something general on eukaryotic taxonomy
TRANSCRIPT
Something general on Something general on Eukaryotic TaxonomyEukaryotic Taxonomy
Alastair SimpsonAlastair Simpson
Dalhousie UniversityDalhousie University
• I will mainly talk about compositions of taxa (“applying names”)
• Higher taxa
• A little on species
• (General, but emphasising where protists are especially problematic).
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
Classifications Phylogenetic trees
Neobodonida
Neobodo Rhynchomonas Dimastigella
Neobodo designis Neobodo saliens Neobodo curvifilus
N. designis N. saliens N. curvifilusRhynchomonas
nasutaDimastigellatrypaniformis
Neobodo
Neobodonida
Neobodo Rhynchomonas Dimastigella
Neobodo designis Neobodo saliens Neobodo curvifilus
N. designis N. saliens N. curvifilusRhynchomonas
nasutaDimastigellatrypaniformis
‘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)
‘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)
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
Two (eukaryotic) codes
Phylum/DivisionClassOrderFamilyGenus
Species
“Zoological”ICZN
“Botanical”(ICN)
~ govern proposing names, not applying them
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.
e.g. Opalozoa1993[A diverse groups of protozoa; never with flagellar hairs]
Opalinida*,
Proteromonadida & Pseudodendromonadida
andApusomonadida, 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
andAnoecida, Bicocoecida, Blastocystida, Borokida, Placidida, Rictida & Uniciliatida,
(~1/2 with flagellar hairs)
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!
Amonas Bemonas Cemonas OtherthingsozoaNewcritta
Which of these two groups ‘should’ be “Amonadidae”?
What if BOTH groups are important enough to deserve names?
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
Phylogenetically defined taxa (usually) ‘exist’ irrespective of the tree (but their composition
Amonas
Bemonas
Cemonas
Otherthingsozoa
Amonadidae
A. laxi C. taii
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
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]
-Morphology by light microscopy
-No type material for many old accounts
23-25: Trimastix marina: Saville Kent 1880-1882
Traditional species criteria
Former Ancyromonas sigmoides
Scheckenbach et al. 2006 (micrograph Heiss, A.A.)18S rDNA
Now ~10 species, in several genera
18S rDNA
Nutomonas limna(form. Planomonas limna)
Cavalier-Smith et al., 2008
N. howae(P. howae)
Within former Ancyromonas sigmoides