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What Phylum? What Class? What Order? What Family? What Next? 24 Options 17 Options 31 Options 129 Options

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What Phylum? What Class? What Order? What Family? What Next? 24 Options 17 Options 31 Options 129 Options From iBOL to Planetary Biodiversity “We are in the midst of the Sixth Mass Extinction, this time caused solely by humanity’s transformation of the ecological landscape.” Hall of Biodiversity American Museum of Natural History “One sixth of all species may go extinct by 2100 under current policies.” Accelerating extinction risk from climate change. Urban MC, Science (2015) Call to Action − Moral Obligation/Aesthetics Call to Action − Planetary Sustainability The nine planetary boundaries Stockholm Resilience Centre, Online (2009) Call to Action − Quest for Knowledge Humanity spends billions of dollars each year to advance understanding of our world New Horizons Mission ($700M) “We explore because we are human, and we want to know.” Stephen Hawking Loss of Species = Irrevocable Loss of Knowledge Books of Life Japanese Canopy Plant: Marbled Lungfish: 150 billion characters 133 billion characters Protecting Books Burning the Books of Life Banking the Library of Life Banking the Library of Life Banking Seeds Banking the Library of Life Indexing the Library of Life Indexing Animal Life Through Morphology Indexing Animal Life Through Morphology $250 Billion to Describe 5 Million Species The cost of describing the entire animal kingdom. Carbayo & Marques, Trends in Ecology & Evolution (2011) Mega-Science Projects: The Limits to Investment Large Hadron Collider $9B Hubble Telescope $10B Advancing Science “No method of advancing science is so productive as the development of new and more powerful instruments and methods of research” George Hale April 28, 1928 New Instruments for Indexing Biodiversity The Rise of Automated DNA Sequencers New Methods of Research for Indexing Biodiversity Registering Species Through DNA Barcodes Mega-Science (>$1B) Projects: Key Components Scientific Plan Management Structure International Long Duration Solidarity Mega-Science 2015: Three Telescopes $2.5B $1.0B European Extremely Large Telescope Brazil & 14 European nations $1.5B Thirty Meter Telescope Giant Magellan Canada, China, India, Japan, Moore Foundation & 2 US universities Australia, Korea, & 8 US universities Rise in Publications for One Mega-Science Project Hubble Space Telescope Hubble Space Telescope 900 800 700 600 500 400 300 200 100 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Publications for Hubble and for DNA Barcoding DNA Barcoding Hubble Space Telescope 900 800 700 600 500 400 300 200 100 0 1 2 3 4 5 6 7 8 9 10 11 12 International Barcode of Life Project (2007) 5 Years 500K Species $100M iBOL Launch — 2010 Nagoya, Japan – Oct 20, 2010 Guelph/Toronto, Canada – Sept 24-26, 2010 Rise of Barcode Coverage — 2010 Rise of Barcode Coverage — 2013 Rise of Barcode Coverage — 2015 The Rise of Barcode Coverage — 500K Species 500 400 300 200 Species (K) Species 100 0 2010 2011 2012 2013 2014 2015 Barcode Coverage for Animals, Fungi and Plants The Rise of Barcode Coverage — 500K Species 500 400 300 iBOL has delivered coverage 200 for Species (K) Species less100 than 10% of all multicellular species 0 2010 2011 2012 2013 2014 2015 Assembling Specimens Sequencing Specimens 1200 Barcode Production at CCDB 1000 800 600 400 Barcodes (K) Barcodes 200 0 Informatics Platform — BOLD Can we Barcode the Planet? How large is the task? 10M species 20M species or more? Canada and Our Planet Surface Area: 7% of global land surface Biodiversity: 1% of the global biota Can We Barcode All Canadian Species? Plants: 10K Animals: 85K Fungi: 15K Protists: 10K Barcoding All Canadian Plants 6K Vascular Plants 5.5K of 5.6K 5K 4K 3K 2K 1K 0K 2009 2010 2011 2012 2013 2014 2015 Barriers to Progress on Animals Identifications Difficult Sequence Recovery Difficult Many Undescribed Species Formalin Preservation Canada’s rank in new species descriptions th 6 8th 14th 1990 2000 2010 Few Taxonomic Specialists Old Specimens Automating Species Counts 1 2 Sequence Clusters 3 versus Species 4 5 6 7 8 9 A DNA-based registry for all animal species: The Barcode Index Number (BIN) System. Ratnasingham & Hebert. PLOS ONE (2013) Biodiversity Automation Automating Species Counts BOLD:AAF3452 BOLD:AAC9004 Sequence Clusters BOLD:AAB4123 versus Species BOLD:AAA3260 BOLD:AAA7781 BOLD:AAF3512 BOLD:AAF3297 BOLD:AAF3129 BOLD:AAE3351 Biodiversity Automation One BIN Page of 420,000 on BOLD BOLD:AAB8479 Biodiversity Automation Species Counts versus BIN Counts 2000 1750 7 1500 1. Mammals 6 2. Butterflies 1250 3. Birds 4. Molluscs 1000 5. Fishes 6. Spiders # of BINs 750 5 7. Noctuoids 4 500 3 250 2 1 0 0 250 500 750 1000 1250 1500 1750 2000 # of Species Biodiversity Automation Species Counts versus BIN Counts 2000 10 1750 1500 1. North American Adelgids 2. Surinam Mammals 1250 9 3. ACG Sphingids 4. Australian Fishes 1000 5. Romanian Butterflies North American Aphids # of BINs 750 6. 