Emerging standards in Phylogenetic Nomenclature

Emerging standards in Phylogenetic Nomenclature

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.

Tree-thinking

Assembling the Tree of Life

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 ECrown 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

Basic Goals To promote:

– Clarity– Universality– Stability

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)

Monot

remata

Ther

iaMult

itube

rculat

a†

Mammalia

Mammalia = the least inclusive clade containingplatypuses (Monotremata) and humans (Theria).

Monot

remata

Ther

ia

Multitu

bercu

lata

Multitu

bercu

lata††

Mammalia

Clade content

Multitu

bercu

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


taxonomy?• Principle of exhaustive subsidiary taxa (a.k.a PEST)

Family B = Family A

A1

A2Instability in the phylogenetic meaning of Family A


taxonomy?• Phylocode Clade B

A1

A2

Clade 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

PhylogeneticDictyoptera 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


taxonomy?

• Organisms have different distances from their common ancestors and ranks are not comparable


taxonomy?• The paradox of monotypic taxaOrder 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


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)


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

AcknowledgmentsEOL-BioSynC

National Evolutionary Synthesis Center (NESCent)

TDWG organizers

Kevin de Queiroz for ideas and material

Thank you!!

Carolus

Documents

Emerging standards in Phylogenetic Nomenclature