1. Prioritize Organism Selection for the Genomic Encyclopedia Project to Optimize Phylogenetic Diversity
Dongying Wu
April 10, 2007

2. Special Thanks:
Sourav Chatterji
Jason Raymond

3. The lack of phylogenetic diversity is evident
in the current whole genome databases
Certain phyla have been heavily sampled
others have only sparse representatives
Many phyla have been ignored
The missing gaps in the current genome data
are the obstacles for us:
Getting the full picture of the “tree of life”
Understanding of a full range of ecosystems and
biological mechanisms
Anchoring Metagenomic sequencing data   
Proteobacteria  
Firmicutes

4. Solutions
Tree of Life
the Genomic Encyclopedia Project for Bacteria and Archaea
Greengenes ssu rRNAs: sequence entries
ATCC: strains in more than 750 genera
DSMZ: cultures representing 6900
species and 1400 genera (1207 bacteria
and 77 archaea genera)

5. Prioritize Organism Selection to Optimize Phylogenetic Diversity
Phylogenetic diversity (PD): if T is a tree whose leaf labels comprise a set X of species,
and whose edges have non-negative real-valued lengths, then for a subset Y of X,
the PD score of Y is the sum of the lengths of the edges of the minimal subtree of
T that connects Y

6. Input: 2 +
A tree
(optional: a sub tree)
A number (N)
Output:
A list of N taxa that gives the maximum PD for the sub-tree

7. Algorithm: Greedy Algorithm
Reference: Vincent Moulton, Charles Semple and Mike Steel, Optimizing phylogenetic
deverusyt under constraints, Journal of Theoretical Biology,
doi: /j.jtbi ,2006

8. Take a tree and a sub-tree
Calculate the added PD for
each taxon to the subtree
Grown the subtree to the taxon that
adds the maximum PD
Repeat the above steps N times,
the resulting subtree is the one gives
the maximum PD given the imposed constrains

9. Glory Details How tree structure is store in PERL ?
Two Dimension Matrix. A C
Node1
Node2 B D

10. Build Subtree: Base upon Index Paths
Chose any taxon from the original sub-tree as a reference taxon,
index all the paths connect the reference taxon and other taxa. A
A is the reference taxon C
B: B, Node1, A
C: C, Node2, Node1, A
D: D, Node2, Node1, A
Node1
Node2 B D

11. { C B: B, Node1, A C: C, Node2, Node1, A D: D, Node2, Node1, A Node1
Build subtree: combine the paths
Subtree A-B-C:
B: B, Node1, A
C: C, Node2, Node1, A
Calculate and grow subtree: Follow each path
Calculate added PD if subtree grows to D: {
D, Node2, Node1, A

12. If no starting subtree is defined, the program will identify the
longest path as the starting subtree
Step 1: pick any taxon, identify the
farthest taxon
Step 2: Start from the taxon picked
from step 1, identify the longest path.
It is the longest path for the whole tree. A A C C B B D D

13. Run the program: On Bobcat:
/home/dwu/dwu_scripts/public_scripts/maxPD.pl -t input_tree -n number -o output -l input_list(optional)
-i: input tree
-n: the number of taxa that the user need for the output list
-o: output
-l: input list, the user can define a list of taxa, that must be included in the PD calculations (for example, species the user have to include)
-gml: yes or no, output gml file option

14. Output Format:
Taxon ID PD Addition to the subtree ID ID ID

15. Results Visualization
Free software to visualize network/tree structure: yEd

16. GML Input format: graph [
node [id 1 label "A" graphics [ w 50 h 50 type "circle" fill "#AA0000"]]
node [id 2 label "B" graphics [ w 50 h 50 type "circle" fill "#666666"]]
node [id 3 label "C" graphics [ w 50 h 50 type "circle" fill "#AA0000"]]
node [id 4 label "D" graphics [ w 50 h 50 type "circle" fill "#666666"]]
node [id 5 label "node1" graphics [ w 3 h 3 type "circle" fill "#666666"]]
node [id 6 label "node2" graphics [ w 3 h 3 type "circle" fill "#666666"]]
edge [source 1 target 5 graphics [ fill "#AA0000" width 4 ]]
edge [source 2 target 5 graphics [ fill "#666666" width 4 ]]
edge [source 5 target 6 graphics [ fill "#AA0000" width 4 ]]
edge [source 6 target 3 graphics [ fill "#AA0000" width 4 ]]
edge [source 6 target 4 graphics [ fill "#666666" width 4 ]] ]

17. Select 300
out of 30000
based upon a
ssu-RNA neighbor
join tree

18. Y - Added PD X- added taxon (30000 picks /30000 taxa)

19. Y – PD of subtree X – added taxon (30000 picks / 30000 taxa)