A community-assembled, continually updated evolutionary history of all life

Karen A. CranstonNational Evolutionary Synthesis Center

Duke University

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

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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

Where can I browse, search and download a complete tree of life?

You can’t. (Yet)

DATA AVAILABILITY

~4% of all published phylogenetic trees

Community norm to archive sequence data

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

+ 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

Dipsicales graphtaxonomy data (578 taxa) +Soltis et al APG III phylogeny (30 taxa)

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

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

AUTOMATIC UPDATING

update trees with new

sequence data

detect and synthesize newly published trees

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

• 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

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• Open Science

• project wiki: opentree.wikispaces.com

• mailing list (opentreeoflife@googlegroups.com)

• development board (trello.org/opentree)

?

• provide complete phylogenetic framework

• link to biodiversity and systematics content

• provide complete phylogenetic framework

• link to biodiversity and systematics content

• API for downloading subtrees to analysis tools

• source / storage of underlying data

• provide complete phylogenetic framework

• link to biodiversity and systematics content

• API for downloading subtrees to analysis tools

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