Evolution

• Define Evolution 


  Biological Evolution is a change over time in the proportions of individual organisms differing genetically in one or more trait
• How do evolutionary changes transpire?

  -by the origin and subsequent alteration of the frequencies of genotypes from generation to generation within populations,– by alterations of the proportions of genetically differentiated populations of a species or– by changes in the numbers of species with different characteristics, thereby altering the frequency of one or more traits within a higher taxon.
• What are Darwin's central postulates? (Adaptation)

  • There is variation

  • Some of the variation is heritable

  • Not all individuals can survive/reproduce

  • Some of the variation affects survival and/or reproduction

  • Traits which enhance survival and/or reproduction will become more common
• What is the relation between Darwin's postulates and HIV?

  Adaptation to Drug Treatment• There is variation– Reverse Transcription has no error checking, so mutation rate is high.• Some of the variation is heritable– Mutation in RT is incorporated into all daughter virions• Not all individuals can survive/reproduce – AZT blocks reproduction of most viruses• Some of the variation affects survival and/or reproduction – Mutants resistant to AZT reproduce more.• Traits which enhance survival and/or reproduction will become more common. – AZT resistance evolves within the host.
• What are the basics of divergence?

  • Different populations occur in different places and/or under different ecological conditions• Populations in different places tend not to mate with one another– And/or• It is difficult/impossible to be well adapted to all sets of conditions.• Populations will each adapt to their separate conditions• Populations will thus become different from one another.
• Explain how evolution is a process that follows FROM the four postulates rather than a process that proceeds towards a 'goal'

  • Mutation generates variation at random – No foresight, no purpose • Selection Filters the Variation– Selection is not random– (also has no foresight) • Variation THEN selection– If a variant doesn’t exist it can’t be selected for no matter how beneficial it might be. • Therefore, biological evolution happens• -> over generations, Not within a generation• ->in populations, Not in individuals
• Elements of evidence for evolution

  • We observe selection in action - HIV, Finch beaks
  • We can make selection happen in the lab - Crop and animal breeding
  • We can observe divergence, and observe that it creates species differences - "Ring" Species
  • We have created new species - Polyploids, e.g. Kew primrose
  • We have even re-created existing species - Desert sunflowers
  • We observe shared traits derived from ancestors - Homologies - Mammalian forelimbs - Genetic defects
  • We observe vestigial remnants of prior ancestral traits - Wings on flightless birds, pelvic bones in snakes, whales
  • We observe transitional forms in the fossil record - Whales - Birds - Terrestrial vertebrates
• How to calculate allele frequencies

  p = freq[AA] + ½ freq[Aa] q = freq[aa] + ½ freq[Aa]• Here we have 25 mice– 0.36 are AA• (9 out of 25)– 0.48 are Aa• (12 out of 25)– 0.16 are aa• (4 out of 25)• 25 mice -> 50 alleles• All of the alleles in AA are A• Half of the alleles in Aa are A
• What are the assumptions for the Hardy-Weinberg equilibrium?

  • Large (Infinite) Population– No Genetic Drift• No Mutation• No Selection• No Migration• Allele Frequencies Do Not Change• Random Mating – Only affects Genotype Frequencies
• How to calculate Hardy-Weinberg equilibrium?

  Genotype Frequencies are– AA p2– Aa 2pq– aa q2
• What does mutation produce?

  New variation

  • In the DNA Sequence of Genes– Point Mutation• In the Number of Genes– Duplication, Polyploidy– New Genes• In the arrangement of Chromosomes– Polyploidy, Aneuploidy, Inversion– Reproductive Isolation b/c Meiosis disrupted in heterozygotes.
• What is mutation rate?

  The frequency at which a mutation is likely to occur in • Per base pair, per generation ≈ 10^-9• Per gene, per generation ≈ 10^-5 - 10^-6• Per genome per generation ≈ 0.1^ – 1
• What are the types of mutations?

  Point mutation, insertion, deletion, mutation into stop codon, transition & transversion
• What is the difference between a transition and transversion?


  Transition: purine-> purine or pyrimidine-> pyrimidine

  Transversion: pyrimidine-> purine purine->pyrimidine
• Describe and/or predict how mutation affects genetic variation and the equilibrium allele frequencies expected under one- and two-way mutation.

