Evolution Exam 1
What was Essentialism
(400 BC) Greek idea that things are essential and everything has its essence (Dominated Western European thought for 2000 years)
What is the mutation rate in HIV
1 x 10^-3 new nucleotides/nucleotide/replication
What is the mutation rate in eukaryotes
1 x 10^-6 to 1 x 10^-9
What are the 5 steps of the HIV life cycle
1. HIV attached to CD4 and enters cell 2. HIV copies itself to make more virus 3. HIV and CD4 cell fight; HIV damages the cell 4. Young HIV leaves the cell 5. HIV matures and invades other cells
What are the 3 components of clonal selection in HIV
1. Random phenotype variation 2. Differences in fitness 3. Heritability of these phenotypes
What are the 3 criteria for evolution by natural selection
1. Variation 2. Relationship between the trait and fitness in a particular environment 3. Heritability
All humans are about ___% genetically different. HIV generations can be _____% different from the previous oone
2; 30
How old is the Earth estimated to be?
4.6 billion years old
How many times has His evolved into Tyr at amino acid position 83 in HIV envelope protein
7
What did Plato believe
All life is a real, pure, eternal form. Variability is due to imperfection with no meaning.
What is AZT
An HIV drug taken with a drug cocktail
In response to rain, Daphne island birds evolved back to small beaks, what was criterion #2 at the time
Beak size vs. fitness, larger beak size now meant lower fitness
How does AZT work?
Blocks DNA reverse transcriptase by incorporating the wrong base into the virus' DNA so there is no protein synthesis and thus no viral replication.
Is the CD4 T allele or C allele more resistant
CD4 C
What cells does HIV infect?
CD4 helper T cells
What are some traits that can evolve in humans in response to HIV
CD4 receptors CCR 5 receptors Immune response proteins
Who established the principles of geology and rejected the young earth theory in the 1830s
Charles Lyell
Why does a drug-cocktail slow down evolution of resistance
Combination of inhibitors puts replication at approximately 0; 3-5 different mutations would have to arise in a single virus for replication to begin (low probability of mutation origin)
How do we represent heritability
Comparing parental average phenotype to offspring average phenotype
What are the 5 classes of antiretroviral agents that currently exist
Coreceptor inhibitors (CCR5 antagonists) Fusion inhibitors Reverse transcriptase inhibitors Integrase inhibitors Protease inhibitors
What is a pseudogene?
DNA with no promoter - noncoding - no protein made - vestigial trait
How can humans evolve resistance to HIV
Delta 32 CCRF - 35 amino acids that are missing from the proteins surface --Cannot be recognized by the virus --The virus cannot infect individuals with two copies of Delta 32 CCRF
What gene locus controls the armor allele
Eda
Why is HIV's asexual nature advantageous
Exact replication of genotype (no breaking of genes by sexual recombination)
How is evolution both a fact and a theory?
Fact = genetic change has been observed through time Theory = the set of processes by which evolution occurs
T or F: We know the proteins an RNA makes by looking at its sequence
False
T or F: HIV can only evolve within hosts
False, it can evolve across hosts as well
What did Rosemary and Peter Grant do?
Followed every single bird in a population to show evidence of evolution on Daphne Island
What geographic patterns did Darwin take note of
Fossil patterns (Law of Succession) Island patterns (Galapagos birds resembled S. American birds)
What are the groups of HIV-2?
Group A (W. Africa) Group B (W. Africa) Groups C-H
What are the groups of HIV-1
Group M (subtypes A-K) Group N Group O
What are the 2 main types of HIV
HIV-1 HIV-2
What is HAART
Highly Active Anti-Retroviral Therapy (use of a drug cocktail with at least 3 classes of inhibitors)
How is phenotypic variation represented
Histogram X = value of trait Y = number of individuals w/ trait
What are homologous and analogous traits
Homologous: similar because they have common evolutionary origin (synapomorphies) Analogous: traits have the same function, but do not have a common evolutionary origin
What are the two questions to ask ourselves when comparing traits across species
How similar are these two things? Are they the same trait?
Why is resistance to HIV not more prevalent in humans?
Humans = slow evolution HIV = fast evolution
What did Karl Popper say about the scientific method
Hypotheses in the realm of science must be falsifiable, in that it is conceivable that one or more predictions could be refuted by observations.
What is our state fossil (Nevada)
Ichthyosaur (A swimming reptile which acted like the dolphins of today)
Where are the highest levels of human HIV resistance actually found? Why?
In North Western Europe where the virus is relatively new and well-treated; disease outbreaks in the past may have driven a high level of CCR5 causing resistance
Genesis (in the Bible) says what about Earth
It is young
Why is heavy armor a cost in freshwater sticklebacks
It reduces growth rate and thus reproductive success
On Daphne Island, dry environments gave rise to ________ seeds, thus favoring _________
Large; large beak size
How do we represent relationship of phenotype and fitness
Line Graph X=phenotype Y=fitness
Who is resistant to HIV?
Long-term host monkeys
Which have more armor: marine or freshwater stickleback
Marine (thus they have improved fitness in an environment with predators)
What large animal did Darwin find the bones of?
