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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
>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!