tag:blogger.com,1999:blog-5350157389434430698.post4946151748481442352..comments2024-02-27T21:23:44.159-08:00Comments on A Three-Pound Monkey Brain: Computer Programs as TaxonomistsMike Keeseyhttp://www.blogger.com/profile/00147156174467903264noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-5350157389434430698.post-56023644220090009212009-02-02T10:45:00.000-08:002009-02-02T10:45:00.000-08:00Actually, the goal is not to have one consensus tr...Actually, the goal is not to have one consensus tree, but to let anyone pick which datasets they want to use. If you look at <A HREF="http://3lbmonkeybrain.blogspot.com/2008/11/names-on-nodes-entities.html" REL="nofollow">this post</A>, you'll see there's something called a "Context" which refers to a set of "Dataset" objects. (A context implicitly also includes all definitions, and all applications of definitions under that context.) So <I>Names on Nodes</I> will allow everyone to piece together their own phylogenetic contexts. For your supertree, you'd probably just upload the NEXUS file or Newick tree string produced by your analysis and have that as the only dataset in your context. (Although you could augment with with a dataset reflecting your own taxonomic opinions for rank-based taxa, e.g., "<I>Tyrannosaurus</I> ICZN 4 includes <I>Tarbosaurus bataar</I> ICZN 4," etc.)<BR/><BR/>If I could sum up my goal in one sentence, it would be: "To fulfill phylogenetic nomenclature's promise of objective application."<BR/><BR/>This monster's taken a while. Hopefully I can put up an alpha version sometime this year.Mike Keeseyhttps://www.blogger.com/profile/00147156174467903264noreply@blogger.comtag:blogger.com,1999:blog-5350157389434430698.post-76979858500461416202009-02-02T03:41:00.000-08:002009-02-02T03:41:00.000-08:00Hi Mike. I'd like to ask a silly question: what is...Hi Mike. I'd like to ask a silly question: what is your ultimate intention with this stuff? From my point of view this looks like a means to getting a kind of consensus tree for dinosaurs/amniotes and hence is a sort of supertree approach. I've often dreamed of doing something along those lines myself, i.e. a database structure (including published cladograms, with labelled nodes as well as lists of taxonomic validity) with scripts that automate the kinds of tasks we did for the recent dinosaur supertree. However, I am nowhere near competent enough with SQL and the like yet. I suspect that your intentions are somewhat different, but by the looks of things your stuff does most of the same tasks.<BR/><BR/>I am therefore looking forwards to the eventual publication of this monster!Malacodahttps://www.blogger.com/profile/02602635447222532525noreply@blogger.comtag:blogger.com,1999:blog-5350157389434430698.post-39186329583337534992009-02-01T11:41:00.000-08:002009-02-01T11:41:00.000-08:00And here are the MathML versions of the definition...And here are the MathML versions of the definitions.<BR/><BR/><I>Dromaeosauridae</I> sensu Padian & al. 1999:<BR/><BR/><apply<BR/> xmlns="http://www.w3.org/1998/Math/MathML"><BR/> <csymbol definitionURL<BR/> ="http://namesonnodes.org/2009/phylo/math::nodeClade"/><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Dromaeosaurus"/><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Velociraptor"/><BR/></apply><BR/><BR/><BR/><I>Dromaeosauridae</I> sensu Sereno 2005:<BR/><BR/><apply<BR/> xmlns="http://www.w3.org/1998/Math/MathML"><BR/> <csymbol