Quizzes exam 1

Bayesian phylogenetic analysis differs from Maximum Likelihood methods in that: -It is based on the principle of parsimony -It infers the likelihood of the data given a tree -It infers the likelihood of a tree given the data -It uses a bootstrapping process to determine confidence in the results

it infers the likelihood of a tree given the data

Chondrodysplasia in domesticated dogs is the result of: -Dogs hybridizing with polyploid wolves to produce a mutant offspring -Genome duplication in some dog breeds -A point mutation leading to the disorder in affected dog breeds -A processed mRNA inserted into the middle of a transposable element

A processed mRNA inserted into the middle of a transposable element

Theta defensin is: -All of the above -A protein that is not made in humans, chimpanzees and gorillas because they have a premature stop codon in the gene that encodes it -A protein that is not made in humans, chimpanzees and gorillas because HIV-1 blocks its transcription -A primate gene that increases susceptibility to HIV-1 in Rhesus macaques -A rodent protein that increases resistance to HIV-1.

A protein that is not made in humans, chimpanzees and gorillas because they have a premature stop codon in the gene that encodes it

Which of the following may explain why HIV-1 is highly lethal? -Because HIV viral loads increase over time -Because evolution is short sighted -Because HIV infects host immune cells -Because the high mutation rate of RNA viruses allows natural selection to act rapidly, enabling HIV to evolve resistance to host defenses -All of the above

All of the above

What can we expect to see happen to delta-32 allele frequencies over time? -New drugs are being created that act on the HIV delta-32 allele. -As HIV acts as a selection factor on human populations we may see an increase in the number of people carrying the delta-32 allele. -The delta-32 allele should eventually evolve back toward the delta-31 allele. -If infection rates go down the delta-32 allele will increase in frequency through natural selection.

As HIV acts as a selection factor on human populations we may see an increase in the number of people carrying the delta-32 allele.

Because finches with large beaks gave birth to chicks with bigger beaks: -This example gives evidence for the inheritance of acquired characteristics -Beak size is a heritable trait -Conspecific nest parasitism probably doesn't occur -Beak size does not influence survival

Beak size is a heritable trait

During years 1-6 of infection, HIV evolution is extremely fast, but it slows down during year 7. What would be the underlying cause for the HIV virus evolution to slow? -Increase in the change of novel epitopes -Replication of the HIV virus decreased -Viral load decrease -CD4 T cell count decrease

CD4 T cell count decrease

HIV initiates replication by latching on to which two proteins? -CD4 and CCR5 (a coreceptor) -A coreceptor and an integrator -Delta32 and CCR5 -TCR and CD4 -CD4 and CCR32 (a coreceptor)

CD4 and CCR5 (a coreceptor

What is it called when two species experience similar environments and evolve the same adaptations? -Coincidence -Co-adaptation -Convergence -Coevolution

Convergence

HIV was introduced into humans only once (from SIV). -True -False

False

In Darwin's era, his theory had three major problems. Which of the following was NOT one of those problems: -Darwin did not know how traits were passed on -Scientists of the time thought that the Earth was 12-20 million years old -Darwin did not know about mutation -Darwin could not explain how evolution led to an increase in adaption

Darwin could not explain how evolution led to an increase in adaption

The example of the male mosquito fish demonstrates what principles? -Different selective pressures can act on the same trait in opposing directions -Adaptations occur in males more than females -Natural selection evolves adaptations that are always perfect -Evolution occurs on individuals

Different selective pressures can act on the same trait in opposing directions

Polyploidy in animals is rare because: -Recombination between parents ensures diploidy in offspring -They frequently have temperature-dependent sex determination -Diploid gametes most often combine with haploids, producing an unstable triploid -They are not as promiscuous as plants or fungi

Diploid gametes most often combine with haploids, producing an unstable triploid

T/F: Artificial selection always produces phenotypes that have higher fitness

False

T/F: Because organisms progress from simpler to more complex forms, evolution violates the Second Law of Thermodynamics

False

T/F: Isotopes with shorter half-lives are more useful for dating the age of Earth

False

Which genes would provide good tools to use as a molecular clock? -Genes that are not exposed to natural selection -Genes that are exposed to natural selection only in the organisms of interest -Genes that are always influenced by natural selection -Genes are not useful tools to use as a molecular clock.

