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

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

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

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

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

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

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

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