Cycle 12: Molecular Evolution

Question 1

State the characteristics of model systems that can be used for experimental evolution

Answer 1

• Organisms that have a small generation time and can have their ancestors frozen/viewed in some way are good model systems
• These include viruses, bacteria, chlamydomonas, drosophila, yeast

Question 2

Describe how the relative fitness of E. coli can be measured

Answer 2

1. Split a culture of bacteria into two
   
   • One we label with a neutral gene that turns the cells red which we call the evolved culture, and the other one is left blank
2. Subject the evolved culture to a condition (ex., low pH for 2000 generations)
   
   • Allow them to replicate
   • Then we mix them and allow them to grow for a short time at low pH
3. Calculate w = relative fitness = the growth rat of the evolved strain / the growth rate of the ancestral strain

Question 3

Assess what it means for W to be <,> or = to 1

Answer 3

• If w > 1, suggests adaptation has taken place
• If w = 1, then there is no adaptation taking place
• If w < 1, this suggests maladaptation

Question 4

Describe the design of Lenski’s long term evolutionary experiment (LEE) with E. coli

Answer 4

• Lenski grows 12 large, identical populations of E. coli and seeks to observe spontaneous mutations that occur from asexual recombination
• Every we day we take an aliquot of each population and put it into fresh medium
  
  • The medium contains reduced glucose as well as Fe-citrate (to main aqueous state of iron)
• Every 75 days we take an aliquot of each population and freeze them to allow us to go “back in time” and look at the ancestral populations later

Question 5

Where does citrate enter metabolism?

Answer 5

• Present in the citric acid cycle
• Acetyl-CoA can combine with oxaloacetate to produce citrate, or citrate can be directly taken up

Question 6

Describe the role of glucose limitation in the experiment and the effects on the role of citrate

Answer 6

• Glucose resources run out after about 8 hours of growth, stopping growth
• Citrate can only be taken up in E. coli under anaerobic conditions, which are non-existent in the lab
• Gives rise to an ecological opportunity! If a cell line could access the citrate under aerobic conditions, it would enable growth only until it runs out of citrate!

Question 7

What is the Cit+ phenotype…that is what did the researchers detect that was different in the Ara-3 line?

Answer 7

• Cit+ phenotype enables cells to grow on citrate under aerobic conditions, giving them a growth advantage once glucose resources run out

Question 8

Describe the actualisation mutation that occured

Answer 8

• In a normal Cit- population, the citrate gene exists under an operon whose promoter is repressed in the presence of oxygen
• In the Cit+ population, actualisation occurred: part of the citrate operon was duplicated and inserted further down the gene, in front of a constitutive promoter!

Question 9

Describe the refinement process of the Cit+ phenotype

Answer 9

Question 10

What is meant by the term potentiation and what is the evidence that a potentiation event occurred after 20,000 generations?

Answer 10

• Contingency believes that each step in evolution is dependent on all the steps before it
  
  • This mutation 1 is called a potentiation mutation: a silent mutation that has no effect on the phenotype but enables mutation 2 (actualisation) to occur
• It was observed that a potentiation event occurred at the 20,000 mark
  
  • Species removed from freezing at the 10,000 mark never developed Cit+, but species thawed after the 20,000 mark did!

Question 11

Is the Ara-3 line a new species?

Answer 11

By definition, E. coli can’t grow on citrate aerobically, so some argue that this is a new species

Question 12

Explain why Cit+ lines do not drive Cit- lines to extinction

Answer 12

Cit+ lines do not drive Cit- lines to extinction because Cit- lines are more effective at using glucose while supplies last, so it is not completely unfavoured

Question 13

What is trichromatic vision?

Answer 13

• Three different types of rhodopsin
• SW, MW, LW

Question 14

What accounts for the differences in absorption characteristics of the different rhodopsins?

Answer 14

• The pigment retinal remains the same in each cone cell, but the protein (opsin) varies slightly
• Each type of opsin is folded slightly differently, and so absorbs slightly different wavelengths by straining the structure of the retinal

Question 15

Describe the major similarities and differences as revealed in protein alignment of SW, MW and LW opsins

Answer 15

• MW and LW opsins are found on the X chromosome (likely originated by duplication) while SW is on chromosome 7 (likely originated via translocation)
• Have the same counterion glutamic acid and same retinal binding sequence lysine

Question 16

Describe the importance of lysine at position 296 and glutamic acid at position 113 of opsins

Answer 16

• Highly conserved amino acids in the different types of opsins
• Lysine at position 296 binds to retinal
• Glutamic acid at position 113 stabilises the interaction between lysine and retinal (it is a counterion)

Question 17

Describe the association between trichromacy, dichromacy, old world monkeys and new world monkeys

Answer 17

• Old world monkeys are found in Africa and Asia and are trichromats
  
  • Originally started as dichromats, evolved to be trichromats
• New world monkeys are dichromats found in South America
  
  • Separation arose from the splitting of Pangea 50 mya

Question 18

State the general distribution of di vs. tri vs. tetrachromacy among vertebrates

Answer 18

• Dichromats: dogs, goats, new world
• Trichromats: humans, old world
• Tetrachromats: reptiles, birds, dinosaurs, common ancestor of vertebrates

Question 19

Mechanisms to explain how and why, over evolutionary time, lineages may lose and regain opsin

Answer 19

• Dichromacy is advantageous if you need to break camouflage or if you have a nocturnal lifestyle where colour vision isn’t necessary
  
  • Ex., early mammals, where 2 opsins are lost
• Trichromacy is advantageous if you need to determine ripeness of food
• in genes
  
  • Ex., old world monkeys, where 1 opsin is gained back
• Thus, complexity is not always better

Question 20

State the mechanism to explain why some new world monkey females have better colour discrimination than any males

Answer 20

Females have 2X chromosomes, so 2 alleles making slightly different opsins that strain retinal in different ways to absorb different wavelengths, therefore better colour discrimination