Separate locus histories from a single species-tree claim

1. Orient: Separate locus histories from a single species-tree claim

A gene tree describes the history inferred for sampled sequence copies; a species tree concerns lineages of organisms. These need not coincide. Sequence duplication can create paralogs, horizontal transfer can move material across lineages, and ancestral polymorphism can persist through successive divergences before different variants are retained.

2. Explain the evidence and inference model

Consider ancestral variants X and Y present before two closely spaced lineage splits. Descendants can retain different variants even when no new transfer occurs after divergence. A sequence tree may then group copies by the older variant history rather than by the most recent species split. This incomplete-lineage-sorting explanation is distinct from duplication/loss or introgression.

The original summary contains100 hypothetical loci assigned to three quartet hypotheses. Controls change how many support each split. These are not bootstrap replicates; a50% locus fraction is not automatically a50% posterior probability for a species tree. Linked loci and shared inference errors can reduce effective independence.

Check orthology, alignment, recombination, taxon sampling and model adequacy before interpreting conflict. Ribosomal sequence comparisons and cellular characters transformed classification of Bacteria, Archaea and Eukarya, but a conventional domain label does not settle every deep branching relationship. Endosymbiotic organelle histories and horizontal transfer add reticulate relationships; no single gene should silently stand for every part of an organism’s history.

3. Reconstruct a worked example

If50 loci supportAB|CD,30 supportAC|BD and20 supportAD|BC, the largest observed locus fraction is0.5. It is legitimate to report that distribution; it is not legitimate to callAB|CD proven or assign it posterior probability0.5 without an inference model.

4. Predict and investigate

Predict first: Would conflicting gene trees necessarily mean one of the DNA alignments was fabricated or every tree method failed?

Compare50/30/20 with40/30/30 locus counts. Retain all conflicts and identify one biological and one methodological explanation. Describe independent orthology or genomic-location evidence that could discriminate them without generating or modifying biological material.

Retain the complete matrix, topology, branch lengths or detection assumptions with the first prediction and all conflicting results. These original hypothetical data are not actual specimen observations or measured evolutionary histories.

5. Transfer and defend a changed case

Apply the mechanism to a changed case

A packet has45 loci supportingAB|CD,40AC|BD and15AD|BC. What is the largest observed fraction, and what does it not establish?

Retain your calculation, units and assumptions in the lesson notebook before opening this public practice response.

Compare a worked response

The fraction is0.45. It does not establish a species-tree posterior probability, independent-locus assumption or the mechanism causing discordance. A close plurality may be sensitive to sampling and model choice.

6. Reflect and preserve uncertainty

Explain which conclusion is conditional on the model, identify an alternative and propose independent discriminating evidence. Use the General Biology II workspace to preserve a first argument, human critique and revision. Public practice and submitted prose do not establish independent phylogenetic, sampling or practical competence.

Supporting scientific reference, checked 30 October 2026. Original prose, numerical packets and diagrams; no source artwork or exercise is reproduced and no organism handling is requested.