Wednesday, May 20, 2015

Is Chilesaurus a basal tetanurine?

I've been away for a few weeks, but came back to find the weird new dinosaur Chilesaurus exists.  Just looking at it, any dinosaur worker would notice an odd mix of characters, making me curious exactly what it's related to.  Novas et al. (2015) used four analyses to determine it belonged in non-orionidan Tetanurae.  To use a Peters-ism, that's one strange bed fellow.  So let's go in for a closer look.

Their analyses

The first analysis was Nesbitt et al.'s (2009) Tawa analysis (315 characters), which focused on basal theropods and saurischians.  This found Chilesaurus to be a coelurosaur, though so was Ceratosaurus.  The authors rightly note the matrix was not designed to test neotheropod phylogeny, and the low Bremer supports show this, though I note the pairing of Chilesaurus with the only included actual coelurosaur Velociraptor is better supported than the other neotheropodan nodes. 15 more steps were needed to constrain it as sister to Avepoda, 16 more to constrain it as a sauropodomorph (ended up sister to Plateosaurus instead of Saturnalia or Efraasia), and 14 more as an ornithischian (as the basalmost one or a heterodontosaurid).  These sound impressive until you realize that the matrix wasn't designed with ornithischian or sauropodomorph apomorphies in mind.  Also, I wonder how many more steps it took to place as a basal tetanurine where Novas et al. ultimately conclude it goes?  And why not use Nesbitt's (2011) larger anlysis which expanded on this and has had a major update by Langer and Ferigolo (2013), or at least Sues et al.'s (2011) version of Nesbitt et al.'s that added Daemonosaurus?  The latter genus also has three premaxillary teeth, a short snout, broad posterolateral premaxillary process and elongate cervicals with pleurocoels, so might help move Chilesaurus out of Avepoda.

The second analysis is a logical follow up, coding Chilesaurus in the sauropodomorph-focused matrix of Otero and Pol (2013) (with Tawa added; 353 characters), that is itself basically Yates' 2007 'prosauropod' matrix.  This finds Chilesaurus in a polytomy with Avepoda, Tawa and Chindesaurus, but placing it in Sauropodomorpha (as the most basal member) is now only five steps longer.  I'd say that's not strong support for Chilesaurus being a theropod, as numerous relationships rejected by five steps in one matrix end up being supported in other or later matrices.  It now takes 11 more steps to place it sister to Ornithischia, but that OTU isn't divided up, making the situation more problematic than above.

The third analysis uses a revised version of Smith et al.'s (2007) theropod matrix that is terribly mis/un-coded.  Not encouraging, though Novas et al. "deeply rescored" "several taxa" "based on new available data" including at least Eoraptor and Megaraptor.  They also added Tawa, Aerosteon, Falcarius, Jianchangosaurus and Therizinosauridae and 56 new characters (total now 412 characters).  Here, Chilesaurus emerges as sister to Piatnitzkysauridae+Orionides.  However, only TWO steps are needed to constrain it as the sister of Avepoda*, and only three are needed to place it as the basalmost coelurosaur.  So even if the authors fixed the matrix, it only very weakly supports a basal tetanurine position.  Suspiciously, Plateosaurus was deleted from the matrix "because of the morphological gap present between the very early sauropodomorphs present in the data set (e.g. Saturnalia) and Plateosaurus."  This is rich when they left Velociraptor in Nesbitt et al.'s matrix, which is at least as different from Allosaurus.  As the only sauropodomorphs left were the incomplete Saturnalia and controversial Eoraptor, and considering Chilesaurus emerged sister to Plateosaurus when constrained as a sauropodomorph in their first analysis, I can't help but wonder if Chilesaurus was sister to Plateosaurus here too until the latter was deleted.  Novas et al. never say how many more steps it takes to place Chilesaurus in Sauropodomorpha in this matrix, and ornithischians weren't included.

* Just looking through their list of characters supporting the position, astragalar ascending process height is miscoded in Smith et al.'s (it's clearly not "higher than the astragalar body, typically covering only lateral half of anterior surface of distal tibia"), as is "ridge on lateral side of tibia for connection with fibula present and clearly separated from proximal articular surface."  So there's the two steps we need to move it outside Avepoda.

Finally, the fourth analysis used Carrano et al.'s (2012) basal tetanurine-focused analysis (351 characters).  Now Chilesaurus emerges in a polytomy with Monolophosaurus, Chuandongocoelurus, Megalosauroidea (including piatnitzkysaurids) and Avetheropoda.  Again, only two more steps are necessary to place it in Megalosauroidea, so its precise position here is very poorly supported.  Seven more steps are needed to place it in Coelurosauria (emerges sister to Compsognathus), but only three coelurosaurs are included in the matrix and they're heavily miscoded.  I added a lot of basal coelurosaurs to it when testing Bahariasaurus and found e.g. Compsognathus has 112 miscodings (of 351 characters).  That these include at least 7 that are actually more similar to Chilesaurus seems likely, though of course they probably also include at least 7 less similar to it, with the conclusion that the original matrix can't tell us how Chilesaurus compares to coelurosaurs.  As no maniraptoriforms were included, it can't tell us if Chilesaurus might belong there either.  No sauropodomorphs except the controversial Eoraptor were included, and no ornithischians.  Though like above matrix, this one wasn't made to test such basal nodes.

