Two graphs, three responses
Download as PPTX, PDF2 likes4,184 views
This document discusses two graphs related to taxonomy and barcoding. It then presents three potential responses: 1) Modernize taxonomy by digitizing specimens, literature, and linking data sources. 2) Imagine a world where only barcodes exist and how we would visualize biodiversity. 3) Integrate taxonomy and barcodes by linking names to barcodes using specimens as the connection point, though challenges remain around building complete trees and visualizing communities. Integrating data from sources like BOLD, GBIF, and literature would help but requires resolving issues of duplicate records and name interpretations.
Two graphs, three responses
- 1. Two graphs, three responses @rdmpage http://iphylo.blogspot.com
- 2. Numbers of new animal names 1923 WWI WWII
- 3. Implications • Taxonomists are working at capacity • Maybe we are running out of species to discover…(!) • Most taxonomic work is in the past (“legacy”)
- 5. Two graphs
- 7. Dark taxa (taxa with sequences but no proper scientific name) http://iphylo.blogspot.ca/2011/04/dark-taxa-genbank-in-post-taxonomic.html
- 10. Dark taxa • Disconnect between taxonomy and genomics • Are “dark taxa” species we already know about, or do they represent new diversity?
- 14. GBIF.org 500 million records
- 16. BioNames http://bionames.org • Linking taxonomic names to published literature • DOIs, BHL, BioStor, PDFs, Gallica, etc. • 4 million names • 400K publications
- 17. Response 1: Modernise taxonomy • Barcoding is digitising life (organism to string of letters) • Mass digitisation of specimens and literature, etc. • Cross-links between data sources
- 18. Response 2: Barcode-only world • Imagine barcodes were all we had (i.e., we’re microbiologists) • How would we visualise biodiversity?
- 20. Page R. Visualising Geophylogenies in Web Maps Using GeoJSON. PLOS Currents Tree of Life. 2015 Jun 23 . Edition 1. doi: 10.1371/currents.tol.8f3c6526c49b136b98ec28e00b570a1e
- 21. These are (too) simple
- 22. Challenges • Can we build a complete tree of barcodes? • Can we (quickly) compute sequence diversity for an area? • Can we visualise ecological communities?
- 23. DNA walks Start at (0,0) and first position in sequence Move in x,y plane according to whether next base is different At end of sequence draw point Plot shows DNA mini-barcodes (127 bp)
- 25. Response 3: Link taxonomy and barcodes
- 26. Integrate using taxonomic names?
- 27. Names need not equal taxa Morethia obscura in GBIF
- 28. BINs for Morethia obscura in BOLD
- 29. Integrate using specimens? • Barcodes have vouchers • GBIF has specimens • Why isn’t BOLD in GBIF? • Actually, parts of it already are…
- 31. BOLD samples in GBIF (twice) (but provided by ZSM and EMBL, not BOLD) BC ZSM Lep 10234 GBIF 883514761 Casbia rectaria Walker, 1866 GU655831 GBIF 1080492017 Lepidoptera 7bcace52-85a0-4c5c-991e-555d4479e42c GWORH520-09 BC ZSM Lep 10234 BOLD:AAA4623 Casbia rectaria GU655831 BC ZSM Lep 10234 Lepidoptera sp. BOLD:AAA4623 GBIF GBIF EMBL BOLD
- 32. The role of type specimens Type specimen Type specimen time of publication
- 33. 11,664 bird holotype specimens: For 6,648 GBIF doesn’t understand the name
- 34. Three responses Make taxonomy digital Sequences eat the world Integrate taxonomy & sequences
Editor's Notes
- #3: http://www.organismnames.com/metrics.htm?page=graphs
- #5: http://www.nature.com/scitable/content/growth-in-nucleotide-sequences-submitted-to-genbank-45068
- #21: Page R. Visualising Geophylogenies in Web Maps Using GeoJSON. PLOS Currents Tree of Life. 2015 Jun 23 . Edition 1. doi: 10.1371/currents.tol.8f3c6526c49b136b98ec28e00b570a1e.
- #23: http://gist.neo4j.org/?50f3a54d21a9b0710009
- #28: http://gbif.org/species/2463730 Phot from Jordan Vos http://www.arod.com.au/arod/reptilia/Squamata/Scincidae/Morethia/obscura
- #32: Based on http://gist.neo4j.org/?50f3a54d21a9b0710009, but not that GBIF sequence has gone, now http://www.gbif.org/occurrence/1080492017 7bcace52-85a0-4c5c-991e-555d4479e42c