definitionURL<BR/> ="http://namesonnodes.org/2009/phylo/math::branchClade"/><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Dromaeosaurus_albertensis"/><BR/> <apply><BR/> <union/><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Troodon_formosus"/><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Ornithomimus_edmontonicus"/><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Passer_domesticus"/><BR/> </apply><BR/></apply><BR/><BR/><BR/><I>Neornithes</I> sensu Sereno 2005:<BR/><BR/><apply<BR/> xmlns="http://www.w3.org/1998/Math/MathML"><BR/> <csymbol definitionURL<BR/> ="http://namesonnodes.org/2009/phylo/math::nodeClade"/><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Struthio_camelus"/><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Passer_domesticus"/><BR/></apply><BR/><BR/><BR/><I>Aves</I> sensu Gauthier & de Queiroz 2001:<BR/><BR/><math<BR/> xmlns="http://www.w3.org/1998/Math/MathML"><BR/> <declare><BR/> <ci>Ratitae</ci><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Struthio_camelus"/><BR/> </declare><BR/> <declare><BR/> <ci>Tinamidae</ci><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Tetrao_major"/><BR/> </declare><BR/> <declare><BR/> <ci>Neognathae</ci><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Vultur_gryphus"/><BR/> </declare><BR/> <apply><BR/> <csymbol definitionURL<BR/> ="http://namesonnodes.org/2009/phylo/math::nodeClade"/><BR/> <ci>Ratitae</ci><BR/> <ci>Tinamidae</ci><BR/> <ci>Neognathae</ci><BR/> </apply><BR/></math><BR/><BR/><BR/><I>Palaeognathae</I> sensu Gauthier & de Queiroz 2001:<BR/><BR/><math<BR/> xmlns="http://www.w3.org/1998/Math/MathML"><BR/> <declare><BR/> <ci>Ratitae</ci><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Struthio_camelus"/><BR/> </declare><BR/> <declare><BR/> <ci>Tinamidae</ci><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Tetrao_major"/><BR/> </declare><BR/> <apply><BR/> <csymbol definitionURL<BR/> ="http://namesonnodes.org/2009/phylo/math::nodeClade"/><BR/> <ci>Ratitae</ci><BR/> <ci>Tinamidae</ci><BR/> </apply><BR/></math><BR/><BR/><BR/><I>Aves</I> sensu Sereno 2005:<BR/><BR/><apply<BR/> xmlns="http://www.w3.org/1998/Math/MathML"><BR/> <csymbol definitionURL<BR/> ="http://namesonnodes.org/2009/phylo/math::nodeClade"/><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Archaeopteryx_lithographica"/><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Passer_domesticus"/><BR/></apply><BR/><BR/><BR/><I>Panpalaeognathae</I> Gauthier & de Queiroz 2001:<BR/><BR/><math<BR/> xmlns="http://www.w3.org/1998/Math/MathML"><BR/> <declare><BR/> <ci>Ratitae</ci><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Struthio_camelus"/><BR/> </declare><BR/> <declare><BR/> <ci>Tinamidae</ci><BR/> <csymbol definitionURL<BR/><BR/> ="urn:isbn:0853010064::Tetrao_major"/><BR/> </declare><BR/> <declare><BR/> <ci>Galloanserae</ci><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Phasianus_gallus"/><BR/> </declare><BR/> <declare><BR/> <ci>Neoaves</ci><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Vultur_gryphus"/><BR/> </declare><BR/> <apply><BR/> <csymbol definitionURL<BR/> ="http://namesonnodes.org/2009/phylo/math::branchClade"/><BR/> <apply><BR/> <union/><BR/> <ci>Ratitae</ci><BR/> <ci>Tinamidae</ci><BR/> </apply><BR/> <apply><BR/> <union/><BR/> <ci>Galloanserae</ci><BR/> <ci>Neoaves</ci><BR/> </apply><BR/> </apply><BR/></math><BR/><apply<BR/> xmlns="http://www.w3.org/1998/Math/MathML"><BR/> <csymbol