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Open Tree at UNCC Jan 2013

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Talk given at UNC Charlotte Bioinformatics department about Open Tree of LIfe

Talk given at UNC Charlotte Bioinformatics department about Open Tree of LIfe


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  • 1. OPEN TREE OF LIFE: SYNTHESIZING PHYLOGENETIC DATA Karen CranstonNational Evolutionary Synthesis Center (NESCent) @kcranstn http://www.slideshare.net/kcranstn
  • 2. Tree of life• ~2million named species• Millions more unnamed / undiscovered
  • 3. 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 setEndemic African mammals demonstrates that insectivores are not monophyletic (Table 2)shake the phylogenetic tree Table 1 Bootstrap support for select clades based on different methodsMark S. Springer*, Gregory C. Cleven*, Ole Madsen†,Wilfried W. de Jong†‡, Victor G. Waddell§, CladeHeather M. Amrine* & Michael J. Stanhope§ Paenungulata Paenungulata aardvark elephant shrew* Department of Biology, University of California, Riverside, California 92521, golden moleUSA Mitochondrial DNA† Department of Biochemistry, University of Nijmegen, PO Box 9101, Parsimony 99 956500 HB Nijmegen, The Netherlands Transversion parsimony 64 90 Minimum evolution‡ Institute for Systematics and Population Biology, University of Amsterdam, PO Tamura–Nei I 100 92Box 94766, 1090GT Amsterdam, The Netherlands Tamura–Nei II 100 78§ Biology and Biochemistry, Queen’s University, 97 Lisburn Road, Logdet 99 90Belfast BT9 07BL, UK Maximum likelihood 100 100......................................................................................................................... vWF ParsimonyThe order Insectivora, including living taxa (lipotyphlans) and All positions 49 99archaic fossil forms, is central to the question of higher-level 1st and 2nd positions 24 65relationships among placental mammals1. Beginning with 3rd positions 51 93 Transversion parsimony 30 95Huxley2, it has been argued that insectivores retain many primi- Minimum evolutiontive features and are closer to the ancestral stock of mammals than Tamura–Nei I 37 99are other living groups3. Nevertheless, cladistic analysis suggests Tamura–Nei II 30 99 Logdet 43 97that living insectivores, at least, are united by derived anatomical Maximum likelihood 78 100features4. Here we analyse DNA sequences from three mito- A2ABchondrial genes and two nuclear (2001) to examine relationships Hedges, B. PNAS 98 genes Parsimony All sites 71 88of insectivores to other mammals. The representative insectivores 1st and 2nd positions 49 81are not monophyletic in any of our analyses. Rather, golden moles 3rd positions 31 67are included in a clade that contains hyraxes, manatees, elephants, Transversion parsimony 71 54 Minimum evolutionelephant shrews and aardvarks. Members of this group are of Tamura–Nei I 83 84presumed African origin5,6. This implies that there was an exten- Tamura–Nei II 28 25sive African radiation from a single common ancestor that gave Logdet 79 78 Maximum likelihood 81 89rise to ecologically divergent adaptive types. 12S ribosomal RNA .............................................................................................................................................................................transversions suggest that the base of this radiation occurred Springer, M.S. et al. Nature (1997) Only two of the three paenungulate orders were represented among the mitochondrial and A2AB sequences. Tamura–Nei27 I and II distances were calculated by using an equal-ratesduring Africa’s window of isolation in the Cretaceous period assumption and aM.J. et al. PNAS of rates, respectively. Stanhope, gamma-distribution (1998) Nature © Macmillan Publishers Ltd 1997
  • 4. EVOLUTION OF HUMAN PATHOGENS Smith et al, Nature, 2009
  • 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"" graph from David Hillis
  • 7. What does it mean to “have” the tree of life?
  • 8. Archiving sequence data is acommunity norm ~4% of all published phylogenetic trees Stoltzfus et al 2012
  • 9. “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).
