Introduction to Evolution
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Course Introduction
Introduction to Evolution offers students a comprehensive overview of the fundamental principles of evolutionary biology. The course explores the history of evolutionary thought, the mechanisms that drive evolution such as natural selection, genetic drift, mutation, and gene flow, and the evidence supporting evolutionary theory from fields including genetics, paleontology, and comparative anatomy. Students will also examine how evolution shapes the biodiversity on Earth and influences the adaptation and survival of species over time. By integrating modern research and case studies, the course prepares students to critically engage with current issues in evolutionary science and understand the ongoing impact of evolution on biology and society.
Recommended Textbook
Evolutionary Analysis 5th Edition by Jon C. Herron
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Chapter 1: A Case for Evolutionary Thinking: Understanding HIV
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Q1) What viral coat protein typically binds first to the CD4 receptor on helper T cells?
Answer: gp120
Q2) Explain the mechanism HIV uses to avoid destruction by antibodies present in the human immune system.
Answer: The virus is constantly mutating its surface proteins,and these frequent changes in epitopes on the viral surface prevent the host cell from being able to recognize the virus over time.
Q3) In what region of the world is the incidence of infection with HIV highest?
Answer: Sub-Saharan Africa
Q4) Originally,HIV was thought to be restricted to transmission during homosexual contact between gay men.List other ways in which HIV is currently known to be transmitted.
Answer: HIV can be transmitted by heterosexual sex,oral sex,needle sharing,transfusion with contaminated blood products,other unsafe medical procedures,childbirth and breast-feeding.
Q5) What does the acronym AIDS stand for?
Answer: Acquired Immune Deficiency Syndrome
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Chapter 2: The Pattern of Evolution
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Q1) What are structural homologies?
Answer: Anatomical features that show an underlying structural similarity even though their superficial structure is different,and that provide evidence of a shared common ancestry.
Q2) The radioactive isotope ________ has a half-life of 5,730 years,and has an effective dating range of 100 to 100,000 years.
Answer: Carbon-14
Q3) The coccyx,a tiny tailbone found in humans,is believed to be a ________ structure. A) terminated B) vestigial C) rudimentary D) redundant
Answer: B
Q4) What are two features that characterize processed pseudogenes,and how do these arise?
Answer: Processed pseudogenes contain no introns or promoters,and arise when processed mRNAs are accidentally reverse transcribed to DNA by reverse transcriptase,and then inserted back in the genome at alternate locations.
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4
Chapter 3: Evolution by Natural Selection
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Q1) Natural selection ________.
A) works on populations, but its long-term effect is rendered on individuals
B) works on individuals, but its long-term effect is rendered on populations
C) can work only on populations of genetically identical individuals
D) works regardless of the amount of genetic variability in populations
Answer: B
Q2) Darwin developed his theory of natural selection despite having an incomplete and/or inaccurate knowledge base from which to work.Which of the following were problems for Darwin?
A) the source of variations in populations
B) an understanding of inheritance patterns from one generation to the next
C) The accepted age of the Earth was far too young to allow for the gradual changes Darwin envisioned.
D) All of the above.
Answer: D
Q3) Before Mendel's work was rediscovered,some argued that natural selection would not work because favorable traits would merge into existing traits over time and become lost.This hypothesis is known as ________.[two words]
Answer: blending inheritance
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Chapter 4: Estimating Evolutionary Trees
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Q1) Explain what parsimony is,and why it is preferred in constructing phylogenetic trees.
Q2) Which of the following phylogeny inference tools is the best at reconstructing the most accurate phylogenetic trees?
A) parsimony
B) maximum likelihood
C) Bayesian inference
D) All of these methods have pros and cons.
Q3) In constructing phylogenetic trees,it is useful to think of monophyletic groups as being defined by ________.