Megatherium - Giant Ground Sloth found in S. America and would have been found in the Vegas Valley as well
Why is it more difficult to evolve resistance to a drug cocktail
Mutations have to occur at more than one amino acid to overcome each inhibitor; and there is no sexual recombination to share these mutations, one virus has to evolve ALL of the mutations
What do convergent evolution and analogous traits tell us
Natural selection in similar environments is a predictable process
Was the Law of Succession Darwin's idea?
No, he just sees the pattern and asks "Why is there an extinct and living form in the same area? Why does one cease to exist?"
What base is replaced by AZT
OH in Thymidine is replaced by AZT-triphosphate
Is the humerus across species analogous or homologous
Only homologous (highly modified function across species)
What is the epigenetic role of our microbiome
Our microbiome's genetics affects our genetics and functions
What is the idea of special creation
Species are immutable; Species created independently by god; perfect in form and function; no genealogy; species not related to each other
What are the components of descent with modification
Species change over time (microevolution) Lineages split and diverge (speciation) New life forms derive from old ones (macroevolution) All life forms are related (common ancestry) Earth and life are old
What were the ideas behind special creation
Species do not change; lineages do not split; each species is independently created; earth and life are young
What factors contribute to fast evolution
Strong natural selection; Selection not disrupted (asexual reproduction)
Why do patients that take their drugs 80-90% of the time see more viral mutation than those who take their medication only 20% of the time
Strong selection is present, but not strong enough to prevent viral replication, so there is a strong selection for drug-resistant viruses to survive (in the 80-90% group)
What did James Ussher do?
Studied the bible to understand Nature, determined the age of Earth to be 6000 years old (Origin of the age of Young Earth)(1600s)
Christian scholars added what to Essentialism
The Great Chain of Being's addition of God and the incorporation of religion (c. 1200s)
What happens if criterion #3 is not met
There is selection but no evolution
How can we use graphs to prove evolution
Use two histograms from different generations that show a shift in phenotypic frequency; or line graph showing mean phenotype vs time
How does the Law of Parsimony apply to phylogenetic trees
We ask ourselves what tree best explains all of the variation with the least number of mutations
What would happen if we were safer with HIV?
We would be less likely to see the rapid evolution of highly virulent forms (because the virus would die with the infected individual)
Would it be beneficial for a species to become asexual
Yes, because favorable traits would be directly passed on if they have high fitness
Has AZT resistance evolved more than once in HIV
Yes, independent mutations have occurred in different AZT treated individuals. There are also different amino acids that provide different ways to be resistant
What will you find if you take and HIV + patient and keep sampling the HIV over 10 years
You will find that the HIV are becoming more and more genetically diverse
Selection results in __________
a shift in frequency
Why doesn't resistance increase when it becomes resistant to both C and B
because it is still being suppressed by the A in the cocktail
What is the T cell
center of the immune system; the cell that is supposed to hunt and find a virus
What is evolution
change in the frequency of a trait over time
What's another name for natural selection
clonal selection
The 1st AZT resistant virus arose due to mutation, the rest is due to __________
clonal selection (Law of Parsimony)
What is sexual dimorphism?
difference between males and females
What kind of virus is HIV
diploid RNA-based retrovirus
When referring to phylogenetic trees, the base of the tree is _________ in time than the tips
earlier
Glypotodons are _________
extinct giant armadillos
What is the Law of Succession
extinct species resemble extant species in same geographic area
What factors give rise to a higher chance for beneficial mutations
fast mutation rate; large population; short generation time; quick replication
What are some traits that could evolve in HIV virus
gp120 transcription or insertion proteins antiviral drug resistance
What viral protein is associated with the binding to the CD4
gp120 (docking glycoprotein)
A phylogenetic tree is a _________
hypothesis about the evolutionary history of a species
How does HIV kill its host
immune system is weakened --> AIDS --> secondary infections --> death
Where is integrase found in relation to HIV
inside the virus
Why was the finding of the Ichythosaur important
it suggests that swimming with a tail evolved 3 times
Why do we care about gp120
it's something that the virus can evolve to be different
What are CD4+ T cells
mature T helper cells express the surface protein CD4
Non-functional pseudogenes evolve with _______ patterns indicating descent with modification of traits that have no function.
nested
What are vestigial genes
pseudogenes
What are vestigial structures?
remnants of features that served important functions in the organism's ancestors (nonfunctional homologous structures)
What are the essential 3 proteins for HIV
reverse transcriptase, integrase, and protease
Low variance = _____ evolution
slower
Natural selection is not a force/pressure, it is a __________
sorting process
What trait could be extremely advantageous to the virus if they evolved it in the presence of a drug cocktail
the ability to swap genes (like some bacteria)
Where in the world would we expect human resistance to HIV to be the highest
the highest frequency would happen where infections are the greatest and have been happening for the longest period of time
The more nucleotides that give resistance = __________________
the more opportunities for drug resistance to arise
The more we suppress something ________
the more selective pressure and the more advantage the surviving virus has
Why does HIV evolution reach a plateau at some point
the patient's immune system is breaking down and the HIV doesn't have a T cell preventing survival and replication
The phase between DNA synthesis and DNA splicing is called ___________
the transitory phase
Why can't we evolve the loss of a pseudogene
there is no cost or trade off in which natural selection can act upon (no protein therefore no phenotype)
The pattern of independent evolution serves as evidence that _______________
there's a predictable process happening over and over again suggesting the impact of the environment
What is an adaptation
trait that has evolved by natural selection and therefore has a functional match with environment