Deck 9: From Genes to Traits: the Evolution of Genetic Networks and Development

Question 1

Some evolutionary biologists argue that, overall, regulatory mutations are more likely to result in adaptation than changes in the protein-coding sequence of genes. Considering the logic underlying their argument, in which case below would this expectation not apply to a particular gene involved in adaptation?

A) The gene is involved in multiple functions.
B) The gene is involved in only one function.
C) The gene is expressed in different tissues.
D) The protein encoded by the gene performs an important function.

Answer 1

B

Question 2

Is the fly eye homologous to the mouse eye, or is it convergent?

A) homologous because of developmental genes that regulate the complex eye are
B) convergent because the fly eye is a compound eye and the mouse eye is a camera eye
C) both, depending on the level of development examined
D) neither; the two types of eyes cannot be compared

Answer 2

C

Question 3

Which of the following statements is accurate regarding antagonistic pleiotropy?

A) The net fitness effect of an allele experiencing antagonistic pleiotropy may depend on the environment.
B) Alleles experiencing antagonistic pleiotropy should always be strongly selected against.
C) Antagonistic pleiotropy results when a trait is influenced by more than one gene.
D) none of the above

Answer 3

A

Question 4

The populations of the ray-finned teleost fish, Astyanax, that repeatedly colonized underground Mexican caves and evolved the same suite of derived traits in cave after cave is an example of

A) deep homology.
B) parallel evolution.
C) convergent evolution.
D) genetic drift.

Question 5

Placental mammals differ from marsupial mammals in that

A) they carry a developing fetus in a uterus.
B) they give birth to live young.
C) they lay eggs.
D) a and b

Question 6

In Lenski's experiments, the key to evolution of citrate feeding in
E) coli was the accidental duplication of the citT ______ together with the rnk _____.

A) gene; promotor
B) gene; gene
C) promotor; promotor
D) promotor; gene

Question 7

What does the following phylogeny suggest?

A) The bilaterian ancestor likely had a nervous system arranged like cnidarians.
B) The bilaterian ancestor may have had a diffuse net of nerves.
C) The evolution of a single nerve cord occurred in the common ancestor of all animals.
D) a and b
E) a, b, and c

Question 8

Which of the following is true of the complex eye?

A) It is an example of convergent evolution because of the borrowed crystallin genes that evolved independently.
B) It is an example of common ancestry because the development of all complex eyes in bilaterians is controlled by the same gene, Pax-6.
C) It is an example of deep homology because its growth and development in different lineages result from underlying genetic mechanisms that are inherited from a common ancestor.
D) a and b
E) a, b, and c

Question 9

What does the following phylogeny of animals suggest?

A) Dorsal-ventral patterning and a single nerve cord may have evolved in three independent lineages.
B) The common ancestor of invertebrates had a single nerve cord.
C) Arthropods have a unique dorsal-ventral pattern.
D) a and b
E) none of the above

Question 10

Why might Darwin disagree that bat wings and fly legs represent a homology?

A) because of the lack of genetic knowledge during his time
B) because flies are not vertebrates
C) because he could only recognize homology in the anatomy that he could see with the naked eye
D) all of the above

Question 11

Gene duplication

A) results in genes that are paralogs.
B) leads to functional redundancy.
C) can result in one of the copies gaining a new function.
D) all of the above

Question 12

The Engrailed (En) gene is an example of a(n)

A) paralog; it is crucial for defining the posterior portion of the limb bud in mice and for defining the leg disc in flies.
B) ortholog; it is crucial for defining the posterior portion of the limb bud in mice and for defining the leg disc in flies.
C) paralog; it is a homologous gene produced by gene duplication within the fly limb development pathway.
D) ortholog; it is a homologous gene produced by gene duplication within the fly limb development pathway.

Question 13

Snakes evolved about ____ million years ago, and their closest living relatives include ____.

A) 60; iguanas and monitor lizards
B) 0.1; iguanas and whiptail lizards
C) 150; iguanas and monitor lizards
D) 300; iguanas and crocodiles

Question 14

Which is the likely order of evolution of snake venom?
I. diversification of venom genes
II. duplication of defensin gene
III. single copy of defensin gene
IV. gene recruitment in venom gland

A) III - II - IV - I
B) III - II - I - IV
C) IV - II - III - I
D) IV - I - III - II

Question 15

What evidence suggests that c-opsins were present in the common ancestor of all living vertebrates?