definitionURL<BR/> ="http://namesonnodes.org/2009/phylo/math::nodeClade"/><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Dromaeosaurus"/><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Velociraptor"/><BR/></apply><BR/><BR/><BR/><I>Dromaeosauridae</I> sensu Sereno 2005:<BR/><BR/><apply<BR/> xmlns="http://www.w3.org/1998/Math/MathML"><BR/> <csymbol definitionURL<BR/> ="http://namesonnodes.org/2009/phylo/math::branchClade"/><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Dromaeosaurus_albertensis"/><BR/> <apply><BR/> <union/><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Troodon_formosus"/><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Ornithomimus_edmontonicus"/><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Passer_domesticus"/><BR/> </apply><BR/></apply><BR/><BR/><BR/><I>Neornithes</I> sensu Sereno 2005:<BR/><BR/><apply<BR/> xmlns="http://www.w3.org/1998/Math/MathML"><BR/> <csymbol definitionURL<BR/> ="http://namesonnodes.org/2009/phylo/math::nodeClade"/><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Struthio_camelus"/><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Passer_domesticus"/><BR/></apply><BR/><BR/><BR/><I>Aves</I> sensu Gauthier & de Queiroz 2001:<BR/><BR/><math<BR/> xmlns="http://www.w3.org/1998/Math/MathML"><BR/> <declare><BR/> <ci>Ratitae</ci><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Struthio_camelus"/><BR/> </declare><BR/> <declare><BR/> <ci>Tinamidae</ci><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Tetrao_major"/><BR/> </declare><BR/> <declare><BR/> <ci>Neognathae</ci><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Vultur_gryphus"/><BR/> </declare><BR/> <apply><BR/> <csymbol definitionURL<BR/> ="http://namesonnodes.org/2009/phylo/math::nodeClade"/><BR/> <ci>Ratitae</ci><BR/> <ci>Tinamidae</ci><BR/> <ci>Neognathae</ci><BR/> </apply><BR/></math><BR/><BR/><BR/><I>Palaeognathae</I> sensu Gauthier & de Queiroz 2001:<BR/><BR/><math<BR/> xmlns="http://www.w3.org/1998/Math/MathML"><BR/> <declare><BR/> <ci>Ratitae</ci><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Struthio_camelus"/><BR/> </declare><BR/> <declare><BR/> <ci>Tinamidae</ci><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Tetrao_major"/><BR/> </declare><BR/> <apply><BR/> <csymbol definitionURL<BR/> ="http://namesonnodes.org/2009/phylo/math::nodeClade"/><BR/> <ci>Ratitae</ci><BR/><BR/> <ci>Tinamidae</ci><BR/> </apply><BR/></math><BR/><BR/><BR/><I>Aves</I> sensu Sereno 2005:<BR/><BR/><apply<BR/> xmlns="http://www.w3.org/1998/Math/MathML"><BR/> <csymbol definitionURL<BR/> ="http://namesonnodes.org/2009/phylo/math::nodeClade"/><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Archaeopteryx_lithographica"/><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Passer_domesticus"/><BR/></apply><BR/><BR/><BR/><I>Panpalaeognathae</I> Gauthier & de Queiroz 2001:<BR/><BR/><math<BR/> xmlns="http://www.w3.org/1998/Math/MathML"><BR/> <declare><BR/> <ci>Ratitae</ci><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Struthio_camelus"/><BR/> </declare><BR/> <declare><BR/> <ci>Tinamidae</ci><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Tetrao_major"/><BR/> </declare><BR/> <declare><BR/> <ci>Galloanserae</ci><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Phasianus_gallus"/><BR/> </declare><BR/> <declare><BR/> <ci>Neoaves</ci><BR/> <csymbol definitionURL<BR/> ="urn:isbn:0853010064::Vultur_gryphus"/><BR/> </declare><BR/> <apply><BR/> <csymbol