Hooper_Collaborating in the Cloud-Managing and sharing the escalating number of sponge unknowns via the SpongeMaps project

Transcript

1. JNA Hooper 1,2, KA Hall 1, M Ekins 1, D Erpenbeck 3, G Wörheide 3,4 & G Jolley-Rogers 5 Collaborating in the Cloud: Managing and sharing the escalating number of sponge “unknowns” via the SpongeMaps project. 1, Natural Environments Program, Queensland Museum. 2, Eskitis Institute for Cell & Molecular Therapies, Griffith University. 3, GeoBio-CenterLMU, Ludwig- Maximilians Universität Munich. 4, Bayerische Staatssammlung für Paläontologie und Geologie. 5, CSIRO Plant Industry.
2. Problem #1: Economic Imperative The Problem we have with Sponges Problem #2: Megadiversity Problem #3: Cosmopolitism and the Morphospecies ‘Problem’ Problem #4: The Thin Taxonomic Pipeline One Solution: An Online, Collaborative, Integrative Taxonomic Infrastructure: SpongeMaps Conclusions (what presently exists) Aspirations (what we might need in the future)
3. 11,000 [Source: Newman & Cragg (2012) ‘Natural Products as Sources of New Drugs over the 30 Years from 1981-2010’. J. Nat. Prod. 75, 311-335] • 49% of all new approved drugs for cancer (1981- 2010) were derived directly from natural sources ... (N = 1355) Average over 30 yrs for all clinical targets = 34% Problem #1: Economic Imperative
4. (Eg. AIMS marine bioactivity) Bayesian hierarchical analyses. Mean (±95% CI) predicted marginal means of percentage of active bioassay samples across Phyla (N ~10,000) [source: courtesy of Libby Evans-Illidge et al. (in press, 2013). PLoS ONE PONE-D-12-08357] Cyto- toxicity Anti- microbial CNS protective
5. (E.g. Sources of quinones across marine taxa) • Class of compound ubiquitous in nature, bioactivity includes cytotoxicity • Brown algae and sponges most prolific producers • Complex secondary metabolite relationship between marine microbes and invertebrate hosts increasingly being shown to be of microbial origin [Source: Sunassee & Davies-Coleman (2012) ‘Cytotoxic and antioxidant marine prenylated quinones and hydroquinones’. Natural Products Reports DOI: 10.1039/c2np0008 6e] Major sources of MNPs
6. [Source: Leal et al. (2012) ‘Trends in the Discovery of New Marine Natural Products from Invertebrates over the Last Two Decades – Where and What Are We Bioprospecting?’ PLoS ONE 7(1): e30580. doi:10.1371/journal.pone.0030580] ~10,000 marine NPs discovered from marine invertebrates between 1990–2009 Porifera Cnidaria Echinodermata Chordata Mollusca
7. Number of “known” (described) species (black columns) and “unknown” (estimated) species (white columns) of the most bioactive marine invertebrate phyla versus number of new Marine Natural Products (MNPs) discovered between 1990-2009 (white dots). [Source: Hooper et al. (2013). Integrative and Comparative Biology, pp. 1–9 doi:10.1093/icb/ict038], based on data reanalysed from Leal et al. (2012), Appeltans et al. (2012a, 2012b). Known spp Unknown spp MNPs 49% 29% 7%
8. [Source: Costello et al., 2010, ‘A Census of Marine Biodiversity Knowledge, Resources, and Future Challenges’. PLoS ONE 5(8): e12110.doi:10.1371/ journal.pone.0012110] State of knowledge Well known Poorly known Predominant marine animal bioactives mean
