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 BCDE 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

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 clade AB XY < A & B < A+B Clade(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 AB C 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 TheriaMonotremata Reptilia > 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 AB C 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)

Monotremata Theria Multituberculata† Mammalia Mammalia = the least inclusive clade containing platypuses (Monotremata) and humans (Theria). Monotremata Theria Mammalia Clade content Multituberculata†

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

Are Linnaean categories compatible with phylogenetic taxonomy? Phylocode Clade B A1 A2 Clade A

Isoptera (Termite) Example Proposed Rank-Based Superorder 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-Based Superorder 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 OrderGinkgoales FamilyGinkgoaceae GenusGinkgo SpeciesGinkgo biloba Contradicts Linnaean hierarchical relationships Different taxon names refer to the same taxon = redundancy

Summary Phylogenetic 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

Summary Phylogenetic 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)

Summary Phylogenetic 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

Thank you!! Carolus