A) All vertebrates carry c-opsin.
B) C-opsins have the same basic molecular shape in all vertebrates.
C) C-opsins have the same basic functional pathway in all vertebrates.
D) all of the above
E) none of the above

Question 16

How does the development of a mouse leg differ from the development of a fly leg?

A) In a mouse leg, the proximal structures develop first.
B) In a mouse leg, the gene Hh controls development.
C) In a fly leg, the proximal segments develop first.
D) In a fly leg, the gene Shh controls development.

Question 17

Which of the following represent(s) homologies?

A) the forelimb structure of vertebrate wings, hands, and flippers
B) the limb structure of bilaterians
C) Hox genes in mice and flies
D) a and b
E) a and c

Question 18

How does bat wing development differ from other tetrapod limbs?

A) The humerus forms first, followed by more distal structures.
B) The digits form first, followed by more proximal structures.
C) Increased expression of Bmp2 drives more cell division in developing digits.
D) Bat wing development does not differ from other tetrapod limbs; there is simple a gene that codes for longer digits.

Question 19

If you examine the phylogeny of animals, you would see that

A) eyes are not present in the common ancestor of all animals.
B) sponges and placozoans have no eyes.
C) eyes are found only within the eumetazoans.
D) all of the above
E) none of the above

Question 20

Which of the following statements accurately describes Hox genes?

A) They code for traits such as legs or wings in the developing embryo.
B) Their expression gives positional information to other genes.
C) They are transcription factors.
D) a and b
E) b and c

Question 21

Meganeura, which lived around 300 million years ago, was

A) a dragonfly-like insect.
B) the size of a seagull.
C) the size of modern insects.
D) a and b
E) a and c

Question 22

Which of the following was the earliest step in the evolution of the vertebrate eye lens?

A) A patch of tissue folds inward into a cup beneath unpigmented skin.
B) The cup, the eye, becomes spherical and evolves greater acuity.
C) Unpigmented skin above a cup of tissue becomes transparent and can focus an image.
D) Light-sensitive regions bulge outward to the sides of the head.

Question 23

Which of the following snakes does not produce venom?

A) garter snake
B) Australian inland taipan
C) eyelash viper
D) none of the above

Question 24

A bacterial spore

A) is an adaptation coded by a single gene.
B) is an adaptation coded by epistatic genes.
C) is a complex adaptation coded by a single gene.
D) is a complex adaption coded by a regulatory network of genes.

Question 25

Which statement is true regarding the evolution of crystallins?

A) They evolved through gene recruitment.
B) They evolved from promiscuous proteins.
C) They evolved from gene duplication.
D) a and c
E) a, b, and c

Question 26

Is the following statement true or false, and why? New adaptations do not evolve from scratch.

A) False; traits can always arise de novo.
B) False; some traits evolve from scratch, and some are modifications of previously existing traits.
C) True; new adaptations are modifications of previously existing traits.
D) none of the above

Question 27

How might complex adaptions evolve in bacteria?

A) Viruses can move genes from one individual to another.
B) Bacteria can exchange plasmid genes via sex pili.
C) Bacteria can take up exogenous DNA from their environment.
D) b and c
E) a, b, and c

Question 28

How do insects get oxygen?

A) through diffusion in their skin
B) through spiracles
C) through lungs
D) through gills

Question 29

Which of the following is not an example of convergent evolution on similar body plans?

A) placental mole and marsupial mole
B) bird wing and butterfly wing
C) anteater and numbat
D) bat forelimb structure and bird forelimb structure

Question 30

Tetrapods evolved from

A) aquatic invertebrate ancestors.
B) terrestrial invertebrate ancestors.
C) scratch.
D) a and b
E) none of the above

Question 31

Which of the following accurately describes the signal cascade in a typical gene regulatory network?

