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If this is the future, where is my tree of life?

Karen Cranston
Karen Cranston

1. The document discusses the Open Tree of Life project, which aims to synthesize a complete draft tree of life from existing phylogenetic trees. 2. The project will release the tree with annotations, areas of uncertainty, links to source data, and tools to download subtrees. It will also automatically update the tree with new sequence data. 3. The goal is to provide a complete phylogenetic framework and link it to biodiversity and systematics content through an open, community-driven effort.

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IF THIS IS THE FUTURE, WHERE IS MY TREE OF LIFE? Karen Cranston National Evolutionary Synthesis Center (NESCent) @kcranstn http://www.slideshare.net/kcranstn
Tree of life ~2million named species Millions more unnamed / undiscovered
If this is the future, where is my tree of life?
Phylogeny'papers,'1978;2008' 12000" 10000" Number'of'papers'published' 8000" Rapid"increase"in"applica?ons"of" phylogeny,"beginning"in"early"1990s" 6000" 4000" 2000" 0" 1978" 979" 980"1981" 982" 983" 984"1985" 986"1987" 988" 989" 990"1991" 992" 993" 994"1995" 996"1997" 998" 999" 000"2001" 002" 003" 004"2005" 006"2007" 008" 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 Year' Source:"ISI"Web"of"Science"" graph from David Hillis
What does it mean to have the tree of life?
If this is the future, where is my tree of life?
Archiving sequence data is a community norm ~4% of all published phylogenetic trees Stoltzfus et al 2012
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 = 95100%, gray/bp = 8894%, white/bp = 8088%). Nodes with im- proved bootstrap values resulting from postanalysis pruning of unstable taxa are marked by stars (black/bp = 95100%, gray/bp = 8894%, 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).
Lander et al. Nature 2001
Rod asks: Why do we need a database of trees?
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 = 95100%, gray/bp = 8894%, white/bp = 8088%). Nodes with im- proved bootstrap values resulting from postanalysis pruning of unstable taxa are marked by stars (black/bp = 95100%, gray/bp = 8894%, 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). extraembryonic development (dorsal amnion closure) (26) miRNAs exhibit a striking phylogenetic pattern of conservation evolved in the stem lineage of Cyclorrhapha and preceded the across the metazoan tree of life, suggesting the accumulation and origin of the schizophoran amnioserosa. maintenance of miRNA families throughout organismal evolution Wiegmann et al. PNAS Early Edition | 3 of 6
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 = 95100%, gray/bp = 8894%, white/bp = 8088%). Nodes with im- proved bootstrap values resulting from postanalysis pruning of unstable taxa are marked by stars (black/bp = 95100%, gray/bp = 8894%, 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
If this is the future, where is my tree of life?
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
Community assembly of the tree of life (Open Tree of Life) Next generation Phenomics (PI OLeary) Arbor: Comparative Analysis Work鍖ows (PI Harmon)
Karen Cranston, lead PI (Duke) Gordon Burleigh (Florida) Keith Crandall (BYU) Karl Gude (MSU) David Hibbett (Clark) Mark Holder (Kansas) Laura Katz (Smith) opentreeo鍖ife.org Rick Ree (FMNH) Stephen Smith (Michigan) Doug Soltis (Florida) Tiffani Williams (TAMU) AVAToL: Assembling, Visualizing and Analysis of the Tree of Life
1. Synthesize a complete draft tree of life from existing phylogenetic trees
1. Synthesize a complete draft tree of life from existing phylogenetic trees 2. Release with: a. ability to add annotations and upload new data sets b. areas of uncertainty / con鍖ict c. links to source data and analysis methods d. utilities to download whole tree and subtrees
If this is the future, where is my tree of life?
Graph database holding thousands of input trees with 鍖lter / weight input trees millions of nodes build synthetic trees compare to alternate trees input new data sets
Dipsicales graph taxonomy data (578 taxa) + Soltis et al APG III phylogeny (30 taxa)
Dipsicales graph Synthesized tree (favouring phylogenetic branches); contains all 578 taxa
AUTOMATIC UPDATING update trees with new sequence data detect and synthesize newly published trees
? 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
? Open Science project wiki: http://opentree.wikispaces.com/ open source software: https://github.com/OpenTreeOfLife public mailing list, meeting notes, management tools
If this is the future, where is my tree of life?
provide complete phylogenetic framework link to biodiversity and systematics content API for downloading subtrees to analysis tools source / storage of underlying data
opentreeo鍖ife.org Weve only just started (June 1 2012) Open to input, feedback and participation: join the mailing list & wiki add publications to the Mendeley group vote / comment on plans on the development boards participate in virtual data curation sprint in 2013
Karen Cranston, lead PI (Duke) Gordon Burleigh (Florida) Keith Crandall (BYU) Karl Gude (MSU) David Hibbett (Clark) Mark Holder (Kansas) Laura Katz (Smith) opentreeo鍖ife.org Rick Ree (FMNH) Stephen Smith (Michigan) Doug Soltis (Florida) Tiffani Williams (TAMU) AVAToL: Assembling, Visualizing and Analysis of the Tree of Life

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If this is the future, where is my tree of life?