9. [Partial source: Van Soest et al., 2012, ‘Global Diversity of Sponges (Porifera)’. PLoS ONE 7(4): e35105. doi:10.1371/journal.pone.0035105] Siliceous sponges ~ 7,200 known (described) spp Problem #2: Megadiversity
10. Glass sponges ~ 600 known spp [Partial source: Van Soest et al., 2012, ‘Global Diversity of Sponges (Porifera)’. PLoS ONE 7(4): e35105. doi:10.1371/journal.pone.0035105]
11. [Partial source: Van Soest et al., 2012, ‘Global Diversity of Sponges (Porifera).’ PLoS ONE 7(4): e35105. doi:10.1371/ journal.pone.0035105] Calcareous sponges ~ 700 known spp
12. ‘Homosclerophorid’ sponges ~ 100 known spp [Partial source: Van Soest et al., 2012, ‘Global Diversity of Sponges (Porifera).’ PLoS ONE 7(4): e35105. doi:10.1371/ journal.pone.0035105]
13. [Sources: (WPD) Van Soest et al., 2012, ‘Global Diversity of Sponges (Porifera)’. PLoS ONE 7(4): e35105. doi:10.1371/journal.pone.0035105. (AFD) ABRS, 2009, ‘Australian Faunal Directory’. Australian Biological Resources Study, Canberra. (Viewed 18 May 2012).] Worldwide “known” species (WPD) Australian (territorial) “known” species (AFD) Global versus regional trends in current biodiversity knowledge (Porifera): KNOWN species diversity ~50 yrs ~20 yrs ~8,450 spp known ~1,650 spp known
14. ~4,800 collection sites, ~30,000 specimen records, ~5,000 morphospecies (OTUs); datapoints all underpinned by verifiable objects “Biodiscovery”: marine sponges - 1991-present 1993-07 R.Quinn Eskitis/ AZ 1995-10 C.Debitus IRD Noumea/ CRISP 2002-11 C.Ireland & L. Matainaho, Univ Utah/ UPNG/ Wyeth 1987-92 P.Murphy, J. Baker AIMS/ US NCI GBR SBD 2004-11 AIMS, CSIRO, QDPI, GBRMPA, FRDC, etc. 2010-12 ABRS, Univ Utah 1985-11 Others (e.g. R.Capon, M.Garson)
15. Scratching further below the surface …
16. Great Barrier Reef Seabed Biodiversity Project: • >23% of all invertebrates processed were sponges (Porifera) (~1300 spp or OTUs) • 2 of the “top 5” most abundant sponges were new to science • 4 of these “top 5” most abundant sponges were not found on the adjacent coral reefs • Most of our knowledge of the GBR so far is based on the coral reefs, with little known of the adjacent shallow seabed • While our collections continue to rapidly expand, our capability to process them within our systematics lags significantly Scratching further below the surface …
17. HIGHER GROUP KINGDOM/ PHYLUM/ CLASS DESCRIBED SPECIES TOTAL SPECIES (LOWER ESTIMATE) TOTAL SPECIES (HIGHER ESTIMATE) POTENTIALLY BIOACTIVE MARINE PHYLA Eukarya Plantae 7593 22,798 22,803 22,803 Chromista 19444 77,930 93,923 93,923 Fungi 1035 16,035 16,035 16,035 Eukarya (Animals) Protozoa 542 2,207 2,207 0 Basal Metazoa (Parazoa) Porifera 8,553 25,853 26,553 26,553 Placozoa 1 29 119 0 Basal Metazoa (Mesozoa) Mesozoa 134 774 1,684 0 Eumetazoa Radiata Ctenophora 190 315 500 0 Cnidaria (Hexacorallia) 3,152 3,976 5,105 0 Cnidaria (Octocorallia) 3,171 4,871 4,871 4,871 Cnidaria (Cubozoa) 37 67 107 107 Cnidaria (Hydrozoa) 3426 4,976 7,526 7,526 Cnidaria (Siphonophorae) 176 276 296 296 Cnidaria (Scyphozoa) 201 338 383 383 Cnidaria (Staurozoa) 48 88 113 0 Myxozoa 700 7,171 9,818 0 HOW MANY MARINE SPECIES ARE THERE ? (with proportion of potentially bioactive marine species based on reported MNPs) (1) Plants to Eumetazoa Radiata [Source: Appeltans W, et al. (2012) The Magnitude of Global Marine Species Diversity. Current Biology, http://dx.doi.org/10.1016/j.cub.2012.09.036] The problem is the sponge “unknowns”
