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Open Tree of Life at Duke Futures

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Presentation given to to Duke Information Future committee, March 2012

Presentation given to to Duke Information Future committee, March 2012

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  • 1. OPEN TREE OF LIFEA community-assembled, continually updated evolutionary history of all life Karen A. Cranston National Evolutionary Synthesis Center Duke University
  • 2. Tree of life • 1.8million named species • Millions more unnamed / undiscoveredAll biodiversity linked through common ancestry; tree of life is a grand challenge; scale ishuge
  • 3. Correspondence and requests for materials should be addressed to C.W. (e-mail: whitlock@oregon. and elephant shrews with paenungulates. What is most unexpected uoregon.edu). is that golden moles, a family of insectivores, are also part of this clade. 12S rRNA sequences earlier suggested an association of golden moles with paenungulates, but did not provide convincing bootstrap support for this hypothesis7. Our expanded data set Endemic African mammals demonstrates that insectivores are not monophyletic (Table 2) shake the phylogenetic tree Table 1 Bootstrap support for select clades based on different methods Mark S. Springer*, Gregory C. Cleven*, Ole Madsen†, Wilfried W. de Jong†‡, Victor G. Waddell§, Clade Heather M. Amrine* & Michael J. Stanhope§ Paenungulata Paenungulata aardvark elephant shrew * Department of Biology, University of California, Riverside, California 92521, golden mole USA Mitochondrial DNA † Department of Biochemistry, University of Nijmegen, PO Box 9101, Parsimony 99 95 6500 HB Nijmegen, The Netherlands Transversion parsimony 64 90 Minimum evolution ‡ Institute for Systematics and Population Biology, University of Amsterdam, PO Tamura–Nei I 100 92 Box 94766, 1090GT Amsterdam, The Netherlands Tamura–Nei II 100 78 § Biology and Biochemistry, Queen’s University, 97 Lisburn Road, Logdet 99 90 Belfast BT9 07BL, UK Maximum likelihood 100 100 ......................................................................................................................... vWF Parsimony The order Insectivora, including living taxa (lipotyphlans) and All positions 49 99 archaic fossil forms, is central to the question of higher-level 1st and 2nd positions 24 65 relationships among placental mammals1. Beginning with 3rd positions 51 93 Transversion parsimony 30 95 Huxley2, it has been argued that insectivores retain many primi- Minimum evolution tive features and are closer to the ancestral stock of mammals than Tamura–Nei I 37 99 are other living groups3. Nevertheless, cladistic analysis suggests Tamura–Nei II 30 99 Logdet 43 97 that living insectivores, at least, are united by derived anatomical Maximum likelihood 78 100 features4. Here we analyse DNA sequences from three mito- A2AB chondrial genes and two nuclear genes to examine relationships Parsimony All sites 71 88 of insectivores to other mammals. The representative insectivores 1st and 2nd positions 49 81 are not monophyletic in any of our analyses. Rather, golden moles 3rd positions 31 67 are included in a clade that contains hyraxes, manatees, elephants, Hedges, B. PNAS 98 (2001) Transversion parsimony 71 54 Minimum evolution elephant shrews and aardvarks. Members of this group are of Tamura–Nei I 83 84 presumed African origin5,6. This implies that there was an exten- Tamura–Nei II 28 25 sive African radiation from a single common ancestor that gave Logdet 79 78 Maximum likelihood 81 89 rise to ecologically divergent adaptive types. 12S ribosomal RNA ............................................................................................................................................................................. Only two of the three paenungulate orders were represented among the mitochondrial and transversions suggest that the base of this radiation occurred A2AB sequences. Tamura–Nei27 I and II distances were calculated by using an equal-rates during Africa’s window of isolation in the Cretaceous period assumption and a gamma-distribution of rates, respectively. Nature © Macmillan Publishers Ltd 1997 NATURE | VOL 388 | 3 JULY 1997 61 Springer, M.S. et al. Nature (1997) Stanhope, M.J. et al. PNAS (1998)Learned amazing things about biodiversity from studying the tree; radically changed views
  • 4. EVOLUTION OF HUMAN PATHOGENS Smith et al, Nature, 2009Importance to human health and disease
  • 5. MODERN BIOLOGY NEEDS TREES Conventional Evolutionarystatistics assume: trees provide: Modified from Garland and Carter, 1994
  • 6. 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""We’ve been extremely productive
  • 7. Where can I browse,search and download acomplete tree of life? You can’t. (Yet)
  • 8. 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""It’s not because we haven’t been productive
  • 9. Reason 1: silos of phylogenetic knowledge
  • 10. DATA AVAILABILITY High archival rate of sequence data ~4% of all published phylogenetic treesReason 2: can’t do synthesis without data; community norm to deposit sequences but nottrees
