2. Taxonomy is described sometimes as a science and sometimes as an art,
but really it’s a battleground
Bill Bryson
A short history of nearly everything

3. Taxonomy: the “common denominator”
from Ancient Greek: τάξις taxis "arrangement" and Ancient Greek: νομία nomia "method"
= the academic discipline of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups.
To bring order into the “chaos” of species, to help scientists in how to deal with species, so they know they are talking about the same creature and to classify them in larger groups.
International Code on Zoological Nomenclature (ICZN)
International Code of Nomenclature for algae, fungi
and plants
Kingdom > Phylum > Class > Order > Family >
Genus > Species

4. Taxonomy: human errors & variation
Taxonomy: prone to spelling variations & mistakes
Some names are harder to spell than others…
Actinobacillus actimomycetemcomitans
Actinobacillus actimycetemcomitans
Actinobacillus actinmycetemcomitans
Actinobacillus actinomicetemcomitans
Actinobacillus actinomy
Actinobacillus actinomyce
Actinobacillus actinomycemcomitans
Actinobacillus actinomyceremcomitans
Actinobacillus actinomycetam
Actinobacillus actinomycetamcomitans
Actinobacillus actinomycetecomitans
Actinobacillus actinomycetemcmitans
Actinobacillus actinomycetemcomintans
Actinobacillus actinomycetemcomitance
Actinobacillus actinomycetemcomitans
Actinobacillus actinomycetemcomitants
Actinobacillus actinomycetemcommitans
Actinobacillus actinomycetemocimitans
Actinobacillus actinomycetencomitans
Actinobacillus actinomycetum
Actinobacillus actinomyctemcomitans
Actinobacillus actinomyectomcomitans
Actinobacillus actinomyetemcomitans
Actinobacillus actinonmycetemcomitans
Actinobacillus actionomycetemcomitans
Actinobacillus actynomicetemcomitans
Actinobacillus antinomycetemcomitans
Difficulties with Latinized Names
Transcription errors
Which one is correct?
Controlled taxonomic vocabulary necessary!
World Register of Marine Species (WoRMS)

5. Taxonomy: prone to computer errors
Automatic “series filling” is not always recommended…
Clupea harengus Linnaeus, 1758
Clupea harengus Linnaeus, 1759
Clupea harengus Linnaeus, 1760
Clupea harengus Linnaeus, 1761
Clupea harengus Linnaeus, 1762 …
Clupea harengus Linnaeus, 2254
Clupea harengus Linnaeus, 2255

6. Taxonomy: many ways to (correctly) spell a name…
Agalinus paupercula borealis
Agalinus pauperculum borealis
Agalinis paupercula var. Borealis
Agalinus pauperculum var. borealis
Agalinus paupercula var. borealis
Agalinus paupercula var. borealis Pennell
Agalinus paupercula Britton var. borealis Pennell
Agalinus paupercula (Gray) Britt. var. borealis Pennell
Agalinis paupercula (A.Gray) Britton var. borealis Pennell
Agalinus paupercula (Gray) Britton var. borealis (Pennell) Zenkert 1934
Gerardia paupercula borealis
Gerardia paupercula var. borealis
Gerardia paupercula var. borealis (Pennell) Deam
Gerardia paupercula (Gray) Britt. var. borealis (Pennell) Deam
Gerardia paupercula (A. Gray) Britton var. borealis (Pennell) Deam
Gerardia paupercula (A. Gray) Britton subsp. borealis (Pennell) Pennell
Gerardia paupercula (Gray) Britt. ssp. borealis (Pennell) Pennell
Gerardia paupercula Britton ssp. borealis Pennell

7. Taxonomy: variation in the author name
Ceratium hirudinella
Ceratium hirudinella (Muller 1773)
Ceratium hirundienella
Ceratium hirundinella
Ceratium hirundinella (Mull )
Ceratium hirundinella (Mull)
Ceratium hirundinella (Muller )
Ceratium hirundinella (Muller 1773)
Ceratium hirundinella (Muller)
Ceratium hirundinella (O. F. Müller) Bergh
Ceratium hirundinella (O.F. Müller) Bergh
Ceratium hirundinella (O.F. Müller) Bergh
Ceratium hirundinella (O.F. Müller, 1773) Dujardin, 1841
Ceratium hirundinella (O.F. M�ller) Bergh
Ceratium hirundinella Dujardin
Ceratium hirundinella O. F. M.
Ceratium hirundinella O. F. Muller
(Example from the Global Names Index - GNI)

8. Taxonomy – a complicated topic
Synonymy
Halichondria (Halichondria) panicea (Pallas, 1766)
Bread-crumb sponge: more than 60 synonyms)

9. Important to know the context of your dataset!
Homonymy
A name for a taxon that is identical in spelling to another such name,
that belongs to a different taxon.
Only one of the two names can stay “valid”, the other becomes “invalid”.
Scientific name: Alebion
Alebion Krøyer, 1863
=> Animalia, Crustacea, parasitic copepods
Alebion Gray, 1867
=> Animalia, Porifera
=> Accepted as Iophon Gray, 1867
Important to know the context of your dataset!

10. Taxonomy: how to deal with all this variation?
Link taxon names with World Register of Marine Species (WoRMS)
WoRMS:
Standard list of marine taxon names
First authoritative list of names of all marine & brackish water taxa worldwide
Managed by VLIZ, directed by taxonomic experts
Open access
Follow international standards & serve permanent Global Unique IDs (LSIDs)
Up-to-date and (near) complete (incl. synonyms &commonly used spelling mistakes)
If no link possible:
Consult with data provider(s)
Consult with taxonomic expert(s) at
Originally delivered name is always safeguarded!

