open tree of life @evolution 2012
DESCRIPTION
Open Tree of Life talk given at 2012 Evolution meetings in Ottawa, CanadaTRANSCRIPT
![Page 1: Open Tree of Life @Evolution 2012](https://reader034.vdocument.in/reader034/viewer/2022052321/554e85a3b4c90573338b46a6/html5/thumbnails/1.jpg)
A community-assembled, continually updated evolutionary history of all life
Karen A. CranstonNational Evolutionary Synthesis Center
Duke University
![Page 2: Open Tree of Life @Evolution 2012](https://reader034.vdocument.in/reader034/viewer/2022052321/554e85a3b4c90573338b46a6/html5/thumbnails/2.jpg)
opentreeoflife.org
Karen Cranston (NESCent) Laura Katz (Smith)Gordon Burleigh (Florida) Rick Ree (FMNH)
Keith Crandall (GWU) Stephen Smith (Michigan)Karl Gude (MSU) Doug Soltis (Florida)
David Hibbett (Clark) Tiffani Williams (TAMU)Mark Holder (Kansas)
AVAToL: Assembling, Visualizing and Analysis of the Tree of Life
![Page 3: Open Tree of Life @Evolution 2012](https://reader034.vdocument.in/reader034/viewer/2022052321/554e85a3b4c90573338b46a6/html5/thumbnails/3.jpg)
0"
2000"
4000"
6000"
8000"
10000"
12000"
1978"1979"1980"1981"1982"1983"1984"1985"1986"1987"1988"1989"1990"1991"1992"1993"1994"1995"1996"1997"1998"1999"2000"2001"2002"2003"2004"2005"2006"2007"2008"
Num
ber'o
f'pap
ers'p
ublishe
d'
Year'
Phylogeny'papers,'1978;2008'
Source:"ISI"Web"of"Science""
Rapid"increase"in"applica?ons"of"phylogeny,"beginning"in"early"1990s"
graph from David Hillis
![Page 4: Open Tree of Life @Evolution 2012](https://reader034.vdocument.in/reader034/viewer/2022052321/554e85a3b4c90573338b46a6/html5/thumbnails/4.jpg)
Where can I browse, search and download a complete tree of life?
You can’t. (Yet)
![Page 5: Open Tree of Life @Evolution 2012](https://reader034.vdocument.in/reader034/viewer/2022052321/554e85a3b4c90573338b46a6/html5/thumbnails/5.jpg)
![Page 6: Open Tree of Life @Evolution 2012](https://reader034.vdocument.in/reader034/viewer/2022052321/554e85a3b4c90573338b46a6/html5/thumbnails/6.jpg)
DATA AVAILABILITY
~4% of all published phylogenetic trees
Community norm to archive sequence data
![Page 7: Open Tree of Life @Evolution 2012](https://reader034.vdocument.in/reader034/viewer/2022052321/554e85a3b4c90573338b46a6/html5/thumbnails/7.jpg)
1. Synthesize a complete draft tree of life from existing phylogenetic trees
2. Publish this draft tree with:
a. ability to add annotations and upload new data sets
b. highlighted areas of conflict and links to source data
c. utilities to download whole tree and subtrees
Year one goals
![Page 8: Open Tree of Life @Evolution 2012](https://reader034.vdocument.in/reader034/viewer/2022052321/554e85a3b4c90573338b46a6/html5/thumbnails/8.jpg)
+ taxonomies of living and extinct species+ digital phylogenetic data: Assembling the Tree of Life (and other) projects recent high-profile phylogenies ribosomal RNA trees for Bacteria and Archaea TreeBASE and Dryad trees
Graph database holding thousands of input trees with millions of nodes
![Page 9: Open Tree of Life @Evolution 2012](https://reader034.vdocument.in/reader034/viewer/2022052321/554e85a3b4c90573338b46a6/html5/thumbnails/9.jpg)
Dipsicales graphtaxonomy data (578 taxa) +Soltis et al APG III phylogeny (30 taxa)
![Page 10: Open Tree of Life @Evolution 2012](https://reader034.vdocument.in/reader034/viewer/2022052321/554e85a3b4c90573338b46a6/html5/thumbnails/10.jpg)
Dipsicales graph Synthesized tree (favouring phylogenetic branches); contains all 578 taxa
![Page 11: Open Tree of Life @Evolution 2012](https://reader034.vdocument.in/reader034/viewer/2022052321/554e85a3b4c90573338b46a6/html5/thumbnails/11.jpg)
Graph database holding thousands of input trees with