  • 11. Most trees published as (beautiful) figures in PDF files EVOLUTION not reusable! Weigmann et al. PNAS, 2011Fig. 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 Most phylogenetic knowledge locked in PDFs; even best case (here): trees and alignments inof 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. treebase, sequences in GenBank but so much more data in this figure!
  • 12. 1. Build and make publicly available the first complete draft tree of life2. Engage the community in refinement and annotation of the draft tree3. Promote a culture of data sharing among systematists through software products that target key bottlenecks in phylogenetic workflows4. Develop, disseminate, and evaluate novel methods for phylogenetic synthesis
  • 13. + NSF Assembling the Tree of Life projects + recent high-profile phylogenies + ribosomal RNA trees for Bacteria and Archaea + unnamed environmental sequences + taxonomies of living and extinct species Draft Tree of Life as seed for collaborationGet all data available! Part of draft tree will be good; parts not so good
  • 14. Tools to browse, update, monitor the draft tree of life Tools that incentivize collaboration Tree image modified from Tree of Life Web Project page http://tolweb.org/Nymphalidae/12172 Pictures by Katja Schulz (queen butterfly; CCAttribution-NonCommercial) and Charles Lam (via Flicker;CCAttribution-ShareAlike)publish refinement tools along with draft tree; invite comment / critique / updating
  • 15. SMART GENERATION OF FIGURES FOR PUBLICATION • Semantic annotation layers • Collaborative editing EVOLUTION • Integrated submission of data and annotations to archivesig. 1. Combined molecular phylogenetic tree for Diptera. Partitioned ML analysis of combined taxon sets of tier 1 and tier 2 FLYTREE data samples (−lnL =44155.6169) calculated in RAxML. Circles indicate bootstrap support >80% (black/bp = 95–100%, gray/bp = 88–94%, white/bp = 80–88%). Nodes with im- Motivated to organize data at this point in pipeline; want to capture digitally at this pointroved bootstrap values resulting from postanalysis pruning of unstable taxa are marked by stars (black/bp = 95–100%, gray/bp = 88–94%, white/bp = 80–8%). 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 numberf 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 ofhe organisms.
  • 16. AUTOMATIC UPDATING update trees with new sequence data detect and synthesize newly published treesCan’t rely on manual refinement alone; need automate based on new data (and need newanalytical method development)
  • 17. community refinementng the major evolutionary relationships recovered in this analysis of Carnivora. Illustrations ofom top): Nandinia binotata; Felidae (Lynx rufus); Viverridae (Viverra zibetha); Hyaenidae (Crocutay carnivorans (Eupleres goudotii); Canidae (Canis lupus); Ursidae (Ursus americanus); Phocidae Odobenidae (Odobenus rosmarus); Ailurus fulgens; Mephitidae (Mephitis mephitis); Procyonidae education and outreach (generalized schematic representing diverse taxa [African polecat and striped marten, badger,telidae, Mustela (Mustela frenata); Mustelidae, Lutrinae (Lontra canadensis).the major evolutionary relationships recoveredin this analysis of Carnivora. Illustrations of nting the major evolutionary relationships recovered in this analysis of Carnivora. Illustrations of top): Nandinia binotata; Felidae (Lynx rufus); Viverridae (Viverra zibetha); Hyaenidae (Crocuta (from top): Nandinia binotata; Felidae (Lynx rufus); Viverridae (Viverra zibetha); Hyaenidae (Crocutagasy carnivorans (Eupleres goudotii); Canidae (Canis lupus); Ursidae (Ursus americanus); Phocidae rnivorans (Eupleres goudotii); Canidae (Canis lupus); Ursidae (Ursus americanus); Phocidae us); Odobenidae (Odobenus rosmarus); Ailurus fulgens; Mephitidae (Mephitis mephitis); Procyonidaedobenidae (Odobenus rosmarus); Ailurus fulgens; Mephitidae (Mephitis mephitis); badger, ids (generalized schematic representing diverse taxa [African polecat and striped marten, Procyonidae Dynamic,Mustelidae, schematic representing diverse Lutrinae (Lontra canadensis). neralized Mustela (Mustela frenata); Mustelidae,taxa [African polecat and striped marten, badger,dae, Mustela (Mustela frenata); Mustelidae, Lutrinae (Lontra canadensis). continually updated cladogram representing the major evolutionary relationships recovered in this analysis of Carnivora. Illustrations ofor lineages include (from top): Nandinia binotata; Felidae (Lynx rufus); Viverridae (Viverra zibetha); Hyaenidae (Crocuta gos mungo); Malagasy carnivorans (Eupleres goudotii); Canidae (Canis lupus); Ursidae (Ursus americanus); Phocidae tree of all lifeZalophus californianus); Odobenidae (Odobenus rosmarus); Ailurus fulgens; Mephitidae (Mephitis mephitis); Procyonidae asal/other mustelids (generalized schematic representing diverse taxa [African polecat and striped marten, badger, ?roup (Gulo gulo); Mustelidae, Mustela (Mustela frenata); Mustelidae, Lutrinae (Lontra canadensis). ? ? automatic ? updating downstream analyses The grand vision
  • 18. opentreeoflife.com Karen Cranston, lead PI (Duke) Laura Katz (Smith) Gordon Burleigh (Florida) Rick Ree (FMNH) Keith Crandall (BYU) 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, $5.76 millionThe team and funding; empirical + computational biologists + comp sci + graphics /communication