Download Midterm 2 - 1996

NAME_______________________________
EXAM#_______
1
1. (15 points) Next to each unnumbered item in the left column place the number from the right
column/bottom that best corresponds:
1) a genomic segment bordered by a pair of long terminal repeats and
3 autopolyploid
containing inactive protein-coding genes
2) a geological principle that influenced Darwin's theory of gradualism
24 Chelex
3) all chromosome sets from one species
4) always transmitted from father to son
6 D1S80
5) an assumption of Darwin's theory of common descent
6) a non-coding locus that shows high levels of variation in human
19 degrees of freedom
populations
7) a segment of mitochondrial DNA with known single-nucleotide
1 endogenous retrovirus
polymorphisms (SNPs) in Trimerotropis saxatilus
8) bead-like condensation visible at telophase of mitosis
11 Harlequin chromosome
9) can be used to determine exactly when two copies of homologous
DNA randomly chosen from the human population coalesce
30 heritability of fitness
10) chromosomes replicate once in presence of 5-bromouracil
11) chromosomes replicate twice in presence of 5-bromouracil
12 identity by descent
12) copies of homologous DNA whose genealogical path of
coalescence
features no mutation
18 interspecific polymorphism
13) equals dN/dS
14) formed by spontaneous hybridization and chromosome doubling
20 mathematical model
15) group of genes that all function in the same biochemical pathway
16) homologous DNA molecules that represent different haplotypes
27 multigene family
17) illustrated by the env gene of HIV 1
18) illustrated by the "standard" gene order for chromosomes 3 of
29 parsimony
Drosophila persimilis and D. pseudoobscura
19) in a contingency table = (number of rows-1)(number of columns-1)
21 patroclinous
20) involves assumptions, abstraction and simplification, and cannot
simultaneously maximize generality, precision and reality
22 telomere
21) like the father in phenotype
22) normal chromosome end
2 uniformitarianism
23) occurs whenever broad-sense heritability exists for the hemoglobin
A/S polymorphism
24) removes from solution positive ions that might interfere with the action of Taq polymerase
25) replicates rapidly in somatic cells, often causing disease symptoms
26) the number of differences between amino-acid sequences of homologous proteins
27) thought to have arisen by gene duplication and divergence
28) used to digest protein in the isolation of template DNA for a PCR reaction
29) used to estimate the ancestral state of a protein sequence from a haplotype tree
30) zero at a selective equilibrium
NAME_______________________________
EXAM#_______
2
2. (6 points) As described in class, Creighton and McClintock studied crossing over in chromosome 9 of
corn. As indicated below, they test crossed plants heterozygous for a normal chromosome 9 and an
unusual chromosome 9 that carried a chromatin knob at the tip of the short arm and a large block of
chromatin at the tip of the long arm.
normal chromosome 9:
unusual chromosome 9:
knob
chromatin block
Assuming that a single crossover occurs in the short arm (between the knob and the centromere) and that
no crossovers occur in the long arm, draw the appearance of these homologs at
a. diplotene
b. anaphase I
NAME_______________________________
EXAM#_______
3
NAME_______________________________
3. (4 points) Give very brief answers to the following:
Name the substages of prophase I in which the following events occur:
a. crossing over
pachytene
b. the initiation of chromosome condensation
leptotene
c. the appearance of chiasmata
diplotene
d. synapsis
zygotene
EXAM#_______
4
NAME_______________________________
EXAM#_______
4) (8 points)
a. What is chiasma interference?
inhibition by one crossover of others occurring nearby
b. What is chromatid interference?
influence of chromatids involved in one crossover on chromatids involved in another
c. Why are triploids usually sterile?
Because segregation of each trivalent is independent of all others, almost all gametes have
unbalanced chromosome numbers.
d. Why are about half of gene conversions associated with crossovers?
because Holliday structures are resolved to produce crossovers half the time
5
NAME_______________________________
EXAM#_______
6
5. (4 points) In corn, the A, B, and D genes are on different (nonhomologous) chromosomes. What are
the expected phenotypes and their frequencies in the cross AaBbDd x AaBbdd? Assume
complete dominance of the A, B and D alleles.
NAME_______________________________
EXAM#_______
7
6. (6 points) a. (3 points) In yeast, a cross is made between B D and b d haploids. Of 100 tetrads
scored, the following numbers of types were observed:
BD
BD
bd
bd
BD
Bd
bD
bd
80
20
Bd
Bd
bD
bD
0
Draw a linkage map showing the positions of these genes and, if possible, their centromere(s). Show
distances in map units.
b. (3 points) A second cross is made between E F and e f haploids. Of 100 tetrads scored, the following
numbers of types were observed:
EF
EF
ef
ef
EF
eF
Ef
ef
eF
eF
Ef
Ef
50
0
50
Draw a linkage map showing the positions of these genes and, if possible, their centromere(s). Show
distances in map units.
E and F on different chromosomes. Both are very close to their centromeres.
NAME_______________________________
EXAM#_______
8
7. (18 points) The following data are used for an analysis of variance in fitness associated with
genotypes at a polymorphic locus where the frequency of allele A is 0.6 and the frequency of allele a is
0.4. Assume Hardy-Weinberg genotypic proportions. The relative fitnesses measured for each genotype
at the locus are as follows:
Genotype:
W
A/A
0.8
A/a
1.0
a/a
0.3
mean
0.6
a. (4 points) Provide a mathematical expression for the genetic variance in fitness for this
population (answer should be left in polynomial form).
0.36(0.8 - 0.6)2 + 0.48(1.0 - 0.6)2 + 0.16(0.3 - 0.6)2
b. (2 points) What, if any, information not derivable from the numbers given above is needed to
calculate the average excesses of the two alleles, A and a?