  • 10. Lander et al. Nature 2001
  • 11. Rod asks: Why do we need a database of trees?
  • 12. 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
  • 13. 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
  • 14. 1. Synthesize a complete draft tree of life from existing phylogenetic trees2. Release with: a. ability to improve tree by uploading new data b. areas of uncertainty / conflict c. links to source data and analysis methods d. utilities to download whole tree and subtrees
  • 15. 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
  • 16. INPUTS a AACCGTGAA e a c f b d b ACACGTTAA computationalphylogenies c AAACGTTAA d AGACGTTAA method e AACCGTTAA f AAACGTGAA e a c f b d g h itaxonomies
  • 17. a b c da b c d a,b c,d a,b,c,d a b c da c b d a,b c,d a,b,c,d Stephen Smith, U Michigan
  • 18. a b c da c b d a,b c,d a,b,c,d a b c d a,c a,b c,d b,d a,b,c,d Stephen Smith, U Michigan
  • 19. a b c da d e f g h i a,c a,b c,d b,d a,b,c,d a b c d e f g ha,c a,b c,d b,d a,b,c,d e,f,g,h,i a,b,c,d,e,f,g,h,i Stephen Smith, U Michigan
  • 20. a b c d e f g h a b c d e f g ha,c a,b c,d b,d a,c a,b c,d b,d a,b,c,d e,f,g,h,i a,b,c,d e,f,g,h,i a,b,c,d,e,f,g,h,i a,b,c,d,e,f,g,h,i a c b d e f g h i Stephen Smith, U Michigan
  • 21. Dipsicales graphtaxonomy data (578 taxa) +Soltis et al APG III phylogeny (30 taxa)
  • 22. Dipsicales graph Synthesized tree (favouring phylogenetic branches); contains all 578 taxa
  • 23. community refinementr evolutionary relationships recovered in this analysis of Carnivora. Illustrations ofndinia binotata; Felidae (Lynx rufus); Viverridae (Viverra zibetha); Hyaenidae (Crocuta education and outreachns (Eupleres goudotii); Canidae (Canis lupus); Ursidae (Ursus americanus); Phocidaeae (Odobenus rosmarus); Ailurus fulgens; Mephitidae (Mephitis mephitis); Procyonidaed schematic representing diverse taxa [African polecat and striped marten, badger,stela (Mustela frenata); Mustelidae, Lutrinae (Lontra canadensis).volutionary relationships recoveredin this analysis of Carnivora. Illustrations of jor evolutionary relationships recovered in this analysis of Carnivora. Illustrations ofNandinia binotata; Felidae (Lynxrufus); Viverridae (Viverra zibetha); Hyaenidae (Crocuta nia binotata; Felidae (Lynx rufus); Viverridae (Viverra zibetha); Hyaenidae (Crocuta ans (Eupleres goudotii); Canidae (Canis lupus); Ursidae (Ursus americanus); Phocidae Eupleres goudotii); Canidae (Canis lupus); Ursidae (Ursus americanus); Phocidae dae (Odobenus rosmarus); Ailurus fulgens; Mephitidae (Mephitis mephitis); Procyonidae Odobenus rosmarus); Ailurus fulgens; Mephitidae (Mephitis mephitis); badger, ed schematic representing diverse taxa [African polecat and striped marten, Procyonidaechematic representing diverse taxa [African polecat and striped marten, badger, ustela (Mustela frenata); Mustelidae, Lutrinae (Lontra canadensis).a (Mustela frenata); Mustelidae, Lutrinae (Lontra canadensis).representing the major evolutionary relationships recovered in this analysis of Carnivora. Illustrations of nclude (from top): Nandinia binotata; Felidae (Lynx rufus); Viverridae (Viverra zibetha); Hyaenidae (Crocuta; Malagasy carnivorans (Eupleres goudotii); Canidae (Canis lupus); Ursidae (Ursus americanus); Phocidaeifornianus); Odobenidae (Odobenus rosmarus); Ailurus fulgens; Mephitidae (Mephitis mephitis); Procyonidaemustelids (generalized schematic representing diverse taxa [African polecat and striped marten, badger,gulo); Mustelidae, Mustela (Mustela frenata); Mustelidae, Lutrinae (Lontra canadensis). ? automatic ? updating ? ? downstream analyses
  • 24. • provide complete phylogenetic framework • link to biodiversity and systematics content • API for downloading subtrees to analysis tools• source / storage of underlying data
  • 25. ?• 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
  • 26. ?• Open Science • project wiki: http://opentree.wikispaces.com/ • open source software: https://github.com/OpenTreeOfLife • public mailing list, meeting notes, management tools
  • 27. 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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