18. HIGHER GROUP KINGDOM/ PHYLUM/ CLASS DESCRIBED SPECIES TOTAL SPECIES (LOWER ESTIMATE) TOTAL SPECIES (HIGHER ESTIMATE) POTENTIALLY BIOACTIVE MARINE PHYLA Eukarya Plantae 7593 22,798 22,803 22,803 Chromista 19444 77,930 93,923 93,923 Fungi 1035 16,035 16,035 16,035 Eukarya (Animals) Protozoa 542 2,207 2,207 0 Basal Metazoa (Parazoa) Porifera 8,553 25,853 26,553 26,553 Placozoa 1 29 119 0 Basal Metazoa (Mesozoa) Mesozoa 134 774 1,684 0 Eumetazoa Radiata Ctenophora 190 315 500 0 Cnidaria (Hexacorallia) 3,152 3,976 5,105 0 Cnidaria (Octocorallia) 3,171 4,871 4,871 4,871 Cnidaria (Cubozoa) 37 67 107 107 Cnidaria (Hydrozoa) 3426 4,976 7,526 7,526 Cnidaria (Siphonophorae) 176 276 296 296 Cnidaria (Scyphozoa) 201 338 383 383 Cnidaria (Staurozoa) 48 88 113 0 Myxozoa 700 7,171 9,818 0 HOW MANY MARINE SPECIES ARE THERE ? (with proportion of potentially bioactive marine species based on reported MNPs) (1) Plants to Eumetazoa Radiata [Source: Appeltans W, et al. (2012) The Magnitude of Global Marine Species Diversity. Current Biology, http://dx.doi.org/10.1016/j.cub.2012.09.036] “The Taxonomic Impediment”
19. • Cryptic/ sibling species increasingly discovered hiding within so-called cosmopolitan or widely distributed species • In many cases high level of genetic divergence is not manifested at the morphological level • Genetic diversity of sponges is probably substantially underestimated • Promise of sponge biodiversity likely much higher than our present understanding Problem #3: Cosmopolitism and the Morphospecies ‘Problem’
20. E.g. “The Appalling Sponges” - morphologically nearly undifferentiated e.g. Lamellodysidea & Dysidea spp [Source: Erpenbeck, Hooper, Bonnard, Sutcliffe, Chandra, Perio, Wolff, Banaigs, Wörheide, Debitus & Petek, 2012, Evolution, radiation and chemotaxonomy of Lamellodysidea, a demosponge genus with anti-plasmodial metabolites. Marine Biology, 159(5): 1119-1127 (DOI 10.1007/s00227-012-1891-z)]
21. • Anti- plasmodial activity based on polybrominated diphenylethers (PBDEs), of suspected bacterial origin • Different PBDE compositions between populations increase with geographic distance ITS1&2 rDNA tree PBDEs Dysidea Lamellodysidea • Confirms taxonomic split & 8 species boundaries, likely co-evolution of bacterial and sponge hosts
22. ~20,000 specimens of sponges 2008-2010
23. ~20,000 specimens of sponges 2008-2010 (Pöppe et al. 2010. CO I Barcoding Reveals New Clades and Radiation Patterns of Indo-Pacific Sponges … PLoS ONE 5(4): e9950.doi:10.1371/journal.pone.0009950) • Cryptic species of Ircinia and Psammocinia – geographic correlates
24. Sponge Barcoding Project website (www.spongebarcoding.org)
25. Sponge Barcoding Project website (www.spongebarcoding.org)
26. Sponge Barcoding Project website (www.spongebarcoding.org) • Challenge of integrating morphometric data and images with nomenclature, literature, georeferenced specimen, molecular and chemical data into a contemporary and dynamic systematics ? ?
