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December 6, 2016 Computable definitions for clades Gaurav Vaidya, Hilmar Lapp, Nico Cellinese

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Campanula latifolia Lobelia cardinalis

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Campanula latifolia Lobelia cardinalis

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Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens Chrysanthemum

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Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens Chrysanthemum

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Hinchliff et al. (2016) www.opentreeoflife.org

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The Solution: Phyloreferences ✤ Explicit definitions for clades. www.phyloref.org

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The Solution: Phyloreferences ✤ Explicit definitions for clades. ✤ Built around ancestral relationships, so they always match monophyletic groups. www.phyloref.org

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The Solution: Phyloreferences ✤ Explicit definitions for clades. ✤ Built around ancestral relationships, so they always match monophyletic groups. ✤ But the group’s composition may change from tree to tree! www.phyloref.org

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Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens Chrysanthemum

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Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens Chrysanthemum

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Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens Chrysanthemum Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis

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Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens Chrysanthemum Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis

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Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens Chrysanthemum Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis

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Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens Chrysanthemum Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis

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Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens Chrysanthemum Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis

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Implementing phyloreferences

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Implementing phyloreferences ✤ Could we use off-the-shelf open source tools to find clades on phylogenetic trees?

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Implementing phyloreferences ✤ Could we use off-the-shelf open source tools to find clades on phylogenetic trees? ✤ Could we design a system flexible enough to match many different kinds of phyloreferences?

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Implementing phyloreferences ✤ Could we use off-the-shelf open source tools to find clades on phylogenetic trees? ✤ Could we design a system flexible enough to match many different kinds of phyloreferences? ✤ Could we create a test set of phyloreferences and their expected matches for testing our software and others?

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Web Ontology Language (OWL) ✤ Designed to classify individuals and classes based on definitions.

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Web Ontology Language (OWL) ✤ Designed to classify individuals and classes based on definitions. ✤ e.g. A Maharashtrian is a Person who was born in the Indian state of Maharashtra.

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Web Ontology Language (OWL) ✤ Designed to classify individuals and classes based on definitions. ✤ e.g. A Maharashtrian is a Person who was born in the Indian state of Maharashtra. ✤ Uses OWL Reasoners to infer unknown facts from known facts.

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Reasoning over facts ✤ :Gaurav a :Person

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Reasoning over facts ✤ :Gaurav a :Person ✤ :Gaurav :bornIn :Mumbai

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Reasoning over facts ✤ :Gaurav a :Person ✤ :Gaurav :bornIn :Mumbai ✤ :Mumbai :partOf :Maharashtra

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Reasoning over facts ✤ :Gaurav a :Person ✤ :Gaurav :bornIn :Mumbai ✤ :Mumbai :partOf :Maharashtra ✤ => :Gaurav :bornIn :Maharashtra

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Reasoning over facts ✤ :Gaurav a :Person ✤ :Gaurav :bornIn :Mumbai ✤ :Mumbai :partOf :Maharashtra ✤ => :Gaurav :bornIn :Maharashtra ✤ Only if :bornIn o :partOf => :bornIn!

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Reasoning over facts ✤ :Gaurav a :Person ✤ :Gaurav :bornIn :Mumbai ✤ :Mumbai :partOf :Maharashtra ✤ => :Gaurav :bornIn :Maharashtra ✤ Only if :bornIn o :partOf => :bornIn! ✤ => :Gaurav a :Maharashtrian

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Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens Chrysanthemum

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Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens Chrysanthemum ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia

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Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens Chrysanthemum ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis

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Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens Chrysanthemum ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis

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Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens Chrysanthemum ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis ✤ :Node_1 a :Node

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Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens Chrysanthemum ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis ✤ :Node_1 a :Node ✤ :has_Child :Campanula_latifolia

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Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens Chrysanthemum ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis ✤ :Node_1 a :Node ✤ :has_Child :Campanula_latifolia ✤ :has_Child :Campanula_rotundifolia

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Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens Chrysanthemum ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis ✤ :Node_1 a :Node ✤ :has_Child :Campanula_latifolia ✤ :has_Child :Campanula_rotundifolia

