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ECOL 409 Final Study

Terms in this set (73)

In the depicted example phylogenetic tree of some vertebrates, what is the bootstrap proportion of the node that depicts the most recent common ancestor of humans and sea turtles? Fill in the bootstrap proportion on that node (a number). (This tree of vertebrates may look different from one you may have seen elsewhere. For the purposes of this question, assume this tree is accurate as depicted and base your answer on this tree only.)
100
Why does genetic drift have a greater effect on smaller populations than on larger populations?
The probability that allele frequencies, especially of rare alleles, change by chance during genetic drift is greater in small populations.
How does a virus start to infect a host cell?
The virus forms specific molecular bonds with particular host cell surface proteins.
What part of the phylogenetic tree does this arrow point to?
Tip
Why are homologous traits similar?
They are derived from a common ancestor
Consider this published phylogenetic tree of HIV-1 (Human Immunodeficiency Virus) strains M/A, M/B, N and O, and several SIVcpz strains (Simian Immunodeficiency Virus of chimpanzees). Don't mind the colors. Which of the following is an accurate statement?
HIV-1 is a paraphyletic group.
Which of the following is NOT an example of indirect transmission?
Vertical transmission
What is an opportunistic infection?
Infection caused by organisms that are often facultatively parasitic and invade hosts with weakened immune systems.
Consider the following population of grasshoppers: 20% have a green color, 50% have a brown color and 30% have red color. This year has been a great year for the grasshopper population: no predators and as much food available as they can eat. All grasshoppers are able to reproduce and all individuals have 2 offspring each. Which of the following statements is CORRECT:
Natural selection for a particular color will not occur because there was no variation in fitness among individuals with different colors.
A patient with a bacterial infection is treated with penicillin (a type of antibiotic). Most bacteria immediately die from the antibiotic treatment, but some cells carry a mutation that ensures they are resistant to the antibiotic. The number of resistant bacteria soon becomes much higher than the number of antibiotic-susceptible bacteria in this patient. What is this process called?
Evolution by natural selection
Which of the following is an accurate statement of relationships?
C is more closely related to D than to B.
Which statement is correct?
Protozoa are a paraphyletic group of eukaryotes.
In a flu patient, millions of virions of influenza A virus are present. They represent a diverse population inside a host. However, when the virus is transmitted to a new host, only a few hundred virions make it to the new host. What is this transmission event an example of?
A population bottleneck.
What is a major goal of evolution?
There are no goals in evolution.
Which statement is false?
Bacteria, Archaea and viruses are asexual organisms therefore genetic recombination does not occur in these groups.
What is a dead-end host?
A host that the parasite is not adapted to infect.
A host from which no or very limited onwards transmission occurs.
A host in which the parasite "accidentally" winds up in.
All of the above.
***All of the above.
In March 2014, a deadly outbreak of a hemorrhagic fever erupted in Guinea, but the causative agent was unknown. Genetic sequences of three patients were obtained, and were compared in a phylogenetic tree with representatives of filoviruses. Based on the information in this phylogenetic tree, write the full and exact name of the virus the unknown isolates are most closely related to.
Zaire ebolavirus
In terms of genome organization, what type of viruses are retroviruses?
Positive sensed, single stranded RNA (+ssRNA) as genome, and at a certain phase the genomic RNA is reverse transcribed to DNA, which is inserted in the host genome.
Which of the following is a way in which fitness (in the evolutionary sense) can be estimated?
How many offspring an individual produces.
Which disease is described here? Each time this disease arises it is an independent evolutionary process in which multiple clones of cells originate through mutation and then compete with each other for resources. Clonal competition fed by genetic heterogeneity among cell clones drives natural selection that favours the better performing clones. Here performance significantly includes both the ability of cells to spread and invade other tissues and the resistance of some clones to chemotherapy. Thus two of the most significant characteristics of this disease are products of natural selection.
Cancer
What is the basic reproductive number R0?
The expected number of secondary cases produced by a single infected individual in a susceptible host population.
When could an epidemic stop and die out?
When R0 < 1.
What does herd immunity mean?
When enough people are vaccinated against a particular infection, so that the number of susceptible people becomes so small that the infection cannot spread.
Which of the following inter-species interactions is NOT an example of antagonism?