27. KeSimpulan.com bigduck.co Evolutionary Barcoding Taxonomic Barcoding Applied Barcoding www.spongebarcoding.org
28. KeSimpulan.com Taxonomic Sponge Barcoding
29. www.dionlabel.com Clade of taxa with equal chemistry (terpenoid sterols - potentially ubiquitous in microbial communities) Barcode “Tree” Applied Sponge Barcoding
30. www.dionlabel.com Clade of taxa with equal chemistry (halogenated (bromine) compounds – potentially sponge-produced) Barcode “Tree” Applied Sponge Barcoding
31. Lake Tanganyika endemic family Lake Tanganyika sponges other endemic families - Colonization several times - Endemic families originate from cosmopolitan families Family Spongillidae bigduck.co Colonization of ancient lakes Sponge Evolutionary Barcoding
32. • Significant lag between: more effectively documenting the world’s sponge fauna still hiding in the oceans • documenting the 100,000’s of unknowns already in coll’ns • defining all these within the Linnaean systematics • making their unequivocal identities and distributions widely accessible [this gap is presently in the order of magnitudes] Problem #4: The Thin Taxonomic Pipeline
33. Solution. An Online, Collaborative, Integrative Taxonomic Infrastructure: SpongeMaps Source of the pipeline: collecting and curating collections (‘dots on maps’) Other end of the pipeline: publishing OTUs that lead to formal taxa and their biological data
34. Source of the pipeline: collecting and curating collections (‘dots on maps’) Other end of the pipeline: publishing OTUs that lead to formal taxa and their biological data The Biodiversity Information Gap: Challenge of better pumping information through the taxonomic pipeline
35. SpongeMaps: collaborations in ‘the cloud’ ‘Super Carl’
36. Version 1: SpongeMaps.wiki (Foswiki Platform) Version 2: SpongeMaps.org (Caspio Bridge Platform)
37. • Works with IE, but better with new browsers (Chrome, Firefox) • Caspio Bridge Platform (http://www.caspio.com/ ) • Online MS Access/ SQL engine • URL: www.spongemaps.com • Public, Member, Editor & Administrator login areas www.spongemaps.org
38. Public access: • no p/w needed • read-only access • species released to ALA (676 spp public access) • Linnaean taxa (+ some OTUs mentioned in publications)
39. Public access: • no p/w needed • read-only access • species released to ALA (676 spp public access) • Linnaean taxa (+ some OTUs mentioned in publications) Search by image match 2013
40. Public access: • no p/w needed • read-only access • species released to ALA (676 spp public access) • Linnaean taxa (+ some OTUs mentioned in publications) Search by image match
41. Inputs & Outputs •Unique “mudmap” number linking specimens • Images, morphological data, chemical SMILES codes stored on SpongeMaps.org • Taxonomic data harvested from AFD & WoRMS • Specimen GIS data harvested from OZCAM • Sequence data harvested from SBD and GenBank • Exported to ALA 1st of month as XML
43. Pressing this “Download” button saves data as a zipped spreadsheet
47. “bushy”, “red”, “Queensland” Returns: 9 spp of 676 spp accessible to the public
55. MEOWs
56. Silicates
57. Salinity
58. SS temperature
59. Endemism
60. Species richness
62. Member access: • p/w protected • can add new taxa (OTUs) but not edit existing taxa • OTUs not released to ALA unless by agreement of data owners (4,354 OTUs visible, >5,000 OTUs in editor section) • 56,066 images, 30,760 specimens
63. chemistry (Search for “sceptrin”)
66. DNA (Search for “CO I mtDNA, partial”)
67. (Link to record in Sponge Barcoding Database)
69. locality inventories “Heron Island”
70. locality inventories “Heron Island” Returns 2056 specimens in 184 OTUs
71. locality inventories “Heron Island” Returns 2056 specimens in 184 OTUs Pressing this “Download” button saves data as a zipped spreadsheet
72. Editor access: • p/w protected • add new data + edit existing data • >5000 OTUs • 56,066 images • 30,760 specimens • active datasets: QM, NTM, WAM, SAM, MV and UU, with others imminent (e.g. AIMS, Naturalis)
73. Add new data Edit existing data
74. Add new data for mudmaps, specimens, images, chemical compounds, sequences etc
75. Add new specimen records manually (batch mode via import template [Darwin 2 core compliant])
76. Add new specimens Add new images Other online templates Add new mudmap Add new sequence data
77. Edit existing data Editable text data fields Check this box to make species page public (via XML data push to ALA / EOL)
78. Links to WPD (WoRMS)
79. User statistics for SpongeMaps since launch in early May Visits (480), Pages/visit (6.43), Aver. visit time (11.31 mins), % new visits (45.62%)