Genes that are not exposed to natural selection

What is a paraphyletic group of organisms? -Groups that include all descendents of a common ancestor. -Groups that include paranormal species and their ancestors. -Groups that include all but one descendent of a common ancestor. -Groups that include several groups that do not share a common ancestor. -Groups that includes a common ancestor and some but not all descendants

Groups that includes a common ancestor and some but not all descendants

The delta-32 allele has the LOWEST frequencies in areas where -HIV infection is rare -HIV strains are missing the viral protein Nef -HIV contains the CD4 receptor within its RNA genome -HIV infection is rampant or abundant

HIV infection is rampant or abundant

How does HIV cause AIDS? -HIV is a DNA virus that parasitizes the immune system cells. -HIV is a RNA virus that parasitizes the immune system cells. -HIV only causes AIDS if the host is infected with multiple HIV-1 types. -HIV is a RNA virus which integrates into red blood cells and causes death.

HIV is a RNA virus that parasitizes the immune system cells

Which type of HIV virus is causing the AIDS epidemic? -HIV-2 subtype B -SIVcpzANT: Chimpanzee -HIV-1 -SIVstm: stump-tailed macaque -HIV-2 subtype A

HIV-1

An HIV virion that reproduces quickly will: -Likely be less lethal. -Will be transmitted only via sexual intercourse. -Have a high transmission rate. -Be less widespread in Europe.

Have a high transmission rate

AZT resistant virions will: -Increase if the AZT is removed from the patient's bloodstream. -Decrease in the presence of AZT, because if AZT is present, selection will favor virions with reverse transcriptase that can incorporate AZT -Decrease in the presence of AZT, because new mutations will produce AZT susceptible virions -Increase in the presence of AZT, because AZT imposes selection for resistant virions.

Increase in the presence of AZT, because AZT imposes selection for resistant virions.

Selection happens to _______, but changes _______ -Individuals, populations -Populations, individuals -Individuals, ecosystems -Ecosystems, populations

Individuals, populations

Viral load in a patient that is HIV positive -Continues to decrease until the patient develops AIDS. -Initially increases, then decreases, and then increases until the patient develops AIDS. -Initially decreases, then increases until the patient develops AIDS. -Continues to increases until the patient develops AIDS.

Initially increases, then decreases, and then increases until the patient develops AIDS.

Fusion inhibitors are a type of antiretroviral drug that -Interfere with gp120 or gp41 binding to host cells -interfere with protein fusion between gp120 and integrase -Inhibit fusase from binding with the integrase protein -Inhibit DNA transcription

Interfere with gp120 or gp41 binding to host cells

How does AZT work? -AZT is not a drug. -Helps reverse transcriptase add more thymidine to the proteins -Interrupts the pathway that adds more nucleotides -Is a HAART cocktail.

Interrupts the pathway that adds more nucleotides

In Sub-Saharan Africa, the primary mode of transmitting HIV is: -Male-female sex -Transfusions with contaminated blood -Consuming bush meat -Male-male sex

Male-female sex

If we want to understand why a particular trait is common in a particular population, we should study how that trait: -Might influence an organism's immune response. -Might influence an organism,s ability to undergo cellular division. -Might influence an organism's heritability. -Might influence an organism's reproductive success and survivability.

Might influence an organism's reproductive success and survivability.

During a drought in the Galapagos, small, easily eaten seeds become less abundant leaving only large, hard-cased seeds only birds with large beaks can eat. If this drought persists for several years, then what would be expected from natural selection? -More birds with small beaks dying than large-beaked birds giving way to offspring produced in subsequent generations having a higher percentage of large-beaked birds -Birds with small beaks mutating their beak genes with the result that later-generation offspring have larger beaks -Birds with larger beaks eating less to save some for birds with smaller beaks. -Small birds growing larger beaks by exercising their mouth parts.