A) apomorphies
B) plesiomorphies
C) synapomorphies
D) clades
Q4) Your textbook states that under optimal conditions,all of the methods discussed (parsimony,maximum likelihood,neighbor joining,and Bayesian inference reveal the true branching pattern of the phylogeny in question with accuracies approaching 100%.However,real phylogenies are rarely inferred under ideal circumstances.Explain,using examples,why this is so.
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Chapter 5: Variation Among Individuals
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Q1) In the mutation accumulation experiments of Dee Denvers and colleagues (2004)with Caenorhabditis elegans,deleterious mutations were observed to accumulate at a slow but steady rate when the populations were grown in a benign environment,with optimal temperature and humidity,minimal crowding of individuals,abundant food,and no predators or parasites.Control lines grown under normal conditions did not accumulate mutations at the same rate.After 240 generations,experimental lines that had accumulated substantial mutations were removed from the benign environment and these lines were propagated.Explain the results once the recovery lines were established,and how this experiment demonstrates the significance of natural selection in the evolutionary process.
Q2) What is the term used to describe the smallest possible mutation in a DNA strand,which involves only one base?
Q3) Genes that are duplicated within a genome and later diverge in function,such as the RNASE1 and RNASE1B genes in douc langur monkeys,are described as ________.
A) duplicated genes
B) orthologous genes
C) homologous genes
D) paralogous genes
E) derived genes
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Page 7
Chapter 6: Mendelian Genetics in Populations I: Selection and Mutation
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Q1) In the study of Gigord and colleagues using Elderflower orchids,the allele frequencies of yellow and purple flowers varied such that when the yellow allele started to become rare,the reproductive success of purple flowers decreased and the reproductive success of yellow-flowered individuals increased in a process known as ________. A) overdominance
B) frequency-dependent selection
C) underdominance
D) Hardy-Weinberg stabilization
E) frequency depression
Q2) A hypothetical population has two alleles for a gene: A and a.In a random sample of 100 individuals,20 are homozygous for a,20 are homozygous for A,and 60 are heterozygous.What is the frequency of A?
A) 20%
B) 25%
C) 50%
D) 60%
E) 80%
Q3) A group of interbreeding individuals and their offspring is known as a(n)________.
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Chapter 7: Mendelian Genetics in Populations II:
Drift, & Nonrandom Mating
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Q1) The most common form of nonrandom mating is inbreeding.Despite the fact that inbreeding will not change allelic frequencies,it can still have a significant impact on the evolution of a lineage.Explain,using examples,why this is so.
Q2) With enough time and in the absence of other evolutionary mechanisms,genetic drift will ________.
A) reduce the genetic variation in a population
B) increase the genetic variation in a population
C) have no effect on the genetic variation of a population
D) None of the above.
Q3) Suppose a founding population carries an allelic frequency not typical of the original population.Which of the following effects would most likely lead to homogenization?
A) genetic drift within the founding population
B) random mating within the founding population
C) no mutations within either population
D) migration between the original and founding populations
E) None of the above.
Q4) The survival and fertility rates of the offspring of related individuals are commonly reduced.This is known as ________.[two words]
Page 9
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Chapter 8: Evolution at Multiple Loci: Linkage and Sex
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Q1) When genotypes at one locus of a chromosome are independent of genotypes at another locus of the same chromosome,the two loci are ________.
A) in linkage equilibrium
B) in linkage disequilibrium
C) nonrandomly associated
D) None of the above.
Q2) The creation of new combinations of alleles,as a consequence of sexual reproduction with meiosis,is called ________.
A) genetic recombination
B) outcrossing
C) genetic drift
D) linkage disequilibrium
Q3) The explanation for the accumulation of deleterious alleles in asexual populations over time,with the resulting genetic load,is known as ________.[two words]
Q4) In cases where a perpetual "arms race" occurs between biological antagonists,such as parasites and their hosts,sex is favored because it reduces linkage disequilibrium by recreating missing genotypes in an oscillating fashion.This hypothesis is called the ________ [two words] hypothesis.