  One way: one allele will become dominant while the other disappears µ

  Two way: equilibrium amongst them, higher mutation rate > more abundant V
• Describe mutation effects on fitness and how experiments provide evidence of this

  usually fitness will drop, way of testing-> 2 groups: control (allow selection) + treatment (no selection) see which of the 2 has higher fitness
• Calculate the change of allele frequency under natural selection (using the ‘selection table’)

  Symbol for fitness= W

  A) p^2

  
• Describe and/or interpret experiments testing the expected outcome of selection (overdominance)

  overdominance: heterozygote adaptation strength > homozygote (fitness higher)

  
• Describe and/or interpret experiments testing the expected outcome of selection (lethal recessive)

  letal recessive: will take time to go away

  
• Describe and/or interpret experiments testing the expected outcome of selection (deleterious)

  deleterious: lowers fitness
• What are the problems when trying to create a vaccine i.e. the case of HIV?

  Rapid diversification of coat proteins• Epitopes evolve to evade host immune system• Vaccine from present strain(s) unlikely to match future virions
• Mutations produce new variation in... (3 things)

  • In the DNA Sequence of Genes– Point Mutation• In the Number of Genes – Duplication, Polyploidy – New Genes• In the arrangement of Chromosomes – Polyploidy, Aneuploidy, Inversion – Reproductive Isolation b/c Meiosis disrupted in heterozygotes
• How does duplication arise?

  unequal cross over during meiosis
• What is the difference between polyploidy and anyploidy?

  • Change in Chromosome number• Polyploidy – complete doubling All Chromosomes• Aneuploidy – Fission, fusion, or doubling of only some Chromosomes.• Prevents mating with Ancestors
• What is the equation for mutation-selection balance?

  q*=√(µ/s)

  
• What is a back mutation?

  The previously mutated allele could return to what it originally was a -> A Mutation rate -> (‘nu’)

  A -> a Mutation rate -> (‘mu’)

  
• How do you find the stable equilibrium?

  p*=v/µ+v (same as the two way mutation)
• How does fitness affect the new (mutated) alleles “Mutation Accumulation Experiment”

  Compare (Control):• Mutation with Selection– If mutations reduce fitness– Mutants will leave fewer offspring• Mutations Eliminated– Average fitness should remain at some equilibrium

  With (Treatment):• Mutation Without Selection– Single individual descent– Each Individual leaves exactly one offspring• Mutations Accumulate• When selection is re-imposed:• See whether Fitness has dropped.
• What is the definition of fitness?

  • The extent to which an individual contributes genes to the next generation• Lifetime reproductive success.• Under a given set of environmental circumstances• Of course, under different ecological conditions, fitness, and therefore selection may change.
• What is the definition of selection?

  • Difference (on average) in survival or fecundity Between groups ofindividuals with different genotypes or phenotypes

  • Difference in contribution of genes (alleles) to the next generation.

  • Consistent across individuals with the same genotype or phenotype under a given set of environmental circumstances
• What is the mean fitness?

  • The Average Fitness of all the individuals in the population• This is just the sum of the “Product” column in the table.– Note: it is NOT the average of the fitness column

  
• What is the mutation-selection equilibrium?


  • Take the result from mutation• Plug it in for selection• Set p" = p (no change) and Solve

  
• What are the mutation selection balances?

  Deleterious dominants-> Fitnesses = 1-s, 1-s, 1

  Deleterious recessives-> Fitnesses = 1, 1, 1-s

  Lethal recessives-> Fitnesses = 1, 1, 0 (s = 1)
• What is genetic drift?

  • Changes in allele frequency due to

  • random sampling variation when drawing alleles to form zygotes or

  • Chance variation in survival, unrelated to genotype.

  • Most pronounced in small populations.
• How can a mutation be neutral?


  What makes a gene neutral is that it has no effect on fitness
• What is expected heterozygosity?

  Expected under random mating (ie HWE) Depends on allele freqs Stays the same even if not in HWE

  =2pq
• Expected heterozygosity in natural populations

  • Expected heterozygosity has been measured in many many species– Molecular techniques• It varies widely from species to species• Usually much less than 0.5 – Unless there are more than two alleles
• Predicting Loss of He

  Multiply each value for He By the probability of it occurring. Add up

  Loss is fastest for Small populations

  
• What is effective population size?

  • Ne

  • The size of an ideal population that loses variation at the same rate as your actual population.

  • Ne usually less than N
• Why is Ne < N?

  Our theoretical calculation assumed what’s called a Poisson distribution

  ->Each allele was equally likely to ‘get picked’

  In the real world, however, there are

  • More individuals that have either very many or very few offspring

  • Fewer individuals that have the “average” number of offspring

  Than we assumed in the calculation