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Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens Chrysanthemum ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis ✤ :Node_1 a :Node ✤ :has_Child :Campanula_latifolia ✤ :has_Child :Campanula_rotundifolia

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Campanula latifolia Campanula rotundifolia Lobelia coronopifolia Lobelia cardinalis Cyphocarpus rigescens Chrysanthemum ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis ✤ :Node_1 a :Node ✤ :has_Child :Campanula_latifolia ✤ :has_Child :Campanula_rotundifolia

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Phyloreferences in OWL Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis

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Phyloreferences in OWL ✤ We’re looking for all the descendants of a Node that: Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis

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Phyloreferences in OWL ✤ We’re looking for all the descendants of a Node that: ✤ :has_Descendant :Campanula_latifolia Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis

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Phyloreferences in OWL ✤ We’re looking for all the descendants of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :excludes_lineage_to :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis

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Phyloreferences in OWL ✤ We’re looking for all the descendants of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :has_Child :Campanula_latifolia ✤ :excludes_lineage_to :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis

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Phyloreferences in OWL ✤ We’re looking for all the descendants of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :has_Child :Campanula_latifolia ✤ :has_Child [:has_Child :Campanula_latifolia] ✤ :excludes_lineage_to :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis

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Phyloreferences in OWL ✤ We’re looking for all the descendants of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :has_Child :Campanula_latifolia ✤ :has_Child [:has_Child :Campanula_latifolia] ✤ :has_Child [:has_Child [:has_Child :Campanula_latifolia]] ✤ :excludes_lineage_to :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis

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Phyloreferences in OWL ✤ We’re looking for all the descendants of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :has_Child :Campanula_latifolia ✤ :has_Child [:has_Child :Campanula_latifolia] ✤ :has_Child [:has_Child [:has_Child :Campanula_latifolia]] ✤ … ✤ :excludes_lineage_to :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis

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Phyloreferences in OWL ✤ We’re looking for all the descendants of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :excludes_lineage_to :Lobelia_cardinalis ✤ Either :has_Sibling :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis

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Phyloreferences in OWL ✤ We’re looking for all the descendants of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :excludes_lineage_to :Lobelia_cardinalis ✤ Either :has_Sibling :Lobelia_cardinalis ✤ Or :has_Sibling that :has_Descendent :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis

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Phyloreferences in OWL ✤ We’re looking for all the descendants of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :excludes_lineage_to :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis

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What are we building? ✤ Software tools and standards for converting phylogenies to logical statements.

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What are we building? ✤ Software tools and standards for converting phylogenies to logical statements. ✤ Ontologies to make these relationships simple and clear.

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What are we building? ✤ Software tools and standards for converting phylogenies to logical statements. ✤ Ontologies to make these relationships simple and clear. ✤ Defining terms like excludes_lineage_to so you don’t have to.

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What are we building? ✤ Software tools and standards for converting phylogenies to logical statements. ✤ Ontologies to make these relationships simple and clear. ✤ Defining terms like excludes_lineage_to so you don’t have to. ✤ Web application and web service to make phyloreferences quick and easy to use.

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What are we building? ✤ Software tools and standards for converting phylogenies to logical statements. ✤ Ontologies to make these relationships simple and clear. ✤ Defining terms like excludes_lineage_to so you don’t have to. ✤ Web application and web service to make phyloreferences quick and easy to use. ✤ Testing to ensure that phyloreferences match the correct nodes on the tree.

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Conclusions

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Conclusions ✤ OWL reasoners can identify parts of a phylogenetic tree based on phyloreferences expressed in OWL.

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Conclusions ✤ OWL reasoners can identify parts of a phylogenetic tree based on phyloreferences expressed in OWL. ✤ But can we make them work fast, through easy-to-use websites and over web services?

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Conclusions ✤ OWL reasoners can identify parts of a phylogenetic tree based on phyloreferences expressed in OWL. ✤ But can we make them work fast, through easy-to-use websites and over web services? ✤ Continuous testing will make sure that all existing phyloreferences continue to work in the future.