More birds with small beaks dying than large-beaked birds giving way to offspring produced in subsequent generations having a higher percentage of large-beaked birds

Domestication of dogs from gray wolves represents an example of: -Artificial adaptation -Natural selection Mutating genes to produce a new phenotype -All of the above -None of the above

None of the above

The fungus Phytopthera infestans caused the Irish potato famine because it infected potato crops and made them rot. Phytopthera infestans is only virulent when it can avoid the potato plant's defenses. A loss-of-function mutation in the Avirulence gene allows this to happen and causes potato disease, but only when fungal strains are homozygous recessive (aa), not when they are AA or Aa. You observe a potato crop where 75/150 plants have rotted from Phytopthera infestans. At the Avirulence locus, what is the frequency of the a allele? -50% -75% -100% -Not enough information

Not enough information

Yellow color in summer squash is determined by a single dominant allele, thus YY and Yy genotypes both produce yellow squash but yy does not. You cross summer squash to a zucchini, which is green and therefore yy. Among your 60 offspring, 100% are yellow. What are the frequencies of the Y and y alleles, respectively, among these 60 offspring? -75%, 25% -25% 75% -50%, 50% -100%, 0% -Not enough information

Not enough information

The age of processed pseudogenes can be estimated by the number of mutations they have accumulated. We expect to find that: -Older pseudogenes are shared by few species -Newer pseudogenes are shared by many species -The older the pseudogene, the less valuable it is for determining relationships -Older pseudogenes are shared by more species

Older pseudogenes are shared by more species

The KISS principle (Keep It Simple, Stupid), is the best example of which type of method for evaluating the best tree -Parsimony -Bayesian Markov Chain Monte Carlo -Maximum Likelihood -Bootstrapping

Parsimony

When natural selection repurposes existing structures, behaviors or genes this is called a(n) _____________ -Reshuffling of alleles -Punctuated equilibrium -Evolutionary jump -Preadaptation or exaptation -Artificial selection

Preadaptation or exaptation

Shared similarity of genetic flows (e.g. mutations) -Provides further evidence of common descent -Cannot yet be explained by evolutionary biologists, but will likely be explained some day -Does not occur -Helps identify symptoms of infections disease

Provides further evidence of common descent

HIV follows which flow of genetic information? -RNA to DNA to mRNA to protein -DNA to RNA to mRNA to protein -protein to DNA to mRNA -RNA to mRNA to DNA to proteins

RNA to DNA to mRNA to protein

Which of the following is true about chromosome inversions? -They are always deleterious -They always reduce fitness -They break apart linkage groups -They are rare in fruit flies

They break apart linkage groups

If a phylogenetic tree depicts extant taxa on the right and the point of most recent common ancestry on the left: -The vertical axis represents time -The horizontal axis represents time -The amount of time since the most recent common ancestor depends on the vertical spacing between taxa -An accurate phylogeny only shows taxa on the top and the most recent common ancestor on the bottom

The horizontal axis represents time

Which of the following does NOT provide evidence for evolution? -The human hemoglobin family -Discovery of Archaeopteryx -The spurs of the rubber boa -The immutability of species -Theory of Plate Tectonics

The immutability of species

T/F: HAART cocktails destroy most but not all of the HIV virions in the host's body.

True

T/F: Historically, snakes had legs and now they are vestigial structures in certain species

True

T/F: In the chronic phase of HIV infection, CD4 T-cell counts decrease continually.

True

T/F: Life on Earth has evolved over time

True

Which of the following can cause AZT to become less effective as a treatment for HIV infection? -Virions inside a person can mutate to a form that allows reverse transcriptase to use AZT as an efficient DNA building block -All of the above. -Virions inside a person can mutate to a form that does not allow reverse transcriptase to incorporate AZT into DNA strands -AZT molecules eventually mutate into regular thymidine

Virions inside a person can mutate to a form that does not allow reverse transcriptase to incorporate AZT into DNA strands

What we, as scientists, cannot explain the formation of an interesting structure: -We should stop looking for naturalistic explanations because the structure was obviously was obviously intelligently designed -We should continue to look for naturalistic explanations, including precursor-like structures in other organisms -We should continue to look for naturalistic explanations, but if we do not find them we should declare a miracle

We should continue to look for naturalistic explanations, including precursor-like structures in other organisms

Mutation rates can be influenced by: -the species -the environment -the gene region -all of the above

all of the above