The new classification of eukaryotes

Sina M. AdlUniversity of Saskatchewan

ISOP taxonomy and revisions,what we learned during this process

1998

• 1980, Levine & 15 others, A newly revised classification of the Protozoa. J. Protozoology 27:37-58.

• Protist classification pre-1997• Glimmer of synthesis, 1998• 1997, Yves van der Peer & Rupert de Wachter, J. Molec.

Evol. 45:619-630– Complete phylogenetic tree of eukaryotes

• ISOP had not shown involvement or leadership– ISEP, IJSEM

• Very exciting period, but loss of name stability• Protists disappeared from text books and courses

1998-2003

• 1998, ISOP was not interested, “too difficult”• Mark Farmer’s attempt (~2000)

– Ranks were a problem– No agreement on names– No agreement on lineages– More than ever before, zoological and botanical

codes were intermingled (and some lineage names duplicated)

– No co-operation– Couldn’t be assembled from the literature

• 1999, the debacle of the Illustrated Guide 2nd edn

– Loss of civility and respectful behaviour– Ego before science and hypothesis testing

• Insufficient data, personal classifications, grounded in imagination and possibilities

• Obvious failure of the Codes (ICZN, ICBN)– No name stability– Independence of individuals to make things up– Incompatible codes

Lesson 1

Some egos are disruptive to science

2002-2005

• Emergence of tree builders, who didn’t know their groups

• Conversations on groups and phylogeny impossible– Every lab its own vocabulary

• Patiently, group by group, microscopists identified, lineages re-described, reassembled, names and authorities discussed– Hard part, how to assemble these groups– which rules to use?

Lesson 2

Beware of b

ioinformatic

ians who don’t

have a cl

ue

Problems with traditional codes

• Based on Aristotle and Linnaeus– Predate idea of “common decent” and

evolution (Darwin 1859)– Believed in fixed number of species

• Moving species changes its name• Rank change causes cascade of

name changes• More emphasis on authority than

name stability

See Adl & 19 others, 2007, J. Systematic Biology 56

Other issues

• ICBN species described in Latin

• The Codes do not accommodate each other

• Type-specimen rules impractical or useless for many protists

Codes failed to provide name stability

• Electron microscopy & DNA sequence information– many changes to groups and names– multiple names created for the same

groups– use of common terms, without specifying

authority or definition or delineation

• Loss of species name, when moved, is a bad system for filing and finding again

Lesson 3

Naming clades correctly is a community effo

rt

Towards a new system

• Provide some formality• Designating group names, authority,

definitions• Clades monophyletic (as possible) • Classification based on name-less

ranks• Prevents name changes in higher

ranks• Easier to revise

Adl & 28 others, 2005, J.E.M. 52 (5).

Lesson 4

Select nice people who can work together

Solutions to consider

• Classification system must ensure species name stability– Genus epithet, genus.epithet, genus-epithet,

genusepithet

Adl & 19 others, 2007, Systematic Biology

• Nested clades as PhyloCode– Separates naming clades from

assembling hierarchy

• To modernise or replace traditional codes– Rules should be few, simple, practical

Lesson 5

Progress re

quires a

n open mind,

it means d

oing things d

ifferently

Solutions to consider (next)

• Phonetic names with descriptions in any language, translatable

• New rules for type specimen– Digital images– DNA sequence– Biological information

• Must be public, free, web-based

Systematics

• Adopted a name-less rank system, with formal definitions– Polyphyletic groups indicated– Retain older names, emended– Eliminate empty ranks– Ignore rank endings as an accident of history– Allows groups to be moved and modified, without

changing their names• Problems with using traditional codes summarised

– Adl & 19 others, 2007, J. Systematic Biology 56

PhyloCode

• A modern code– Apomorphy– Branch-based– Node-based– Groups related “by common descent”

• Corrects most problems in ICBN & ICZN• Did not deal with naming species and

type-specimen• Code is ready, not implemented

Cantino & de Queiroz 2006, Phylocode

2005

• 2004, ISOP interested in the manuscript– An issue of J. Euk. Microbiol.

• 1 CD of emails over 3 years of discussions– 1 manuscript

• To distinguish between phylogeny and classification– Separation of assembling nested hierarchies,

from naming clades– Standardising names of clades– The return of name stability

Phylogeny vs classification

• Phylogeny guides classification– Wrong end of the tree– Common terms, informal names

• Delineation of groups missing, which genera are in, and which are excluded?

…but what are species?

• How much sequence divergence?• How much biogeographical sampling?• Identical morphology but different

species!• Selection acts on ecological

parameters– 3D niche space must be part of the

solution

• Issues now facing environmental data

Lesson 6

With progress, the fie

ld is shifting

Organiser, non-partisan, knows the field and people well,well-known, diplomat, arbitrator

Subject expert, respected, works well with people

Basic modular structure

Group or subject experts,detailed deep knowledge,diversified opinions

External comments on outcome, discussions, revisions

Work in progress…

• New rules for protist type specimen– Digital web-based species data-base

• Your good ideas and discussions are welcome

International codes of nomenclature

• Rules of the system for classifying and naming species – Int. Code Botanical Nomen.– Int. Code Zool. Nomen.– Int. Code Cultivated Plants– Int Code Microbiol. Nomen.– PhyloCode

Definitions

• Systematics– According to a system

• Taxonomy– A system of classifying

• Classification– Placing into categories

• eg. Species into named groups, by common descent

• Nomenclature– A system (set of rules) of

naming Source: Oxford dictionary of current English 3rd edn, 2001