(BIO3240) Final Exam

Which of these was a challenge for Darwin to explain under his theory of evolution? a. Complex structures such as eyes b. The source of phenotypic variation c. Elaborate traits with no fitness advantage d. All of these were challenges for Darwin to explain

d. All of these were challenges for Darwin to explain

Which of these is a conclusion of the Hardy-Weinberg model? a. Allele frequencies in a population will not change over time if the assumption of random mating is met b. If no other processes are operating, populations will reach Hardy-Weinberg Equilibrium in one generation c. If the allele frequencies in a population are given by A1 and A2, the genotype frequencies will be given by A12, 2A1A2, and A22 d. These are all conclusions of the Hardy-Weinberg model

d. These are all conclusions of the Hardy-Weinberg model

What is population genetics?

the study of variation in allele frequencies over time and space within populations

Population 2

Who has higher relative fitness within its population, the brown mouse in population 1 or population 2?

Heterochrony describes:

Changes that affect the time of onset of reproductive traits, Changes that affect the timing of onset of somatic traits, Differences in developmental timing between ancestors and descendent species

Extinction debt occurs because:

Clades that survive a mass extinction are unable to adapt to new ecological conditions, so they go extinct later

In class we discussed why there are different ecomorphs of anoles on Caribbean islands. What is the most likely hypothesis for the evolution of these ecomorphs?

Competition for resources led natural selection to favor traits that enabled individuals to use different habitats on the same islands

Analysis of residues in the apparatus of the Miller-Urey (organic soup) experiments showed that:

Conditions present in a primordial "soup" could give rise to organic compounds and amino acids

In class we discussed the above plot showing the percentage of female elephants without tusks before the Mozambique civil war and the percentage of tuskless females after the war. Now that the war is over and poaching has declined, what do you predict will happen in this population of elephants?

The percent of tuskless females will decline, because tusklessness is no longer adaptive

What is relative fitness?

The relative genetic contribution of individuals to the next generation

Tree #1 & #3

Which trees are equivalent?

In class, we discussed evidence that there are prezygotic reproductive barriers in Darwin's finches. What evidence did researchers use to establish that these barriers exist? a. Mount experiments that determined whether males only courted females of their own species b. Genetic testing of hybrid offspring to assess evidence of infertility c. Playback experiments that measured response of males to the songs of their own and other species d. Assessment of the viability of hybrid embryos

a, c

In class we discussed the domestication of maize from teosinte. One of the genes hypothesized to be involved in domestication is tb1. If you wanted to figure out if tb1 is responsible for changes in branching patterns between teosinte and maize, which experiments would help answer this question? a. Compare the regulatory region sequence of tb1 between maize and teosinte b. Compare introns between maize and teosinte c. Compare the coding region sequence of tb1 between maize and teosinte d. Insert the tb1 gene from maize into teosinte and see if the plant develops maize-like branching patterns

a, c, d

What is not a benefit of using DNA over RNA as a storage system? a. It can catalyze chemical reactions, unlike RNA b. It is more stable than RNA c. It has better repair mechanisms than RNA d. It can store more information than RNA

a. It can catalyze chemical reactions, unlike RNA

Which is not evidence that mitochondria and chloroplasts arose from endosymbiosis? a. Mitochondria and chloroplasts often survive and reproduce outside of eukaryotic cells b. Mitochondria and chloroplasts have their own ribosomes that are different from nuclear ribosomes c. Mitochondria and chloroplasts have their own DNA that is more similar to proteobacteria and cyanobacteria, respectively, than to eukaryotic DNA d. Mitochondria and chloroplasts are enclosed by two membranes

a. Mitochondria and chloroplasts often survive and reproduce outside of eukaryotic cells

Which statement correctly describes how mutations and natural selection interact? a. Mutations randomly generate genetic variants, and natural selection acts on those variants b. Mutations generate deleterious mutations that are then removed from the population by natural selection c. The environment stimulates beneficial mutations, on which natural selection then acts d. Mutations generate beneficial variants for the organisms, and natural selection acts on those variants

a. Mutations randomly generate genetic variants, and natural selection acts on those variants

The principles of succession and superposition provide evidence of natural selection, because:

Newer layers of sediment cover older layers of sediment, allowing scientists to observe changes in fossil organisms over predictable periods of time

Can adaptive evolution produce any phenotype?

