Name_____________________
BZ508 - Exam 1 – Fall 05
50 pts Total
(1 pt each) Match the letter from THE LIST with the following statements:
_e_1. The “watch-maker” metaphor is used to support this form of creationism
_j_2. A group of species that share a common ancestor
_i_3. Proposed transformational evolution and inheritance of acquired characteristics
_c_4. Father of taxonomy
_k_5. Stochastic process that makes it difficult to reconstruct phylogeny during an
adaptive radiation
_h_6. Independent evolution of the same characteristic among taxa that don’t share an
immediate common ancestor
_f_7. Variation in this trait allows amphibians to adapt to aquatic habitats
_r_8. Uniquely derived character state
_j_9. Shared derived character state
_p_10. Philosophy that the simplest explanation is probably correct one
_o_11. Model of nucleotide sequence evolution
_a_12. Different forms of a gene
xxx13. Variant sequence of a gene BAD QUESTION; NOT COUNTED
_u_14. A coherent body of interconnected statements that explain a variety of
observations
s or m15. Origin of new species
THE LIST
a. allele
b. Pauley
c. Linneaus
d. synapomorphy
e. intelligent design
f. developmental timing
g. flat earth
h. convergent evolution
i. Lamarck
j. monophyletic group
k. incomplete or lineage sorting
l. polyphyletic group
m. macroevolution
n. hypothesis
o. jukes-cantor model
p. parsimony
q. maximum likelihood
r. autapomorphy
s. Darwin
t. microevolution
u. scientific theory
(1 pt each) Multiple Choice
1. What sources contribute to variation in the phenotypes of organisms?
a. environmental factors
c. nervous energy
b. genetic differences
d. both a and b
2. True or False. Assuming that only bifurcations occur in a tree, there are 4 possible
ways to draw an unrooted tree to show evolutionary relationships among 3 taxa.
a. true
b. false
3. Darwin proposed that the evolution of new species _______.
a. occurs gradually as a result of natural selection
b. occurs suddenly as a result of orthogenesis
c. only requires mutation
d. is a directed process that anticipates future environmental change
4. According to binomial nomenclature, which shows a correct hierarchical order from
the most inconclusive taxon to the more exclusive taxon?
a. phylum, order, class, species, genus
b. class, order, family, genus
c. family, species phylum
d. species, genus
5. Originated the idea that organisms were arranged hierarchically according to a “Scale
of Nature”, with humans on top.
a. Darwin
c. Sharkey
b. Lemarck
d. Aristotle
6. True or False. Adaptation is an evolutionary process that requires genetic change.
a. True
b. False
7. The Scopes Trial concerned
a. the teaching of evolution in a public Tennessee classroom
b. disclaimers on Louisiana textbooks
c. equal time for creationism in Louisiana science classrooms
d. legal battle over mouthwash
8. According to the idea of anti-elitism, why do many Americans respect people that are
expert in sports, entertainment, and finance but disrespect scientists and teachers?
a. because scientists and teachers are pure evil
b. because entertainers do not prompt Americans to think deeply about
issues that threaten religous beliefs
c. because knowledge of science and nature is not as important as the World
Series, the Oscars, and casino gambling.
d. because Americans are as shallow as the new I-POD is thin.
9. What is the difference between phylogenetic analysis and taxonomy?
a. there is no difference; both attempt to classify organisms hierarchically
b. taxonomy is based upon the idea of common decent
c. phylogenetics is the study of evolutionary relationships among species
d. taxonomy is a form of systematics; phylogenetics is not
10. Why is homoplasy a problem in DNA sequence data?
a. because transversional substitutions occur often
b. because the rate of transversional substitution is higher than the rate of
transitional substitution
c. because there are only 4 character states for each nucleotide position
d. because DNA sequence variation is very low in typical populations
11. If 25 nucleotide substitutions are observed between two DNA sequences, how many
substitutions will be estimated after applying the Juke-Cantor model of sequence
evolution?
a. < 25
c. = 25
b. > 25
d. 250
12. Natural selection is best defined as
a. Differential survival and reproduction among individuals of a population
that vary in genetically-based traits
b. Survival of the fittest
c. Common descent with modification
d. Evolution with purpose
13. Which of the following is not an example of homology?
a. Human hand and seal fin
b. Butterfly wing and bird wing
c. Human brain and chimp brain
d. Human prolactin gene and chimp prolactin gene
14. Which of the following statements is true?
a. maximum likelihood will always do the best job of resolving evolutionary relationships
among species
b. parsimony will always do the best job of resolving evolutionary relationships among
species
c. maximum likelihood analysis incorporates a model for character evolution
d. parsimony analysis incorporates a model for character evolution
15. What does a bootstrap percentage of 70% mean for a given clade (monophyletic
group) within a phylogenetic tree?
a. that there is a 70% probability that maximum likelihood will do a better job of
reconstructing evolutionary relationships than parsimony
b. there is a 70% probability that the corresponding clade shows true evolutionary
relationships among species when the data are re-sampled with replacement
c. the corresponding clade is observed in 70% of the trees that are re-generated by
re-sampling the original dataset with replacement
d. none of the above
(5 pts) Answer the following question pertaining to the figure below
1
2
3
4
5
Large body size
Small body size
1. How many monophyletic groups? 4
2. You are interested in the evolution of body size among these 5 related species of frog.
The phylogenetic tree shows the true evolutionary relationships among the species, and
also shows the body size of each species (large vs small). Please show/describe how body
size evolves on the tree for each of the two following conditions:
(a) the ancestral condition is small body size
(b) the ancestral condition is large body size.