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Page 10
Chapter 9: Evolution at Multiple Loci: Quantitative Genetics
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Q1) ________ selection and ________ selection tend to reduce the amount of variation in a population,whereas ________ selection tends to increase the amount of variation in a population.
Q2) It becomes possible to predict evolutionary changes in a population after we have measured two attributes affecting the population in question.What two measures allow us to make such predictions?
Q3) ________ refers to the fraction of the total variation in a trait that is due to variation in genes.
Q4) Estimating heritability using twin studies has been useful for certain human phenotypes,such as general cognitive abilities.Explain the logic behind this,and how such studies are performed.
Q5) Three distinct modes of selection have been proposed and studied in natural populations.Each mode is different in its effects on the mean value and distribution of phenotypes.Compare and contrast each of these three modes.
Q6) Continuously variable traits typically have a(n)________,[two words] otherwise known as a "bell-curve."
Q7) Compare and contrast qualitative traits/genetics with quantitative traits/genetics.
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Chapter 10: Studying Adaptation: Evolutionary Analysis of
Form and Function
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Q1) In the Kotukutuku plant,fuchsia excortiata,why do pollinated flowers remain attached to the plant for several days after pollination occurs and nectar is no longer produced?
Q2) To demonstrate the response of several Daphnia genotypes across a wide range of environments,Luc De Meester (1996)measured the change in phototactic behavior of Daphnia sampled from lakes that contained different numbers of predatory fish.Some genotypes altered their behavior in the presence versus absence of fish.The variation in response is termed ________.
A) phenotype-by-environment interaction
B) genotype-by-environment interaction
C) induced response interaction
D) reactive response interaction
Q3) Huey and colleagues (1989)performed experiments to examine thermoregulation in garter snakes.Explain the factors that were examined in their experiments,how the temperature of the snakes was monitored,and the specific details of how the snakes can regulate their temperature by selective movements.
Q4) In their experiments with the flowers of Begonia involucrate,Agren and Schemske (1991)observed that there was a trade-off between what two characteristics?
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Chapter 11: Sexual Selection
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Q1) Which of the following statements is true regarding the involvement of sexual selection on male function (pollen donation)leading to sexual dimorphism in flowers?
A) Female flowers typically receive far more pollen than is needed to fertilize their seeds.
B) Delph and colleagues (1996) found that out of 42 animal-pollinated plant species, 29% of females had the largest reproductive parts, but males had the largest perianths.
C) Studying wild radishes, Stanton and colleagues (1996) found that reproductive success through pollen donation was limited by pollinator visits, whereas reproductive success through seed production was not.
D) All of the above statements are true.
Q2) Natural selection would appear to act against long tails in male red-collared widowbirds,given that longer tails reduce body condition over the mating season.Based on the experiments of Pryke and Andersson (2005),why do long tails appear to be favored despite their obvious disadvantage?
Q3) In general,mothers typically make a larger parental investment in each offspring than males do.What is meant by the term parental investment?
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Chapter 12: The Evolution of Social Behavior
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Q1) A measure of the reproductive fitness of genetic relatives resulting from the actions of an individual is called ________.
A) direct fitness
B) indirect fitness
C) inclusive fitness
D) kin selection
Q2) Social behavior in which the "actor" benefits at the expense of the "recipient" is termed ________.
Q3) Which hypothesis has been proposed to explain the evolution of eusociality?
A) the haplodiploidy hypothesis
B) the Monogamy hypothesis
C) the ecology/life history hypothesis
D) All of the above.
Q4) A measure of the reproductive fitness of an individual without the help of others is known as ________.
A) direct fitness
B) indirect fitness
C) inclusive fitness
D) kin selection
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Chapter 13: Aging and Other Life-History Characters
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Q1) The theory of aging that posits that aging is caused by irreparable damage to the cells,tissues,and organs of an organism brought about by such things as errors in protein synthesis and the accumulation of toxic metabolites is the ________.
