Informatics Infrastructure at the start of the Second Decade of DNA Barcoding
- 1. Informatics Infrastructure at the start of the Second Decade of DNA Barcoding SUJEEVAN RATNASINGHAM BIODIVERSITY INSTITUTE OF ONTARIO UNIVERSITY OF GUELPH
- 2. 10+ Years 4M+ Records 0.5M+ Species 100+ Nations
- 3. Decade 1 - Capacity Building Community DatabaseCollaborative Networks Software Tools Data Standards
- 5. Building the Library 10,000 100,000 1,000,000 10,000,000 2004 2006 2008 2010 2012 2014 barcodes Linnean Species BINs
- 6. Spiders Birds Lepidoptera Of North America Birds of Argentina IUCN RedList CITES Fish Bees Amphibians Mammals Taxonomic Thematic Geographic Community Benchmarks Mosquitoes
- 7. Collaborative Networks 0 2 4 6 8 10 12 14 16 2004 2006 2008 2010 2012 2014 RegisteredUsers(Thousands) Data Sharing 2005 – 102 users from 30 institutions
- 8. 1000+ Institutions from 94 countries sharing data on BOLD AcrossNations Within Nations 100K+ 10K – 100K 1K – 10K BOLD User Network - 2015
- 9. CanadaFranceUSA GermanyCosta Rica United Kingdom Switzerland AcrossNations Within Nations 100K+ 10K – 100K 1K – 10K Finland BOLD User Network - 2015
- 10. KenyaBelgium Madagascar Norway Austria Sweden Jordan Argentina China Brazil Spain Mexico Panama Portugal Pakistan Egypt South Africa India New Zealand Netherlands AcrossNations Within Nations 100K+ 10K – 100K 1K – 10K BOLD User Network - 2015
- 11. AcrossNations Within Nations 100K+ 10K – 100K 1K – 10K BOLD User Network - 2015 66 Other Countries from Every Continent
- 12. Testing the Library Depth BBC Tree of Life, 2014 400K+ 163K+ 80% 500+ Species with Full Taxonomy of the BOLD Library Orders Animals Test Data: 4000 species from 200 orders, 20 per order
- 13. Reference Queries Testing the Library Depth
- 14. 0 25 50 75 100 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 TopMatchSimilarity >98% >95% >92% >90% Testing the Library Depth
- 15. Testing the Library Depth −0.05 0.00 0.05 0.10 0.15 −0.06−0.04−0.020.000.02 PCA1 PC2 Coleoptera Diptera Ephemeroptera Hemiptera Hymenoptera Lepidoptera Plecoptera Thysanoptera Trichoptera −0.05 0.00 0.05 0.10 −0.04−0.020.000.020.04 PC1 PC2 Coleoptera Diptera Ephemeroptera Hemiptera Hymenoptera Lepidoptera Plecoptera Thysanoptera Trichoptera K-mers (k=3) Ratnasingham, Ma, Hebert, in prep. Amino Acid Composition
- 16. Barcode Index Number (BIN) Algorithm Registry • Tuned to the marker (COX1) • Fixed parameters for balanced OTU generation • Uses prior threshold but refines for each group • Occurrence of DNA Barcode (place and time) • Aggregation of all associated metadata • Reusable - works across studies
- 17. BOLD:AAF2716 Notioplusia illustratataOraesia Janzen 03 Ctenoplusia sp. ANIC1
- 18. 0 50000 100000 150000 200000 250000 300000 Mammalia Birds Insecta Fish Araneae Mollusca Plants Fungi Importance of registering OTUs Species Barcode Index Numbers Unregistered OTUs 0 10,000 20,000 30,000 40,000 50,000 60,000 LATITUDINAL RANGE
- 20. Allow anyone, anywhere, to identify any organism
- 21. MAIL
- 23. LifeScanner Solution Overview Species Identification ID Engine Sample Collection Sequencing PCR Prep Partner Sequencing Labs
- 26. Moving into decade 2
- 27. EmbraceBigData Impact Reporting Analysis Monitoring Forecasting Complexity (Data volume & Dimensionality) What happened? Why it happened? What is happening? What might happen?
- 28. Support for multiple scales 102 103 104 104
- 29. Support for NGS based Barcoding
- 30. BOLD4 Launch of Beta on Sept 29,2015 Advancing the Automation of Species Identification
- 31. Community Curated Libraries Tier 3 Tier 2 Tier 1 Purpose generated & reference specimens available Barcode compliant & consistent Key species (e.g. Dirty 22, Domesticated & Bush meat) Curated for consistency in taxonomic assignments Barcode compliant & consistent CITES/REDLIST (e.g. Endangered & controlled species) Mined from BOLD Limited verification and only to be used as last resort Disease vectors & invasive species 78% 20% 25%
- 32. Community Defined Metadata Extensions Rougerie R, Smith AM, Fernandez-Triana J, Lopez-Vaamonde C, Ratnasingham S Hebert PDN. 2011.Molecular analysis of parasitoid linkages (MAPL): gut contents of adult parasitoid wasps reveal larval host. Mol Ecol 20:179-186.
- 34. Community Developed Analytical Tools Plug-in Framework 6000+ Analytical Packages in CRAN
- 36. BOLD 4 + SAP Lumira
- 37. BOLD4 – Some other features • Checklist Support (synonyms, progress, shopping lists) • Data portal for core facilities • Complete record histories • RESL algorithm on your own datasets • Storage and analysis of pre-clustered NGS data
- 38. Support for Metabarcoding mBRAVE Linkages & Partners Metabarcoding Research And Visualization Environment
- 39. Acknowledgements BOLD Team Paul Hebert Dan Janzen & Winnie Hallwachs Scott Miller Axel Hausmann Stefan Kremer Many others! Biodiversity Institute Collections Team Canadian Center for DNA Barcoding Team BOLD Users