1. OPEN TREE OF LIFE:
SYNTHESIZING
PHYLOGENETIC DATA
Karen Cranston
National Evolutionary Synthesis Center (NESCent)
@kcranstn
http://www.slideshare.net/kcranstn
2. Tree of life
• ~2million named
species
• Millions
more
unnamed / undiscovered
9. Archiving sequence data is a
community norm
~4% of all published
phylogenetic trees
Stoltzfus et al 2012
10. “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).
13. 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.
15. 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
16. 1. Synthesize a complete draft tree of life from existing
phylogenetic trees
2. Release with:
a. ability to improve tree by uploading new data
b. areas of uncertainty / conflict
c. links to source data and analysis methods
d. utilities to download whole tree and subtrees
17. 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
18. INPUTS
a AACCGTGAA e a c f b d
b ACACGTTAA
computational
phylogenies c AAACGTTAA
d AGACGTTAA method
e AACCGTTAA
f AAACGTGAA
e a c f b d g h i
taxonomies
19. a b c d
a
b
c
d
a,b c,d
a,b,c,d
a b c d
a
c
b
d
a,b c,d
a,b,c,d
Stephen Smith, U Michigan
20. a b c d
a
c
b
d
a,b c,d
a,b,c,d
a b c d
a,c a,b c,d b,d
a,b,c,d
Stephen Smith, U Michigan
21. a b c d
a
d
e
f
g
h
i
a,c a,b c,d b,d
a,b,c,d
a b c d e f g h
a,c a,b c,d b,d
a,b,c,d e,f,g,h,i
a,b,c,d,e,f,g,h,i
Stephen Smith, U Michigan
22. a b c d e f g h a b c d e f g h
a,c a,b c,d b,d a,c a,b c,d b,d
a,b,c,d e,f,g,h,i a,b,c,d e,f,g,h,i
a,b,c,d,e,f,g,h,i a,b,c,d,e,f,g,h,i
a
c
b
d
e
f
g
h
i
Stephen Smith, U Michigan
24. Dipsicales graph Synthesized tree (favouring
phylogenetic branches); contains
all 578 taxa
25. community
refinement
r evolutionary relationships recovered in this analysis of Carnivora. Illustrations of
ndinia binotata; Felidae (Lynx rufus); Viverridae (Viverra zibetha); Hyaenidae (Crocuta
education and
outreach
ns (Eupleres goudotii); Canidae (Canis lupus); Ursidae (Ursus americanus); Phocidae
ae (Odobenus rosmarus); Ailurus fulgens; Mephitidae (Mephitis mephitis); Procyonidae
d schematic representing diverse taxa [African polecat and striped marten, badger,
stela (Mustela frenata); Mustelidae, Lutrinae (Lontra canadensis).
volutionary relationships recoveredin this analysis of Carnivora. Illustrations of
jor evolutionary relationships recovered in this analysis of Carnivora. Illustrations of
Nandinia binotata; Felidae (Lynxrufus); Viverridae (Viverra zibetha); Hyaenidae (Crocuta
nia binotata; Felidae (Lynx rufus); Viverridae (Viverra zibetha); Hyaenidae (Crocuta
ans (Eupleres goudotii); Canidae (Canis lupus); Ursidae (Ursus americanus); Phocidae
Eupleres goudotii); Canidae (Canis lupus); Ursidae (Ursus americanus); Phocidae
dae (Odobenus rosmarus); Ailurus fulgens; Mephitidae (Mephitis mephitis); Procyonidae
Odobenus rosmarus); Ailurus fulgens; Mephitidae (Mephitis mephitis); badger,
ed schematic representing diverse taxa [African polecat and striped marten, Procyonidae
chematic representing diverse taxa [African polecat and striped marten, badger,
ustela (Mustela frenata); Mustelidae, Lutrinae (Lontra canadensis).
a (Mustela frenata); Mustelidae, Lutrinae (Lontra canadensis).
representing the major evolutionary relationships recovered in this analysis of Carnivora. Illustrations of
nclude (from top): Nandinia binotata; Felidae (Lynx rufus); Viverridae (Viverra zibetha); Hyaenidae (Crocuta
; Malagasy carnivorans (Eupleres goudotii); Canidae (Canis lupus); Ursidae (Ursus americanus); Phocidae
ifornianus); Odobenidae (Odobenus rosmarus); Ailurus fulgens; Mephitidae (Mephitis mephitis); Procyonidae
mustelids (generalized schematic representing diverse taxa [African polecat and striped marten, badger,
gulo); Mustelidae, Mustela (Mustela frenata); Mustelidae, Lutrinae (Lontra canadensis).
?
automatic ?
updating ?
?
downstream
analyses
26. • provide complete phylogenetic
framework
• link to biodiversity and systematics
content
• API for downloading subtrees to analysis tools
• source / storage of underlying data
27. ?
• 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
28. ?
• Open Science
• project wiki: http://opentree.wikispaces.com/
• open source software: https://github.com/OpenTreeOfLife
• public mailing list, meeting notes, management tools
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