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This document summarizes a case study analyzing and visualizing large collections of trees representing relationships within Chalcidoidea (Insecta: Hymenoptera). The study used sequences from 525 terminals and 2992 characters to generate 30,000 trees across 5 analyses. Tree sets were compared using operations like union and intersection in TreeZip. MrsRF was used to calculate Robinson-Foulds distances between trees and consensus trees, visualized with heatmaps. While inconsistencies emerged, the consensus tree agreed across analyses and recognized taxonomic groups were recovered.

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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
The tree space The number of possible trees is given Criteria exist to determine which ones are better hypotheses Heuristics
The tree space The number of possible trees is given Criteria exist to determine which ones are better hypotheses Heuristics
Case study 525 terminals 2992 characters, rDNA (18S and 28S D2-D5) sequences Structural alignment + MAFFT alignment of the RAA's (EINSI)
Secondary structure is characterized by stems (paired bases) and loops (unpaired bases): alignment
Case study: symptoms Inconsistencies across repeated analyses Spurious relationships Why?
low support results highly sensitive to the method used recognized tribes and subfamilies group, but not in a plausible place
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?
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
1. Portability and set operations File size comparison a print screen of file structure [hashing?] Reference for details
Set Operations All trees were unique in every set but Union = 32,300 (unique) trees, not 150,000 Intersection = 28,422 trees Consensus.
2. Comparisons: MrsRF 5x5 heatmap
Large heatmap
Distance between consensus trees = 0
Color strict consensus tree
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Acknowledgements

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