No, adaptation is constrained by available genetic variation

Does selection act to generate new species?

No, species are typically by-products of evolutionary processes operating in isolation

In a population of birds, you notice that 50% of individuals have blue heads and 50% have red heads. You also see that 50% have yellow tails, and 50% have green tails. What proportion of birds have red heads and yellow tails?

Not enough information to determine

Why might traits that act as proxies for direct benefits evolve?

females can efficiently evaluate the benefits provided by that male, males can quickly assess the competitive ability of their rivals, males can avoid costly fights they might lose

When we use parsimony to build a tree based on molecular data rather than character data, we:

Can use the exact same approach, in which we treat nucleotide mutations at a particular site as changes in character state

12/20

What is the frequency of the red allele in this population?

If you find that the coefficient of linkage disequilibrium in your population is a large positive number, what might that mean?

The frequency of a particular haplotype is more common than expected under independent assortment

Dogs and gray wolves

Based on this tree, which species share a common ancestor most recently (and are therefore more closely related)?

How do we know that the first ancestral cells to use DNA for storage gave rise to all other living things?

Because all living things use DNA for information storage

When we quantify viability selection at a particular locus, we calculate the average viability across many individuals. Why do we do focus on averages?

Because many loci typically affect fitness, so we need to average across many individuals to detect the impact of one particular locus

QUIZZES

...

In class we discussed changes in the beak depth of Darwin's finches in response to drought. We showed that x0 = 9.2, x1=9.8, and x2=9.5. What is the heritability of this trait?

0.5

You measure a population of 16 rock pocket mice. 4 individuals have the recessive dd (q2) genotype, which gives them light-colored fur. If the population is at Hardy-Weinberg equilibrium, what is the frequency of q?

0.5

In class we discussed changes in the beak depth of Darwin's finches in response to drought. We showed that x0 = 9.2, x1=9.8, and x2=9.5. What is the selection differential of this trait?

0.6

A population of plants has red or blue flowers, and large or small leaves. Red flowers are under positive selection. If red flowers and large leaves are in linkage disequilibrium, what pattern might you expect to find?

An increase in the frequency of large leaves in the population

Why would molecular mutualisms be favored in a closed system?

Any sacrifices a molecule makes to its own replication to benefit replication of another molecule are regained through the closed system

What is the expected outcome of negative frequency dependent selection?

Both alleles are maintained in the population, with fluctuating frequencies

Tephritid flies have a black stripe pattern on their wings. When approached, they wave their wings in a display that mimics the territorial behavior of one of their predators, the jumping spider. To test the hypothesis that wing pattern and/or waving behavior evolved to deter spiders, researchers created experimental treatment groups where they manipulated presence/absence of both the black stripe pattern and wing waving behavior in flies. They then measured the response of spiders to the flies. Based on the figure above, what can you conclude about the effect of wing pattern and waving behavior on spiders?

Both wing pattern and waving behavior are required to deter spiders

In class we discussed the frequency of light- vs. dark-colored rock pocket mice living on light- vs. dark- colored substrates. Based on the figure above, which phenotype has the overall highest selective advantage? Remember, dd is light-colored and both Dd and DD are dark-colored.

Dark colored mice have the greatest overall selective advantage

In mountain lions, one male typically establishes a large territory that overlaps with the smaller territories of several females. He then breeds with these females. He defends his territory and chases off migrant male mountain lions that may appear to challenge him. What impact do you think this breeding system has on effective population size of mountain lions?

Decreases effective population size, because it creates a founder effect

When the teosinte version of the branching gene tb1 is inserted into maize, it causes the maize plants to have more branches, and when the maize version of tb1 is inserted into teosinte, teosinte plants develop fewer branches. However, when you compare the protein-coding sequence of tb1 in maize and teosinte, there are no differences. What might you conclude from this observation?

