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

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Talk given at Duke biology, November 2012

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

  1. 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. 2. Tree of life• ~2million named species• Millions more unnamed / undiscovered
  3. 3. Phylogenypapers,1978;2008 12000" 10000"Numberofpaperspublished 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
  4. 4. What does it mean to “have” the tree of life?
  5. 5. Archiving sequence data is acommunity norm ~4% of all published phylogenetic trees Stoltzfus et al 2012
  6. 6. “Publishing a tree” = picture in a PDF EVOLUTIONFig. 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, 2011344155.6169) 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.thermore, a paraphyletic relationship of phorids and syrphids To test this hypothesis, we used a relatively recent phylogenomicwould support the hypothesis that their shared special mode of marker: small, noncoding, regulatory micro-RNAs (miRNAs).
  7. 7. Lander et al. Nature 2001
  8. 8. Rod asks: Why do we need a database of trees?
  9. 9. 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.thermore, a paraphyletic relationship of phorids and syrphids To test this hypothesis, we used a relatively recent phylogenomicwould 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 conservationevolved in the stem lineage of Cyclorrhapha and preceded the across the metazoan tree of life, suggesting the accumulation andorigin of the schizophoran amnioserosa. maintenance of miRNA families throughout organismal evolutionWiegmann et al. PNAS Early Edition | 3 of 6
  10. 10. assemblyalignmentinferenceexpertise 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 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
  11. 11. NSF IDEAS LABi. Pre-proposal / application iv. Pitch high risk proposal ideas at endii. 5 day highly facilitated workshop v. NSF invited full proposalsiii. Self-assembly into groups
  12. 12. • Community assembly of the tree of life (Open Tree of Life)• Next generation Phenomics (PI O’Leary)• Arbor: Comparative Analysis Workflows (PI Harmon)
  13. 13. Karen Cranston, lead PI (Duke) Gordon Burleigh (Florida) Keith Crandall (BYU) Karl Gude (MSU) David Hibbett (Clark) Mark Holder (Kansas) Laura Katz (Smith)opentreeoflife.org Rick Ree (FMNH) Stephen Smith (Michigan) Doug Soltis (Florida) Tiffani Williams (TAMU) AVAToL: Assembling, Visualizing and Analysis of the Tree of Life
  14. 14. 1. Synthesize a complete draft tree of life from existing phylogenetic trees
  15. 15. 1. Synthesize a complete draft tree of life from existing phylogenetic trees2. Release with: a. ability to add annotations and upload new data sets b. areas of uncertainty / conflict c. links to source data and analysis methods d. utilities to download whole tree and subtrees
  16. 16. Graph database holdingthousands of input trees with • filter / weight input trees millions of nodes • build synthetic trees • compare to alternate trees • input new data sets
  17. 17. Dipsicales graphtaxonomy data (578 taxa) +Soltis et al APG III phylogeny (30 taxa)
  18. 18. Dipsicales graph Synthesized tree (favouring phylogenetic branches); contains all 578 taxa
  19. 19. AUTOMATIC UPDATING update trees with new sequence data detect and synthesize newly published trees
  20. 20. ?• 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
  21. 21. ?• Open Science • project wiki: http://opentree.wikispaces.com/ • open source software: https://github.com/OpenTreeOfLife • public mailing list, meeting notes, management tools
  22. 22. • provide complete phylogenetic framework • link to biodiversity and systematics content • API for downloading subtrees to analysis tools• source / storage of underlying data
  23. 23. opentreeoflife.org• We’ve 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
  24. 24. Karen Cranston, lead PI (Duke) Gordon Burleigh (Florida) Keith Crandall (BYU) Karl Gude (MSU) David Hibbett (Clark) Mark Holder (Kansas) Laura Katz (Smith)opentreeoflife.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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