What does the gamma rate parameter model?

• The number of species in the tree
• The age of the oldest fossil
• Rate variation across sites

Which model allows each nucleotide pair its own rate plus unequal base frequencies?

• Jukes-Cantor
• The general time reversible model
• HKY

A tree likelihood sums over all possible ancestral states at the internal nodes.

Circle one:   True   False

HKY adds which ingredients over Jukes-Cantor?

• Fewer parameters and no rates
• Unequal base frequencies plus a transition bias
• Fossil dates and tip ordering

A study ignores rate variation although sites evolve at very different speeds. What goes wrong?

• Nothing ever goes wrong
• All branch lengths become infinite
• Long branches shrink unfairly and fast lineages may group wrongly

Two candidate trees swap winner when the model moves from Jukes-Cantor to GTR plus gamma. What does this show?

• Model choice directly changes which tree wins
• Likelihood never depends on any model
• The alignment contains no information

Reading a tree by the left-to-right order of tip names gives the correct relationships.

Circle one:   True   False

A tree groups two fast evolving lineages with sky-high support under a no-gamma model, but the grouping vanishes under GTR plus gamma. What is the likely story?

• Coincidental matches fooled the simple model; the grouping is suspect
• The rich model must be wrong because support was high
• Fast lineages always form true clades