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Two graphs, three responses
@rdmpage
http://iphylo.blogspot.com
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Numbers of new animal names
1923
WWI WWII
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Implications
• Taxonomists are working at capacity
• Maybe we are running out of species to discover…(!)
• Most taxonomic work is in the past (“legacy”)
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Two graphs
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Two graphs
taxonomy sequen
cing
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Dark taxa(taxa with sequences but no proper
scientific name)
http://iphylo.blogspot.ca/2011/04/dark-taxa-genbank-in-post-taxonomic.html
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Mammals
Proper Linnaean names
Aus sp.
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“Invertebrates”
BOLD
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Dark taxa
• Disconnect between taxonomy and genomics
• Are “dark taxa” species we already know about, or do they represent new diversity?
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Two graphs
taxonomy sequen
cing
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Three responses
Make taxonomy digital
Sequences eat the world
Integrate taxonomy & sequences
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https://www.flickr.com/photos/nhm_beetle_id/15930177695
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GBIF.org 500 million records
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Digitise the literature
http://biodiversitylibrary.orghttp://biostor.org
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BioNameshttp://bionames.org
• Linking taxonomic names to published literature
• DOIs, BHL, BioStor, PDFs, Gallica, etc.
• 4 million names
• 400K publications
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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
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Response 2: Barcode-only world
• Imagine barcodes were all we had (i.e., we’re microbiologists)
• How would we visualise biodiversity?
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Visualise all barcodes
http://iphylo.org/~rpage/bold-map
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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
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These are (too) simple
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Challenges
• Can we build a complete tree of barcodes?
• Can we (quickly) compute sequence diversity for an area?
• Can we visualise ecological communities?
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DNA walksStart 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)
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“Symbiome”
http://iphylo.blogspot.ca/2011/03/visualising-symbiome-hosts-parasites.html
Insects Crustacea
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Response 3: Link taxonomy and barcodes
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Integrate using taxonomic names?
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Names need not equal taxa
Morethia obscura in GBIF
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BINs for Morethia obscura in BOLD
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Integrate using specimens?
• Barcodes have vouchers
• GBIF has specimens
• Why isn’t BOLD in GBIF?
• Actually, parts of it already are…
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http://doi.org/10.15468/tfpnkp
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BOLD samples in GBIF (twice)(but provided by ZSM and EMBL, not BOLD)
BC ZSM Lep 10234GBIF 883514761Casbia rectaria Walker, 1866
GU655831GBIF 1080492017Lepidoptera
7bcace52-85a0-4c5c-991e-555d4479e42c
GWORH520-09BC ZSM Lep 10234BOLD:AAA4623Casbia rectaria
GU655831BC ZSM Lep 10234Lepidoptera sp. BOLD:AAA4623
GBIF
GBIF EMBL
BOLD
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The role of type specimens
Type specimen
Type specimen
time of publication
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11,664 bird holotype specimens:
For 6,648 GBIF doesn’t understand the name
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Three responses
Make taxonomy digital
Sequences eat the world
Integrate taxonomy & sequences