A) environmental signal triggers transcription factor; transcription factor binds cis-regulatory element; protein-coding gene activated
B) environmental signal binds cis-regulatory element; cis-regulatory element triggers transcription factor; protein-coding gene activated
C) environmental signal triggers expression of protein-coding gene; transcription factor binds cis-regulatory element; cis-regulatory element activated
D) none of the above

Question 32

Olfactory receptor evolution provides an example of

A) gene duplication; the 855 genes for olfactory receptors belong to the same "gene family."
B) gene recruitment; once duplicated, the genes for olfactory receptors likely diverged, taking on new functions.
C) promiscuous proteins; the genes duplicated after new functions arose.
D) a and b
E) a, b, and c

Question 33

The gene recruitment for venom production

A) evolved independently in each lineage of venomous snakes.
B) evolved in the ancestor of snakes.
C) evolved in the ancestor of snakes and their closest living relatives.
D) evolved in the ancestor of snakes and mammals.

Question 34

Which of the following statements about venom evolution is accurate?

A) The earliest venoms evolved after fangs and other parts of the venom delivery system.
B) The earliest venoms evolved before fangs and other parts of the venom delivery system.
C) All reptiles produce venom even if they do not have fangs or other components of the venom delivery system.
D) b and c

Question 35

Which of the following is an incorrect match between animal and eye type?

A) flatworms-light-sensitive spots
B) insects-compound eye
C) scallops-light-sensitive spots
D) cephalopods-camera eye

Question 36

Some evolutionary biologists argue that changes in the regulation of genes rather than changes in the coding sequence are more likely to be involved in adaptation. Which of the following statements forms part of the basis for this argument?

A) Coding sequence changes are constrained because most genes perform multiple functions.
B) Regulatory mutations are more likely to occur than coding sequence mutations.
C) Regulatory changes likely affect all processes that a gene is involved in.
D) all of the above

Question 37

In Näsvall's experiments, the purpose of the mutation to the HisA enzyme in Salmonella was to

A) create a promiscuous enzyme that could only synthesize histidine.
B) create a promiscuous enzyme with the ability to synthesize histidine and tryptophan.
C) create a paralog of a promiscuous enzyme.
D) simulate a gene duplication event.

Question 38

Why are there no gigantic insects alive today?

A) There is no niche for gigantic insects.
B) There are gigantic insects in remote regions of the tropics; we just have not discovered them.
C) The concentration of oxygen in the atmosphere is too low to make gigantic body size in insects efficient.
D) There is no evidence of gigantic insects in the past, so there can not be any alive today due to constraining evolution.

Question 39

The detoured nerve in giraffes results from

A) the imperfection in complex adaptations.
B) the nerves in aquatic vertebrate ancestors.
C) natural selection retooling the form and function of characters present in a population.
D) all of the above
E) none of the above

Question 40

Almost all mammals have seven cervical vertebrae. There is a fitness disadvantage to mammals that have a different number of cervical vertebrae; for example, in humans, fetuses with an abnormal number of cervical vertebrae are often stillborn, and such children are more prone to pediatric cancers. This is an example of

A) convergent evolution.
B) phenotypic plasticity.
C) constraining evolution.
D) pleiotropy

Question 41

Please describe at least two different ways that a patterning network can be perturbed to create an altered phenotype.

Question 42

Based on the development of snakes, which lack forelimbs, hypothesize how you could genetically engineer a chicken that lacks wings.

Question 43

Why do sloths have eight cervical vertebrae, even though most mammals have seven?

A) because they have low metabolic rates
B) because they are arboreal and require extra flexibility in their neck
C) because they are a more basal mammal taxon with different metabolic constraints
D) all of the above
E) none of the above

Question 44

Two genes that are orthologs

A) are derived from a common ancestral gene.
B) arose from gene duplication.
C) always perform the same function.
D) all of the above
E) none of the above

Question 45

Given the similar genetic network of developmental genes among bilaterians, what can we say about their common ancestor?

A) It may have grown some kind of outgrowth from its body wall.
B) It most likely had limbs used in movement.
C) It most likely had three pairs of legs, similar to insects.
D) none of the above

Question 46

Crystallins evolved through

A) gene recruitment from heat-shock proteins.
B) gene recruitment from GPCR proteins.
C) heat-shock protein gene duplication and subsequent mutation.
D) an unknown mechanism, but we know they are related to heat-shock proteins.

Question 47

In Lenski's E. coli experiment, what evidence suggests that the ability to effectively exploit citrate was a complex adaptation that involved more than a single mutation?