80. SpongeMaps.wiki • Works best with modern browsers like Google Chrome or Firefox • Foswiki enterprise collaboration platform (http://foswiki.org/) • URL: (https://wiki.trin.org.au/ Marine.Sponges.WebH ome) •Currently only Member login area (no public access)
81. • 3 points of access species (OTUs) Phylogeny Specimens (GIS data and images etc)
82. • Access via OTU (species) portal
83. Species pages include mapping tool and aggregated OTU images
84. Editing tool for text, forms, images on same page as viewing tool
85. Mapping tool allows viewing and editing of data points directly
86. • Entry via Character list
87. Ability to filter via any character
88. Full map has a number of cadastral layers built in (not requiring external tools)
89. Marine Ecoregions of the World (MEoWs)
90. Marine mean oxygen
91. • Entry via Specimen list
92. Choose specimen
93. • Entry via Image list
94. Choose image
95. • Entry via Phylogeny (Phylowidget)
96. Sponge Maps To be linked to Sponge GeneTree Server (www.spongegenetrees.com)
97. Sponge Maps
98. Sponge Maps
99. Conclusions (what presently exists) (Source: doi:10.1093/icb/ict038) • Move multiple collections of sponges and datasets (including raw taxonomic data), into a collaborative online workspace, providing opportunities for collaborators to debate taxonomic identifications and annotate descriptions in real time and behind password protection. Purpose of SpongeMaps • Objectify the early processes of sponge taxonomy through a ‘‘universal’’ system of OTUs, in an attempt to escalate the flow of data of the “unknowns” through the ponderous taxonomic pipeline • Produce outputs in formats useful to the more sophisticated online biodiversity informatics tools (e.g. ALA, EOL etc) • Provide biological context to specimen GIS datapoints within the various online biodiversity databases, and develop support tools to integrate morphometric data with genetic barcodes and chemical dataset (both of special value to sponge systematics), including the Porifera Tree of Life project (PorTOL)
100. Aspirations (what we might need in the future) Future functionality • Add a GIS mapping capability within SpongeMaps.org to ground-truth specimen distributions within each of the alleged OTUs (i.e. those not yet released to the ALA/ EOL – a proven tool that provides better GIS data accuracy) • Resolve the problems of data delivery from SpongeMaps.org to the ALA / EOL, and some minor data formatting issues within the latter two • Incorporate PhyloJIVE into SpongeMaps.org to depict aggregated biodiversity information into compact phylogenetic trees, based on integrative datasets • Build infrastructure that might better support testing the competing hypotheses that: (1) a certain proportion of sponges are “allegedly widely ranging (‘cosmopolitan’) in their distributions”, versus (2) “there are allegedly a plethora of ‘short-range’ endemic species that defy the previous hypothesis”, but which may be artefacts of a sampling bias – this dichotomy presently confounds sponge systematics • Maintain a policy of keeping the scope of the SpongeMaps.org as simple as possible, to maintain its functionality and uptake by the community, while promoting the outputs of SpongeMap.org to support the more sophisticated biodiversity informatics tools (such as ALA & EOL)
101. With thanks to all our current and future collaborators !
102. Courtesy of Dr Michael NICKEL, Phyletischem Museum Jena, Germany (http://www.porifera.net/index.php?option=com_content&task=blogcategory&id=86&Ite mid=121) This might change your perception of sponges
103. Atlas of Living Australia (ALA): http://www.ala.org.au Caspio Bridge: http://www.caspio.com/ Encyclopaedia of Life (EOL): http://www.eol.org Marine Barcoding of Life (MarBOL): http://www.marinebarcoding.org/ Marine Natural Products Database (MarinLit): http://www.chem.canterbury.ac.nz/marinlit/marinlit.shtml Morphbank: http://www.morphbank.net/ The Ocean Biogeographic Information System (OBIS): http://www.iobis.org/ Online Zoological Collections of Australian Museums (OZCAM): http://www.ozcam.org.au/ Porifera Tree of Life Project (PorTol): http://www.portol.org/ Sponge Barcoding Project (SBP): http://www.spongebarcoding.org/ SpongeMaps (Caspio): http://www.spongemaps.org/ SpongeMaps wiki (TRIN): https://wiki.trin.org.au/Marine/Sponges/WebHome Taxonomic Research & Information Network (TRIN): http://www.taxonomy.org.au World Register of Marine Species (WoRMS): http://www.marinespecies.org World Porifera Database (WPD): http://www.marinespecies.org/porifera A Guide to the Monumental List of Acronyms