Talk given at Duke biology, November 2012

1. IF THIS IS THE FUTURE,
WHERE IS MY TREE OF LIFE?
Karen Cranston
National Evolutionary Synthesis Center (NESCent)
@kcranstn
http://www.slideshare.net/kcranstn

2. Tree of life
• ~2million named
species
• Millions
more
unnamed / undiscovered

4. Phylogeny'papers,'1978;2008'
12000"
10000"
Number'of'papers'published'
8000"
Rapid"increase"in"applica?ons"of"
phylogeny,"beginning"in"early"1990s"
6000"
4000"
2000"
0"
1978" 979" 980"1981" 982" 983" 984"1985" 986"1987" 988" 989" 990"1991" 992" 993" 994"1995" 996"1997" 998" 999" 000"2001" 002" 003" 004"2005" 006"2007" 008"
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2
Year'
Source:"ISI"Web"of"Science""
graph from David Hillis

5. What does it mean to “have” the tree of life?

7. Archiving sequence data is a
community norm
~4% of all published
phylogenetic trees
Stoltzfus et al 2012

8. “Publishing a tree”
= picture in a PDF
EVOLUTION
Fig. 1. Combined molecular phylogenetic tree for Diptera. Partitioned ML analysis of combined taxon sets of tier 1 and tier 2 FLYTREE data samples (−lnL =
Weigmann et al. PNAS, 2011
344155.6169) calculated in RAxML. Circles indicate bootstrap support >80% (black/bp = 95–100%, gray/bp = 88–94%, white/bp = 80–88%). Nodes with im-
proved bootstrap values resulting from postanalysis pruning of unstable taxa are marked by stars (black/bp = 95–100%, gray/bp = 88–94%, white/bp = 80–
88%). Colored squares on terminal branches indicate the presence, in at least one species of a family, of ecological traits as shown to lower left. The number
of origins of each trait was estimated with reference to the phylogeny, the distribution of each trait among genera within a family, and the known biology of
the organisms.
thermore, a paraphyletic relationship of phorids and syrphids To test this hypothesis, we used a relatively recent phylogenomic
would support the hypothesis that their shared special mode of marker: small, noncoding, regulatory micro-RNAs (miRNAs).

9. Lander et al. Nature 2001

10. Rod asks: Why do we need a database of trees?

11. Fig. 1. Combined molecular phylogenetic tree for Diptera. Partitioned ML analysis of combined taxon sets of tier 1 and tier 2 FLYTREE data samples (−lnL =
344155.6169) calculated in RAxML. Circles indicate bootstrap support >80% (black/bp = 95–100%, gray/bp = 88–94%, white/bp = 80–88%). Nodes with im-
proved bootstrap values resulting from postanalysis pruning of unstable taxa are marked by stars (black/bp = 95–100%, gray/bp = 88–94%, white/bp = 80–
88%). Colored squares on terminal branches indicate the presence, in at least one species of a family, of ecological traits as shown to lower left. The number
of origins of each trait was estimated with reference to the phylogeny, the distribution of each trait among genera within a family, and the known biology of
the organisms.
thermore, a paraphyletic relationship of phorids and syrphids To test this hypothesis, we used a relatively recent phylogenomic
would support the hypothesis that their shared special mode of marker: small, noncoding, regulatory micro-RNAs (miRNAs).
extraembryonic development (dorsal amnion closure) (26) miRNAs exhibit a striking phylogenetic pattern of conservation
evolved in the stem lineage of Cyclorrhapha and preceded the across the metazoan tree of life, suggesting the accumulation and
origin of the schizophoran amnioserosa. maintenance of miRNA families throughout organismal evolution
Wiegmann et al. PNAS Early Edition | 3 of 6

