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New Buchholtz-Wagner Taxon Definition Shorthand for Phylogenetic Taxonomy on the Dinosaur List



This has sat around all summer waiting. Pete and I came to a consensus on PT
shorthand about four months ago, but we've been too busy to get the draft
proposal for the list finished... it is not entirely complete. We don't
think we've contradicted anything that has been established concerning PT,
and the only "improvements" we've made are terminological. Comments would be
appreciated!
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The phylogenetic literature is replete with examples of shorthand
notations for describing clades. Some examples include Newick notation, used
to describe tree topology [e.g. "(taxon x, (taxon y, taxon z))"] and various
ad hoc notations used for the description of clade content within a
particular tree or description/shorthand definition of taxa [e.g. "taxon
A ( = taxon x + (taxon y + taxon z))"]. While such notations are adequate for
the purposes they serve within descriptive papers, the authors' intent is
not explicitly clear. For example, does "Dinosauria (Ornithischia +
Saurischia)" describe the topology of the author's cladogram, the composition
of an ingroup OTU, the content of a clade discovered or inferred from an
analysis, or the definition of a phylogenetic taxon?
        Peter Buchholz and I have developed a consensus system of
abbreviated notation which we believe will serve the purpose of allowing
explicit discrimination of phylogenetic taxon definitions. We believe this
system to be internally consistent and we expect that it will not be
objectionable to the dinosaur list community. We hope that you will join us in
testing our system, to see if it really makes definitions explicit, readily
accessible, and shorter than a full text description.
        Note that we do not advocate the abandonment of formal text
definition of phylogenetic taxa. Although a taxon is only defined
once, the definition will be applied many times. If everyone takes the time
to explicitly state the definition which is currently accepted in a
consistent format the process of phylogenetic taxonomy may proceed more
smoothly in the future than it does today.
        The following is a much much shorter (!) version of a posting which was
way too long for the dino list. We hope to find a home (or homes) for the
full-length version as soon as possible. Anyone wishing to provide a home,
please feel free to contact us.

      BUCHHOLZ-WAGNER CONSENSUS NOTATION PHYLOGENETIC TAXON DEFINITION

DEFINITIONS:
        Anchor Taxa: An anchor taxon is a taxon (preferably generic or
specific) which is explicitly included or excluded from the taxon being
defined. The relationships among anchor taxa serve to outline the
composition of the taxon being defined. The "role" of an anchor taxon is
specifically whether it is included in the taxon or excluded from the taxon
(i.e. is an exclusive or inclusive anchor taxon). Note that in phylogenetic
taxonomy, objective synonyms have identical anchor taxa in identical roles.
        Inclusive Anchor Taxon: A taxon which is by definition included in
the taxon being defined.
        Exclusive Anchor Taxon: A taxon which is by definition excluded from
the taxon being defined.
                                ...

FORMAT:
        A shorthand phylogenetic definition should consist of three primary
descriptors: name, definition sign, definition. Three additional
descriptors, author, definition author, and synonymy are appropriate for
inclusion in taxonomic works, but may be omitted from casual usage.

PRIMARY DESCRIPTORS:

NAME:
        All definitions should be preceded by the name of the taxon being
defined.

DEFINITION SIGN:
        The taxon name should be linked to its definition by a "defined as"
or "three barred equal" sign. For ASCII format text, where such a sign
cannot be duplicated, the "==" or "exactly equals" sign should be
substituted. A single "equal" sign should never be used, to preserve the
distinction between definition and synonymy (or clade content).

DEFINITION:
        The definition of a phylogenetic taxon should be set off in "{}" or
"curly brackets". Spaces should be left just within the brackets. The curly
brackets denote the process of common ancestry and descent, and imply the
inclusion of taxa other than anchor taxa. As such, they will distinguish
definition from other forms of clade notation which use parentheses, such as
Newick notation or various other ad hoc schemes.
        
