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

• I will mainly be talking about compositions of taxa

• Higher taxa

• A little on species

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 – how the (eukaryote) codes work

Species

Name-bearing types (usually holotypes)

‘Taxonomic judgment’

‘Taxonomic judgment’

Splitting species ‘red’ - what remains ‘red’

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

Neobodo designis (main clade)

von der Heyden et al., 2004

SSUrDNA

= Hundreds of species?