Term
| What are the 3 enzymes in HIV |
|
Definition
| reverse transcriptase, integrase and protease |
|
|
Term
| Describe the immune response |
|
Definition
Regulatory T cells regulate, dendritic cells present viral protein to naive helper T cells which divide into memory T cells and Effector T cells . Effector t cells stimulate B cells to mature into plasma cells that produce antibodies
Effector T cells also stimulate macrophages to ingest infected cells and activate naive killer T cells which become effector Killer T cells and memory killer T cells |
|
|
Term
| describe compensatory evolution with AZT |
|
Definition
| compensatory evolution makes resistant forms more efficient with longer exposure to the drug (AZT) |
|
|
Term
| TRUE OR FALSE: during the AIDS phase of HIV there is the most divergence in the gp120 binding site gene |
|
Definition
| FALSE: there is little immune system challenges during the AIDS phase, however during the CHRONIC phase there is rapid evolutionary change from pressure of immune system challenge for virions to evolve novel eptitopes and evade immune system |
|
|
Term
| what are the reasons the HIV retrovirus evolves so fast?? |
|
Definition
1) many thousands of generations of HIV in victim
2) RT is so error prone (~50% of transcripts are mutated)
3) rapid generation time |
|
|
Term
| what is in an HIV drug cocktail? |
|
Definition
RT inhibitors: mimic nucleotides or block active site
protease inhibitors: dont let protease cleave viral precursor proteins
fusion inhibitors: dont let HIV enter host cell (interfere with gp120s in virus)
integrase inhibitors: bloack insertiong of HIV DNA into host genome |
|
|
Term
|
Definition
| highly active anti retroviral therapy (cocktails of TR,protease,fusion and integrase inhibitors) |
|
|
Term
|
Definition
1) burns through hosts supply of naive and memory t cells
2) population in host evolves to be more aggressive
3) strains of HIV evolves that can infect naive T cells (progenitors of memory and effector T cells) |
|
|
Term
| what does the evolution of HIV strains that use CXCR4 show? |
|
Definition
| the short-sighted nature of HIV evolution because these strains cannot be transmitted to new hosts. |
|
|
Term
|
Definition
1) evolution does not plan ahead
2) Virulence (all hosts die, the virus has to colonize new hosts) |
|
|
Term
| what affects the fitness of the virion? |
|
Definition
1) intrahost success x 2) interhost transmission
1) traits that predispose HIV to kill also enhance ability to infect new hosts
2) benign strains of HIV are transmitted from host ot host at low rates |
|
|
Term
when are intrahost sucess and interhost transmission negatively correlated?
and positively? |
|
Definition
when hosts are rare are transmissibility is correlated with repeated exposure
when hosts are common and transmissability is correlated with virulence |
|
|
Term
|
Definition
got malaria in the congo
-interested in the idea that people picked up the disease thru contamination of the polio vaccine by vaccines being grown in monkey liver but this is not supported by the evolutionary trees |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| why cant we make AIDS vaccines? |
|
Definition
| there are many different strains of HIV, strains have jumped from primates, diversified and will probably continue to do so --> evolution is too rapid |
|
|
Term
|
Definition
| rudimentary or degenerate body parts in a species that have a function in close relative are suggestive of common ancestry and an evolutionary process |
|
|
Term
|
Definition
| modern organisms tend to be more similar to extinct ones found as fossils in the same place than those found in other places |
|
|
Term
|
Definition
| evolutionary change over a short period |
|
|
Term
| where did all dogs come from? |
|
Definition
| 10 thousand YA from Asian Grey Wolf |
|
|
Term
|
Definition
| can be changed dramatically by selection |
|
|
Term
| what is higher oil content of corn an example of? |
|
Definition
| sustained selection (artificial selection) |
|
|
Term
| what does the sliding jello refer to? |
|
Definition
| increasing a trait beyond the standing variation from the ancestor |
|
|
Term
| where does variation come from? |
|
Definition
1) mutation
2) recombination
2) expression of hidden variation |
|
|
Term
|
Definition
1) there is variation in populations
2) part of this variation is heritible
3) variation influences FITNESS: some individuals are more succesful in survival and reproduction than others |
