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Must-Read Paper



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