11. Taxonomy: a challenge (and head-ache?) for data managers
Dataset
Before tax. check
After tax. check 1
Amphiura sunderali 2
Amphiura sundevali
Amphiura sundevalli 3
Amphiura sundvali 4
Dataset
Before tax. check 1
Amphiura sunderali 2
Amphiura sundevali 3
Amphiura sundvali 4
Amphiura sundevalli

12. “… In total, 6,172 unique taxon names were submitted
“… In total, 6,172 unique taxon names were submitted... After a thorough quality control, however, this number was reduced to 4,525, mostly due to spelling variations and synonymy. Such [taxonomic] quality control is highly needed, since a misspelled or obsolete name could be compared to the introduction of a rare species, with adverse effects on further (biodiversity) calculations…”
Source: Vandepitte et al. (2010). Data integration for European marine biodiversity research: creating a database on benthos and plankton to study large-scale patterns and long-term changes. Hydrobiologia.

13. Uncertain identifications
Sp. 1, Sp. a, Sp. X …
Cfr., aff. …
Aphelochaeta spp./ Chaetozone spp.
=> Link to first higher taxonomic level!
Dataset A (Spain)
Dataset B (Greece)
Acantholaimus sp. 1
Acantholaimus sp. 2 ?
Which equals which?
Specimen comparison!?
Reduction of information till genus level (Acantholaimus)
= loss of biodiversity, but underestimation is preferred to overestimation

14. Cf. & aff.
The term “cf” (or “cfr”) stands for “confer”, and loosely interpreted, means “looks like”.
Acanthonchus duplicatus <> Acanthonchus cf. duplicatus
Acanthonchus
Bolbolaimus abebei <> Bolbolaimus aff. abebei
Bolbolaimus

15. Aphelochaeta sp./Chaetozone sp.
Identify higher classification of both genera
Find first common higher level
Aphelochaeta:
Animalia – Annelida – Polychaeta – Terebellida – Cirratulidae
Chaetozone:
Chaetoceros socialis/radians => Chaetoceros
Pterosperma/Pachysphaera
Pterosperma:
Plantae – Chlorophyta – Prasinophyceae – Halosphaerales - Pterospermataceae
Pachysphaera:
Plantae – Chlorophyta – Prasinophyceae – Chlorodendrales - Halosphaeraceae
Classification: Biota > Plantae (Kingdom) > Chlorophyta (Phylum) > Prasinophyceae (Class) > Halosphaerales (Order) > Pterospermataceae (Family)

16. Avoid abbreviated names: Calanus finmarchicus 15
C. affinis 20
C. pacificus 1
Caligulus sp. 48
C. affinis 9
Acartia tonsa 7
A. danae 8
Balanus balanus 156
B. crenatus 54
Balanetta baylii 2
Abarenicola devia 8
A. affinis 518
Achnanthes subaffinis 5
A. affinis 2
A. affinis 2
A. affinis 518
A. danae 8
Abarenicola devia 8
Acartia tonsa 7
Achnanthes subaffinis 5
B. crenatus 54
Balanetta baylii 2
Balanus balanus 156
C. affinis 20
C. pacificus 1
C. affinis 9
Calanus finmarchicus 15
Caligulus sp. 48

17. How to deal with “common names”?
“translate” the common name to a scientific name
When doubt => consult your data provider!
Provided common name
Scientific name
Knobby brain coral
Diploria clivosa
Lobster
Homarus americanus
Homarus gammarus
Seaweeds ?
Shark
World Register of Marine Species
Contains lots of common names => search option
DarwinCore / IPT
Move common name to field “VernacularName”
Add corresponding scientific name to field “ScientificName”

18. How to deal with unaccepted names?
Dataset name = Ameira ambigua Scott, 1903
According to WoRMS:
Ameira ambigua = unaccepted, synonym of Ameira minuta Boeck, 1865
Protocol as manager:
Keep originally provided name as scientific name (Ameira ambigua)
Link with LSID of this name: urn:lsid:marinespecies.org:taxname:348659
Inform data provider on fact that this name is currently unaccepted
=> provider decides whether to keep or change the name
=> manager follows decision of the provider
If your name matches an ‘unaccepted’ name in WoRMS:
Choice to populate with the WoRMS info assocaited with the original name OR populate the fields with the accepted name info…WHICH IS RECOMMENDED?
What if one populates the classification fields using the accepted name info but populates the scientificname, authority and LSID with the provided name WoRMS content?

19. Taxonomy & DarwinCore fields
33 fields related to partim “taxon” in DwC…
Most important ones:
ScientificNameID (=LSID)
ScientificName
ScientificNameAuthorship
(VernacularName) => check with provider to link to a scientific name
Lots of other fields can be derived by the link to WoRMS and do not need to be completed
ALWAYS keep originally provided name as ScientificName!
When name not in WoRMS
=> check other registers (QC)
=> send with name + source to

20. Taxonomic QC – in summary
Taxon name matches with WoRMS? No
Yes
Spelling errors/common names of WoRMS name?
Uncertain identification?
Yes
Reduce taxonomy to first common higher classification level No
Contact provider
Yes
Need to comply with a certain taxonomic standard, to be able to compare data from different datasets

21. Questions? Part 2 in a few minutes… 