Differences in branching are likely caused by mutations in the regulatory region of tb1

Superhero movies like the X-Men series often refer to the next "step" or "stage" of human evolution. Why is this type of thinking incorrect?

Evolution is not a directed process, and there are therefore no planned evolutionary "steps"

How does anisogamy result in a skewed operational sex ratio?

Females invest more time and resources in reproduction, so at any particular time point there are more males ready to mate than there are available females

Why would cells that are clones of each other be more likely to form cooperative multicellular clusters?

Genetically related individuals are more likely to cooperate because it can increase the survival of their genes

Under Darwin's hypothesis of a common ancestry of all living things, we would expect to observe:

Hierarchical clustering and a branching tree of life among all living things, wherein species that appear to be more similar are more likely to be closely related

You are studying a population of birds and notice that some birds have red heads while others have yellow heads. Head color is controlled by a single locus, with AA individuals having red heads and aa individuals having yellow heads. You discover that the red- headed birds prefer to mate with each other, and the yellow-headed birds also prefer to mate with each other. What will happen to the frequency of heterozygotes at the head color locus in this population over time?

The frequency of heterozygotes will decrease

Tree A

In the video we watched about Caribbean anoles, we saw that different anole ecomorphs have evolved via convergent evolution. Which of these trees correctly illustrates convergent evolution in anoles?

Dr. Kingsley's research shows that if you insert the deleted portion of the Pitx1 pelvic switch into a freshwater stickleback without pelvic spines, what happens?

It grows pelvic spines

Why is language not heritable?

It has no genetic basis, and therefore cannot be passed from parents to offspring

Which is not true about horizontal gene transfer?

It is the mechanism by which offspring resemble their parents

Homeotic genes are broadly conserved (relatively invariant) across animals because:

Mutations in these genes often have large or lethal phenotypic effects

The above picture shows the frequency of predator attacks on models of white and dark mice presented against light (left panel) and dark (right panel) substrates. According to this figure, what are the results of this experiment?

Mouse models are attacked less frequently when they match the color of their substrate

What does it mean for a trait to be condition dependent?

Only the highest-quality males have the resources to produce the most exaggerated versions of the trait

You are studying a group of birds, and notice that females seem to prefer mating with males that have the brightest, reddest wings. However, you can't find any evidence that males with bright red wings are in higher condition or are better quality than males with duller red wings. Which is a reasonable hypothesis for the evolution of red wing color?

Red wings evolved via Fisherian runaway because females have an arbitrary preference for bright red color

What pattern would you expect to observe in a region of genome where there is selection against a deleterious mutation?

Reduced heterozygosity around the deleterious allele

Methodological naturalism set the stage for the modern scientific method by

Seeking explanations for the natural world driven by physical laws

Two populations of frogs have been isolated in different lakes for several thousand years. Flooding brings them back into contact with each other, but when they interbreed they produce unfit hybrid offspring. The frogs use calls to attract mates, but the calls of the two populations are very similar. What might you hypothesize will happen to calls over time in the contact area?

Selection will cause calls to become more different to prevent maladaptive hybridization

What are transitional forms?

Species with intermediate characteristics between major groups

Above is a phylogeny of several flowers in the genus Phlox. When you find all these flowers outside, you assume that red P. drummondii are more distantly related to the other species, because they are red but all other species are purple. However, when you build a phylogeny based on DNA sequence data, you find the above tree. Purple color is therefore most likely to be a:

Symplesiomorphy

According to Dr. Shubin's research, late-phase expression of the Hox gene cluster d8-11 is is involved in the development of:

Tetrapod digits and distal fish fins

Santa Ana

The above figure shows the genetic structure of mountain lion populations in California, with the each color/ shaded area corresponding to a different genetic cluster. Which population would you predict has the lowest heterozygosity based on this figure?

Western Sierra Nevada

The above figure shows the genetic structure of mountain lion populations in California, with the each color/shading corresponding to a different genetic cluster. Imagine a new, beneficial mutation arises in both Santa Ana and in the Western Sierra Nevada. In which population is this new adaptation most likely to increase in frequency? Consider the relationship between population size, genetic drift, and selection.

