The new classification of eukaryotes
Transcript of The new classification of eukaryotes
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The new classification of eukaryotes
Sina M. AdlUniversity of Saskatchewan
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ISOP taxonomy and revisions,what we learned during this process
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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
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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
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• 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
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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
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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
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Other issues
• ICBN species described in Latin
• The Codes do not accommodate each other
• Type-specimen rules impractical or useless for many protists
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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
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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
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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
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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
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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
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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
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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
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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?
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…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
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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
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Work in progress…
• New rules for protist type specimen– Digital web-based species data-base
• Your good ideas and discussions are welcome
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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
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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