A) theory of senescence
B) rate of living theory of aging
C) evolutionary theory of aging
D) particulate theory of aging
Q2) Some researchers argue that short telomeres actually facilitate a longer life span in mammals.The reasoning for this argument includes the idea that ________.
A) the activity of telomerase expression the enzyme that can restore lost bits of telomeres is repressed
B) a reduction in the telomere size for every DNA replication event can serve as an accurate counting mechanism for the number of times a cell has divided
C) reducing the number of divisions a cell will go through will also reduce the likelihood of mutation events occurring in the cell's DNA
D) All of the above are included in this idea.
Q3) Alleles that influence more than one trait are referred to as ________.
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Page 15
Chapter 14: Evolution and Human Health
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Q1) Your text discusses Paul Ewald's studies of how evolutionary trade-offs might have influenced the evolution of virulence in human pathogens.One thing your text did not mention is disease caused by food-borne pathogens such as Salmonella,Campylobacter,and Escherichia coli O157:H7.In industrialized nations,fresh food is often shipped in bulk quantities for thousands of miles from where it is grown.This means that food-borne outbreaks can sicken large numbers of people,and also may force the costly recall of large amounts of contaminated food,over wide regions.This is a relatively recent development; for almost all of human history,fresh food had to be eaten close to where it was produced.Apply Ewald's ideas to food-borne diseases.Can we make any predictions of future trends in virulence? Are there steps we can take,specifically based on evolutionary biology,to decrease the incidence and severity of food-borne disease?
Q2) A group of lineages such as viral strains that all descend from a common ancestor makes up a ________.
Q3) Your text discusses one of the most well-known examples in which human populations have evolved in response to selection imposed by changes in lifestyle.Specifically,this example has to do with a change toward the life-long production of an enzyme that allows humans to digest something our ancestors normally would have ingested only as infants.What is the name of this enzyme?
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Page 16
Chapter 15: Phylogenomics and the Molecular Basis of Adaptation
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Q1) How does a gene tree differ from a species tree?
A) A gene tree shows the relationships among all the genes in a species genome, whereas a species tree shows the relationships among species.
B) A gene tree is based on gene sequences, whereas a species tree is based on morphological features of each species.
C) A gene tree is a phylogeny of individual genes, and can include multiple genes from a single species and/or samples of the same gene from multiple species; in a species tree, each species is represented by only a single branch.
D) A gene tree is a subcategory of species tree, in which the data used to create the tree comes from gene sequences.
Q2) Describe how mobile genetic organisms function,how they affect host organisms,and the mechanisms that host organisms possess to interact with mobile genetic elements.
Q3) Briefly describe the difference between adaptation from new mutation and adaptation from standing genetic variation in natural populations.
Q4) Briefly describe the escape from adaptive conflict hypothesis for the preservation of duplicate genes.
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Chapter 16: Mechanisms of Speciation
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Q1) Geographic isolation of populations can generally come about in two ways.What are they?
Q2) Your textbook authors make the claim that "sympatric species with matching chromosome numbers are rare." Why is this?
A) because allopatric speciation is far more common
B) because sympatric speciation has only been hypothesized but not documented C) because coexisting populations need a boundary to gene flow before divergence can occur, and differences in chromosome numbers provide this D) because macroevolution is just a theory
Q3) Species divergence due to mating behavior and sexual selection,as has been documented in the Hawaiian crickets,is termed ________.[two words]
Q4) The species concept that relies most heavily on the criterion that species are evolutionarily independent units that are isolated by gene flow is ________.
A) the morphospecies concept
B) the phylogenetic species concept
C) the biological species concept
D) This criterion is common to all of these concepts.
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Chapter 17: The Origins of Life and Precambrian Evolution
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Q1) Carl Woese has controversially proposed that all three domains of life evolved from a(n)________.