        NODE-BASED TAXA:
        A node based taxon definition will consist of a listing of inclusive
anchor taxa separated by "+" or "addition" signs with spaces and without
commas or other punctuation. It will be read as "the most recent common
ancestor of [all of the inclusive anchor taxa] and all of its descendants."

        e.g. {taxon x + taxon y + taxon z} is "the most recent common
ancestor of taxon x, taxon y, and taxon z and all of its descendants."

        STEM-BASED TAXA:
        A stem based taxon definition will consist of an inclusive anchor
taxon listed first followed by ">" or "greater-than" sign with a space on
either side, and one or more exclusive anchor taxa separated by commas and
spaces. It will be read as "[The inclusive anchor taxon] and all taxa
sharing a more recent common ancestor with [the inclusive anchor taxon] than
with [each of the exclusive anchor taxa]."

        e.g. {taxon x > taxon y, taxon z} is "Taxon X and all taxa sharing a
more recent common ancestor with taxon x than with taxon y or with taxon z."

        Note that the commas are not intended to be read as "and", nor are
they meant to imply any particular phylogenetic structure among the
exclusive anchor taxa.

                                ...
 
ADDITIONAL DESCRIPTORS:

AUTHOR:
        Taxonomy has always credited the original namer of a taxon,
regardless of the author of the currently valid definition. The original
namer of the taxon (whether phylogenetic or otherwise), and the year it was
named, should be listed.

DEFINITION AUTHOR:
        It is recommended that the author of the definition with priority be
listed along with the original namer. This will prevent confusion as to
which definition is considered to have priority. The last name of the
definition author should be preceded by the abbreviation "def." and
separated from the original author by a colon. If the original author's
definition is phylogenetically valid, only the original author should be listed.

SYNONOMY:
        Taxa synonymous with the taxon being defined (i.e. taxa describing the
common ancestor or the same clade which were defined later regardless of
when they were named (De Quiroz and Gauthier XXXX, Padian and May 1993);
node- and stem-based taxa may never be synonyms Holtz pers. com.) should be
listed in parentheses after a single "equal" sign along with their authors
and the definition authors separated by a colon. Readers are cautioned that
since synonymy may be objective or subjective, the definition provided
cannot be assumed to apply to all synonymous taxa.

INTEGRATED EXAMPLES:

Arctometarsalia == { _Ornithomimus_ > "modern birds" }, Holtz 1994:def.
Holtz 1996

Conjugate-conjoined node-stem triplets:
STEGOSAUROMORPHA=={Stegosaurus + Ankylosaurus} Cooper 1985, (=EURYPODA Sereno
1986)
STEGOSAURIA=={Stegosaurus > Ankylosaurus} Marsh 1877:def Sereno 1986
ANKYLOSAURIA=={Ankylosaurus > Stegosaurus} Osborn 1923:def Sereno 1986

HYPSILOPHODONTIA=={Hypsilophodon + Iguanodon} Cooper 1985 (=Ornithopoda Marsh
1881:def Sereno 1986, =Euornithopoda Sereno 1986:def Weishampel 1990)
HYPSILOPHODONTOIDEA=={Hypsilophodon > Iguanodon} Cooper 1985
(=Hypsilophodontia Cooper 1985:def Sereno 1986)
IGUANODONTIA=={Iguanodon > Hypsilophodon} Dollo 1888:def Cooper 1985
            
An abreviated node-stem triplet example (nodes with asterisc):

        *Dinosauria     == { _Triceratops_ + Neornithes }
        Ornithischia    == { _Triceratops_ > Neornithes }
        Saurischia      == { Neornithes > _Triceratops }
                *Unnamed node
                Sauropodomorpha == { _Diplodocus_? > Neornithes }
                Theropoda       == { Neornithes > _Diplodocus_? }
                        *Eumaniraptora    == { _Deinonychus_ + Neornithes }
                        Deionychosauria == { _Deinonychus_ > Neornithes }
                        Avialae         == { Neornithes > _Deinonychus_ }

        Note substitution of anchor taxa in conjugate stems and conjoined nodes.

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    Jonathan R. Wagner, Dept. of Geosciences, TTU, Lubbock, TX 79409-1053
                    "...To fight legends." - Kosh Naranek