Re: Must-Read Paper

[Mar Qos Aker <marqosaker@yahoo.com>]

Dr. Mortimer: Some of us are really rank amateurs and would like to
read this article, however, how would one get a copy of it? Online?
>From Dr. Jenner? Please, oh please help. Thanks in advance for all the
help. Peace.

Marc Bauer
--- Mickey Mortimer <Mickey_Mortimer111@msn.com> wrote:

> Jenner, R. A. (2004). The scientific status of metazoan cladistics:
> why
> current research practice must change. Zoologica Scripta, 33,
> 293-310.
> 
> Anyone even remotely interested in cladistics or who follows
> phylogenies
> arrived at through cladistic methods needs to read this paper
> (available on
> request).  Yeah, it's about metazoans, but it works just as well for
> dinosaur phylogenetics.
> 
> Jenner basically divides the cladistic process into three steps. 
> Step one
> is choosing taxa and characters and scoring them.  Step two is
> finding the
> best trees.  Step three is interpreting the results.  He finds while
> step
> two is advancing well, step three and especially step one need much
> work.
> 
> "It is an acknowledged dictum of cladistics that all known pertinent
> information should be included within an analysis, lest the results
> be
> unjustifiably biased towards certain conclusions."
> The only published theropod analysis which approaches this condition
> is
> Holtz (2000). Any coelurosaur analysis created now should by all
> rights have
> 500+ characters, given the amount that have been used in prior
> analyses.
> 
> "In order to find the most corroborated and most severely tested
> cladogram,
> it thus becomes critical to establish 'how honestly the relevant data
> are
> surveyed for those synapomorphies that actually have the potential to
> refute
> a cladistic hypothesis, those synapomorphies that can count as
> independent
> ad hoc hypotheses of homoplasy' (Kluge 1998: 350)."
> I've discussed this in terms of consistancy indeces before, and noted
> though
> some analyses like Holtz's and the TWG's are good, others like
> Sereno's and
> Bolotsky and Godefriot's are not.
> 
> "Unfortunately, although some studies justify the exclusion of
> several
> characters from their analyses, explicit justification for the
> inclusion and
> exclusion of all previously proposed and potentially informative
> characters
> is never given."
> Very true for dinosaurian analyses as well, which are just starting
> to
> justify some of the characters they exclude, but by no means a
> significant
> portion of them.
> 
> Jenner goes into detail about the controversial placement of
> entoprocts
> among metazoans.  A strong parallel between the issues involved and
> those
> surrounding alvarezsaurid placement among maniraptoriformes can be
> made.  He
> notes Haszprunar (1996) proposed six synapomorphies linking
> entoprocts with
> mollusks, but later authors never used all of them.  Zrzavy et al.
> (1998)
> and Giribet et al. (2000) used four, Sorensen et al. (2000), Nielsen
> (2001)
> and Peterson and Eernisse (2001) used one, Zrzavy et al. (2001) used
> two,
> and Zrzavy et al. (2003) used four.  Unsurprisingly, none of these
> later
> analyses found entoprocts grouping with mollusks.  Even when the same
> character is included, it's sometimes defined differently, so as to
> not have
> the same distribution.  Jenner describes how one of Haszprunar's
> characters
> was a chitin cuticle, but some later analyses which used the
> character coded
> for only alpha chitin cuticles.
> 
> Take Sereno's (1999) 16 suggested arctometatarsalian characters for
> alvarezsaurids.  There have been three anatomically extensive (so
> Hutchinson's femur-only analysis wouldn't count, for instance)
> phylogenetic
> analyses since then that have included both ornithomimosaurs and
> alvarezsaurids- Holtz (2000-2001), TWG (2001-2004) and Maryanska et
> al.
> (2002).  Holtz included 3 of Sereno's 16 characters, the TWG included
> 2, and
> Maryanska et al. included 1.  Though Suzuki et al. (2002) correctly
> rejected
> a few of Sereno's characters, most are valid (see
> http://dml.cmnh.org/2003Jan/msg00160.html ).  As an example of
> different
> character definitions, Sereno used the large metacarpal I/II ratio to
> group
> alvarezsaurids with ornithomimosaurs (and segnosaurs).  But just look
> at the
> TWG's most recent (Hwang et al., 2004) description of this character
> -
> "character 149 - Metacarpal I half or less than half the length of
> metacarpal II, and longer proximodistally than wide transversely (0)
> or
> subequal in length to metacarpal II (1) or very short and wider
> transversely
> than long proximodistally (2)."  Alvarezsaurids are coded for state
> 2, while
> most ornithomimosaurs are coded for state 1, and it's unordered.  But
> state
> 2 measures metacarpal I length/width proportions, while state 1
> measures
> metacarpal I/II ratio!  Why are they even in the same character!?  It
> forces
> PAUP to view alvarezsaurids as not having a homologous state with
> ornithomimosaurs.  The topology is being decided before the matrix is
> run.
> Most other analyses including alvarezsaurids have not even included