A) single last unique common ancestor (LUCA)
B) extremophilic archaean
C) fusion of a bacterium with an archaean
D) universal gene-exchange pool
E) very large virus
Q2) James Ferris discovered that clay minerals are capable of ________.
A) joining pyrimidines to simple sugars
B) catalyzing the polymerization of activated nucleotides
C) breaking down biomolecules to release energy
D) activating nucleotides by adding phosphate groups
E) forming microscopic spheres from short polymers of amino acids
Q3) The organisms formerly classified in the Kingdom Protista ________.
A) all contain chloroplasts
B) form a single monophyletic group
C) include the last universal common ancestor (LUCA) of life
D) are scattered throughout all branches of the eukaryote family tree
E) have a fossil record extending back 3.4 million years
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Chapter 18: Evolution and the Fossil Record
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Q1) We may be living in the middle of the sixth great mass extinction,as human activity directly and indirectly drives species to extinction.How might the study of past mass extinctions show us how the current extinction might play out? Can paleontology give us any information that might help us mitigate the effects of the current extinction?
Q2) Comparing DNA sequences from living taxa and calibrating their rates of change with at least one well-dated fossil allows scientists to create time-calibrated trees with minimum and maximum age estimates for all branch points.Such studies are called ________ [two words] studies.
Q3) Rock layers right at the K-Pg boundary have enriched concentrations of the element iridium.This is significant for understanding the mass extinction that happened at the time,because ________.
A) iridium is toxic to life and could have killed off many species
B) iridium is very rare in the Earth's crust but relatively common in meteorites
C) iridium forms under conditions of extreme shock and heat
D) iridium would have caused an episode of severe acid rain
E) iridium-rich dust is particularly effective at blocking incoming solar radiation
Q4) An exceptionally rich fossil deposit is known as a(n)________.
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Chapter 19: Development and Evolution
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Q1) Despite a great deal of variation across the animal kingdom,Hox genes tend to appear along a chromosome or chromosomes in the same order that they are expressed in along the anteroposterior axis of an embryo.This pattern of Hox gene expression is called the ________.[four words]
Q2) South American anteaters have no teeth and a long sticky tongue; they rip open anthills and termite mounds and capture insects with their tongues.An Australian marsupial known as the numbat (Myrmecobius fasciatus)is not closely related to anteaters,but it too has highly reduced teeth and a long sticky tongue,and it feeds by ripping open termite burrows and lapping the insects up.Such similarities between species that are not inherited from a common ancestor are known as ________.
Q3) Unlike all other honeybees,worker bees in the South African subspecies Apis mellifera capensis can lay eggs that develop asexually into queens,which makes it possible for them to "nest parasitize" other subspecies of honeybees.This is due to ________.
A) the effects of many genes integrated together (epistasis)
B) a homeotic mutation of a gene in the Hox cluster
C) the appearance of new genes that are paralogous with Hox genes
D) a deletion of nine nucleotides in the gemini transcription factor gene
E) horizontal gene transfer from a distantly related insect species
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Chapter 20: Human Evolution
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Q1) "Robust australopithecines," now classified in the genus Paranthropus,are distinctive as compared to other hominins because of their ________.
A) great height
B) unusually large brains
C) knuckle-walking ability
D) cave paintings and other artwork
E) huge teeth, faces, jaws, and jaw muscles
Q2) All of the following traits are shared by all great apes,except ________.
A) increased flexibility of the wrist and thumb
B) spoken language
C) absence of a tail
D) increased flexibility of hips and ankles
E) relatively large brains
Q3) The peoples of Africa have often been negatively stereotyped by Europeans and Americans as "primitive" and "less advanced" than other peoples.Recent genetic analyses show that Africans make up the earliest branches of the human family tree.But do these two statements mean the same thing? Does genetic research imply anything about the relative "advancement" (or lack thereof)of different human groups?
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