Docsity
Docsity

Prepare for your exams
Prepare for your exams

Study with the several resources on Docsity


Earn points to download
Earn points to download

Earn points by helping other students or get them with a premium plan


Guidelines and tips
Guidelines and tips

EEB Study Guide 2022., Study notes of Evolutionary biology

Study guide with answers filled in

Typology: Study notes

2021/2022

Uploaded on 02/15/2023

luke-bird
luke-bird 🇺🇸

2 documents

1 / 8

Toggle sidebar

This page cannot be seen from the preview

Don't miss anything!

bg1
1. Provide an example of how knowing about evolution (the history of humans, diseases, and how they
change today) affects medical diagnosis, prevention, and treatment, being able to illustrate each
with a specific example. The course description and opening day poses a question: What, if
anything, should medical practitioners know about evolution to do their job? Another way to ask
this is, what would a doctor, nurse, or public health official do differently in their job when they
understand evolution? I suggest you return to these questions as you study, and clearly frame an
answer. This might be the basis for a question on the exam. If so, I would look for a
well-structured and compelling answer clearly illustrated with detailed examples.
2. Know the difference between allele frequencies and genotype frequencies, and how to calculate each. You
should be able to use the basic formulas associated with Hardy Weinberg equilibrium. If I give
you the frequency of a particular genotype, you should be able to calculate allele frequencies,
and vice versa. These are calculations we will draw on much more in the second half of the class.
Some Hardy-Weinberg problems are provided at the end of this document.
• genotype to phenotype
• how many copies of A vs a
• going backwards would apply assumptions (phenotype to genotype)
• Ex.
3. Explain what genetic drift does to allele frequencies, and the relationship between population size
and genetic drift
• Genetic Drift leads to a random loss of alleles over time
• Random luck leading to more reproduction and one alleles will dominate over others unit it is the only
one left
• Diversity is eroded by a random loss of alleles
• Coalescent Theory
4. Know how evolutionary neutral theory relates to molecular clocks and our ability to infer the
timing of past evolutionary changes
• Using phylogenetics, we can determine when mutations occurred that caused a change in alleles in a
species and can also determine the time frame when it likely occurred
pf3
pf4
pf5
pf8

Partial preview of the text

Download EEB Study Guide 2022. and more Study notes Evolutionary biology in PDF only on Docsity!

  1. Provide an example of how knowing about evolution (the history of humans, diseases, and how they change today) affects medical diagnosis, prevention, and treatment, being able to illustrate each with a specific example. The course description and opening day poses a question: What, if anything, should medical practitioners know about evolution to do their job? Another way to ask this is, what would a doctor, nurse, or public health official do differently in their job when they understand evolution? I suggest you return to these questions as you study, and clearly frame an answer. This might be the basis for a question on the exam. If so, I would look for a well-structured and compelling answer clearly illustrated with detailed examples.
  2. Know the difference between allele frequencies and genotype frequencies, and how to calculate each. You should be able to use the basic formulas associated with Hardy Weinberg equilibrium. If I give you the frequency of a particular genotype, you should be able to calculate allele frequencies, and vice versa. These are calculations we will draw on much more in the second half of the class. Some Hardy-Weinberg problems are provided at the end of this document.
  • genotype to phenotype
  • how many copies of A vs a
  • going backwards would apply assumptions (phenotype to genotype)
  • Ex. 3. Explain what genetic drift does to allele frequencies, and the relationship between population size and genetic drift
    • Genetic Drift leads to a random loss of alleles over time
    • Random luck leading to more reproduction and one alleles will dominate over others unit it is the only one left
    • Diversity is eroded by a random loss of alleles
    • Coalescent Theory 4. Know how evolutionary neutral theory relates to molecular clocks and our ability to infer the timing of past evolutionary changes
    • Using phylogenetics, we can determine when mutations occurred that caused a change in alleles in a species and can also determine the time frame when it likely occurred