> ornithomimosaurs (any of Chiappe's [1993-2002] and their varients,
> Gishlick,
> 2002, Chatterjee, 1999).  It's really no wonder these other analyses
> have
> never come up with arctometatarsalian alvarezsaurids.
> 
> "This case study makes clear that recent phylogenetic studies have
> not
> selected characters with the express purpose of constructing an
> effective
> test of available hypotheses for the position of the entoprocts
> within the
> Metazoa. Or, if they have done so, the decisions underlying character
> selection remain entirely hidden."
> Replace "entoproct" with "alvarezsaurid" and "Metazoa" with
> "Maniraptoriformes", and the statement's just as true.
> 
> "The arbitrary selection of characters becomes even more strikingly
> clear
> when we compare the choice of characters in subsequent analyses of
> the same
> research group."
> Jenner describes a situation where Zrzavy et al. (1998) identified
> nine
> characters to link entoprocts and cycliophorans, but later (2001)
> only
> included two of those characters, then in 2003, only included one of
> them.
> "Consequently, the change in the phylogenetic placement of the
> entoprocts
> and Cycliophora from Zrzavy
> et al. (1998) to Zrzavy et al. (2001) and Zrzavy (2003) does not
> reflect any
> increased understanding of phylogeny and synapomorphies."
> The same could be said about new variants of coelurosaurian analyses.
>  Lu et
> al. (2002) used Chiappe et al.'s (1996) characters, and all of the
> taxa,
> while adding three more taxa.  Yet Lu et al. didn't include 26 of
> Chiappe et
> al.'s characters in their matrix.  Why?  One of these (81) supports
> placing
> oviraptorids outside of Aves, and another (89) supports alvarezsaurid
> monophyly (both which Lu et al.'s most parsimonious tree does not
> support).
> Another character was altered from "caudal vertebral count more than
> 35 (0);
> fewer than 25-26 (1); fewer than 15 (2)" to "caudal vertebral count -
> more
> than 35 (0); 36-25 (1); fewer than 25 with fused distal vertebrae
> (2)." Note
> that the previous character in both lists is for the presence of a
> pygostyle.  So Lu et al. purposely change this character to weight
> for
> pygostyle presence, and with oviraptorosaurs coded as polymorphic for
> having
> a pygostyle (thanks to Nomingia), it helps them be the sister group
> of
> Pygostylia.  I won't even go into the five unjustifiable miscodings
> for this
> character alone in Lu et al.'s matrix.
> "The power of cladistics to test alternative phylogenetic hypotheses
> breaks
> down when potential synapomorphies incongruent with the obtained
> results are
> left out of the analysis without justification."
> People need to read this and learn it well.  How are Lu et al.
> testing their
> hypothesis of avialan oviraptorosaurs if not only do they not include
> any of
> the hundreds of other relevent characters used in the literature, but
> don't
> even include all the competing data in the one matrix (Chiappe et
> al.'s)
> they use for their analysis (excepting the two from Chiappe et al.
> 1998 and
> the three "new" characters, all of which had been used previously by
> other
> authors)?
> 
> "A survey of the literature leaves no doubt that uncritical character
> selection contributes significantly to the
> existence of multiple competing hypotheses for the phylogenetic
> position of
> phyla ranging from the gastrotrichs and brachiopods to the arthropods
> and
> tardigrades."
> The same could be said of many theropod groups.  Along with taxon
> selection
> (covered next), this basically is responsible for why alvarezsaurids
> and
> other controversial taxa have such wildly varying placement in
> current
> cladograms.  If you analyze alvarezsaurids in a bird matrix, without
> including the eumaniraptoran and maniraptoran characters they lack,
> or the
> arctometatarsalian characters they have, they'll come out near
> archaeopterygids (Chiappe).  If you analyze them in a coelurosaur
> matrix,
> without including the avialan or arctometatarsalian characters they
> have,
> they'll come out at the base of Maniraptora (TWG).  If you analyze
> them in a
> coelurosaur matrix, and don't include the maniraptoran characters
> they have,
> but include lots of arctometatarsalian characters they have, they'll
> be
> arctometatarsalians (Sereno).
> 
> "I consider uncritical selection of characters in recent phylogenetic
> analyses of the Metazoa as an important factor crippling the
> objectivity and
> testing efficacy of these studies. Of course, it would not be fair to
> criticize workers for not considering all possible evidence that
> could bear
> on a phylogenetic problem. However, good scholarship necessitates
> inclusion,
> or at least discussion, of available data treated in previous
> studies. In
> this sense, recent phylogenetic hypotheses are no better than the
> older
> precladistic scenarios that cladistics was intended to supersede."
> 
> Jenner then goes into critiques of authors who don't include all
> relevent
> taxa.
> "Astonishingly, several recent authors (Nielsen 2001: 496; Zrzavy
