bio sheet2 Cheat Sheet (DRAFT) by bioevocrib

Mode of transm­ission is region dependent - Likely mode of transm­ission is mainly hetero­sexual sex or injection in indo, kenya, Russia but MM sex in US and canada (hetero in uk!)

Immune system response - Dendrite captures virus and activates naïve helper T, these produce effector helper T (some also become memory helper T cells) - Effectors stimulate B cells which make antibodies that inactivate the virus, also activate killer T which destroy hosts who have the virus - But macrop­hage, effectors and memory Ts have CD4 and CCR5 which makes them targets for HIV

Where and when did HIV originate - HIV can evolve in one person and then an ancestor goes to the next patient, new enviro=new evo, we can build an accurate diagram with some parts! - HIV-1 was transf­ected from chimps to people many times HIV-2 was from monkeys o HIV2 is not as transm­issible or fatal and didn’t cause the epidemic, group M HIV1 is the most prevalent strain and our species had no T to deal with it - HIV evolves rapidly which makes vax hard - To estimate the time we had to guess the starting point, used unrooted phenogram, genetic differ­ences and linear regression (molecular clock) 159 strains and do pairwise compar­ison, estimate divergence from common ancestor and extrap­olate (back to 1914-1915)

Affects on body - Chronic infection damaged lymp leading to less T, HIV depletes CD4+ T in gut damaging it, allows bacteria into blood, bacteria in blood induces immune system which causes T cell prolif, giving HIV more cells to target (it does best in activated CD4+ Ts)

Why are infections fatal - Not intuitive, generally HIV evolves to be more aggressive and virulent over time, comp fitness increases then levels off, short sighted because host will die - We see more virulent means less time until aids, greater virulence over time too (more transm­iss­ible), overall transm­ission is max right in the middle (fits with fraction of patients with viral loads too) - As rate of mutation increases time to aids decreases, response by host can contribute to fatality (t cells in response helps viral prolif­era­tion) - Sometimes HIV virons produce variants the immune system can’t recognize, we can display p24 or HLA, in patients with HLA-B alleles the mutations to TSN makes it less detectable than the original TST in virus epitope - HIV can also bind to CXCR4 coreceptor and these viruses evolves faster to kill more T progre­ssing to aids faster, more transm­issible as they get more lethal Unit 2 – support for evolution

HAART - Highly active antire­tro­viral therapy (3+ drugs), increased survival, takes longer to evolve resistance to multiple drugs - Risk of evolving HIV resistance increases when you have done 80-90 prescr­ipt­ions, many stop here because side effect is so bad  resistant popula­tions

Selective lab breeding with mice (MICRO change over time) - High runners from each fam, selected for physical ability as they ran longer and faster against control Natural popula­tio­ns(­MICRO) - Three types of flower, one late flowering and one early, crossed and got middle! Vestigial struct­ure­s(M­ICRO) - Kiwi reduced wings, limbs in verteb­rates, tail bones (coccyx) and arrector pili in humans - Can also be genetic: we have a gene (CMAH 92bp) that creates an enzume with no function from chimps (incom­plete sugar coversion but grants malaria resist­ance!) - Develo­pme­ntal: chicks digits are homologous to ours when developing then they lose 1 Lab and natural experi­men­ts(­spe­cia­tion: new from old) - Lab flies feeding on starch vs maltose for a year, virgins preferred own diet flies - Warblers have to go around tiberan plateau, larger distance to travel will be more different when they meet, genetic diff and song diff, change occurs!

Extinction (MACRO new forms from old) - Irish elk, giant deer who went extinct Succession - Extant form is a succession of fossil form before it (slight changes) Transi­tional forms - Archeo­pteryx, link between dinos and birds this helped as more evidence for evolution - Turtle shells - Ribs expand outside shoulder blades to form shell, amniotes should have ribes inside, we have a transi­tional form - Leeping blenny (terre­strial fish) infer aquatic then see transition to amphib, then terres­trial

Geological time scale – Early is likely 148,00­0,000 (based on Pangaea drift, how long to get gap) Unifor­mit­ati­anism: Processes from past continue today Superp­osi­tion: New material goes on top Original horizo­nta­lity: Originally laid down horizo­ntally Cross cutting relati­ons­hips: Upper layer are younger Inclus­ions: Inclusions are older than host Faunal succes­sion: extant resembles extinct - Eras aren’t even because it is based on mass extinc­tions usually, red dots are the minimal divergence year

Ex. Shared dervived molecular trait, PMP-22 locus on chromo 17, CMT1A is on both sides leading to unequal crossing can lead to neuropathy and Charcot marie tooth disease 1A, shared in chimps and humans Ex. Shared loss, pseudo­genes of only exons are shared most with closest related ancestors Ex. Shared derived develo­pmental traits like pharyngeal pouches (gills in fish) and tail in fetus Ex. Shared derived structural trait: vertebrate forelimbs and orchid elements Homoplasy: cannot represent as synapo­morphic trait, must have evolved separately

Darwin’s finches (he rarely said finch or evolution in first additi­on)­/Gr­ant’s finches - Captured and tagged medium ground finch on daphne major, showed variation in beak depth (1), that beaks correlated in parents and offspring (2), indivi­duals competed for food (3) only large food was left so only those who ate it survived survival and repro was skewed (4), changed pop into large bird with large beaks o (2) Specif­ically Bmp4 mRNA differs in embryos, more means larger beak depth Natural selection operates at the individual and phenotypic level in past and present but produces changes at the population and genotypic level (average moves), cannot operate FOR the future, operates on existing traits but may yield new ones (ex corn kernel inc into new species)

- Evolution is a historical science but preada­ptation is wrong, they are random, we use exaptation instead (new use or had no use but is now an adapta­tion) ex. Panda thumbs due to malformed wrist, this actually outcom­peted! - Natural selection may yield many adapta­tions none of which can be perfect ex. NOT gono! finch beaks are wide as well, not perfectly deep and narrow - Natural selection is not exactly random, biased to those with best traits but operates on random variation - Survival of fittest, this is circular, we just see if 4 postulates and say evolution should eveolve - Macro and micro (species shall not beget species if you are cladist)