1. Taxonomy and taxonomic systems
Elements important for data management

2. Taxonomy Science concerned with
Nomenclature: give ‘scientific’ names to species
Strictly regulated, different ‘codes’ for botany, zoology, bacteria
Classification: create and name groups, ‘taxa’
‘Systematics’ is often used as an equivalent

3. Scientific names In principle, Latin or Latinised names
Regulated by the codes:
Codes are drafted and maintained by Commissions
International Code for Zoological Nomenclature
International Code for Botanical Nomenclature
International Code for Bacterial Nomenclature
Commissions are arbiter in case of disputes
Problem: many unicellular organisms are neither plants nor animals, have two names

4. Classification
1,700,000 names! We need a system to organise this information
Hierarchical classification
Classification is based on phylogeny (common descent)
Hypothesis: life only originated once; all organisms descend from a single ancestor
Basis of objectivity in classification

5. Hierarchy: common descent

6. Hierarchy: sub-sets Biota Animalia Plantae Echinodermata Arthropoda …
Crustacea …
Fungi … … … … …

7. Hierarchy: ranks Regnum: Animalia, Plantae…
Phylum: Arthropoda, Echinodermata…
Classis: Crustacea, Insecta…
Ordo: Decapoda, Amphipoda, Isopoda…
Familia: Xanthidae, Diogenidae…
Genus: Xantho, Progeryon…
Species: Xantho granulicarpus, Xantho hydrophilus…

8. Extra ranks ‘Super-’, ‘Sub-’, ‘Infra-’
Subordo, infraordo, superfamilia…
Not for genus and species (except subspecies)
Tribus: between family and genus
Infraspecific
Subspecies only rank recognised in zoology
Botany: varietas, forma
Botany: ‘Divisio’ instead of ‘Phylum’

9. Standard endings Rank Botany Bacteriology Zoology
Divisio (-phyta/-mycota)
Subdivisio (-phytina/-mycotina)
Classis (-phyceae/-mycetes/-opsida)
Subclassis (-phycidae/-mycetidae/-idae)
Ordo -ales -ales
Subordo -ineae -ineae
Superfamilia (-oidea)
Familia -aceae -aceae -idae
Subfamilia -oideae -oideae -inae
Tribus -eae -eae (-ini)
Subtribus -inae -inae

10. Uni-, bi- et multinomens
Names of rank of genus and above consist of a single part
E.g. ‘Hominidae’, ‘Homo’
Names of rank species and below consist of several parts
E.g. ‘Homo sapiens’
Subspecies… indicated with extra parts
E.g. ‘Homo sapiens erectus’
Several name parts, one name

11. Format of taxonomic names
Names of genera and lower are often written in italics
E.g. ‘Homo’ and ‘Homo sapiens’
Subgenus is written between brackets between genus and specific epitheton
Holothuria (Thymiosicya) impatiens
Subgenus and above are written with initial capital
Genus name often abbreviated to first character at subsequent mentions
E.g. H. sapiens

12. Specific epitheton Second part of species name Is often an adjective
Takes gender from the genus name (which is always a noun)
Can be other than adjective
Noun in apposition
Locality
Named after a person
genitive

13. Classification can change
Phylogeny = scientific study,
Research results can alter understanding
Interpretation of facts can be different between scientists
Difficult to construct a complete and consistent classification
Can result in name changes
Species moves from one genus to another…
Epitheton changes when genus has other gender

14. Nomenclature Publication
To be valid, name has to be published in a publication acceptable to the code
Name has to be unique within the domain of the code
Zoological name can be same as botanical
Typification
Name has to be supported by a type

15. Publication Names have to be published to be valid
Rules for validity are part of the code
No thesis, nor WWW!
Date of publication determines seniority of the name
Important in case of dispute
Start of the nomenclature:
Zoology: Linnaeus (1758). Systema naturae… 10th ed.
Botany: Linnaeus (1753). Species plantarum. 1st ed.

16. Authority
Author of the publication that contains the description becomes ‘author’ of the taxon name
Date of description is the date that the publication became publicly available
Not necessarily the same as the date on the cover of the publication
Journals have a tendency to be published late
Differences in calendars (e.g. Russia in the beginning of the 20th century)

17. Authority
Authority is very important in taxonomy, often added to the name
For many journals mandatory for taxa of rank genus and below
E.g. Homo sapiens Linnaeus, 1758
Zoology: with year of publication
E.g. Zostera noltii Hornemann
Botany: without year

18. Names are unique… … but not absolutely so
Botanical name can be same as zoological
There is no central register (yet), so this leaves a lot of scope for mistakes
‘Preoccupied name’
Has to be replaced with another name – ‘replacement name’

19. Name changes
If a species is transferred from one genus to another, the species’ name changes
Zoology: the original author’s name is placed between brackets
Spongia aurea Montagu, 1818
Hymeniacidon aurea (Montagu, 1818)
Botany: parentheses + author of the new ‘combination’
Halophila stipulacea (Forsskål) Ascherson

20. Name changes
Specific epitheton is often adjective, has to be declined according to rules of latin grammar
Turbo littoreus Linnaeus, 1758
Littorina littorea (Linnaeus, 1758)
Specific epitheton can be noun, which has its own gender
Tellina (Moerella) pygmaeus Lovén, 1846
Taxonomists, but especially other users of taxonomic names, are often mistaken!
Tellina pygmaea: wrong!!

21. Typification Type serves as an anchor, to stabilise taxonomy
Type of a species: specimen
Zoology
Type of a genus: species
Type of a family: genus
Botany: type is always a specimen

22. Synonyms Objective synonyms Subjective synonyms Preoccupied name…
Objective synonyms have the same type
Subjective synonyms
An author has described a taxon, but a subsequent author has stated that the specimens of that species actually belong to a taxon that has been described before

23. Interpretation of the literature
Difference between misidentifications and synonyms not always clear
List of names below a taxonomic name in a taxonomic revision often contain both!
Different authors use different classifications
Importance of having an intelligent database, that aids in interpreting names
Has to have information on synonyms, spelling variations…

24. Problems with names With names themselves With identification
Synonyms
With identification
=applying name to specimen
Name will often depend on source of information used
Need to document identification keys
Problem integrating data from different sources
Need for quality control

25. Types of tax info systems
‘Nomenclators’: list of names
Taxonomic
List of names, plus taxonomic information (author, reference for description publication…)
Who’s valid??
Species database
Information on biology, identification…
Distribution
For a group of species or for a region

26. Indexing literature Zoological record Some free resources
Started 1864, now available electronically
Originally Linnaean Society, now commercial
Unfortunately ridiculously expensive
Some free resources

27. Nomenclators Index Kewensis Index animalium Nomenclator Zoologicus
Included in the IPNI database,
Index animalium
Nomenclator Zoologicus

28. Taxonomic databases Global Regional Taxonomic
Integrated Taxonomic Information System (ITIS)
Species 2000
Regional
Species 2000 Europe, European Register of Marine Species (ERMS)
Marine Species Database for Eastern Africa (MASDEA)
Taxonomic
Fungi…

29. Biogeographical DBs Global Biodiversity Information Facility (GBIF)
OBIS
And its regional nodes
Taxonomic names are not always integrated

30. Species databases FishBase Hexacorallia CephBase, Brachnet, NeMys…
Tree of Life project

31. FishBase

32. Algaebase