Models of Sequence Evolution and Maximum Likelihood Trees · seed 1 · A4, ink-friendly. The answer key prints on its own page for grown-ups.
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The model behind the tree

Science · Genetics & Evolution · ages 22-23
Name ______________________   Date ____________

  1. In a model with gamma site-rate variation, what does the gamma shape parameter control?

    • The spread of fossil ages among sampled species
    • The spread of population sizes among sampled species
    • The spread of substitution rates among sites

  2. Which model allows unequal equilibrium base frequencies and a separate exchangeability for each of the six nucleotide pairs?

    • JC
    • GTR
    • HKY

  3. For unobserved ancestral bases, likelihood sums over possible assignments using the probabilities specified by the model.

    Circle one:   True   False

  4. Which features does HKY allow beyond the Jukes-Cantor constraints?

    • Unequal base frequencies and a separate exchangeability for every pair
    • Unequal base frequencies and a transition/transversion parameter
    • Equal base frequencies and a separate exchangeability for every pair

  5. Sites evolve at very different rates, but a fitted model assumes equal site rates. Which statement correctly describes the risk?

    • Fitting branch lengths removes bias
    • The rate assumption can bias branch lengths but not topology
    • Branch lengths and topology can be biased

  6. For the same alignment, the preferred topology changes when the substitution model changes. What does this demonstrate?

    • The preferred topology is sensitive to model choice
    • The richer model has proved its topology historically true
    • The alignment has lost all phylogenetic information

  7. For the same alignment, a richer nested model with a higher maximized likelihood must be the better model choice, regardless of its extra parameters.

    Circle one:   True   False

  8. A GTR model has equilibrium frequencies A = 0.30 and G = 0.15, with a positive shared AG exchangeability. What is the ratio of the A-to-G rate to the G-to-A rate?

    • 1:2
    • 1:1
    • 2:1
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Answer key

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The model behind the tree W1-mt_Ujtg0xul9N-s1

  1. The spread of substitution rates among sites · The shape parameter controls variation in relative rates among alignment sites. With the mean fixed, smaller positive values mean greater variation.
  2. GTR · GTR permits six pair exchangeabilities. Fixing the overall rate scale leaves five free relative exchangeability parameters.
  3. True · Ancestral assignments contribute according to their model probabilities. The calculation sums those contributions rather than selecting one assignment or giving every assignment equal weight.
  4. Unequal base frequencies and a transition/transversion parameter · HKY allows unequal equilibrium frequencies and a parameter distinguishing transition from transversion exchangeabilities. Separate exchangeabilities for all six pairs belong to GTR.
  5. Branch lengths and topology can be biased · Fitting branch lengths does not remove the mismatch in site rates. Ignoring site-rate variation can bias branch lengths and sometimes topology; the effect depends on the data and analysis.
  6. The preferred topology is sensitive to model choice · Likelihood scores depend on model assumptions. A change in the preferred topology demonstrates sensitivity, not proof that either topology is true.
  7. False · More parameters can improve fit without establishing a better model choice. Compare complexity, model fit and the sensitivity of conclusions.
  8. 1:2 · The rates use the destination frequencies: 0.15 for A to G and 0.30 for G to A. Their shared exchangeability and scale factor cancel, giving 0.15:0.30 = 1:2.
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