definitionURL<BR/> ="http://namesonnodes.org/2009/phylo/math::branchClade"/><BR/> <apply><BR/> <union/><BR/> <ci>Ratitae</ci><BR/> <ci>Tinamidae</ci><BR/> </apply><BR/> <apply><BR/> <union/><BR/> <ci>Galloanserae</ci><BR/> <ci>Neoaves</ci><BR/> </apply><BR/> </apply><BR/></math>Mike Keeseyhttps://www.blogger.com/profile/00147156174467903264noreply@blogger.comtag:blogger.com,1999:blog-5350157389434430698.post-18945120749587972702009-02-01T11:18:00.000-08:002009-02-01T11:18:00.000-08:00While I'm at it, here are the prose definitions:Dr...While I'm at it, here are the prose definitions:<BR/><BR/><I>Dromaeosauridae</I> sensu Padian & al. 1999: "The most recent common ancestor of <I>Dromaeosaurus</I> and <I>Velociraptor</I> and all of its descendants."<BR/><BR/><I>Dromaeosauridae</I> sensu Sereno 2005: "The most inclusive clade containing <I>Dromaeosaurus albertensis</I> Matthew and Brown 1922 but not <I>Troodon formosus</I> Leidy 1856, <I>Ornithomimus edmontonicus</I> Sternberg 1933, <I>Passer domesticus</I> (Linnaeus 1758)."<BR/><BR/><I>Neornithes</I> sensu Sereno 2005: "The least inclusive clade containing <I>Struthio camelus</I> Linnaeus 1758 and <I>Passer domesticus</I> (Linnaeus 1758)."<BR/><BR/><I>Aves</I> sensu Gauthier & de Queiroz 2001: "'<I>Aves</I>' refers to the crown clade stemming from the most recent common ancestor of <I>Ratitae</I> (<I>Struthio camelus</I> Linnaeus 1758), <I>Tinamidae</I> (<I>Tetrao</I> [<I>Tinamus</I>] <I>major</I> Gmelin 1789), and <I>Neognathae</I> (<I>Vultur gryphus</I> Linnaeus 1758)."<BR/><BR/><I>Palaeognathae</I> gauthier & de Queiroz 2001: "'<I>Palaeognathae</I>' refers to the crown clade stemming from the most recent common ancestor of <I>Tinamidae</I> (<I>Tetrao</I> [<I>Tinamus</I>] <I>major</I> Gmelin 1789) and <I>Ratitae</I> (<I>Struthio camelus</I> Linnaeus 1758)."<BR/><BR/><I>Aves</I> sensu Sereno 2005: "The least inclusive clade containing <I>Archaeopteryx lithographica</I> Meyer 1861 and <I>Passer domesticus</I> (Linnaeus 1758)."<BR/><BR/><I>Panpalaeognathae</I> sensu Gauthier & de Queiroz 2001: "Therefore, we propose the name '<I>Panpalaeognathae</I>' (new clade name), defined as the most inclusive clade containing both <I>Tinamidae</I> (<I>Tetrao</I> [<I>Tinamus</I>] <I>major</I> Gmelin 1789) and <I>Ratitae</I> (<I>Struthio camelus</I> Linnaeus 1758) but neither <I>Galloanserae</I> (<I>Phasianus</I> [<I>Gallus</I>] <I>gallus</I> Linnaeus 1758) nor <I>Neoaves</I> (<I>Vultur gryphus</I> Linnaeus 1758)."Mike Keeseyhttps://www.blogger.com/profile/00147156174467903264noreply@blogger.comtag:blogger.com,1999:blog-5350157389434430698.post-59279687577239926092009-02-01T11:12:00.000-08:002009-02-01T11:12:00.000-08:00Thanks. Whoops, meant to put those in the post. He...Thanks. Whoops, meant to put those in the post. Here they are:<BR/><BR/>((Dromaeosaurus, Velociraptor), (Troodon, (Archaeopteryx,(Confuciusornis, (Hesperornis,(Ichthyornis, ((Passer, Vultur), (Struthio, Tinamus)))))))))<BR/><BR/>((archaeopteryx_lithographica, confuciusornis_sanctus), (troodon_formosus, (microraptor_gui, (dromaeosaurus_albertensis, deinonychus_antirrhopus, velociraptor_mongoliensis))))Mike Keeseyhttps://www.blogger.com/profile/00147156174467903264noreply@blogger.comtag:blogger.com,1999:blog-5350157389434430698.post-59875704317363236632009-02-01T09:17:00.000-08:002009-02-01T09:17:00.000-08:00Pretty awesome. What were your two different phylo...Pretty awesome. What were your two different phylogenies that you used?Anonymousnoreply@blogger.com