Download NAME_______________________________ EXAM

NAME_______________________________ EXAM#_______
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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 Darwinian theory of phenotypic evolution influenced by Lyell's
20 abnormal 4:4 segregation
principles of geology
2) a geographically widespread population subdivided into local demes
21 colchicine
among which migrant individuals are exchanged
3) a molecular evolutionary phenomenon that illustrates traditional
8 constitutive heterochromatin
Darwinian natural selection
4) a species concept that pertains only to sexually reproducing lineages
27 fundamental niche
5) a specific endogenous retrovirus in humans
6) common in a population whose inbreeding effective size is very
small
1 gradualism
7) condensed in interphase in only some cells
8) contains highly repeated DNA sequences
15 HIV
9) Darwin's theory of the spatial dimension in multiplication of species
10) factors that prevent members of a sexually reproducing species
from
6 identity by descent
recognizing members of another species as appropriate mates
11) factors that disrupt the development of zygotes formed by fusion
of
24 Mendel's Second Law
gametes drawn from two different species
12) four chromatids to same pole in meiosis I
2 metapopulation
13) illustrated by replacement of hemoglobin ß alleles A and S by
allele
C in some western African populations
25 phylogenetic species concept 14) inhibits chromosome movement by binding to centromeres
15) Its envelope protein evolves by natural selection during the
infection
19 polytene chromosomes
of a host.
16) Law of Segregation
10 prezygotic barriers
17) most frequent in populations that have high heterozygosity
18) occurs when the average excesses for fitness of all alleles at a
18 selective equilibrium
polymorphic locus equal zero but broad-sense heritability is
nonzero
19) permit construction of haplotype trees for chromosomes 3 of Drosophila
22 selfish DNA elements
persimilis and D. pseudoobscura
20) postmeiotic segregations present
29 Turner's syndrome
21) prevents formation of spindle
22) retrotransposons and retroviruses are examples
23) reveal extensive translocation polymorphism in Drosophila pseudoobscura.
24) segregation of each gene pair independent of all others
25) taxonomically recognizes all diagnosably distinct evolutionary lineages
26) the actual resources used by a species at a given time and place
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27) the set of environments/resources that a species is capable of using
28) violates assumptions of the two-dimensional stepping-stone model of population structure
29) XO
30) XXY
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2. (4 points) You are given two pure-breeding strains of snapdragon. One has white flowers and the
other has red flowers. When plants from the two strains are intercrossed, the F1 plants are all red
flowered. When these F1 plants are crossed to plants from the pure-breeding white strain, 3/4 of the
progeny are white flowered and 1/4 are red flowered. Explain these results using gene symbols of your
own choice.
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NAME_______________________________ EXAM#_______
3) (10 points) Draw the appearance of a pair of telocentric homologs and state in words the main
chromosomal event(s) that occur in each of the stages of meiosis I listed below. Be sure to
indicate when the following events occur: synapsis, crossing over, and loss of sister chromatid
adhesion. In your drawings, assume a single crossover occurs between the two homologs, and
distinguish sister chromatids from the two homologs by using different colors or by using smooth
and wiggly lines.
zygotene
pachytene
diplotene
metaphase I
anaphase I
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4) (5 points) In corn, the genes for tassel length (alleles T and t) and pale leaves (alleles P and p) are
known to be on different (nonhomologous) chromosomes. In the course of making routine
crosses, a geneticist noticed that one T/t; P/p plant gave unusual results in a testcross with the
double recessive homozygote t/t; p/p. The results were:
Progeny:
T/t; P/p
t/t; p/p
T/t; p/p
t/t; P/p
1032
1016
14
16
a. Draw the appearance of the chromosome(s) carrying these genes at pachytene in the unusual
T/t; P/p plant. Indicate positions of the T, t, P, and p alleles in your drawing.
b. Explain very briefly the origin of the classes of progeny having 14 and 16 members.
