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Phylogeny

• hypothesis about relationships and patterns of descent with modification
• tips: species in a larger group
• internal nodes: inferred lineage split from special events
• outgroups: indicates last common ancestor group
• clades: branches that include all things sprouted from them
• root:holds single common ancestor; starts from bottom or left
• branch: independent evolution of lineage that happened

Common Tree reading misconceptions

• 1.Species ranked from lowest to highest on tree.
• 2.Main line of species leads to distinct endpoint (not true b/c all siblings equally related to shared cousins.)
• 3. Reading across the tips does not show closeness in relationship.
• 4. Similarity is not relatedness (crocs > related to birds than lizard
• 5. Siblings not ancestors (primates disappeared and humans evolved)
• 6. Long branches are"t ancestral to other lineages and branches don't occur along lineages.
• 7. Different lineage age for modern species.
• 8.Time axis goes backward to show more modern species
• 9. More nodes = more distantly related
• 10. internal node indicate exact moment of physical change

HIV orgin

• HiV-1 (within hosts)
• SIV [cpz] chimpanzee --> transmission--> natural selection
• causing AIDS
• 3 independent transmissions
• More origin
• 3 groups : M, N, O ( M biggest)
• more virulent, so kills host fast, short time to infect new hosts
• favors monogamous system
• HIV-2 (affecting new hosts)
• SIV [sm] from Sooty Mangabeys (West Africa)--> humans--> natural selection
• less virulent than HIV-1

HIV and Vaccines

• hard to design vaccines because HIV rapidly growing w/ high mutation rate; more epitopes
• resistant alleles exist; more frequent in human population as epidemic continues
• best defense against HIV is education and changed behavior
• earliest strain found 1959

Less prone to evolve HIV resistant strains

• prescribe combination therapies ( lots of drugs in combination) to buy time and slow evolution of resistant strains
• Suspend drug for a while. Reintroduce drug. removes body's favoring of resistance.

Cost/ Benefits of Sexual reproduction hypothesis

• 1. purging deleterious mutations " DELETE THIS"
• 2. Red Queen hypothesis: sexual reproduction to stay ahead of the game

Two Fold Cost of Sex. Production

• TFC: if each sexual and asexual had the same # of offspring in a generation, asexual produces 2x as much offspring as sexual
• isogamy is a benefit of asexual reproduction: both sexes equally make zygote
• TWF is the cost to anisogamy not sexual reproduction (different size gametes)

HWE

• Conclusion: allele/ genotype frequency does not change from generation to generation w/o evolutionary changes
• if allele frequency in population is P and Q, then we have P^2+ 2PQ+Q^2=1
• random mating
• test if in HWE with chi square if P< 0.05
• Evolution: change in frequency of alleles in a gene pool of a population over time if influenced by mutations, and selection, which violates HWE assumptions