2 CHANGES
2 CHANGES
(5 points each) Answer 3 of the following 4 Short Essay Questions/Problems
1. What were the two major ideas about evolution that were contributed by Darwin?
Compare these ideas with Lamarck’s evolutionary ideas.
Darwin contributed the idea of evolution by common descent and the idea of
adaptation and evolution by natural selection. The 1st idea suggests that species
originate from ancestral species and thus all organisms share common ancestry. The
2nd idea suggests that adaptation and evolution of species occurs via the mechanism
of natural selection. Lamarck’s idea of Transformational Evolution is similar to
Darwin’s idea of Common Decent: Larmack proposed that organisms are connected
through transformation and one species type evolves into another type over long
periods of time….this is similar to Darwin who proposed that organisms are
connected by common ancestry and ancestral species give rise to new species via
natural selection if given enough time. Lamarck’s idea of inheritance of acquired
traits is similar to Darwin’s idea of natural selection because both emphasize the
importance of variation of traits within species and both provide a mechanism by
which species adapt to their environment.
What did Darwin propose as a mechanism for evolution? According to Darwin’s
gradualistic model of evolution, what is the relationship among character similarity, time,
and relatedness of species?
Darwin proposed natural selection as a mechanism for evolution. He believed that
natural selection brought about gradual changes in the characteristics of species
over time. He proposed that newly derived lineages from an ancestral stock or
population would initially share many characteristics, but after a sufficient amount
of time they would evolve many character differences. Thus, species that share
many similarities in characteristics are more closely related in an evolutionary sense
because they probably arose from a common ancestor in the recent past. In
contrast, species that share fewer similarities in characteristics presumably shared a
common ancestor in the more distant past.
List and refute 3 creationist arguments against evolution.
See Chapter 22 in your Text Book.
How does Natural Selection bring about evolution? Explain how this mechanism works.
Natural selection is a process of differential survival and reproduction that operates
within populations. Individuals of a population are variable for traits that may
affect the probability of survival and reproduction. Conditions of the environment,
which are constantly changing, favor some trait values over others. Individuals with
trait values that confer a higher probability of survival and reproduction will be
more likely to mate and contribute offspring to the next generation. If the traits in
question have a genetic basis, the population will evolve in the direction of the trait
values of the selected individuals.
The mean rate of nucleotide substitution between two sequences that are sampled from
two different species is defined as:
r = K / 2T=
Draw a branching network/tree, label the network/tree, and state verbally what 2T
represents?
Ancestral Sequence
T
Sequence 1
T
Sequence 2
2T = Total
amount of time
since divergence
from common
ancestral
sequence
You are interested in the convergent evolution of eyelessness between 2 closely related
species of fish that are isolated among different cave systems in Kentucky. You decide to
focus your attention on the gene Pax 6, which is known to be a master regulatory gene of
eye development in metazoans; in other words, Pax 6 tends to commit cells during
development in metazoans towards photoreceptor like cells. Propose a hypothesis that
can be tested by examining Pax 6 nucleotide sequence, and describe how the data will be
analyzed to test the hypothesis. A limited amount of embellishment is ok.
Hypothesis: Eyelessness is a derived trait that evolved independently from unrelated
species with eyes. This hypothesis could be tested by building a phylogenetic tree for
multiple, related species of fish that either have eyes or do not have eyes. If the
eyeless species form a monophyletic group within the overall phylogenetic tree (to
the exclusion of the species with eyes), this would suggest that all eyeless forms arose
from a single common ancestor and not independently from different species with
eyes. Although the question required that the phylogenetic tree be based upon
character differences identified from Pax 6 sequences, this might not be such a good
idea if convergent nucleotide changes were selected among eyeless species. In other
words, if the same convergent changes were selected in the independent evolution of
eyelessness, and these changes provided information for building a phylogenetic
tree, this would bias the analysis for grouping the eyeless species together as a
monophyletic group even though they might have evolved independently. In
building phylogenetic trees, it is important to choose characters whose evolution is
presumably neutral and not biased by natural selection or homoplasy.
Is it possible for two different genes to imply different phylogenetic relationships among
a group of species. What are the possible reasons for this?
One reason is lineage or allele sorting. This is a stochastic process whereby alleles at
some gene loci are passed from ancestral species to derived species in a way that
does not reflect the process of speciation. This is especially likely in rapidly radiating
species groups. Another possibility is the differential transmission of alleles at one
gene locus but not another gene locus via hybridization (mtDNA vs nuclear DNA) or
by horizontal gene transfer, which is known to occur somewhat frequently in
prokaryotes.