millions of nodes• filter / weight input trees• build synthetic trees
• compare to alternate trees• input new data sets
![Page 12: Open Tree of Life @Evolution 2012](https://reader034.vdocument.in/reader034/viewer/2022052321/554e85a3b4c90573338b46a6/html5/thumbnails/12.jpg)
AUTOMATIC UPDATING
update trees with new
sequence data
detect and synthesize newly published trees
![Page 13: Open Tree of Life @Evolution 2012](https://reader034.vdocument.in/reader034/viewer/2022052321/554e85a3b4c90573338b46a6/html5/thumbnails/13.jpg)
SMART GENERATION OF FIGURES FOR PUBLICATION
thermore, a paraphyletic relationship of phorids and syrphidswould support the hypothesis that their shared special mode ofextraembryonic development (dorsal amnion closure) (26)evolved in the stem lineage of Cyclorrhapha and preceded theorigin of the schizophoran amnioserosa.
To test this hypothesis, we used a relatively recent phylogenomicmarker: small, noncoding, regulatory micro-RNAs (miRNAs).miRNAs exhibit a striking phylogenetic pattern of conservationacross the metazoan tree of life, suggesting the accumulation andmaintenance ofmiRNA families throughout organismal 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 =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 numberof 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 ofthe organisms.
Wiegmann et al. PNAS Early Edition | 3 of 6
EVOLU
TION
• Semantic annotation layers
• Collaborative editing
• Integrated submission of data and annotations to archives
Weigmann et al. PNAS, 2011
![Page 14: Open Tree of Life @Evolution 2012](https://reader034.vdocument.in/reader034/viewer/2022052321/554e85a3b4c90573338b46a6/html5/thumbnails/14.jpg)
• Increasing availability of digital data associated with phylogeny publications
• Making synthetic tree open to community annotation and data submission
• Simple access to search and download the tree of life
?
![Page 15: Open Tree of Life @Evolution 2012](https://reader034.vdocument.in/reader034/viewer/2022052321/554e85a3b4c90573338b46a6/html5/thumbnails/15.jpg)
• Open Science
• project wiki: opentree.wikispaces.com
• mailing list ([email protected])
• development board (trello.org/opentree)
?
![Page 16: Open Tree of Life @Evolution 2012](https://reader034.vdocument.in/reader034/viewer/2022052321/554e85a3b4c90573338b46a6/html5/thumbnails/16.jpg)
![Page 17: Open Tree of Life @Evolution 2012](https://reader034.vdocument.in/reader034/viewer/2022052321/554e85a3b4c90573338b46a6/html5/thumbnails/17.jpg)
• provide complete phylogenetic framework
• link to biodiversity and systematics content
![Page 18: Open Tree of Life @Evolution 2012](https://reader034.vdocument.in/reader034/viewer/2022052321/554e85a3b4c90573338b46a6/html5/thumbnails/18.jpg)
• provide complete phylogenetic framework
• link to biodiversity and systematics content
• API for downloading subtrees to analysis tools
![Page 19: Open Tree of Life @Evolution 2012](https://reader034.vdocument.in/reader034/viewer/2022052321/554e85a3b4c90573338b46a6/html5/thumbnails/19.jpg)
• source / storage of underlying data
• provide complete phylogenetic framework
• link to biodiversity and systematics content
• API for downloading subtrees to analysis tools
![Page 20: Open Tree of Life @Evolution 2012](https://reader034.vdocument.in/reader034/viewer/2022052321/554e85a3b4c90573338b46a6/html5/thumbnails/20.jpg)
opentreeoflife.org
• We’ve only just started (June 1)
• Looking for input, feedback and participation:
• join the mailing list
• add publications to the Mendeley group
• vote / comment on plans on the Trello boards
• participate in virtual data curation sprint in August