|
|
Term
|
Definition
| codiscovered the principle |
|
|
Term
|
Definition
| divergence of a clade into populations, adapted to many different ecological niches |
|
|
Term
| Prerequisites for selection |
|
Definition
1. Genetic variation in the population in a trait is related to fitness
2. Agent of selection |
|
|
Term
| 2 approaches to finding out if variation is hertible |
|
Definition
1) similarity between relatives
2) response to selection |
|
|
Term
|
Definition
| the proportion of variation observed in a population that is due to variation in genes (varies b/n 0 and 1) |
|
|
Term
|
Definition
|
|
Term
| how to measure heritability |
|
Definition
basic QG: measure the correlation between the offspring and parents
plot graph of offspring vs. mid-parent value
Degree to positive correlation is suggestive of greater genetic effect |
|
|
Term
| problems with heritability |
|
Definition
1) maternal effects
2) conspecific nest parasitism
3) misidentified paternity
4) shared environments |
|
|
Term
|
Definition
due to differences in nutrient stores or hormonal contents of eggs
avoid: estimate heritability from father+ offspring |
|
|
Term
|
Definition
| correlation due to shared environment inflates estimate of heritability |
|
|
Term
|
Definition
| socially monogamous species sometimes have extrapair copulation, reduces estimate of heritability |
|
|
Term
| conspecific nest parasitism |
|
Definition
| females sneak into anothers nest to lay eggs, reduces estimate of heritability |
|
|
Term
| is having 2 eyes heritable or inherited ? why? |
|
Definition
| is it genetically based so it is inherited but there is so variation therefore no heritability |
|
|
Term
| TRUE OR FALSE: life history STRONGER heritability than morphological because they are linked to fitness |
|
Definition
FALSE: the closer a trait is to fitness, the less Vg we expect because there is less genetic contribution
because selection is relentlessly operating on these traits |
|
|
Term
| Bigger isn’t always better. why? |
|
Definition
1. May be poorer at manipulating smaller objects
2. More energetically expensive to produces
3. Affects vocal communication, other aspects of mate choice (Sexual selection)
4. Genetically correlated with other traits also under selection? |
|
|
Term
|
Definition
1. Evolution can occur very rapidly and dramatically
2. Sources of natural selection often shift, so evolution reverses itself or takes new directions
3. The see-saw of selection in changing environments may give the impression of stately gradual change |
|
|
Term
| Bone morphogenetic protein 4 (BMP4) |
|
Definition
found to be linked to outgrowth and shaping of beak
-Calmodulin interacts with BMP4 to define size & shape |
|
|
Term
|
Definition
| = (ln X2 – ln X1)/million years |
|
|
Term
| Adding predator to low predation site you predict |
|
Definition
Decrease in age and size at reproduction
Loss of bright colouration |
|
|
Term
| Migration (gene flow) between locally adapting populations is also a _________ force |
|
Definition
|
|
Term
| what are the 2 types of selection on viruses? |
|
Definition
1) selection of different virus strains within one host
2) selection of strains that are able to transmit from host to host |
|
|
Term
| when will evolution occur |
|
Definition
1) population varys
2) and reproduces
3) variance is heritable
4) there is a selection pressure that causes a difference in survival and reproduction so that certain heritable ways leave more offspring |
|
|
Term
| which two traits are linked in HIV ? |
|
Definition
| virulence and transmission-appear to be linked: HIV-2 has lower viral load (number of virus particles in blood and bodily secretions), which lowers virulence but also apparently lowers transmission rate to new hosts. |
|
|
Term
| why is HIV fatal? (3 hypothesis) |
|
Definition
| (1) Short-sighted evolution: Within each patient, competition between HIV virions results in evolution of HIV strains that are more aggressive, replicate more rapidly, and can evade attack by that host's T cells. This evolution is not to the virus' long-term benefit, however, because it ultimately kills the host-and kills all virions within that host. (2) Evolution for transmission to new hosts: Traits such as high viral load that can cause high virulence may also allow HIV to spread to new hosts. (3) Host has not had time to counterevolve: HIV is a new disease for humans, and our species has not yet had time to evolve defenses. We are still within the first generation of humans to be exposed to HIV. |