No more information is needed
c. (2 points) What, if any, information not derivable from the numbers given above is needed to
calculate the expected change in frequency of the A allele after one generation of selection?
No more information is needed.
d. (2 points) What, if any, information not derivable from the numbers given above is needed to
calculate the heritability of fitness associated with this polymorphism?
total variance in fitness or environmental variance in fitness
e. (2 points) What, if any, information not derivable from the numbers given above is needed to
calculate the dominance variance in fitness associated with this polymorphism?
No more information is needed.
f. (3 points) Is a balanced polymorphism expected for the A and a alleles in this population?
Why?
Yes. Because selection favors the heterozygous genotype, it will act to maintain this
polymorphism rather than to cause fixation of one allele.
g. (3 points) What three major components of fitness are summarized by relative fitness
values as used above?
NAME_______________________________
viability, mating success, fertility/fecundity
EXAM#_______
9
NAME_______________________________
EXAM#_______ 10
8. (9 points) Referring to exercise 3 from our Evolve II experiment in lab (the last experiment with
multiple trials at three different population sizes), what part of the analysis demonstrated each of the
following properties of genetic drift?
a) drift is cumulative
1. The range of allele frequencies gets bigger as generation time increases.
OR
2. The histograms broaden (show more spread form the center of the x-axis) as generation time
increases.
OR
3. The likelihood that the allele goes to fixation increases as generation time increases.
b) drift is non-directional
1. The average change in allele frequency over all trials is always about zero.
OR
2. Over ten trials, the allele frequency goes up from 0.5 about as often as it goes down from 0.5.
c) drift typically shows a larger effect on a smaller population size
1. The range of allele frequencies gets bigger as population size gets smaller.
OR
2. The histograms broaden (show more spread form the center of the x-axis) as population size
gets smaller.
OR
3. The likelihood that the allele goes to fixation increases as population size gets smaller.
NAME_______________________________
EXAM#_______ 11
9. (16 points) For each of the following statements regarding Darwinian evolutionary theory, indicate
whether the statement is true or false. For false statements, explain why the statement is false.
a. Darwin's theory of natural selection explains most amino-acid substitutions occurring in
fibrinopeptides during vertebrate evolution.
False - Rapid evolution of fibrinopeptide sequences was used to support neutrality theory
because most have no apparent functional consequence.
b. Molecular applications of Darwin's theories of common descent and natural selection allow
researchers to predict which amino-acid substitutions in a protein are most likely to cause
disease in human populations.
True
c. Darwin's theory of common descent is the basis for current biological concepts of homology
and phylogeny, on which all comparative biology depends.
True
d. Variation among human populations on a worldwide basis illustrates Darwin's theory of
multiplication of species.
False - These populations collectively represent a single cohesive evolutionary lineage.
e. R. A. Fisher's quantitative-genetic models of variation in fitness and related phenotypes
synthesize Darwin's theories of gradualism and natural selection with Mendel's theory of
particulate inheritance.
True
f. A major problem with Darwin's original theory of natural selection was that it could not
explain conservation of genetic variance across generations for selected traits.
True
g. The basic idea of organic evolution was not original with Darwin but was greatly strengthened
by his work and many subsequent studies stimulated by Darwin's theories.
True
h. Analyses based on Darwin's theory of common descent permit biochemical characterization of
some extinct proteins.
True
NAME_______________________________
EXAM#_______ 12
10. (14 points) Provide brief answers to the following questions regarding uses of measured genotype
approaches to study the genetic basis of quantitative phenotypes.
a. (4 points) What information about the history of a human population is important for choosing
that population to conduct a genome scan to identify which chromosomes carry loci whose variation
may influence a particular disease phenotype, such as diabetes? Why is this information important?
Population must have (1) variation for the phenotype of interest, such as high incidence of the
disease and (2) history of a population-size bottleneck/founder event to produce linkage
disequilibria between closely linked loci. Without linkage disequilibria, there will be no
association between the disease phenotype and SNP markers genetically linked to the locus
causally associated with the disease.
b. (3 points) How can you use information on variation in your chosen population for a large number
of SNP loci located within 10 cM of each other on a single chromosome to confirm the wisdom of
your choice?
If the choice was a good one, pairs of SNP loci drawn from a 10 cM region should include many
that show high levels of linkage disequilibrium.
c. (3 points) Suppose that a genome scan indicates statistically significant association between
variation in the disease phenotype and variation at multiple SNP markers located within a 10-cM
region of chromosome 6. What is the logical next step in identifying variation causally associated
with the disease phenotype?
Consult information from the human genome project to see which genes are located within the
chromosomal region highlighted by the scan. A gene within the region whose function is
related to the phenotype of interest is a candidate locus for further investigation of variation.
d. (4 points) Candidate-locus studies indicate that elevated levels of LDL cholesterol are associated
with an epistatic interaction between a genotype at the LDLR locus (homozygotes for allele 2) and
genotypes at the apoE locus (genotypes containing at least one copy of allele 4). Allelic frequencies
for alleles at both loci are given below for two hypothetical populations. Indicate for each population
which of the two loci (apoE or LDLR) is expected to make the greatest contribution to heritability of
cholesterol level, and explain why.
ApoE
LDLR
Allele
2
3
4
1
2
Population 1
0.08 0.77
0.15
0.2
0.8
Population 2
0.02 0.03
0.95
0.8
0.2
Population 1 - apoE. Population 2 - LDLR. When epistatic interactions produce a phenotype,
population-level variation is associated primarily with the rarer factor. In population 1, the
apoE 4 allele is relatively uncommon whereas a majority of the population has the homozygous
2 genotype for LDLR. In population 2, most people have a copy of the apoE 4 allele, whereas
the homozygous 2 genotype for LDLR is rare.