect”? (6 pts)
“fast-X effect”: an expected increase in the rate of adaptive evolution on the X chromosome due to the fixation of recessive, beneficial mutations in hemizygous males.
“large-X effect”: the X is enriched for loci that cause hybrid incompatibilities, such as hybrid male sterility, suggesting that the X plays a disproportionately large role in speciation – at least in the evolution of postzygotic reproductive isolation.
A 900-kb inversion on chromosome 17 is polymorphic in humans. What two observations suggest that the inverted form (H2) has been positively selected in European populations? (4 pts)
- H2 is very rare in most populations, except in Europe where it is in high frequency (≈ 20%)
- In Iceland, women with the H2 inversion had more children (on average 3% more) than women with H1
Below is a DNA sequence alignment. Each sequence comes from a different individual from within the same species. (8 pts.)
17. What is the number of segregating sites (S)?
18. How many of the segregating sites involve transitions?
19. How many of the segregating sites involve transversions?
20. How many haplotypes are there?
17. What is the number of segregating sites (S)? 6
18. How many of the segregating sites involve transitions? 4
19. How many of the segregating sites involve transversions? 2
20. How many haplotypes are there? 3
The Scala Naturae refers to
Consider two biallelic loci A and B. Which of the following notation refers to a haplotype?
In female heterogametic species like birds the mutation rate of the Z chromosome compared to autosomes is expected to be
Two alleles A and a segregate at a single bi-allelic locus. Assuming finite population size, random mating and no selection, the A allele will eventually be
Which of the following statements is correct? Linkage disequilibrium
You calculate F-statistics for a set of two subpopulations in a diploid organism. In subpopulation 1 you find FIS to be positive. What does that mean?
What does the Wahlund effect refer to?
Which of the following conditions would most likely lead to an increase in the frequency of altruistic behavior in a population?
In a diploid population with alleles A and a the aa genotype has a selective disadvantage s of 40%. The dominance coefficient h in heterozygotes is 0.3. What is the fitness of the three genotypes?
One obligate cross-over per chromosome arm is required for successful meiosis. Consider an organism with 23 metacentric chromosomes. What is the minimum genetic map length of the genome?
Using a linear regression of the phenotypic values of the offspring over the mean of the two parental phenotypic values we can estimate:
The biological species concept is useful because
Draw a 2-dimensional model of evolution after a) Carolus Linnaeus b) Jean-Baptiste Lamarck and c) Charles R. Darwin. Use ‘time’ for the y-axis and ‘species’ for the x-axis in all cases. (3p)
Consider the code table below and assign the correct answer (A, B, C or D) to the blank on the left. (2p)
Which of the following mutations of the coding strand sequence 5’ – TAC – 3’
a) TAC > TAT
b) TAC > TAG
c) TAC > CAC
d) TAC > TCAC
are
___ missense mutation
___ frameshift mutation
___ non-sense mutation
___ silent mutation
___ missense mutation = C
___ frameshift mutation = D
___ non-sense mutation = B
___ silent mutation = A
le 20 genotypes each from two populations. Genotyping each individual with a codominant molecular marker you infer the following genotype frequencies:
AA
Aa
aa
Pop1
5
10
Pop2
2
4
14
a) What are the allele frequencies p1 and p2 for the A allele in population 1 and 2 respectively? (1p)
b) What is average proportion of heterozygote individuals in the subdivided populations assuming Hardy-Weinberg equilibrium? (1p)
c) What is the expected frequency of heterozygotes assuming Hardy-Weinberg equilibrium if population structure is ignored? (1p)
d) Calculate the following F statistics (round to three decimals) (2p)
____ FIS for population 1
____ FIS for population 2
____ FST What do you infer from these values? ?
Remember Wright’s fixation index relating heterozygosity across hierarchical levels X and Y as FXY=1-HX/HY. Round the results to three decimals where necessary.
0.5 = p1 0.2 = p2
0.41 = HS
0.455 = HT
Methods for DNA-sequencing were developed in:
1970
Homolog of Pax6 in invertebrates:
"eyeless"
Negative value of Tajimas'D suggests excess of:
rare variants
Human gene associated with 'risk taking':
DRD4
Consequences of chromosome 17 inversion in Iceland:
number of children increased
If the observed proportion of differences (D) between two protein sequences is 0.42, the expected proportion of differences (K) is:
If all nucleotides are used with equal frequency, the maximum divergence we expect between two DNA sequences is:
If all amino acids are used with equal frequency, we expect two random protein sequences to be _____ identical:
Which type of site is expected to show the least divergence between species?
Which of the following represents a typical value of the transition/transversion ratio for DNA substitutions?
The ratio dN/dS is also sometimes referred to as:
Which of the following is expected for a pseudogene?
According to the molecular clock, sequence divergence between species depends on:
Methods for determining the amino acid sequence of proteins were developed in the:
The most parsimonious tree is the one that:
Which one of the following statements about the great apes is correct?
Which of the following represents a rare genetic change (RGC)?
Which of the following statements about mammalian mitochondrial DNA is true?
Mexican and South American dog breeds:
Clone-by-clone genome sequencing is also known as ________ genome sequencing?
What type of species has the largest known genome?
Which of the following methods are used for gene expression profiling?
Who is known for the hypothesis “ontogeny recapitulates phylogeny”?
The defining feature of a cis-regulatory variant is that it:
Which pair of species/taxa are male-heterogametic?
What is the expected proportion of differences in DNA sequences?
k = -3/4 (1-4d/3)
The least divergence in protein sequences between humans and chimps is seen in..
brain
How long are the homeo domain proteins
60aas
Which uses distance matrix?
Heterozygosity over time due to genetic drift
heterozygosity loss
N_e : effective Pop sizeS
Effective population size with sex ratio differences
The probability of fixation of a new mutation is
1/2N
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