|
|
Term
| why is the evidence for evolution? |
|
Definition
1. evidence from living species
a) direct observation of change thru time (soapberry bugs)
b) vestigial organs
2. evidence from the fossil record
a) fact of extinction
b) law of sucession
c) transitional forms
3. evidence of descent with modification
4. evidence of common ancestry
a) ring species
b) homology
c) relationships among species
5. the age of the earth |
|
|
Term
| evidence from living species of evolution? |
|
Definition
a) direct observation of change thru time (soapberry bugs)
b) vestigial organs |
|
|
Term
| 2. evidence from the fossil record of evolution? |
|
Definition
a) fact of extinction
b) law of sucession
c) transitional forms |
|
|
Term
| soapberry bugs getting longer beaks and birds evolving from dinos are examples of ______ ___ __________ |
|
Definition
| 3. evidence of descent with modification |
|
|
Term
| 4. evidence of common ancestry in evolution ? |
|
Definition
a) ring species
b) homology
c) relationships among species |
|
|
Term
|
Definition
| trait that has developed via natural selection over many generations in terms of relative reproductive fitness, |
|
|
Term
|
Definition
| variation exists, the variation is heritable, survival & reproduction are not equal, and survival and reproduction are not random. |
|
|
Term
|
Definition
| selection of a trait that is detrimental to the individual carrying the trait, but that is favorable to other members in the group. |
|
|
Term
| 3 objections to darwins th |
|
Definition
| Three major objections to Darwin's theory were: there is not enough variability for evolution to continue for very long; new traits would disappear by "blending" with other traits; and, the earth's temperature implies that the earth is too young for evolution to have occurred. |
|
|
Term
| 3 objections to darwins th |
|
Definition
| Three major objections to Darwin's theory were: there is not enough variability for evolution to continue for very long; new traits would disappear by "blending" with other traits; and, the earth's temperature implies that the earth is too young for evolution to have occurred. |
|
|
Term
| what is the sesamoid thumb of the panda an example of? |
|
Definition
|
|
Term
| if boostrap support for a particular branch is less that 0.5, what will the research do? |
|
Definition
| conclude the branching pattern is uncertain in that part of the tree and collapse the branch into a polytomy (point of uncertainty) |
|
|
Term
|
Definition
| duplicated genes found in the same genome; describes the relationship among members of the same gene family ( a type of genetic homology) |
|
|
Term
|
Definition
| DNA sequences that are homologous to functioning genes but are not transcribed |
|
|
Term
|
Definition
| genes that diverged after a speciation event; describes the relationship among homologous genes found in different species. |
|
|
Term
| difference between orthologous and paralogous |
|
Definition
| Orthologous genes diverge by speciation events, whereas paralogous genes are the result of gene duplication. |
|
|
Term
| what kind of force in migration |
|
Definition
| migration= gene flow so its a homogenizing force |
|
|
Term
|
Definition
| speciation over very small distances – mate choice |
|
|
Term
| what does selection change in a population? |
|
Definition
|
|
Term
| selection acts upon ____ of ______ but evolution only occurs when it acts upon _________ |
|
Definition
| 1. phenotypes 2. individuals 3. heritable variation |
|
|
Term
| what iis the result of over specialization? |
|
Definition
|
|
Term
| what are two examples that show selection is not progressive? |
|
Definition
| vestigial organs and parasites that de-evolve free living structures |
|
|
Term
| why is survival of the fittest not a tautology? |
|
Definition
| because fitness is an HERITABLE estimable and objective entity related to survival and reproductive success of variants that can be inherited. |
|
|
Term
| characters that are coopted for new purposes are called? |
|
Definition
|
|
Term
| van valen called the evolution/counter evolution between species what? |
|
Definition
| the red queen principle, competitors are always getting better too |
|
|
Term
|
Definition
| allows slower growing organisms to stay a little bit ahead of parasites etc. |
|
|
Term
| what maintains variation for fitness? |
|
Definition
1)Mutation: ultimate soure of variation
