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Emerging standards in Phylogenetic Nomenclature

This article discusses the emerging standards in phylogenetic nomenclature, which aims to represent the relationships between organisms based on their phylogenetic relationships. It explores the distinction between taxonomy and nomenclature, the challenges of tree-thinking and assembling the Tree of Life, and the distinctive properties of phylogenetic nomenclature. The article also introduces various phylogenetic definitions and discusses the compatibility of Linnaean categories with phylogenetic taxonomy.

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Emerging standards in Phylogenetic Nomenclature

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  1. Emerging standards in Phylogenetic Nomenclature Nico Cellinese Florida Museum of Natural History University of Florida

  2. 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

  3. Phylogenetic systematics Reconstruction/estimation of phylogenetic relationships (Discovers relationships) Phylogenetic Taxonomy System of names representing relationships (Represents relationships)

  4. TAXA = CLADES Clades = groups that include one ancestor and all of its descents (monophyletic groups) Clades are the entities to be named

  5. 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.

  6. Tree-thinking

  7. Assembling the Tree of Life

  8. 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?

  9. Phylogenetic Nomenclature • An approach to biological nomenclature that applies names to taxa based common ancestry and descent.

  10. 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.

  11. Phylogenetic Nomenclature ≠ Cladistic Classification • Cladistic classification (principle of monophyly) is a taxonomic principle. • Phylogenetic nomenclature (principle of phylogenetic definitions) is a nomenclatural principle.

  12. Naming convention: set of rules and principles that govern the establishment, definition, and usage of names B C D E Crown clades clades where all branches originating from the basal node have extant or Recent taxa Branches Apomorphies (characters) We want to name the things we discover

  13. Basic Goals • To promote: • Clarity • Universality • Stability

  14. 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

  15. Phylogenetic definitions • Node-based definition: The clade originating with the last common ancestor of A and B. A B X Y Node-based clade < A & B < A+B Clade(A+B) The least inclusive clade containing A and B (and C and D, etc.), where A, B, C, D-etc. are specifiers.

  16. Phylogenetic definitions • Node-based definition: Mammalia Monotremata Marsupialia Theria < Homo sapiens + Ornithorynchus anatinus The least inclusive clade containing Monotremata and Theria where Ornithorynchus anatinus [platypus] and Homo sapiens are specifiers.

  17. Phylogenetic definitions • Branch-based definition: The clade originating with the first ancestor of A that is not an ancestor of C. A B C Branch-based clade Clade(A <-- C) A ¬ C > A ~ C The most inclusive clade containing A but not C (and D, E, F, etc.)

  18. Phylogenetic definitions Monotremata Theria Reptilia • Branch-based definition: Mammalia Branch-based clade > Homo sapiens+Ornithorynchus anatinus ~ Crocodylus niloticus The most inclusive clade containing Theria and Monotremata but not Reptilia

  19. Phylogenetic definitions • Apomorphy-based definition: The clade originating with the first ancestor of A to evolve M A B C Apomorphy-based clade Clade(M in A ) A + M > M(A) M The most inclusive clade exhibiting character (state) M synapomorphic with that in A.

  20. Phylogenetic definitions • Apomorphy-based definition: Mammalia Reptilia Monotremata Theria Apomorphy-based clade > M(Ornitorhynchus anatinus) The most inclusive clade exhibiting dentary-squamosal jaw joint synapomorphic with that in Ornitorhynchus anatinus

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

  22. 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.

  23. Are Linnaean categories compatible with phylogenetic taxonomy? • Principle of exhaustive subsidiary taxa (a.k.a PEST) Family B Family A A1 A2

  24. 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

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

  26. 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 Isoptera (Termite) Example 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

  27. Are Linnaean categories compatible with phylogenetic taxonomy? • Organisms have different distances from their common ancestors and ranks are not comparable

  28. 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

  29. 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

  30. 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)

  31. 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

  32. Acknowledgments EOL-BioSynC National Evolutionary Synthesis Center (NESCent) TDWG organizers Kevin de Queiroz for ideas and material

  33. Thank you!! Carolus

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