EukRef Workshop 2015

1. Something general onSomething general on
Eukaryotic TaxonomyEukaryotic Taxonomy
Alastair SimpsonAlastair Simpson
Dalhousie UniversityDalhousie University

2. • I will mainly talk about compositions of taxa
(“applying names”)
• Higher taxa
• A little on species
• (General, but emphasising where protists are
especially problematic).

3. Some notable features of
Biological classification
• Hierarchical
– Traditionally also with named ranks
• Has a ‘base’ rank: Species
• Species are binomial (strange).
• Classification is ‘real’ rather than arbitrary
(in many ways this is a curse)
• Governance (by codes of nomenclature):
partial, fragmented, inconsistent

4. Classifications  Phylogenetic trees
Neobodonida
Neobodo Rhynchomonas Dimastigella
Neobodo designis Neobodo saliens Neobodo curvifilus
N. designis N. saliens N. curvifilus
Rhynchomonas
nasuta
Dimastigella
trypaniformis
Neobodo

5. Neobodonida
Neobodo Rhynchomonas Dimastigella
Neobodo designis Neobodo saliens Neobodo curvifilus
N. designis N. saliens N. curvifilus
Rhynchomonas
nasuta
Dimastigella
trypaniformis

6. ‘Real’ not arbitrary (in many ways a curse)
• Tension of correctness vs stability
• Different views on exact relationship between
taxonomy and phylogeny (a ‘protist problem’)
Almost everyone active:
Taxa are to be monophyletic
where-ever possible
Cavalier-Smith:
Paraphyletic taxa are
perfectly okay (and I
have made lots, BTW)

7. ‘Real’ not arbitrary (in many ways a curse)
• Tension of correctness vs stability
• Different views on exact relationship between
taxonomy and phylogeny (a ‘protist problem’)
• [genuinely non-tree-like history]
• And ~ real not same as ~ objective
Almost everyone active:
Taxa are to be monophyletic
where-ever possible
Cavalier-Smith:
Paraphyletic taxa are
perfectly okay (and I
have made lots, BTW)

8. Some notable features of
Biological classification
• Hierarchical
– Traditionally also with named ranks
• Has a ‘base’ rank: Species
• Species are binomial (strange).
• Classification is ‘real’ rather than arbitrary
(in many ways this is a curse)
• Governance (by codes of nomenclature):
partial, fragmented, inconsistent

9. 9
Two (eukaryotic) codes
Phylum/Division
Class
Order
Family
Genus
Species
“Zoological”
ICZN
“Botanical”
(ICN)
~ govern proposing names, not applying them

10. Diagnosis / Description of a higher taxon
• Usually:
1) Some sort of description, differentiating it from
other taxa (sometimes with apomorphies identified)
2) A list of included taxa:
–‘Typified’ taxa – one subordinate taxon IS the type
Limited information about how to apply names
(once changing information considered)
All of this, except the type (if there is one), is
essentially unregulated.

11. e.g. Opalozoa
1993
[A diverse groups of protozoa;
never with flagellar hairs]
Opalinida*,
Proteromonadida &
Pseudodendromonadida
and
Apusomonadida, Cercomonadida,
Cryomonadida, Diphylleida, Ebriida
Heliomonadida, Hemimastigida,
Histionida, Katheblepharida,
Jakobida, Leucodictyida,
Nephromycida, Phagomyxida,
Plasmodiophorida, Pseudosporida,
Spongomonadida, Telonemida &
Thaumatomonadida
2013
[A subgroup of stramenopiles, a taxon
distinguished by flagellar hairs]
Opalinida,
Proteromonadida &
Pseudodendromonadida
and
Anoecida, Bicocoecida,
Blastocystida, Borokida,
Placidida, Rictida & Uniciliatida,
(~1/2 with flagellar hairs)

12. Applying names:
The drifting basal node problem
Amonas Bemonas Cemonas
Amonas
Bemonas
Cemonas
Otherthingsozoa
Amonadidae
Newcritta**
Amonadidae
** = there are a LOT of
these in protistology!

13. Amonas Bemonas Cemonas OtherthingsozoaNewcritta
Which of these two groups ‘should’ be
“Amonadidae”?
What if BOTH groups are important enough to deserve names?

14. Phylogenetic definitions (and the like)
Amonas Bemonas Cemonas
Otherthingsozoa
Amonadidae
A. laxi C. taii
Amonadidae is the most recent common ancestor of
Amonas laxi, and Cemonas taii, and all of its descendants

15. Phylogenetically defined taxa (usually) ‘exist’
irrespective of the tree (but their composition
Amonas
Bemonas
Cemonas
Otherthingsozoa
Amonadidae
A. laxi C. taii

16. • I will mainly be talking about
compositions of taxa
• Higher taxa
• A little on species

17. Species
• Harder to do without than other ranks
• Rank has more ‘reality’ (or perceived reality)
– “species concepts”:
e.g. Biological Species Concept many others
• Eukaryotic codes govern names, not
species concepts

18. Species – how the (eukaryote) codes work

19. Species
Name-bearing types (usually holotypes)

20. ‘Taxonomic judgment’

21. ‘Taxonomic judgment’

22. Splitting species ‘red’ - what remains ‘red’

23. Species in (most) Protists
• Type material frequently absent or useless
• No universal criteria for species distinction
• Nomenclatural species breadth hugely variable
• ‘Maximum’ breadth changing (narrowing) rapidly
• [reminder: this is essentially unregulated]

24. -Morphology by light microscopy
-No type material for many old accounts
23-25: Trimastix marina: Saville Kent 1880-1882
Traditional species criteria

25. Former Ancyromonas sigmoides
Scheckenbach et al. 2006 (micrograph Heiss, A.A.)18S rDNA
Now ~10 species, in several genera

26. 18S rDNA
Nutomonas limna
(form. Planomonas limna)
Cavalier-Smith et al., 2008
N. howae
(P. howae)
Within former Ancyromonas
sigmoides

27. Neobodo designis (main clade)
von der Heyden et al., 2004
SSUrDNA
= Hundreds of species?