2)Diploidy – recessive traits “hidden”
3)Fluctuating selection pressure over time (or space)
4)Trade offs: improvement in one character results in loss of another
5)Disruptive selection:
Over space, time, use of different elements of habitat
6)Immigration and spatial variation – mixing genes between populations |
|
|
Term
|
Definition
| how many grand kids does this individual produce? |
|
|
Term
|
Definition
| organism has best phenotype already and selection is removing the outer bounds, pushing the population to everyone being intermediate – average is best |
|
|
Term
|
Definition
| selection is moving in two different directions simultaneously |
|
|
Term
|
Definition
| individuals moving towards another trait |
|
|
Term
| what is the problem with blending? |
|
Definition
| doest provide for genetic variation |
|
|
Term
|
Definition
| genotype frequencies and gene frequencies of a LARGE, RANDOMLY breeding population remain constant provided that MUTATION, IMMIGRATION and SELECTION don't take place |
|
|
Term
| science and culture discovery institute |
|
Definition
| supports research by scientists for intelligent design |
|
|
Term
| flagella counter argument |
|
Definition
| homologous proteins of Yersinia bacteria has pointy spine that doesnt actually move |
|
|
Term
|
Definition
| showed a phylogeny started from one cell of e.coli |
|
|
Term
| findings from the e.coli experiment |
|
Definition
1) new beneficial mutations are frequent enough to fuel rapid adaptive change in e.coli
2) population structure can be complicated when multiple beneficial mutations arise in different genotypes
3) "mutator" genotypes were favored later in the selection response
4) historical contingency may be important to the evolution of novelty |
|
|
Term
|
Definition
|
|
Term
| what happened with the cit e.coli ? |
|
Definition
| earlier mutation events "potentiated" the genome of A3 making mutation to cit+ far more likely |
|
|
Term
|
Definition
1) competition: compare to see which survives best under limited conditions
2) intinsic rate of increase: how many progeny |
|
|
Term
|
Definition
|
|
Term
| TRUE OR FALSE: not all synapomophies are homolgous |
|
Definition
|
|
Term
|
Definition
| synapamorphy of the tetrapods |
|
|
Term
|
Definition
| classifying things based on common ancestry |
|
|
Term
| true or false: humans evolved from chimps |
|
Definition
| false, they have a shared common ancestor |
|
|
Term
|
Definition
|
|
Term
| based on which characteristics do whales belong to which group? |
|
Definition
|
|
Term
| cladistic analysis vs phenetic |
|
Definition
cladistic looks at groups by indivdual synapamorphies but phenetic looks at % synapamorphy and throws out individual ones
cladistic uses principle of MONOPHYLY, all descendants of a common ancestor are part of a clade and groups that dont include some descendants are paraphyletic
PHENTIC approaches stress MORPHOLOGICAL similarity
PHYLOGENETIC approaches stress COMMON ANCESTRY |
|
|
Term
|
Definition
| lowest number of branches, simplest model wins |
|
|
Term
|
Definition
| algorithm evaluates many possible trees, calculates probability of obtaining particular data given a model of change |
|
|
Term
|
Definition
| similar to ML, different statistical principle |
|
|
Term
|
Definition
discrete traits used to infer a quantitative degree of differentiation
implies a model of change easiest to imagine with molecular clock |
|
|
Term
|
Definition
early mamle linked to whales
phylogeny places whales within artiodactyls, but not close to hippos
hippos have recent orgin in fossil record (~7MYA) but whales date back to 50MYA |
|
|
Term
| indohyous synapomorphies with whales |
|
Definition
bone density
ear morphology |
|
|
Term
| advantages and disadvantages of molecular data |
|
Definition
adv: less likely to contain homoplasy due to convergent evolution, thousands of characters can be used through the genome (which is getting cheaper), many mutations occur in DNA that arent in phenotype, you can use models to account for probability
disadv: the mutation rate varies from gene to gene and there are only 4 bases so reversals occur and homoplasy difficult to reconize |
|
|
Term
| whales were traditionally considered to be an order within ____ |
|
Definition
|
|
Term
molecular clocks assumption
3 problems |
|
Definition
that all molecules change at a consistent predictable rate
1)different parts of a codon are expected to change at different rates
2) loci will vary by functional significance