In Darwin's finches, we learned that abundant food after an El Nino year led to ongoing genetic introgression between cactus finches and medium ground finches. What is one consequence of this genetic introgression?

The beak shape of cactus finches is becoming more similar to medium ground finches

What is reproductive isolation?

The cessation of gene flow between populations

Imagine you are reconstructing a phylogeny of four species. Three of them are red and one is blue. Why is color not a useful trait for resolving the evolutionary history of this group under parsimony?

The change in color in one species requires only one evolutionary step, and could therefore be produced by any evolutionary history

The D statistic (coefficient of linkage disequilibrium) measures:

The difference between observed haplotype frequency and haplotype frequency expected under independent assortment

In the forest you discover green birds and red birds. The green birds are harder to see in the trees, and you hypothesize that they are better adapted to their environment than red birds due to natural selection. What is one piece of evidence that would support this hypothesis?

The green birds have more surviving offspring than the red birds

What does a phylogeny illustrate?

The hypothesized evolutionary relationships among groups of organisms

A consequence of Malthus's idea that populations will outstrip their available resources is that:

The individuals best able to monopolize resources in a particular environment will survive

You notice that your dog wags his tail constantly, but you can't imagine there is a fitness benefit to wagging. What is an alternative explanation for the high frequency of tail wagging in dogs?

The locus associated with wagging behavior is in linkage disequilibrium with a different locus that is under selection

What are the two variables that cause skew in the operational sex ratio?

The number of males vs. females available to mate and the ability of males to monopolize access to females`

In class, we learned that many populations of Hawaiian crickets have evolved to be silent (unable to produce courtship songs) because a parasitic wasp is attracted to their courtship songs and kills them. However, the figure above shows the proportion of females from these silent populations that respond positively to recordings of ancestral courtship songs. What can you infer based on this figure?

There is a genetic basis to female preference, so that even if the song is absent in the population the preference for it remains

The Pitx1 gene is expressed in the jaws, pituitary glands, and hindlimb of marine sticklebacks. Freshwater sticklebacks have normal jaws and pituitary glands, but no hindlimb. What is the most likely explanation for this phenomenon?

There is a mutation in the regulatory enhancer sequence in freshwater stickleback that causes Pitx1 to not be turned on in the hindlimb

We observe a plant with pink and yellow flowers. The pink plant produces 1000 offspring and the yellow plant produces 400 offspring. What can we infer selection coefficients and changes in allele frequency in this population?

There is a selection coefficient of 0.6 against yellow flowers, and the pink allele will increase in frequency over time

Sperm cells exhibit some of the fastest rates of evolution and greatest variation in morphology of all cell types. Why might this be?

They are in an arms race to overcome the defenses of the female reproductive tract

It has a low heritability and is strongly environmentally determined

This figure shows a regression of mean body mass between parents and offspring. What might you hypothesize about body mass based on this figure?

The average age of the population decreased and heterozygosity increased after the introduction from Texas

This figure shows changes in average age and heterozygosity in Florida panther populations after the introduction of individuals from Texas. What pattern was observed?

Each line is a genotype. The same genotype can produce different numbers of leaves in different light intensities.

This figure shows reaction norms for the number of leaves on plants grown at different light intensities. What is the correct interpretation of this figure?

Positive frequency dependent selection: fitness of P1 increases as it becomes more common

This figure shows:

You sequence a particular gene in several different species. In one of these species you notice that there are many more non-synonymous mutations in the third codon position than expected. What might this mean?

This gene is under positive selection in that species

When is parapatric speciation most likely to occur?

When populations are distributed along an ecological or geographic gradient

When would you expect the frequency of allele A to increase in frequency most rapidly?

When saa = 0.6 and u from A--> a is low

Under what conditions do we expect to observe most rapid fixation of the dominant D allele? (Think about your observations in class on the rate of fixation of p.)

When the Dd and dd genotypes both have lower fitness than the DD genotype

When does Fisherian Runaway stop?