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Conclusions ✤ OWL reasoners can identify parts of a phylogenetic tree based on phyloreferences expressed in OWL. ✤ But can we make them work fast, through easy-to-use websites and over web services? ✤ Continuous testing will make sure that all existing phyloreferences continue to work in the future. ✤ We need you to submit useful phyloreferences and tricky phylogenies, to complain about phyloreferences that don’t make sense to you, and to use our infrastructure to identify clades in your datasets.

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We need a postdoc! ✤ “Specifically, you will work with other projects funded by NSF’s GoLife program to obtain large phylogenies, gather sources for meaningful phyloreferences, and develop phyloreferencing proof-of-concept applications for these. These applications will include aggregating trait and other domain-relevant data.” ✤ “Strong background in Systematic Biology required. You should be well versed in all aspects of theoretical phylogenetics and related topics.” ✤ http://www.phyloref.org/blog/2016/10/postdoc2-ad/

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Acknowledgements ✤ NSF: “An Ontology-Based System for Querying Life in a Post-Taxonomic Age” (NSF-DBI 1458604) ✤ Available on FigShare: http://dx.doi.org/10.6084/ m9.figshare.1401984.v1

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Questions? phyloref.org @phyloref

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References ✤ Hinchliff et al. (2016): http://dx.doi.org/10.1073/ pnas.1423041112

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Images ✤ https://commons.wikimedia.org/wiki/ File:Tree_of_life_SVG.svg ✤ https://commons.wikimedia.org/wiki/ File:Lobelia_cardinalis_-_Cardinal_Flower.jpg ✤ https://commons.wikimedia.org/wiki/ File:Campanula_latifolia_(7814338584).jpg ✤ https://commons.wikimedia.org/wiki/ File:Unclesamwantyou.jpg

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A database of clades: PhyloRegnum Name Definition Campanulaceae The clade originating with the most recent common ancestor of Campanula latifolia Linnaeus 1753 and all extant organisms or species that share a more recent common ancestor with Campanula latifolia than with Roussea simplex J. E. Smith 1789, Pentaphragma ellipticum Poulsen 1903, or Stylidium graminifolium Swartz ex Willdenow 1805. Campanuloideae The clade originating with the most recent common ancestor of Campanula latifolia Linnaeus 1753, Wahlenbergia linifolia A. de Candolle 1830, and Platycodon grandiflorus (Jacquin) A. de Candolle 1830.

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:Campanula_latifolia :Campanula_rotundifolia ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis ✤ :Node_1 a :Node ✤ :has_Child :Campanula_latifolia ✤ :has_Child :Campanula_rotundifolia

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:Campanula_latifolia :Campanula_rotundifolia has_Sibling ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis ✤ :Node_1 a :Node ✤ :has_Child :Campanula_latifolia ✤ :has_Child :Campanula_rotundifolia

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:Campanula_latifolia :Campanula_rotundifolia has_Sibling :Node_1 … ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis ✤ :Node_1 a :Node ✤ :has_Child :Campanula_latifolia ✤ :has_Child :Campanula_rotundifolia

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:Campanula_latifolia :Campanula_rotundifolia has_Sibling :Node_1 has_Child … ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis ✤ :Node_1 a :Node ✤ :has_Child :Campanula_latifolia ✤ :has_Child :Campanula_rotundifolia

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:Campanula_latifolia :Campanula_rotundifolia has_Sibling :Node_1 has_Child has_Child … ✤ :Campanula_latifolia :has_Sibling 
 :Campanula_rotundifolia ✤ :Lobelia_coronopifolia :has_Sibling 
 :Lobelia_cardinalis ✤ :Node_1 a :Node ✤ :has_Child :Campanula_latifolia ✤ :has_Child :Campanula_rotundifolia

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A SEMANTIC CLADE Node-based Branch-based Apomorphy-based A A A B B B C C C Last common ancestor of B and C X Last ancestor of B that is not an ancestor of A Last ancestor of B that exhibits apomorphy X The clade originating with:

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A SEMANTIC CLADE Node-based A B C Last common ancestor of B and C The clade originating with:

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A SEMANTIC CLADE Node-based Branch-based A A B B C C Last common ancestor of B and C Last ancestor of B that is not an ancestor of A The clade originating with:

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