Sunday Discussion on Biological Issues

The discussion was moderated by John Luecke. Susan Holmes opened the discussion by suggesting that we might ask the biologists: what mathematical or biological questions related to phylogenetic trees are most important to biologists? She also invited clarifications about things that have been addressed in talks earlier in the day.

Q. What properties of phylogenetic trees make them different from random trees? Is there some kind of structure that makes them different? (Epstein)

Q. What are the characteristics that a ``distance between trees'' should have that biologists would want? (Luecke)

Q. Is there a difference between some real distribution of trees on tree space rather than some random distribution? (Holmes)

Q. Problem: make notions of distances accessible to biologists, so they might use them. (Huelsenbeck)

More comments about tree space topology and branch lengths:

Q. How to pick a tree (or tree average) from a set of trees resulting from data?

Q. How to understand or deal with residuals, such as non-tree like data?

More comments on distances:

Q. Which is better: concatenating DNA sequences first or averaging trees later?

Q. What is the right notion of an ``average'' of trees?

Q. What are good properties of averaging? (Luecke)

Q. What would be the distribution on trees that gives majority rule consensus as its average? (Holmes)

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