When the cost of the trait to survival is greater than the benefit from mate choice

You are studying a population of lizards, and you notice that males seem to have two different mating strategies: they either defend territories that attract females, or they sneak up to females and try to steal copulations. You hypothesize that females have evolved cryptic choice to guard against sneaker males. Which observation would support this hypothesis?

When you mix sperm from sneaker males and territorial males in a petri dish with a female egg and female ovarian fluid, the sneaker male sperm has higher fertilization success

Tapirs and rhinoceroses

Which are sister taxa on this tree?

Node #3

Which node indicates the common ancestor of mammals and coelacanths?

According to Dr. Shubin's research, do fish have wrists?

Yes- homologous enhancers are involved in gene expression in tetrapod wrists and the distal surface of fish fins

What is an allele?

any part of the genome that varies among individuals

Under Hardy-Weinberg equilibrium, what is the chance that an individual offspring has a heterozygote genotype?

fA1fA2 + fA2fA1

Which of these is not a testable hypothesis? a. Species do not change over long periods of time b. An intelligent force designs organisms to be well-suited to their environments c. Organisms acquire beneficial traits during their lifetimes, which they then pass on to their offpsring d. Most geologic change on earth is caused by catastrophic events

b. An intelligent force designs organisms to be well-suited to their environments

Which is correct about Darwin's views on natural and artificial selection? a. He thought natural and artificial selection could produce new varieties, but not new species b. He viewed them as essentially the same process, with only the selective agent differing c. He believed only artificial selection could produce new species d. He viewed them as fundamentally different processes

b. He viewed them as essentially the same process, with only the selective agent differing

Which process does not increase the likelihood of allopatric speciation? a. Drift b. Migration c. Mutation d. Selection

b. Migration

Which of these is NOT a component of natural selection as described by Darwin? a. Individuals within species are variable b. Organisms reproduce via sexual reproduction c. Survival and reproduction are non random: individuals carrying specific variations survive and reproduce the most d. Individuals pass their variants on to their offspring

b. Organisms reproduce via sexual reproduction

Which is not a challenge of studying speciation? a. Most species are old b. Speciation usually happens instantaneously c. No species concept works for 100% of cases d. Speciation is a continuous process, but defining species requires drawing a "line" defining discrete groups

b. Speciation usually happens instantaneously

Which is not true about homeotic genes? a. They include MADS-box genes that affect spatial development in plants b. They code for fine-scale differences between closely related species c. They are involved in proper ordering of the body plan d. They encode transcription factors that bind to regulatory enhancers and guide development

b. They code for fine-scale differences between closely related species

Why does random mating not change allele frequencies under Hardy-Weinberg equilibrium?

because our model assumes no mutation or natural selection, so random mating just reshuffles alleles each generation without increasing or decreasing the frequencies

Why are mutations at degenerate codon positions often considered "silent"?

because they are unlikely to affect the phenotype

Which is an example of adaptive introgression? a. There is strong selection against interbreeding within a hybrid zone b. Traits involved in species recognition become more divergent in sympatry c. A few beneficial loci move from one population to another across a hybrid zone d. Two differentiated populations collapse due to extensive hybridization

c. A few beneficial loci move from one population to another across a hybrid zone

Which of these is NOT true: a. Experiments allow us to test hypotheses about evolution b. Evolution can be predictable and repeatable over time c. Evolution always produces identical results in similar environments d. Similar phenotypic changes can arise independently in similar environments

c. Evolution always produces identical results in similar environments

Which is true about Hox genes? a. Mutations in Hox genes have small phenotypic effects b. Hox genes cannot be swapped between different species c. The position of the Hox gene along a chromosome corresponds to the position of the structure it controls on the body d. They are not conserved and vary widely across species

c. The position of the Hox gene along a chromosome corresponds to the position of the structure it controls on the body

Which observation supports Mendel's inference that offspring must receive genetic material from both parents?

offspring in the F2 generation exhibit both parental phenotypes

Under what conditions do you expect the fastest increase in frequency of the favored p allele? (Remember what we learned in our in-class activity on the impact of starting allele frequency and selection coefficients on rates of increase in allele frequencies.)

when starting p = 0.5 and s =0.8