12. assembly
alignment
inference
expertise Fig. 1. Combined molecular phylogenetic tree for Diptera. Partitioned ML analysis of combined taxon sets of tier 1 and tier 2 FLYTREE data samples (−lnL =
344155.6169) calculated in RAxML. Circles indicate bootstrap support >80% (black/bp = 95–100%, gray/bp = 88–94%, white/bp = 80–88%). Nodes with im-
proved bootstrap values resulting from postanalysis pruning of unstable taxa are marked by stars (black/bp = 95–100%, gray/bp = 88–94%, white/bp = 80–
88%). Colored squares on terminal branches indicate the presence, in at least one species of a family, of ecological traits as shown to lower left. The number
of origins of each trait was estimated with reference to the phylogeny, the distribution of each trait among genera within a family, and the known biology of
the organisms.
time thermore, a paraphyletic relationship of phorids and syrphids
would support the hypothesis that their shared special mode of
extraembryonic development (dorsal amnion closure) (26)
evolved in the stem lineage of Cyclorrhapha and preceded the
origin of the schizophoran amnioserosa.
To test this hypothesis, we used a relatively recent phylogenomic
marker: small, noncoding, regulatory micro-RNAs (miRNAs).
miRNAs exhibit a striking phylogenetic pattern of conservation
across the metazoan tree of life, suggesting the accumulation and
maintenance of miRNA families throughout organismal evolution
$$$ Wiegmann et al. PNAS Early Edition | 3 of 6

14. NSF IDEAS LAB
i. Pre-proposal / application iv. Pitch high risk proposal
ideas at end
ii. 5 day highly facilitated
workshop v. NSF invited full proposals
iii. Self-assembly into groups

15. • Community assembly of the
tree of life (Open Tree of Life)
• Next generation Phenomics
(PI O’Leary)
• Arbor: Comparative Analysis
Workflows (PI Harmon)

16. Karen Cranston, lead PI (Duke)
Gordon Burleigh (Florida)
Keith Crandall (BYU)
Karl Gude (MSU)
David Hibbett (Clark)
Mark Holder (Kansas)
Laura Katz (Smith)
opentreeoflife.org Rick Ree (FMNH)
Stephen Smith (Michigan)
Doug Soltis (Florida)
Tiffani Williams (TAMU)
AVAToL: Assembling, Visualizing and Analysis of
the Tree of Life

17. 1. Synthesize a complete draft tree of life from existing
phylogenetic trees

18. 1. Synthesize a complete draft tree of life from existing
phylogenetic trees
2. Release with:
a. ability to add annotations and upload new data sets
b. areas of uncertainty / conflict
c. links to source data and analysis methods
d. utilities to download whole tree and subtrees

20. Graph database holding
thousands of input trees with • filter / weight input trees
millions of nodes
• build synthetic trees
• compare to alternate trees
• input new data sets

21. Dipsicales graph
taxonomy data (578 taxa) +
Soltis et al APG III phylogeny (30 taxa)

22. Dipsicales graph Synthesized tree (favouring
phylogenetic branches); contains
all 578 taxa

23. AUTOMATIC UPDATING
update trees
with new
sequence data
detect and synthesize newly
published trees

24. ?
• Open Data
• increasing
availability of digital data associated with
phylogeny publications
• synthetic
tree open to community annotation and
new data submission
• whole tree / subtrees available for download

25. ?
• Open Science
• project wiki: http://opentree.wikispaces.com/
• open source software: https://github.com/OpenTreeOfLife
• public mailing list, meeting notes, management tools

27. • provide complete phylogenetic
framework
• link to biodiversity and systematics
content
• API for downloading subtrees to analysis tools
• source / storage of underlying data

28. opentreeoflife.org
• We’ve only just started (June 1 2012)
• Open to input, feedback and participation:
• join the mailing list & wiki
• add publications to the Mendeley group
• vote / comment on plans on the development boards
• participate in virtual data curation sprint in 2013

29. Karen Cranston, lead PI (Duke)
Gordon Burleigh (Florida)
Keith Crandall (BYU)
Karl Gude (MSU)
David Hibbett (Clark)
Mark Holder (Kansas)
Laura Katz (Smith)
opentreeoflife.org Rick Ree (FMNH)
Stephen Smith (Michigan)
Doug Soltis (Florida)
Tiffani Williams (TAMU)
AVAToL: Assembling, Visualizing and Analysis of the Tree of Life