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TAXA
In traditional taxonomy, organisms are grouped into taxa because they share similar traits
Phylogenetic taxonomy seeks to communicate the discoveries of phylogenetic systematics. Organisms are grouped into taxa based on their phylogenetic relationships
Phylogenetic systematics
Reconstruction/estimation of phylogenetic relationships (Discovers relationships)
Phylogenetic Taxonomy
System of names representing relationships(Represents relationships)
TAXA = CLADES
Clades = groups that include one ancestor and all of its descents (monophyletic groups)
Clades are the entities to be named
Distinction between Taxonomy and Nomenclature
Taxonomy is concerned with the representation of relationships.
Nomenclature is concerned with the application of names (to taxa).
Taxonomy and nomenclature are logically independent.
Do we want to generate classifications that reflect our knowledge of taxon relationships?
Can we still generate accurate classifications based on traditional assumptions?
Is the Linnaeus system of nomenclature still practical?
Phylogenetic Nomenclature
An approach to biological nomenclature that applies names to taxa based common ancestry and descent.
Distinctive Properties of Phylogenetic Nomenclature
Application of taxon names is based on explicit phylogenetic definitions (as opposed to implicit rank-based definitions).
Tree-based approach to nomenclature.
Phylogenetic Nomenclature ≠ Cladistic
Classification Cladistic classification (principle of
monophyly) is a taxonomic principle.
Phylogenetic nomenclature (principle of phylogenetic definitions) is a nomenclatural principle.
Naming convention: set of rules and principles that govern the
establishment, definition, and usage of names
B C D E
Crown clades
Branches
We want to name the things we discover
Apomorphies(characters)
clades where all branches originating from the basal node have extant or Recent taxa
Phylogenetic definitions
Specifiers:– Species, specimens, and apomorphies
(characters) cited in phylogenetic definitions are called specifiers because they specify the clade to which the name applies.
Reference Phylogenies
Phylogenetic definitions Node-based definition: The clade originating with the last common ancestor of A
and B.
The least inclusive clade containing A and B (and C and D, etc.), where A, B, C, D-etc. are specifiers.
Node-based cladeA BX Y
< A & B< A+BClade(A+B)
Phylogenetic definitions Node-based definition: Mammalia
The least inclusive clade containing Monotremata and Theria where Ornithorynchus anatinus [platypus] and Homo sapiens are specifiers.
TheriaMarsupialiaMonotremata
< Homo sapiens + Ornithorynchus anatinus
Phylogenetic definitions Branch-based definition: The clade originating with the
first ancestor of A that is not an ancestor of C.
The most inclusive clade containing A but not C (and D, E, F, etc.)
Branch-based clade
A BC
Clade(A <-- C) A ¬ C> A ~ C
Phylogenetic definitions Branch-based definition: Mammalia
The most inclusive clade containing Theria and Monotremata but not Reptilia
Branch-based clade
TheriaMonotremataReptilia
> Homo sapiens+Ornithorynchus anatinus ~ Crocodylus niloticus
Phylogenetic definitions Apomorphy-based definition: The clade originating with the first ancestor
of A to evolve M
The most inclusive clade exhibiting character (state) M synapomorphic with that in A.
Apomorphy-based clade
A BC
Clade(M in A ) A + M > M(A)
M
Phylogenetic definitions Apomorphy-based definition: Mammalia
The most inclusive clade exhibiting dentary-squamosal jaw joint synapomorphic with that in Ornitorhynchus anatinus
Apomorphy-based clade
TheriaMonotremataReptilia
> M(Ornitorhynchus anatinus)
Mon
otre
mat
a
Ther
iaMul
titub
ercu
lata
†
Mammalia
Mammalia = the least inclusive clade containingplatypuses (Monotremata) and humans (Theria).
Mon
otre
mat
a
Ther
ia
Mul
titub
ercu
lata
Mul
titub
ercu
lata
††
Mammalia
Clade content
Mul
titub
ercu
lata
†
Sources of Compositional Instability
Traditional nomenclature has two sources:
– Changes in ideas about relationships.
– Changes in ranks.
Phylogenetic nomenclature has only one source:
– Changes in ideas about relationships.
Are Linnaean categories compatible with phylogenetic
taxonomy?• Principle of exhaustive subsidiary taxa (a.k.a PEST)
Family AFamily B
A1
A2
Are Linnaean categories compatible with phylogenetic
taxonomy?• Principle of exhaustive subsidiary taxa (a.k.a PEST)
Family B = Family A
A1
A2
Instability in the phylogenetic meaning of Family A
Isoptera (Termite) Example
Proposed Rank-BasedSuperorder Dictyoptera Order Mantodea Order Blattodea Family Polyphagidae Family Nocticolidae Family Blattidae Family Cryptocercidae Family Termitidae Subfamily Mastotermitinae Subfamily Hodotermitinae Subfamily Termopsinae Subfamily Kalotermitinae Subfamily Rhinotermitinae Subfamily Serritermitinae Subfamily Termitinae Family Blattaridae Family Blaberidae
Phylogenetic
Dictyoptera
Mantodea
Blattodea
Polyphagidae
Nocticolidae
Blattidae
Cryptocercidae
Isoptera
Mastotermitidae
Hodotermitidae
Termopsidae
Kalotermitidae
Rhinotermitidae
Serritermitidae
Termitidae
Blattaridae
Blaberidae
Original Rank-BasedSuperorder Dictyoptera Order Mantodea Order Blattodea (roaches) Family Polyphagidae Family Nocticolidae Family Blattidae Family Cryptocercidae Family Blattaridae Family Blaberidae Order Isoptera
(termites) Family
Mastotermitidae Family
Hodotermitinae Family Termopsinae Family
Kalotermitidae Family
Rhinotermitinae Family
Serritermitidae Family Termitidae
Are Linnaean categories compatible with phylogenetic
taxonomy?
• Organisms have different distances from their common ancestors and ranks are not comparable
Are Linnaean categories compatible with phylogenetic
taxonomy?• The paradox of monotypic taxa
Order Ginkgoales
Family Ginkgoaceae
Genus Ginkgo
Species Ginkgo biloba
• Contradicts Linnaean hierarchical relationships• Different taxon names refer to the same taxon = redundancy
SummaryPhylogenetic Nomenclature
A new approach to biological nomenclature based on evolutionary principles.
Functions analogously to, but differently from, traditional rank-based nomenclature.
Taxon names are associated with monophyletic taxa (clades) NOT ranks.
Functions better than traditional rank-based nomenclature in terms stability and changes
It maybe undesirable to many, but it’s a reality that is not going away
SummaryPhylogenetic Nomenclature
Phylonyms Volume will be published together with the PhyloCode in 2010
At least 333 clade names:
– Vertebrate: 112 - Other animals: 82
– Land plants: 98 - Red and green algae: 22
– Fungi: 4 - Other eukaryotes: 14
– Prokaryotes: 1
At least 136 authors (2 in Australia, 93 in USA, 12 in Canada, 28 in Europe, 1 in S. America)
SummaryPhylogenetic Nomenclature
Authors include: Michael Donogue, David Hillis, Tim Rowe, Kevin Padian, Chris Brochu, Pam & Doug Soltis, Jim Doyle, Walter Judd, David Baum, Brent Mishler, Sina Adl, Birgitte Bremer, David Cannatella, Dick Olmstead, David Archibald, Robert Reisz, David Hibbett
Acknowledgments
EOL-BioSynC
National Evolutionary Synthesis Center (NESCent)
TDWG organizers
Kevin de Queiroz for ideas and material