User:R. Eric Collins/MBL/PAML

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PAML Lab

Exercise 1

omega minimum at 0.067

Exercise 2

Objective:

  1. Test effect of transition / transversion ratio (κ)
    • κ goes up when estimated
    • S goes up when κ goes up
    • omega goes up when κ goes up
  2. Test effect of codon frequencies (π’s )
    • log likelihoods: F61 (-756.57) < F3x4 (-842.21) < Fequal (-926.28)
  3. Determine which assumptions yield the largest and smallest values of S, and what is the effect on ω
    • largest S/largest ω: F61 + κ=1
      • S = 165.8
      • ω = 0.320
    • smallest S/smallest: Fequal + κ=est
      • S = 40.5
      • ω = 0.063

Exercise 3

Objective: Use LRTs to evaluate the following hypotheses:

  1. The mutation rate of Ldh-C has increased relative to Ldh-A
    • =H2: is omega of C0/1 greater than A0/1?
      • omega_A 0.0755 omega_C 0.2394
      • yes the mutation rate has increased, and it is significant (LRT = 66 >> 3.84)
  2. A burst of positive selection for functional divergence occurred following the duplication event that gave rise to Ldh-C
    • =H1: is omega of C0 greater than C1&A0/1?
      • omega_A0 0.1319 omega_C0 0.192
      • yes the mutation rate has increased, but it is not significant (LRT=2.12 < 3.84)
  3. There was a long term shift in selective constraints following the duplication event that gave rise to Ldh-C
    • = H3: is omega of C0/1 different from A0 and A1?
      • omega_A0 = 0.0642 omega_A1 = 0.0949 omega_C0/1 = 0.2403
      • A0 and A1 are slightly different and C0/1 is greater and may have relaxed constraints
      • but it is not a significantly better explanation than H2 (LRT=3.05<3.84)