3) organisms vary in generation time |
|
|
Term
| transition beween fish and modern reptiles |
|
Definition
| panderichitis and tiktaalik |
|
|
Term
|
Definition
| small (less than 5%) and have few deleterious effects |
|
|
Term
|
Definition
| disproportionately stronger selection against multiple mutants |
|
|
Term
| DNA polymerase aries what? |
|
Definition
| heritably in error rate, leading to variation in u |
|
|
Term
| reasons mutation can be adaptive |
|
Definition
1) asexual bacteria require mutation for evolutionary change
2) DNA polymerase varies heritably in error rate (higher u)
3) HIV evades host with mutation (higher u) |
|
|
Term
| most mutations alter existing ____ creating new ______ |
|
Definition
|
|
Term
| what happens to the second copy from unequal crossover? |
|
Definition
can be conserved and produce multiple copies [homolog] - same gene
paralog: creating gene family with slight differences and novel function (globins)
can accumulate mutations sheltered from selection
(pseudogenes)- are devolved into junk DNA |
|
|
Term
| what happened with the extra copies of hsp 70 in d. melanogaster |
|
Definition
extra copies improved susvival under EXTREME thermal stress but were DISADVANTAGEOUS under LOW stress
--> TRADEOFF because unnecessary production of hsp is costly and evolution will strike a balance |
|
|
Term
|
Definition
| reduce recombination, generates linkage disequilibirum |
|
|
Term
|
Definition
|
|
Term
|
Definition
| suppress recombination and have dominant markers |
|
|
Term
|
Definition
| makes sure there is no recombination on certain chromosome but redirects recombination elsewhere |
|
|
Term
|
Definition
u=frequency of mutations
s= effect of mutation on viability |
|
|
Term
| TRUE OR FALSE: mutations can reduce the viability up to 100% in harsh conditions |
|
Definition
|
|
Term
| why are MA results an underestimate? |
|
Definition
1) all lethal mutations are lost
2) silent mutations are not measured
3) viability only one component of fitness (didnt measure fertility, longevity ect) |
|
|
Term
| MA in c. elegants found how many new mutations/ genome/ generation? |
|
Definition
|
|
Term
|
Definition
| multiple mutations may have a stronger negative impact thta tthe sum of the individual effects |
|
|
Term
| how does a second copy create a new gene |
|
Definition
| it accumulates mutations sheltered from selection and if one works it gives a new gene |
|
|
Term
| effects of inversion in linkage (2) |
|
Definition
1) gene combinations kept together and selected together
2) some exhibit clinal variation (over latitudinal gradient) |
|
|
Term
| invasion of north america by d. subobscura showed |
|
Definition
identical cline in Est frequencies as in europe
-larger bodies and extended growth related to cold wet climates |
|
|
Term
|
Definition
1. genetic hitchhiking (with superstars!)
2. background selection (good combo cant escape bad background) |
|
|
Term
| 2 consequences of speciation by polyploidization |
|
Definition
1. individuals are reproductively isolated
2. if they can self fertilize they are an instant species |
|
|
Term
factors 1. against polylpoidization
2. for? |
|
Definition
1. rare, inbreeding cost, gamete wastage from 3n fertilizations
2. 4n sometimes bigger (slower, but stress tolerant), self-fertilization common in some species (less inbreeding cost and low gamete wastage) and extra chromo set is freer to evolve as in gene duplication example |
|
|
Term
|
Definition
-triploids have some fertility (produce 2n gametes)
-these 2N gametes can serve as a bridge to allow 4N polylpooid population to establish
-increases genetic diversity and less inbreeding than plants compared to selfing
-essential for plants that dont self |
|
|
Term
| why can polyploids prosper at the range limits? what is the effect? |
|
Definition
| because they are robust! concentrates them in an area that fosters successful reproduction |
|
|
Term
|
Definition
| that most alleles are equivalent; diversity results from genetic drift. |
|
|
Term
|
Definition
| argue that forces like shifting NS, heterozygote advantage, frequency- dependence (advantage to being rare) supports variation. |
|
|
Term
| measures of genetic diveristy (2) |
|
Definition
| 1. heterozygosity (frequency of heterozygotes in a population) 2. proportion of genes polymorphic |
|
|
Term
|
Definition
• practically, it serves as a null model. Deviations from H-W equilibrium point to interesting problems for investigation.