A vulture and a hyena both eating from one carcass.
Two bacterial species live together in Frank's oral cavity. Frank takes particular antibiotics, which kills off only one of the two species in his oral cavity. Bacterial cells of the remaining species now proliferate and occur in numbers 2 times higher than originally before the antibiotic treatment. What was the type of interaction the different bacteria species experienced with each other?
Competition
What is an evolutionary explanation for mutualism?
The benefit of receiving a service from a partner outweighs the cost of performing a service for a partner.
Why can we make an analogy between this quote in an Alice in Wonderland book ("Now, here, you see, it takes all the running you can do, to keep in the same place") by the Red Queen character, and an evolutionary arms race between antagonists?
Organisms in an antagonistic interaction need to keep on evolutionarily changing to be able to survive in an ever-evolving environment, while the interaction can remain antagonistic through time.
What is an endosymbiont? Choose the best definition.
An organism that lives inside a host body or cells.
Which of the following would provide evidence that a parasite and its host have co-evolved?
Infectivity is higher when a host is challenged in the lab with parasites from the same year, than when challenged with parasites revived from the previous year or from the subsequent year.
Which interpretation(s) of the comparison between this host and parasite phylogenetic tree from Moran & Bauman 1994 paper could be correct? Choose the best answer.
Parasites and hosts are co-evolving and therefore their evolutionary lineages have been co-diverging too.
Parasite lineages diverged whenever the lineages of their hosts diverged too.
The evolutionary divergence of the parasite is linked to the evolutionary history of the host.
All of the above could be correct.
***All of the above could be correct.
What kind of inter-species interactions can members of the human microbiome experience?
Competition, mutualism, commensalism and parasitism.
Humans harbor an immense diversity of bacteria in their microbiomes. One of these is bacteria species A. Which of the following describes a commensalistic interaction between humans and bacteria species A?
Species A receives food from the food ingested by its human host and requires the host gut to live in, but Species A has no effect on its human host.
In which of these situations could virulence of a pathogen in humans expected to be a coincidence and not an adaptive trait?
The pathogen is usually transmitted among a different host species.
Approximately how long does an epidemic of Zaire ebola virus usually last in humans?
A few weeks or months, a few years tops.
What is a zoonosis?
An infection normally circulating in non-human animals that humans sometimes acquire via cross-species transmission events.
In which situation could virulence be an adaptive trait?
If transmission probability and virulence are positively coupled.
Which of the following are components of the virulence-transmission tradeoff hypothesis? Select all that apply.
Lower levels of virulence will always be favored by natural selection.
***Through increased mortality rates, high virulence can decrease transmission rate.
***Virulence is an unavoidable cost to the pathogen for using the host resources for replication.
***An intermediate level of virulence is expected to evolve under the virulence-transmission tradeoff hypothesis.
According to the virulence-transmission trade-off hypothesis and using this equation of the basic reproductive number, R0 = BaN/mu+a+Va, why would decreasing virulence not necessarily lead to an increase in R0?
Because the recovery rate v would increase and the transmission probability B would decrease.
When transmission probability and virulence are positively coupled, which of the following would influence the level of virulence that is expected to eventually evolve?
Best guess: The mode of transmission of the infection.
Besides the literal definition of the basic reproductive number R0, what can R0 be a measure of?
A parasite's fitness.
In which scenario would a microbial symbiont be particularly constrained to evolve a cooperative trait for its host?
If the microbial symbiont species was first in a parasitic relationship with its host.
What does PCR do?
It makes many copies of a particular targeted segment of DNA.
Of the following options, which have the highest evolutionary rates?
ssRNA viruses
How can phylogenetics inform epidemiology? Choose all that apply.
***Identification of the course of the epidemic.
***Tracking routes of geographic spread of the epidemic.
***Identification of disease agent.
***Demarcating epidemic clusters.
Why has the invention of Nanopore MinION device impacted the field of outbreak epidemiology?
Because the MinION is small, portable and fast, one can perform sequencing at the site of an epidemic and in real-time.
From which animal host species did HIV-1 group M originate?
Chimpanzee
If there would be only human-to-human transmission of Lassa virus after a single spillover event from rodent, what would be a feature of the phylogenetic tree build from both rodent-derived and human-derived Lassa virus sequences?
