All The Clades In The World Building a Semantically-Rich and Testable Ontology of Phylogenetic Clade Definitions Gaurav Vaidya, Hilmar Lapp, Nico Cellinese www.phyloref.org
What’s in a name? • Names and Concepts do not reconcile that easily • Names are text strings • Context is lacking or subjective • Meaning is not computable
A clade, also known as monophyletic group, represents a branch on the tree of life. It is a group of organisms that consists of a common ancestor and all its descendants. What is a clade? Node = ancestor Descendants
Tree-thinking Berberidopsidaceae Opiliones Zingiberaceae Hamamelidaceae Sarcolaenaceae Lingulidae Hymenoptera Mammalia Apocynaceae Galliformes Rubiaceae Anarthriaceae Lineidae Crocodylidae Stylosiphonia Andrenidae Cracidae Gavialis Globba Glottidia Micrella Streptotham nus Rhodoleia Phalangiidae Tachyglossa Lyginia Mediusella Chamaeclitandra These names are not generated in an evolutionary-based framework (Groups defined by character similarity vs. common descent)
Both the Encyclopedia of Life (EOL) and the Open Tree of Life suggest that Campanuloideae is a misspelling of Campaniloidea (marine gastropods!) GBIF does not currently have Campanuloideae in its backbone taxonomy.
Phylogenetic Definitions Statements formally expressing the patterns we discover (analogous to map coordinates) Node-Based (minimum clade) Branch-Based (maximum clade) Apomorphy-Based A B C A B C A B C X The clade originating with the last common ancestor of B and C. The clade originating with the first ancestor of B that is not an ancestor of A. The clade originating with the first ancestor of C to evolve X.
Phyloreferences • Portable to any phylogeny that has all the specifiers • Resolvable on any phylogeny represented in RDF by using an OWL 2 DL reasoner • Extensible to other kinds of definitions if need be • Working on better ways to match specifiers