• conceptually, it solved a major dilemma for early population genetics: how variation can be maintained. |
|
|
Term
|
Definition
| Similarity in traits that is not due to inheritance from a common ancestor. |
|
|
Term
|
Definition
| disproportionately stronger selection against multiple mutants. |
|
|
Term
| nature of natural selection 8 misconceptions |
|
Definition
1. natural selction acits on individuals but sonequences occur in populations
2. natural selection acts on phenotypes but evolution is changes in allele frequencies
3. natural seleciton is not forward looking
4. new traits evolve though natural selection acts on existing traits
5. natural selection does not lead to perfection
6. natural selction is NON random but it is also NON progressive
(parasites, vestigial organs)
7. fitness is not circular
8. selection acts on individuals not for the good of the species |
|
|
Term
| 3 reasons using fossils is tough |
|
Definition
1) palaeontologists are rare
2) soft things don't fossilize
3) lots of environments are not very accessible |
|
|
Term
|
Definition
| found indohyus has similiarties with whales based on bone density and ear morphology but place them from far from hippos within the artiodactyls |
|
|
Term
|
Definition
| put whales back near hippos |
|
|
Term
|
Definition
balancers suppress recombination and have dominantly expressed marker,therefore they shelter genes from homozygosity
-can be used to isolate chromosomes
-minimize selection maximize drift to create mutations
-they found that mutations accumulate to decrease viability |
|
|
Term
| why are MA results an underestimate? |
|
Definition
lethal mutations are loss
silent mutations not measured
viability is not the only component of fitness
most measurements done under lax conditions |
|
|
Term
| kondrashov's middle class neighbourhood |
|
Definition
an alternate to balancing, you stop selection to observe mutations accumulate
-kids are random picks and fertility is standardize so there is no selection |
|
|
Term
| denver et all mutation accumulation in c elegans |
|
Definition
-indels are most common
-genome can never be in equilibrium
-mitochondrial DNA is even more mutable |
|
|
Term
| name 3 instances where mutating can be adaptive |
|
Definition
1) DNA polymerase varies heritably in error rate leading to variation in per genome mutation rate (u)
2) HIV/pathogens evade host defence in higher mutation rate
3) the lenski lines that became mutators suddenly = source of evolution in asexual bacteria
4) when colonizing new environments |
|
|
Term
|
Definition
| 3/12 mutations became mutator strains |
|
|
Term
| true or false: recombination and mutation create new alleles and genes |
|
Definition
| FALSE: meiosis reshuffles but doesnt create new alleles |
|
|
Term
|
Definition
| studied chromsome rearrangements in dros subobscura |
|
|
Term
| the latitudinal cline in the Est genes of d.subobscura showed |
|
Definition
-probably an association between the genes in Est and something related to temperature
-inversion polymorphisms can exibit clinal variation
-clines result from natural selection! |
|
|
Term
| true or false: clonal organisms are never in linkage dis-equilibirum |
|
Definition
|
|
Term
|
Definition
|
|
Term
| chromosome inversions create |
|
Definition
| supergenes: alleles likely to be transmitted as a unit |
|
|
Term
|
Definition
| new genes that can acquire new functions by mutations |
|
|
Term
| The most important source of new genes is probably ___________ the underlying mechanism for this is _________ |
|
Definition
| Most new genes probably originate from gene duplication due to unequal cross-over, as diagrammed in Figure 5.6 and discussed in Section 4.2. Gene duplication also creates new genes, and is associated with some major evolutionary events (such as the radiation of ray-finned fishes), but occurs less frequently that duplication of individual genes. |
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|
