Phylogenomics: Gene Trees, Species Trees and Why They Disagree · seed 1 · A4, ink-friendly. The answer key prints on its own page for grown-ups.

Why genes disagree about the species tree

Science · Genetics & Evolution · ages 22-24
Name ______________________   Date ____________

  1. What does a coalescent summary method do?

    • It discards every gene that disagrees with the majority
    • It strings all genes into one giant alignment
    • It infers each gene tree, then finds the species tree fitting their distribution

  2. What is incomplete lineage sorting?

    • Gene variants failing to sort neatly when large ancestral populations split quickly
    • The loss of all gene copies during a population bottleneck
    • The transfer of genes between unrelated species by infection

  3. A gene tree always matches the species tree when the data are clean.

    Circle one:   True   False

  4. Discordance clusters at one short internal branch and matches coalescent frequencies. What is it?

    • Proof of laboratory contamination
    • Real incomplete lineage sorting to be modeled
    • A rooting error that longer sequences must fix

  5. Your concatenated alignment gives full support, but single genes strongly disagree. What do you suspect?

    • Concatenation converged on the wrong answer under genuine discordance
    • The species tree is now proven beyond doubt
    • Longer sequences would remove the need for any model

  6. One topology is enriched among gene trees and linked sites share the pattern. What does that show?

    • Symmetric sorting with no gene flow
    • Random estimation error across the genome
    • Introgression grouping the exchanging partners

  7. If conflict fades as sequences get longer and models improve, it was likely estimation error rather than true discordance.

    Circle one:   True   False

  8. A colleague averages conflicting genes into one tree and calls the conflict noise. What is the error?

    • Averaging is always the safest choice
    • True biological conflict is signal to model, and averaging can lock in the wrong tree
    • Gene trees may never be inferred separately
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Answer key

For grown-ups. Fold this page away before handing over the rest.

Why genes disagree about the species tree W1-mt_rg7feIg1D4-s1

  1. It infers each gene tree, then finds the species tree fitting their distribution · The two stage logic respects that genes have genuinely different histories.
  2. Gene variants failing to sort neatly when large ancestral populations split quickly · Big ancestral populations plus fast splits leave variants unsorted across descendant species.
  3. False · Genes have their own histories, so a gene tree can differ for biological reasons.
  4. Real incomplete lineage sorting to be modeled · Sorting concentrates at short branches and follows predicted frequencies, so it is signal.
  5. Concatenation converged on the wrong answer under genuine discordance · Concatenation assumes one shared tree, so real discordance can mislead it with confidence.
  6. Introgression grouping the exchanging partners · Flow enriches exactly the topology of the exchanging partners, with matching site patterns.
  7. True · Noise shrinks with more data and better models, while biological conflict persists with structure.
  8. True biological conflict is signal to model, and averaging can lock in the wrong tree · Genuine disagreement needs a method that expects conflict instead of hiding it.
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