Open Tree of Life, v 1.0Karen Cranston!National Evolutionary Synthesis Center!@kcranstn @opentreeoflife!http://slideshare.net/kcranstn

Community-enabled phylogenetic synthesis

Gordon Burleigh!Keith Crandall!

Karl Gude!David Hibbett!Mark Holder!Laura Katz!

Rick Ree!

Stephen Smith!Doug Soltis!

Tiffani Williams!+ many postdocs, grad students and

undergrads

@NESCent: Karen Cranston, Jonathan Rees, Jim Allman

http://avatol.org

If we had the tree of life…

❖ complete = contains all biodiversity!

❖ dynamic = updates when new results published!

❖ digitally available = browse, query, download

❖ Synthesize published phylogenetic trees!

❖ Enable comment & feedback on synthetic tree!

❖ Allow updating through upload of new data

❖ Expectation: Tree of life that represents our collective phylogenetic knowledge!

❖ Reality: Tree of life that illustrates digital availability of open phylogenetic and biodiversity data

Inputs: Published phylogenies Taxonomic hierarchies

• filter / weight input trees • synthesize into binary tree

• process feedback • input new data sets

complete tree of life

NCBI taxonomy (578 taxa)

Soltis et al APG III phylogeny (30 taxa)

Dipsicales graph

Dipsicales graph

Synthesized tree; phylogenetic

structure with all 578 taxa

More details about synthesis❖ Smith, Brown, and Hinchliff. "Analyzing and

Synthesizing Phylogenies Using Tree Alignment Graphs." PLoS computational biology 9.9 (2013): e1003223.!

❖ phyloseminar.org/recorded!

❖ Cranston: Technical and social challenges to synthesizing the tree of life!

❖ Smith: Exploring graphs for mapping and synthesizing phylogenies

2.22 million tips !!

7 taxonomies, including NCBI,

GBIF, SILVA!!

~3000 phylogenetic studies; 335 in synthetic tree

tip = lineage with >= 500 descendants!grey = lineage with > 1 tip from a phylogeny

Open Tree of Life, v 1.0

node provenance

http://tree.opentreeoflife.org

edge provenance

http://tree.opentreeoflife.org

>10000 per year

~ 4% deposited in TreeBASE / Dryad

publ

ishe

d ph

ylog

enie

s

estimates from Stoltzfus et al 2012, Drew et al 2013

phylogenetic knowledge

digitally available phylogenetic knowledge

increase to 16% by contacting authors

directly

TREE Fig._S1 = [&R] (2,1,((3,7),(4,(6,(33,(15,((20,(47,((51,(49,50)),(46,(48,(52,16)))))),(((44,45),((18,(12,(13,(43,42)))),((41,((39,38),(40,17))),((35,9),(34,(36,37)))))),(32,(((21,19),

((30,14),(22,((11,31),((27,25),(23,((28,(24,8)),(10,(26,(5,29)))))))))),((((72,(63,57)),((65,64),((66,67),(68,(69,(70,(71,54))))))),(((82,59),(60,(61,(62,55)))),((80,(81,56)),((53,(77,78)),((75,73),(76,(58,74))))))),((88,((86,87),((85,84),

(83,89)))),(79,((91,(93,(95,(92,(96,(94,90)))))),((100,(99,98)),(97,(((168,((172,185),((159,101),(109,157)))),(((181,(179,180)),((102,(183,187)),(175,(176,(178,177))))),(212,((195,(210,211)),

(199,((201,(196,202)),((194,197),((203,(192,205)),(204,(193,((209,(208,206)),(198,(200,207))))))))))))),(113,(((154,((169,170),(103,191))),((131,126),(128,((134,135),(129,(125,((132,130),

(104,133)))))))),((((190,166),((162,171),((116,120),(115,114)))),((122,(188,(186,108))),((118,(119,105)),(117,(158,(184,189)))))),

((123,124),(((148,((165,161),(174,182))),((106,121),(163,(167,127)))),((173,(156,(155,160))),(164,(((136,137),(139,(138,107))),((153,145),(112,(((146,143),(144,(140,141))),

((142,152),(147,((110,111),(149,(150,151)))))))))))))))))))))))))))))))));

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

re-root!clean up taxon labels!

add annotations

How do I get OpenTree data?

❖ browse: http://tree.opentreeoflife.org!

❖ synthetic tree: http://files.opentreeoflife.org/trees!

❖ taxonomy: http://files.opentreeoflife.org/ott !

❖ input trees: http://github.com/OpenTreeOfLife/phylesystem !

❖ API access: https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-of-Life-APIs

@opentreeoflife @iEvoBio

❖ Using a git-based datastore for community contributed phylogenies : Emily Jane McTavish!

❖ Using peyotl and Open Tree of Life APIs : Mark Holder!

❖ Taxonomic data exchange as expression and synthesis of phylogenetic claims : Jonathan Rees

http://ievobio.org

For further information:! bit.ly/1ioPPMc

Tree-for-all!A hackathon to develop / access

Open Tree of Life data and services

Leaf

Tree of LifeOPEN

September 15 to 19!University of Michigan, Ann Arbor

Applications open now! Due July 8!