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5) (15 points) Identify each of the following equations and its relevance to population genetics,
including an explanation of all parameters. Indicate as appropriate any assumptions made by these
expressions regarding the number of alleles present at any locus or variable site being studied. (3 points
each)
a. p' = p2 + 1/2(2pq)
The expected frequency of an allele following one generation of random mating (p') equals the
initial frequency of homozygous genotypes for that allele in the population (p2) plus half the
frequency of heterozygous genotypes (2pq; assumes that only two alleles are present in the
population).
b. D’ = D/Dmax where D = gABgab - gAbgaB and Dmax = lower value of p1 q2 or p2 q1
D’ is a standardized measure of linkage disequilibrium between two loci or variable SNP sites that
varies from 0 (no disequilibrium) to 1 (maximum disequilibrium). D is an unstandardized
measure of linkage disequilibrium. p1 = frequency of allele A at the first site/locus, p2 = frequency of
allele a at the first site/locus, q1 = frequency of allele B at the second site/locus, q2 = frequency of
allele b at the second site/locus. g terms are the gametic frequencies of haplotypes AB, ab, Ab and
aB as indicated by the subscript. Dmax is the maximum level of disequilibrium possible for the
population with the given allelic frequencies. The equation assumes two allelic forms at each
locus/site in the population.
c. Rate of Evolution =Rate of Input X Rate of Loss = (2N)µ1/2N = µ
T
long-term
of neutral evolution of a locus or protein. Rate of input of neutral
mutations is twice the inbreeding effective size (N) of the population times the neutral mutation
rate per locus. The rate of loss of alleles is 1/ 2N. The N terms cancel, so the long-term rate of
neutral evolution equals the rate of mutation to neutral alleles.
d. dn = do(1-2m)n
ifference in frequency of an allele between two populations at generation n (dn) equals the
difference in frequency at generation 1 (do) times 1 minus 2m to the nth power, where m is the
portion of each population that migrates to the other one each generation. The expression
assumes that m is symmetrical and constant across generations.
e. FST = (HT - HS)/HT
FST is the standardized variance in allelic diversity (varies from 0 to 1) between two or more demes
(= subpopulations) of a population. Heterozygosity for the total population (HT) equals 1 minus
the sum of squared allelic frequencies measured for the population as a whole. Heterozygosity for
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subpopulations is the average of 1 minus the sum of squared allelic frequencies calculated for each
subpopulation separately. FST measures the interaction between gene flow between subpopulations
(lowers FST) and genetic drift within subpopulations (raises FST). (Heterozygosities may be
calculated also as the sum of all heterozygote [2pq] terms for all pairs of alleles in a population.)
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6) (15 points) Identify each of the following equations and its relevance to quantitative genetics,
including an explanation of all parameters. Indicate as appropriate any assumptions made by these
expressions regarding the number of loci or alleles present at any locus being studied. (3 points each)
a. s2 = [(x1- µ)2 + (x2-µ)2 + … + (xn- µ)2]/n
The variance (s2) of a phenotypic trait in a population is calculated as the average squared
deviation of each individual phenotype (x1, x2 . . . xn) from the population mean (µ), where n =
number of individuals in the population.
b. σ2p = σ2a + σ2d + σ2i + σ2e
Fisher's analysis of phenotypic variance (σ 2p) into components including additive genetic variance
(σ 2a), dominance genetic variance (σ 2d), epistatic genetic variance (σ 2i) and environmental
variance (σ 2e, the variance not explained by the modeled genetic variation). At least two loci must
be considered to have epistatic variance.
c. Corr(Sib1,Sib2) = 1/2h2 +1/4σd2/σp2
The measured correlation coefficient between siblings for a phenotype (left term of equation)
equals half the narrow-sense heritability (h2 , ratio of additive genetic variance to total phenotypic
variance) plus one quarter of the ratio of the dominance genetic variance (σ d2) to the total
phenotypic variance (σ p2). (Results may be compared to correlation coefficient between parents
and offspring to partition genetic variance into additive and dominance components.)
d. aA = p(WAA-W) + q(WAa-W)
The average excess for fitness of allele A in a population (aA) equals the probability that a gamete
carrying A will be fertilized by another A gamete (p) times the genotypic deviation for fitness of
the resulting genotype (AA) plus the probability of fertilization by an a gamete (q) times the
genotypic deviation of the resulting Aa genotype. WAA = average fitness of AA genotype; WAa =
average fitness of Aa genotype; W = average fitness of the population. The expression assumes two
alleles (A and a) at the locus being studied.