> 2003: 66)
> have excluded taxa from their phylogenetic analyses because their
> relationships are uncertain! For example, Zrzavy (2003) excludes
> Xenoturbella from his analysis because its position is 'still
> contentious.'
> But what is phylogenetics all about, if not the testing of the
> phylogenetic
> placement of taxa?"
> Hilarious, but sad.  Looking at our alvarezsaurid example, of the
> fourteen
> published analyses (and derivitives) that include alvarezsaurids,
> only nine
> include ornithomimosaurs, once as an outgroup.
> Looking at another aspect of this problem, look at how many taxa
> aren't
> included in supposedly extensive phylogenetic analyses.  Chiappe
> never
> includes any of the most bird-like dromaeosaurs in his analyses,
> despite the
> obvious ramifications for tree topology around archaeopterygids,
> Rahonavis
> and alvarezsaurids.  None of the 'oviraptorosaurs are birds' papers
> (Lu et
> al., 2002; Maryanska et al., 2002) have either, despite the fact they
> are
> the best evidence for placing dromaeosaurs closer to birds than
> oviraptorosaurs.  Taxa are as important to testing hypotheses as
> characters
> are, and more people need to realize this.
> 
> Finally (for the sake of this review), Jenner describes the appalling
> state
> of character coding in metazoan analyses.
> "Rather than representing occasional lapses of judgement, most of the
> identified errors are symptomatic of a generally cavalier attitude
> towards
> character study. A major aim of future cladistic analyses of the
> Metazoa
> must therefore be the correction of the many errors through a more
> detailed
> and explicit approach to character study."
> Here's an amusing story involving such attitudes in theropod
> phylogenetics.
> Back in 1996, Sereno et al. create the character "fibular fossa
> occupying
> all of the medial aspect of the proximal end" (63 in their matrix). 
> This is
> the fossa on the fibula, used to diagnose coelurosaurs including
> their new
> taxon Deltadromeus.  Note their wording in the text (pg. 988),
> "...coelurosaur is based on the ... presence of a large deep fossa on
> the
> proximal end of the fibula", referencing figures which show and label
> the
> "fibular fossa" on the fibula.  In 1998, Harris was the first to use
> it
> again.  But he misunderstands it as being on the tibia!  His
> character 130
> is "incisura tibialis (= fibular fossa) occupies all of medial aspect
> of
> proximal end of tibia - no (0); yes (1) (Sereno et al., 1996)."  Now
> yes,
> the incisura tibialis is on the tibia, but that's not the fibular
> fossa
> Sereno et al. discussed and coded.  Currie and Carpenter (2000)
> follow
> Harris without checking Sereno et al. (probably, since their codings
> are
> identical to Harris, and very different from Sereno et al.'s), and
> keep the
> mistake in the literature with their character 106 - "Tibia, fibular
> fossa
> occupied all of medial aspect of proximal end: 0 - no. 1 - yes." 
> Finally,
> Holtz (2000) completes the transformation, leaving out any use of the
> term
> "fibular fossa" in his character 347- "Incisura tibialis cranialis:
> 0,
> occupies less than 50% of medial surface of proximal tibia; 1,
> occupies more
> than 66% of medial surface of proximal tibia. (HARRIS, 1998)."  He
> has
> another character (355) for the fibular fossa itself.  Holtz's
> codings for
> the incisura tibialis are completely different than Harris', but they
> clearly aren't codings for a fibular fossa either.
> 
> "It is a striking observation that none of the recent cladistic
> studies of
> the Metazoa comprehensively support all data matrix entries with
> source
> citations."
> Same with theropod matrices, with a few applaudable exceptions (e.g.
> Rauhut,
> 2003).
> 
> There is much other good in this paper, and it comes with my highest
> recommendation.  I know I'll be looking out for his other papers as
> well-
> 
> Jenner, R. A. (2001). Bilaterian phylogeny and uncritical recycling
> of
> morphological data sets. Systematic Biology, 50, 730-742.
> 
> Jenner, R. A. (2002). Boolean logic and character state identity:
> pitfalls
> of character coding in metazoan cladistics. Contributions to Zoology,
> 71,
> 67-91.
> 
> Jenner, R. A. (2003). Unleashing the force of cladistics? Metazoan
> phylogenetics and hypothesis testing. Integrative and Comparative
> Biology,
> 43, 207-218.
> 
> Jenner, R. A. (in press). Towards a phylogeny of the Metazoa:
> evaluating
> alternative phylogenetic positions of Platyhelminthes, Nemertea, and
> Gnathostomulida, with a critical reappraisal of cladistic characters.
> Contributions to Zoology, 72, in press.
> 
> Jenner, R. A. & Schram, F. R. (1999). The grand game of metazoan
> phylogeny:
> rules and strategies. Biological Reviews of the Cambridge
> Philosophical
> Society, 74, 121-142.
> 
> Mickey Mortimer
> Undergraduate, Earth and Space Sciences
> University of Washington
> The Theropod Database -
> http://students.washington.edu/eoraptor/Home.html
> 



                
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