Question 48

Why do scientists think that insects are constrained to be relatively small? What evidence was used to test this hypothesis?

Question 49

Which of the following correctly describes the elements of DNA?

A) Some regions encode proteins.
B) Some regions encode RNA.
C) Some regions bind repressors or transcription factors.
D) a and b
E) a, b, and c

Question 50

Which is true regarding the homologous Hox genes for dorsal-ventral patterning in mice and flies?

A) Bmp4 is homologous to Dpp, and both play a role in location of gut formation.
B) Chordin is homologous to Bmp4, and both play a role in the location of nervous system formation.
C) Bmp4 is homologous to Dpp, and both play a role in the location of nervous system formation.
D) Sog is homologous to Chordin, and both play a role in location of gut formation.

Question 51

Why are microbes ideal model organisms for evolutionary studies?

A) diversity
B) rapid reproduction
C) slow mutation rate
D) a and b
E) a, b, and c

Question 52

Male pipefish have a brood pouch in which they carry and protect developing embryos. The gene patristacin plays a major role in the formation and function of the pouch. An evolutionary analysis revealed that patristacin is involved in liver and kidney function in all other fish (other male fish do not produce a brood pouch). This is an example of

A) gene recruitment.
B) irreducible complexity.
C) gene duplication.
D) antagonistic pleiotropy.

Question 53

A paralog is a(n) ________, while an ortholog is a(n) ________.

A) homologous gene within a species; analogous gene separated by a speciation event
B) homologous gene separated by a speciation event; homologous gene that arises from a duplication event
C) homologous gene within a species; homologous gene separated by a speciation event
D) analogous gene within a species; homologous gene within a species

Question 54

Two genes that are paralogs

A) arose from gene duplication.
B) are found in the same genome.
C) may perform the same or different functions.
D) all of the above
E) none of the above

Question 55

The field of evo-devo proposes that many major morphological changes result from changes in gene __________ of regulatory genes. The premise for this argument is that these changes _______.

A) expression; will change the outcome of interactions with all genes that regulatory genes interact with
B) protein-coding sequence; will change the outcome of interactions with all genes that regulatory genes interact with
C) expression; can be compartmentalized and need not interfere with the outcome of all interactions
D) protein-coding sequence; can be compartmentalized and need not interfere with the outcome of all interactions

Question 56

Bilateral symmetry in plants

A) is a complex adaptation that evolved from developmental regulatory genes.
B) may have evolved 70 separate times.
C) was a key innovation for flowering plants by increasing pollination efficiency.
D) a and b
E) a, b, and c

Question 57

Which of the following statements is accurate regarding opsin evolution?

A) The common ancestor of jellyfish and humans had only one type of opsin.
B) In deuterostomes, r-opsins evolved into the primary photoreceptors.
C) The earliest bilaterians had three types of opsins.
D) none of the above

Question 58

The gene for snake venom crotamine is most closely related to

A) other snake venom genes.
B) defensin genes, which are used to fight infections.
C) cobra venom factor gene.
D) The evolutionary history for crotamine is not known.

Question 59

How are tetrapod limbs and fish fins developmentally similar?

A) Both start out as buds bulging from body wall.
B) Hox genes are used to produce both phenotypes.
C) Both grow from ectodermal tissue when Hox gene expression ceases.
D) a and b
E) b and c

Question 60

Compare and contrast the formation of the gut in vertebrates and invertebrates.

Question 61

Provide at least three examples of complex adaptions that are far from perfect, but still provide fitness advantages.

Question 62

Describe how gene duplication can lead to the formation of a gene with a different function.

Question 63

What is parallel evolution? Please give an example.

Question 64

Please describe why some evolutionary biologists argue that cis-regulatory elements are particularly likely to be involved in morphological adaptation.
Answer Key

Question 65

Please describe Lamb et al.'s hypothesis for the evolution of the vertebrate eye.

Question 66

Many years in the future, humans have altered the environment on the Galápagos Islands so much that the only plants left produce very large seeds. As a result, many small-beaked species of Darwin's finches are not able to eat the seeds, and they are in danger of going extinct. You are tasked with trying to save these species through genetic engineering of larger beak size. How would you do it?

Question 67

Describe the evolution of the snake venom crotamine in the context of gene duplication and recruitment.