5. Be able to explain the principles of natural selection (including the Breeder’s equation and Fisher’s fundamental theorem of natural selection), and provide biomedically relevant examples of natural Selection in the lab, and in real life. - Breeder’s Equation: R = h^2 S → used for forecasting quantitative trait evolution - R = response to selection, h = heritability, S = selection differential - h^2 = VA (additive Genetic Variance) / VP (phenotypic variance) - Fisher’s Fundamental Theorem of Natural Selection - fitness increases throughout time proportional to speed and fitness Ex. mosquitoes where they have a fungal pathogen that kills them. Using the pathogen to control mosquitoes was more effective if you use it earlier Ex. looking for drug combinations for therapy, want a negative pleiotropy so that one trait won't promote resistance. In the lab you want to reduce fitness difference between strains that are resistant vs susceptible to the drug and target something that has negative pleiotropy so it doesn't kill all of the resistant things so the next drug can target what is left - Over time, natural selection leads to adaptations 6. Know what fitness is, and what fitness is not - Fitness is the ability of an organism to reproduce viable offspring - An adaptation can be developed throughout generations to help increase the likelihood of producing offspring - we are not adapted to the present day, we are adapted to generations ago 7. How do we measure / detect natural selection? - We can measure and detect natural selection by comparing the relative fitnesses of different phenotypes of different species and see which ones have the highest fitness - With natural selection, previous sequences of a phylogeny will vanish or stop reproducing, and new ones will start to flourish 8. What is a phylogeny, and what information do we gain from them, with an emphasis on medical practice and epidemiology? - A phylogeny is the historical relatedness between individuals, populations, or species - We are able to determine how closely two species are related to each other - With emphasis on medical practices and epidemiology, we can use it to look at the spread of a disease - “Superspreader” events, we can track down the relative time that the infection was passed to other people, and we can also look to figure out who the individual was, and what kind of mutations occurred between the different spreads of infection to see if new variants arised 9. What does a phylogeny look like for a pathogen under positive selection versus genetic drift - Genetic drift on the left, Natural selection on the right

