1. Analysis and visualization of
large collections of trees
A case study in Chalcidoidea (Insecta:
Hymenoptera)
Ana Dal Molin, Suzanne Matthews
James Munro, John Heraty, Jim Woolley

2. The tree space



The number of possible
trees is given
Criteria exist to
determine which ones
are better hypotheses
Heuristics

3. The tree space



The number of possible
trees is given
Criteria exist to
determine which ones
are better hypotheses
Heuristics

4. Case study



525 terminals
2992 characters, rDNA (18S and 28S D2-D5)
sequences
Structural alignment + MAFFT alignment of the
RAA's (EINSI)

5. Secondary structure is characterized by stems (paired bases) and loops
(unpaired bases): alignment

6. Case study: symptoms

Inconsistencies across repeated analyses

Spurious relationships

Why?

7. “low support”
“results highly
sensitive to the
method used”
recognized tribes
and subfamilies
group, but not in a
plausible place

8. Problems
1. Growing data sets lead to growing number of trees,
sometimes too large to be compared by eye
2. Dozens of thousands of trees with hundreds of
terminals = really large files

Can I even load them?
3. Inconsistencies and polytomies in consensus trees:

Do we have rogue taxa?

Has the search run enough?

Do we have enough signal?

9. Methods


TNT, 5 seeds, unweighted parsimony
5 different seeds resulted in 30,000 trees, 20061
steps, CI=0.165, RI=0.62

Portability: TreeZip

Set operations: TreeZip

Comparison via matrices of RF distances: MrsRF
−
Heatmaps of the distance matrices plotted using R

10. 1. Portability and set operations
File size comparison
• a print screen of file
structure
• [hashing?]
• Reference for details

11. Set Operations
• All trees were unique in
every set
but
• Union = 32,300 (unique)
trees, not 150,000
• Intersection = 28,422
trees
• Consensus….

12. 2. Comparisons: MrsRF

5x5 heatmap

13. Large heatmap

14. Distance between consensus trees =
0

15. Color strict consensus tree

16. More Information

17. Acknowledgements