7. Aquarium Fishes 500 8 8. Argentine Birds 7 6 9. UK Lepidoptera 250 3 4 10. Finnish Beetles 12 5 0 0 250 500 750 1000 1250 1500 1750 2000 # of Species Biodiversity Automation Species Counts versus BIN Counts 1400 1200 1000 The Automation of 800 Species Counts A species count can now be 600 obtained for any site by # of BINs barcoding many specimens 400 and allowing BOLD to assign the sequences to BINs 200 0 # of Species Biodiversity Automation How Many Species are Shared Between Sites? Biodiversity Automation How Many Species are Shared Between Sites? 1% shared Canada Costa Rica Biodiversity Automation How Many Species are Shared Between Sites? 18% shared Costa Rica Argentina Biodiversity Automation Automating Taxonomic Assignments Plutellidae - Ypsolophidae Brachodidae - Sesiidae Hesperiidae - Papilionidae Lycaenidae - Riodinidae Sphingidae - Saturniidae Ichneumonidae - Braconidae Formicidae - Vespidae Apidae - Crabronidae Biodiversity Automation Automating Taxonomic Assignments What Phylum? What Class? What Order? What Family? What Next? 24 Options 17 Options 31 Options 129 Options Lepidoptera Insecta Arthropoda Complete Linnaeus New BIN Achlya flavicornis Drepanidae BIN Only BOLD:AAC2792 Biodiversity Automation Recollecting Canada’s Insect Species Recollecting Canada’s Insects Species Count 29,985 Known Canada’s Biodiversity Mosquin et al. Canadian Museum of Nature (1995) Recollecting Canada’s Insects Species Count 55,000 Estimated Canada’s Biodiversity Mosquin et al. Canadian Museum of Nature (1995) 1. Barcoding Insects in 68 Schoolyards 68 schools 3 weeks 1. Barcoding Insects in 68 Schoolyards 3000 2929 BINs 2500 2000 1500 BINs 1000 500 10% of our known insects 0 0 2000 4000 6000 8000 10000 12000 14000 Specimens Sequenced 2. Barcoding Insects in One Backyard GUELPH 2. Barcoding Insects in One Backyard 5000 4700 BINs 4500 4000 3500 3000 2500 BINs 2000 1500 1000 500 16% of our known insects 0 0K 5K 10K 15K 20K 25K 30K 35K 40K Specimens 3. Barcoding Insects in 45 National Parks 2012 2013 2014 3. Barcoding Insects in 45 National Parks 45 39,808 BINs 40 35 30 29,985 Species Known 25 BINs (K) 20 15 10 5 133% of our known insects 0 0 200 400 600 800 Specimens (K) Barcoding Canadian Insects 60K 50K 57,350 BINs 40K 30K 29,985 Species Known 20K 10K 191% of our known insects 0K 1 200K 400K 600K 800K 1.0M 1.2M Barcoding Canadian Animals 80K 70K 69,200 BINs 60K 50K 49,500 Species Known 40K 30K 20K 10K 0K 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 Probing Biodiversity with DNA Barcodes 1. Are estimates of global number of animal species accurate? ? 2. Has competition been the primary force in limiting the number of animal species? ? 3. Are most species old? ? How Many Species of Insects? “The question of how many terrestrial species exist is all but reduced to one of how many arthropod species there are. With beetles accounting for about 40% of all described arthropod species, the truly pertinent question is how many beetle species exist.” Beetle Species Mean: 1.5M Insect Species Mean: 5.5M New approaches narrow global species estimates for beetles, insects, and terrestrial arthropods. Stork et al. PNAS (2015) Canadian Insect Orders — BINs vs Species 5 4.5 4 3.5 Coleoptera 3 Lepidoptera Hemiptera BINs 2.5 10 2 Log 1.5 1 0.5 0 0 0.5 1 1.5 2 2.5 3 3.5 4 Log10 Known Species Canadian Insect Orders — BINs vs Species 5 4.5 Diptera 4 Hymenoptera 3.5 Coleoptera 3 Lepidoptera Hemiptera BINs 2.5 10 2 Log 1.5 1 0.5 0 0 0.5 1 1.5 2 2.5 3 3.5 4 Log10 Known Species Canadian Insect Orders — BINs vs Species 36K Known Species BIN Estimate 17K Species/BINs Observed 7.2K 6.7K 7K 4.9K 4.5K 4.5K 3.2K 3K 3.1K 2K Diversity of 99 Families of Diptera — BINs vs Species 10,000 1000 100 BINs Observed 10 Diploid Haplodiploid 1 1 10 100 Number of Known Species in Family Diversity of Canadian Cecidomyiidae Number of BINs Number Log2 Number of Specimens What Did We Learn About Insect Diversity? 50K 20K 9K 6K 5K 4K Diptera Hymenoptera Coleoptera Lepidoptera Hemiptera Others Insect Species (Canada) — 94K estimated Prior work — 55K estimated What Did We Learn About Insect Diversity? 50K 20K 9K 6K 5K 4K Diptera Hymenoptera Coleoptera Lepidoptera Hemiptera Others Insect Species (Canada) — 94K Insect Species (Global) — 9.4M (versus 5.5M) What Did We Learn About Cecidomyiidae Diversity? Cecidomyiidae (Canada) —20K estimated Prior work —1K estimated What did We Learn About Cecidomyiid Diversity? Estimated Species (Canada) — 20K Estimated Species (Global) — 2M “It would appear that God has an inordinate fondness for stars and beetles.” J.B.S. Haldane “On further thought, it would appear that God has an inordinate fondness for stars and midges.” More Hyperdiverse Lineages Harpacticoids Nematodes Acarina Implications of Species Counts
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