    1. Old human diseases that spread into new areas (Zika, monkeypox)
    1. Old human pathogens that mutate to become more severe (bubonic plague)
    1. New species of human diseases arising from an old species (Lice, increased resistance to antibiotics) 14. Be able to explain when and why infectious diseases evolve to be more, or less, virulent, with a case study examples of each. Be able to relate this to our definition of Ro.
  • Infectious diseases will be more virulent when Ro is > than 1
  • How are beta and alpha related? (more contact = high beta)
  • They will be less virulent when Ro is < than 1
  • cholera in areas with good sanitation, when it was virulent, high alpha, 15. What conditions help bacteria evolve antibiotic resistance?
  • When bacteria undergo mutations, it allows for evolution of the species to create new strains, which may be less susceptible to dying under antibiotic conditions, leaving them behind so now they have no competitors and can grow quickly (high mutation rate = high genetic diversity)
  • Horizontal Gene Transfer → give a plasmid with a resistant gene to other bacteria in the area 16. How can we use evolutionary ideas to fight antibiotic resistance? Know the broad ideas and an example of each
    1. Reduce initial genetic diversity
  • Do a surgery, cut out most of the tumor as possible, now less diverse because less population
    1. Inhibit addition of new variation (mutation, immigration, recombination)
  • suppress pool of variation required for evolution by natural selection
    1. Apply weaker selection
  • not killing the pathogen, but keeping it under control
  • applying pesticides earlier in life in mosquitoes to prevent malaria
    1. Apply so much selection nobody survives
  • if all of the pathogen dies, then there is no variants (no adaptation)
  • Combination Therapy
    1. Select against resistant genotypes
  • counterselection, favor drug susceptible types, drive total population to be treatable
    1. Set an evolutionary trap: allow evolution of resistance, then use a second drug that kills resistant phenotypes
  • temp them to being resistant, then use something that kills all resistant forms 17. Explain how vaccination works, and what considerations affect the target number of people who have to be vaccinated for herd immunity.
  • Get an injection containing antigens, these antigens are taken up by macrophages where they are chopped up, and then pieces are loaded into an empty groove on MHC (HLA), where it is then exported to the cell surface, where the antigen is shown
  • MHC-antigen complex is recognized by T cells, which then present the antigen to B-cells to activate it
  • These B cells secrete antibodies that coat a pathogen so it cannot attach to cells, aid in phagocytosis, and activate Complement cascade (punch holes in things, flagged by antibodies) that can lyse cells
  • This immune memory can prevent 2nd infection immediately or minimize its severity and duration
  • When considering the target number of people who have to be vaccinated for herd immunity, you have to look at Scrit, and use that to find Pcrit 18. I often invoke the idea that you can’t have your cake and eat it too: that there are tradeoffs that constrain organisms’ ability to be good at everything. Have in mind at least one example of how trade-offs (aka negative pleiotropy) affects the evolution of pathogens.
  • Trade-offs, aka negative pleiotropy, affect the evolution of pathogens because even though the bacteria may be resistant to the first antibiotic, they will be very susceptible to the second antibiotic. This causes the bacteria to have a harder time evolving because after the second antibiotic, it has lost a ton of its genetic diversity. 19. What are the strategies by which bacteria evolve resistance to antibiotics? Same for insect pests and pesticides
    1. Changes in protein shape of antibiotic target (chemical that binds to the receptor that take the bacteria and inhibit its function)
    1. Reduced cell permeability (drug has to get into the cell to do its job, if peptidoglycan layer, it blocks the import of the drug)
    1. Increases efflux (pump the drug back out of the cell using porins and efflux transporters)
    1. Metabolize drug into other compounds (take a dangerous chemical and turn it into something harmless) 20. When bacteria evolve resistance to one antibiotic, they may become more susceptible to another antibiotic (negative pleiotropy) or less susceptible. How is this important in guiding antibiotic prescriptions?
  • Negative pleiotropy → one gene that has 2 traits with opposite fitness effects
  • You want to choose drugs that have a negative pleiotropy so that one drug can kill all of the susceptible bacteria and that the other antibiotic will kill off the resistant bacteria
  • There is going to be less adaptation when using drugs that are antagonistic against bacteria vs ones that are synergistic 21. What are some environmental considerations that affect the risk of antibiotic resistance?
  • Use of antibiotics in agriculture and how they are very widespread for nonmedical purposes, bacteria are good at sharing genes, if you target a bacteria in pork, you wouldn't think its a problem for humans
  • Water runoff 22. What environmental considerations affect the risk of zoonotic disease?
  • Risk Factors:
  • Some cells cheat because they want to dominate over the other species and use all the nutrients to thrive 27. Be able to explain, with examples, how natural selection acts within tumors.
  • Mutations cause genetic diversity which can allow resistance to antibiotics, allowing for growth of the tumor, and overtime if chemotherapy is used, eventually it will get to a point where the whole tumor is made up of resistant cells, which will be selected for by the use of the chemo drugs
  • Natural selection can drive evolutionary changes that benefit tumor cells in the short run, but in the long run, it is stuck with that human and is not passed on to the next generation 28. Compare and contrast the evolution of antibiotic resistance, and evolution of chemotherapy resistance what are some shared features, and how are they radically different?
  • 20
  • The evolution of chemotherapy is different from antibiotic resistance because cancer is unique to each patient who has it. Each time someone goes through chemo, all of the cells die except for the resistant cells, which then over time will proliferate, and it is harder to find a drug that will kill all of them. Unlike antibiotics, resistance to chemotherapy drugs isn’t becoming more common, this is because tumor drug-resistant cells cannot be given to someone else, every new tumor is starting out with drug susceptible cells 29. Be able to explain evolutionary ideas of adaptive radiation, key innovations, and parallel evolution, and how they relate to cancer
  • 19
  • Adaptive Radiation is the relatively fast evolution of a species from a single common ancestor (ex. Darwin's finches)
  • Parallel evolution → shows that evolution is repeatable, replication of same evolutionary change in 2 different bodies of water with fish
  • Key Innovations → new physiologies that open up new opportunities (adaptations that enable tumor cells to establish new niches and escape predation)
  • Cancer: every cancer patient is a brand new origin of a tumor, cancer is somewhat parallel but mostly non-parallel 30. How are evolutionary principles being used to change how we treat cancer? How is phylogenetics being applied to the study of cancer?
  • 18
  • Because a tumor is a genetically diverse population, it will have a branched evolution, which allows us to determine when mutations occurred, and which stem cell acted as the most common ancestor
  • In a phylogenetic analysis of cancer, we can trace the stem cell source of the tumor and diagnose the cancer, identify which mutations initiated the tumor, identify the timing of tumor origin, and identify genetic diversity and spatial complexity of the tumor to guide treatment
  • We can now bar-code tag tumor cells to watch how the evolution unfolds → these barcodes are delivered by a virus, which insert a unique “SSN” into each tumor cell, and if one of these cells with a barcode divides, all of its descendents will have the barcode as well, and this allows us to determine if the tumor is evolving or not

SIR Model:

  • S = susceptible, I = infected, R = resistant
    • going from S → I is β (transmission rate), going from I → R is 𝛾 (rate of recovery)
  • R is the average number of new infections that will result from one current infection, Ro is the “basic reproductive rate” of the disease
  • Scrit is the minimum number of susceptible people for a disease to spread, Pcrit is the minimum number of people we have to vaccine to reach herd immunity = (N - Scrit)/N - An infection will decline when the susceptible population is less than Scrit, but will increase when S is greater than Scrit - If we vaccinate at least Pcrit proportion of the population, then we reduce S (# of susceptible people) to below Scrit and the disease declines
  • Vaccination moves people from the susceptible bin and moves them to the resistant bin without going through the infected bin

β𝛼𝛾μ