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The iPlant Collaborative: A Cyberinfrastructure for the Life Sciences Naim Matasci BIO5 / The iPlant Collaborative EEB, University of Arizona Oct 4, 2011.

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Presentation on theme: "The iPlant Collaborative: A Cyberinfrastructure for the Life Sciences Naim Matasci BIO5 / The iPlant Collaborative EEB, University of Arizona Oct 4, 2011."— Presentation transcript:

1 The iPlant Collaborative: A Cyberinfrastructure for the Life Sciences Naim Matasci BIO5 / The iPlant Collaborative EEB, University of Arizona Oct 4, 2011

2 Ancestral state of Hawaiian lobelioids Lobelia niihauensis (Image: David Eickhoff) Cyanea leptostegia (Image: Karl Magnacca)

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4 (Schulter et al. 1997, Paradis 2004) Continuous Ancestral Character Estimation ?

5 Obtain sequences GetSeq Obtain sequences GetSeq Align sequences Muscle Align sequences Muscle Build Tree FastTree (aML) Ninja (NJ) PHYLIP (MP, NJ, ML) RAxML (ML) Build Tree FastTree (aML) Ninja (NJ) PHYLIP (MP, NJ, ML) RAxML (ML) Visualize Tree iPlant Tree Viewer Visualize Tree iPlant Tree Viewer Integrate Data Lopper TNRS Integrate Data Lopper TNRS Run Analysis CACE DACE Contrast OUch Picante Penalized likelihood Run Analysis CACE DACE Contrast OUch Picante Penalized likelihood

6 Obstacles Number of taxa Taxa names

7 Taxonomic uncertainty 1.Non-existent names Misspellings Contamination Annotations Morphospecies Digitization issues (frame shifts, character encoding)Lexical variants (digitization conventions) 2.Synonymy Nomenclatural synonyms Taxonomic synonyms / concepts 3.Misidentifications, incomplete identifications

8 a) Centaurium curvistamineum (Wittr.) Abrams (1951) b) Centaurium minimum (Howell) Piper (1915) c) Centaurium muhlenbergii (Griseb.) Wight ex Piper (1906) d) Centaurium muhlenbergii (Griseb.) Wight ex Piper forma albiflorum (Suksd.) St. John (1937) e) Centaurium muhlenbergii (Griseb.) Wight ex Piper var. albiflorum Suksd. (1927) f) Centaurodes muhlenbergii (Griseb.) Kuntze (1891) g) Erythraea curvistaminea Wittr. (1886) h) Erythraea minima Howell (1901) i) Erythraea muhlenbergii Griseb. (1839) Image: Gordon Leppig & Andrea J. Pickart

9 How to figure that out? …or ask around at My-Plant.org

10 Makemake at de.wikipedia

11 Hans Hillewaert

12 Taxonomic Name Resolution Service Computer assisted standardization of plant names Corrects spelling errors and alternative spellings to a standard list of names Convert out-of-date names to currently accepted names

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16 Lobelia kauaensis Lobelia villosa Galeatella gloria-montis Trematolobelia kauaiensis Trematolobelia macrostachys Lobelia hypoleuca Neowimmeria yuccoides Lobelia niihauensis Brighamia insignis Brighamia rockii Delissea rhytidosperma Delissea subcordata Cyanea acuminata Cyanea hirtella Cyanea coriacea Delissea leptostegia Clermontia kakeana Clermontia parviflora Clermontia arborescens Clermontia fauriei

17 Obtain sequences GetSeq Obtain sequences GetSeq Align sequences Muscle Align sequences Muscle Build Tree FastTree (aML) Ninja (NJ) PHYLIP (MP, NJ, ML) RAxML (ML) Build Tree FastTree (aML) Ninja (NJ) PHYLIP (MP, NJ, ML) RAxML (ML) Visualize Tree iPlant Tree Viewer Visualize Tree iPlant Tree Viewer Integrate Data Lopper TNRS Integrate Data Lopper TNRS Run Analysis CACE DACE Contrast OUch Picante Penalized likelihood Run Analysis CACE DACE Contrast OUch Picante Penalized likelihood

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