Best guess: Each human-derived Lassa virus sequence would form a separate monophyletic group with a rodent-derived Lassa virus sequence.
When did HIV-1 group M likely first emerge in humans in central Africa?
Early 1900's.
Whose work in the late 19th century was seminal in proving that infectious diseases are caused by microorganisms, and devised a number of postulates through which one could determine the microbial agent of a disease?
Robert Koch
What do we call the rate at which novel mutations arise (per site or per genome) per genome replication event?
Mutation rate
If there is a positive correlation between root-to-tip divergence distance and the sampling date of sequences in a phylogeny, what can we conclude?
The sequenced population is probably measurably evolving across the observed time window.
Which of the following is an appropriate definition of clonal deletion?
The removal through apoptosis of B cells and T cells that have expressed receptors for self molecules
Which of the following cell types can kill cells that present antigens via MHC on their cell surface?
Cytotoxic T cell
For which of the following receptor proteins do the corresponding genes undergo somatic recombination?
T cell receptor
True or false. In both the 2009 swine flu and 1918 flu pandemics, one or more RNA segments of the circulating influenza strains had its origins in a non-human animal.
True
Which of the following is NOT a region of the heavy chain of B-cell receptors?
B (B-cell)
A mutation in a virus arises that changes the amino-acid sequence of a viral protein that contains the dominant epitope for the host's CTL mediated immunity. In which of the following situations would this lead to CTL escape?
If the affinity of TCR binding is reduced with the new epitope.
If the processing of peptides in the proteasome is affected with the new viral protein.
If the efficiency of binding to MHC molecules is reduced with the new epitope.
***In all of the above situations.
Which of the following is a reason why people need to get a new and different flu shot (vaccine) every year to remain protected from influenza?
Influenza virus continuously evolves and as such evades immune recognition via antigenic drift
Which of the following is an appropriate explanation for the large diversity of lymphocyte receptors?
Diversity is generated largely by somatic recombination of the genes that encode for lymphocyte receptors
Which of the following is a correct function of the CD4 protein on T cells?
It binds to MHC class II molecules
What is the role of proteasomes in T cell mediated immune response?
Proteasomes cleave proteins in to small peptides that will be presented by MHC molecules on the cell surface.
What is the basis of antigenic variation in fast-evolving viruses such as HIV and hepatitis C?
Continuous molecular evolution
Covid-19 is caused by what kind of pathogen?
A positive-sense single-stranded RNA (+ssRNA) virus
Which of the following could lead to cytotoxic T lymphocyte (CTL) escape?
An amino acid substitution that leads to reduced binding of a parasite's peptide to MHC molecules
How can a doctor measure progression of AIDS in a patient infected with HIV-1?
Counting the number of CD4 T cells
When you determine the sequence of the MHC class I B gene (also called HLA-B) in two different persons, it is possible you find four different DNA sequences. How is this possible?
There are many different HLA-B alleles circulating in the human population and many people are heterozygous in this gene.
In LCMV infection in lab mice, a single Y to F substitution in the epitope KAVYNFATM leads to a 100-fold reduction in affinity with the dominant T cell receptor. What is the consequence of this?
The ability of the dominant cytotoxic T cells to bind to that epitope will be reduced.
What is an appropriate definition of antigenic variation?
Alterations in parasite proteins in order to avoid a host immune response
Which of the following attributes of covid-19 make it an especially challenging infectious disease for public health authorities to control?
Human-to human transmission
Asymptomatic and pre-symptomatic transmission
Relatively high R0
***All of the above
Which of the following is an appropriate definition for immunological memory?
The persistence of pathogen-specific antibodies and lymphocytes after the original infection has been eliminated so that reinfection can be prevented.
Which of the following statements is true?
One lymphocyte carries a single type of antigen-recognizing receptor
What is likely an important factor that increases mortality induced by avian influenza viruses H5N1 and H7N9 (the two influenza viruses talked about in the second part of Michael Worobey's seminar)?
Whether the first exposure to influenza virus as a child was by an influenza strain with a hemagglutinin (HA) gene from a different genetic group
Approximately how many people died worldwide in the 1918 influenza virus pandemic?
~50 million
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