  • 1. IF THIS IS THE FUTURE, WHERE IS MY TREE OF LIFE? Karen Cranston National Evolutionary Synthesis Center (NESCent) @kcranstn http://www.slideshare.net/kcranstn
  • 2. Tree of life ~2million named species Millions more unnamed / undiscovered
  • 4. Phylogeny'papers,'1978;2008' 12000" 10000" Number'of'papers'published' 8000" Rapid"increase"in"applica?ons"of" phylogeny,"beginning"in"early"1990s" 6000" 4000" 2000" 0" 1978" 979" 980"1981" 982" 983" 984"1985" 986"1987" 988" 989" 990"1991" 992" 993" 994"1995" 996"1997" 998" 999" 000"2001" 002" 003" 004"2005" 006"2007" 008" 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 Year' Source:"ISI"Web"of"Science"" graph from David Hillis
  • 5. What does it mean to have the tree of life?
  • 7. Archiving sequence data is a community norm ~4% of all published phylogenetic trees Stoltzfus et al 2012
  • 8. 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 = 95100%, gray/bp = 8894%, white/bp = 8088%). Nodes with im- proved bootstrap values resulting from postanalysis pruning of unstable taxa are marked by stars (black/bp = 95100%, gray/bp = 8894%, 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).
  • 9. Lander et al. Nature 2001
  • 10. Rod asks: Why do we need a database of trees?
  • 11. 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 = 95100%, gray/bp = 8894%, white/bp = 8088%). Nodes with im- proved bootstrap values resulting from postanalysis pruning of unstable taxa are marked by stars (black/bp = 95100%, gray/bp = 8894%, 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). extraembryonic development (dorsal amnion closure) (26) miRNAs exhibit a striking phylogenetic pattern of conservation evolved in the stem lineage of Cyclorrhapha and preceded the across the metazoan tree of life, suggesting the accumulation and origin of the schizophoran amnioserosa. maintenance of miRNA families throughout organismal evolution Wiegmann et al. PNAS Early Edition | 3 of 6
  • 12. 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 = 95100%, gray/bp = 8894%, white/bp = 8088%). Nodes with im- proved bootstrap values resulting from postanalysis pruning of unstable taxa are marked by stars (black/bp = 95100%, gray/bp = 8894%, 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. 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
  • 15. Community assembly of the tree of life (Open Tree of Life) Next generation Phenomics (PI OLeary) Arbor: Comparative Analysis Work鍖ows (PI Harmon)
  • 16. Karen Cranston, lead PI (Duke) Gordon Burleigh (Florida) Keith Crandall (BYU) Karl Gude (MSU) David Hibbett (Clark) Mark Holder (Kansas) Laura Katz (Smith) opentreeo鍖ife.org Rick Ree (FMNH) Stephen Smith (Michigan) Doug Soltis (Florida) Tiffani Williams (TAMU) AVAToL: Assembling, Visualizing and Analysis of the Tree of Life
  • 17. 1. Synthesize a complete draft tree of life from existing phylogenetic trees
  • 18. 1. Synthesize a complete draft tree of life from existing phylogenetic trees 2. Release with: a. ability to add annotations and upload new data sets b. areas of uncertainty / con鍖ict c. links to source data and analysis methods d. utilities to download whole tree and subtrees
  • 20. Graph database holding thousands of input trees with 鍖lter / weight input trees millions of nodes build synthetic trees compare to alternate trees input new data sets
  • 21. Dipsicales graph taxonomy data (578 taxa) + Soltis et al APG III phylogeny (30 taxa)
  • 22. Dipsicales graph Synthesized tree (favouring phylogenetic branches); contains all 578 taxa
  • 23. AUTOMATIC UPDATING update trees with new sequence data detect and synthesize newly published trees
  • 24. ? 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
  • 25. ? Open Science project wiki: http://opentree.wikispaces.com/ open source software: https://github.com/OpenTreeOfLife public mailing list, meeting notes, management tools
  • 27. provide complete phylogenetic framework link to biodiversity and systematics content API for downloading subtrees to analysis tools source / storage of underlying data
  • 28. opentreeo鍖ife.org Weve only just started (June 1 2012) Open to input, feedback and participation: join the mailing list & wiki add publications to the Mendeley group vote / comment on plans on the development boards participate in virtual data curation sprint in 2013
  • 29. Karen Cranston, lead PI (Duke) Gordon Burleigh (Florida) Keith Crandall (BYU) Karl Gude (MSU) David Hibbett (Clark) Mark Holder (Kansas) Laura Katz (Smith) opentreeo鍖ife.org Rick Ree (FMNH) Stephen Smith (Michigan) Doug Soltis (Florida) Tiffani Williams (TAMU) AVAToL: Assembling, Visualizing and Analysis of the Tree of Life