. Δp = paA/W
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The expected change of frequency of allele A caused by selection (Δp) following a generation in
which the initial frequency of A is p, the average excess for fitness of A is aA, and the average
fitness of the population is W.
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7) (12 points) The accompanying figure is a haplotype tree constructed from sequences of homologous
protein-coding genes from 10 primate species. Branches on the tree are designated by letters (A-R).
Numbers on the branches are the inferred dN/dS values.
a. (4 points) Identify and describe the methodological principle used to construct a haplotype tree
(as shown) from haplotype data and to identify the substitutions occurring on each branch.
Parsimony - Find the tree that requires the smallest total number of substitutions to explain the
observed haplotypic variation.
b. (2 points) Define the terms dN and dS.
dN - the number of nonsynonymous substitutions per nonsynonymous site inferred for a branch
dS - the number of synonymous substitutions per synonymous site inferred for a branch
(A nonsynonymous base substitution causes an amino acid substitution in the encoded protein; a
synonymous substitution does not cause an amino acid substitution in the encoded protein.)
c. (2 points) Considering the tree as a whole, what is the most prevalent consequence of natural
selection with respect to evolution of the encoded protein? What data support this conclusion?
Selection mainly acts to conserve the amino-acid sequence of the protein because most branches
have a higher rate of synonymous than nonsynonymous substitution (dN/dS < 1).
d. (2 points) Which branches contain the strongest evidence for selectively-driven amino-acid
substitutions in the protein?
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H and M
e. (2 points) Which single branch would be the main focus of attention for someone looking for
mutations whose reversal is likely to be associated with genetic disease in humans? Why?
H, because selectively-driven amino-acid substitutions are indicated for this branch (dN/dS > 1),
and it is ancestral to humans.
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8) (8 points) Match the organism in the first column with the concept that was illustrated in lab
using that organism (in the second column). Choose all concepts that apply to each organism (some
may have more than one answer).
____H____
onion
____A____
corn pollen
___E, F____ Drosophila
___I, C____ Brassica rapa
___C, D___
humans
A. Mendel’s first law
B. Mendel’s second law
C. polygenic traits
D. Hardy-Weinberg equilibrium
E. chromosomal aberration
F. sex linkage
G. meiosis
H. mitosis
I. artificial selection
J. gene flow
9) (4 points) In the HIV computer lab, we were testing the hypothesis that the presence of an SI
mutation in more than half of the HIV sequences present in an HIV+ patient is associated with a
severely compromised immune system.
a. What data from your chosen subject did you examine to test the hypothesis?
We looked at the HIV sequences present from the last visit of a given patient.
b. What did the ClustalW program do? Describe how using ClustalW was important for testing the
hypothesis.
ClustalW aligned all of the HIV sequences, so it was easy to find the amino acid residue present at
the site of interest (usually position 306) for determining whether or not the SI mutation was
present.
10) (2 points) In general, did the FST values you calculated in the gene flow experiment with T. saxatilis
indicate that there was a lot of gene flow among the grasshopper subpopulations, or very little gene
flow?
a lot of gene flow
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11) (10 points) Identify by name the concept corresponding to each of the following statements. (2
points each)
a. An evolutionary lineage that maintains its cohesiveness over time because it is a reproductive
community capable of exchanging gametes and/or an ecological community sharing a derived
adaptation or adaptations needed for reproduction.
cohesion species concept or Templeton's species concept
b. “. . . all our plants and animals have descended from some one form into which life was first
breathed.”
common descent (Darwin's theory of common descent or Darwin's theory of descent with
modification)
c. Past geological events can be explained using laws of physics and chemistry that have remained
constant since the origin of the earth.
uniformitarianism
d. Formation of a new species by hybridizing two different species followed by endoreduplication
giving complete copies of the diploid genomes of each parent species in the genome of the new
species.
allotetraploidy or allopolyploidy
e. The synthesis of Darwinism and the chromosomal theory of inheritance.
neo-Darwinism