KHAEMENES ACADEMY · BIOLOGY 10 · WEEK 30 · DAY 04

Molecular Trees, Gene Trees & Conflict

Explain why different genes can yield different tree histories and how scientists reconcile conflict.

Safety and evidence boundary

Use supplied character matrices, public fossil/sequence data, and fictional taxa. No personal belief is graded. Scientific common-ancestry and phylogenetic models must be explained accurately; theological or philosophical claims may be discussed respectfully but are not interchangeable with empirical models unless they generate testable evidence.

Explicit science instruction

Gene sequences have their own histories. Gene duplication, lineage sorting, hybridization, recombination and horizontal transfer can make a gene tree differ from a species tree. Scientists compare multiple loci and models rather than assuming one gene is the whole history.

Worked example with reasoning

Gene X groups A+B while Gene Y groups B+C. If X duplicated before species divergence or Y introgressed between lineages, the conflict can be biologically informative rather than mere error. Additional loci and genomic context can discriminate explanations.

Guided question

Why is disagreement among gene trees not automatic evidence that phylogenetics has failed?

Independent work

  1. Compare three small gene trees.
  2. Identify conflict.
  3. List three biological causes.
  4. Propose evidence to distinguish them.

Investigation / Data Lab

Character-matrix phylogeny comparison

Question: Which of two candidate trees requires fewer character-state changes for the supplied fictional taxa?

  1. Score a supplied character matrix with at least five characters across four or five taxa.
  2. Map every character change onto Tree A and Tree B using the same coding rules.
  3. Count total changes and identify any homoplasy or ambiguous state.
  4. Compare the parsimony scores with a short molecular-distance dataset.
  5. Explain whether the evidence streams agree and why parsimony alone does not prove the true history.

Evidence standard: preserve the matrix, mapped trees, scores, and one model limitation.

Misconception check

A single “DNA similarity percentage” cannot by itself determine a complete species relationship.

Formative understanding check

What is a gene tree?

Worked response

A hypothesis about the historical relationships among copies/sequences of a gene, which may differ from the organismal species tree.

Open-book formative practice only; not an official mastery attempt or grade.

Mentor evidence conference

Ask Archaemenes to challenge your model topology, evidence classification, calculation, and stated uncertainty without substituting belief or protected answers for science mastery.

Open Archaemenes

Teacher guidance

Foundation: use side-by-side tree diagrams. Core: explain at least two conflict mechanisms. Extended: evaluate multilocus concordance and network-like histories.

Preserve learning evidence

Keep models, data work, corrections, source classifications, and limitations in the matching Week 30 evidence field.