Given these results, Novas et al.'s conclusion seems to be stated far more strongly than their evidence indicates.  They say "the four independent phylogenetic data matrix [sic] favours a position as a neotheropod [avepod in my terminology], and particularly as a basal tetanuran", "The results of the four analyses are detailed below, but all of them agree in the position of Chilesaurus as a tetanuran theropod", and "Remarkably, all these analyses placed Chilesaurus as a member of Theropoda, near the origin of tetanurans."  Only the first two matrices have the needed basal taxa to test whether Chilesaurus is in Avepoda, and the second doesn't place it any closer to avepods than Tawa or Chindesaurus and supports Sauropodomorpha as a highly plausible alternative.  Further, the first places it as a ceratosaur not a tetanurine, the second doesn't even split Avepoda into multiple OTUs so can't weigh in, and the third is basically ambiguous whether Chilesaurus is actually sister to Avepoda or a coelurosaur.  Only the fourth analysis may strongly support placing Chilesaurus as a monolophosaur-piatnitzkysaur grade tetanurine, though we don't know how easy it is to place outside Avepoda in that one.

I'd say that even if we trusted these matrices accuracy 100%, they only tell us it's quite possible Chilesaurus is the basalmost sauropodomorph or coelurosaur and is about equally likely to be sister to Avepoda, a non-orionidan tetanurine or a basal megalosauroid.  Not actually much agreement there.

My analyses

Will come next...

References- Smith, Makovicky, Hammer and Currie, 2007. Osteology of Cryolophosaurus ellioti (Dinosauria: Theropoda) from the Early Jurassic of Antarctica and implications for early theropod evolution. Zoological Journal of the Linnean Society. 151, 377-421.

Yates, 2007. The first complete skull of the Triassic dinosaur Melanorosaurus Haughton (Sauropodomorpha, Anchisauria). Special Papers in Palaeontology. 77, 9-55.

Nesbitt, Smith, Irmis, Turner, Downs and Norell, 2009. A complete skeleton of a Late Triassic saurischian and the early evolution of dinosaurs. Science. 326, 1530-1533.

Nesbitt, 2011. The early evolution of archosaurs: Relationships and the origin of major clades. Bulletin of the American Museum of Natural History. 352, 292 pp.

Sues, Nesbitt, Berman and Henrici, 2011. A late-surviving basal theropod dinosaur from the latest Triassic of North America. Proceedings of the Royal Society B. 278(1723), 3459-3464.

Carrano, Benson and Sampson, 2012. The phylogeny of Tetanurae (Dinosauria: Theropoda). Journal of Systematic Palaeontology. 10(2), 211-300.

Langer and Ferigolo, 2013. The Late Triassic dinosauromorph Sacisaurus agudoensis (Caturrita Formation; Rio Grande do Sul, Brazil): Anatomy and affinities. Geological Society, London, Special Publications. 379(1), 353-392.

Otero and Pol, 2013. Postcranial anatomy and phylogenetic relationships of Mussaurus patagonicus (Dinosauria, Sauropodomorpha). Journal of Vertebrate Paleontology. 33(5), 1138-1168.

Novas, Salgado, Suarez, Agnolın, Ezcurra, Chimento, Cruz, Isasi, Vargas and Rubilar-Rogers, 2015. An enigmatic plant-eating theropod from the Late Jurassic period of Chile. Nature. doi:10.1038/nature14307

Thursday, February 26, 2015

Lingham-Soliar's (2015) Galileo complex

Hooo-eeee, Theagarten Lingham-Soliar (2015) just published volume 2 of his work "The Vertebrate Integument."  Sure sounds scholarly, and parts of it are, but the last chapter is something else.

Before the end

The preceding chapter also has some fun parts, such as section 6.4- "Sinosauropteryx, A Basal Theropod."  Well, it's not exactly basal, that would be more like Eodromaeus, or coelophysoids.  He then goes on to say "Given the importance of Sinosauropteryx as a basal dinosaur with alleged protofeathers."  Wait, now it's a basal dinosaur?!  He repeats this again in section 7.4.1.  Try 'basal coelurosaur' if you want the term to be meaningful.

Lingham-Soliar follows this with section 6.5- "Pushing Feathered Dinosaurs into the Mid-Triassic", based on Xu et al.'s (2009) Beipiaosaurus paper.  The Mid-Triassic part is based on a quote in their concluding paragraph where they note the resemblance of coelurosaurian integument to Psittacosaurus' quills and pterosaurian pycnofibers, though Lingham-Soliar conveniently cuts out the pterosaur part from his quote.  Perhaps the greater similarity to pycnofibers and certainty of a Middle Triassic (if not earlier) basal ornithodiran wasn't as insultable as dragging feathers rootward to hypothetical Middle Triassic dinosaurs based solely on quills in one ornithischian?

Notably, Lingham-Soliar doesn't seem to believe in pycnofibers either.  At least he finally realizes the vast majority, if not all, of pterosaur researchers accept fuzzy pterosaurs (unlike his 2003 paper, or Feduccia from 1996 onward*), though in the end he punts the question- "Given the dismal accounts in the literature of so-called protofeathers in non-avian dinosaurs, e.g., Sinosauropteryx (see Chap. 6), the subject of pycnofibers and their alleged functions such as thermo-regulation and warm-bloodedness will not be discussed any further here."

* The funny thing here is he says "Although it was thought to have been based on an unfortunate interpretation of Sharov’s (1971) description of hair-like structures in the pterosaur Sordes pilosus", in reference to the idea of fuzzy pterosaurs, he leaves out who thought that.  The answer is himself and Feduccia.  But instead of taking responsibility and admitting the BANDits and himself were so grossly ignorant of the pterosaur literature that they misunderstood fuzzy pterosaurs as being based on a misunderstanding of a 1971 paper, he uses the passive "it was thought."  "Mistakes were made..."

I'm being oppressed! (these titles write themselves)

Anyway, on to chapter 7- "The Last Best Hope."  Lingham-Soliar actually begins by retelling the story of Galileo's persecution by the Catholic church and of Nazis excluding Jews from scientific research in 1930s Germany.  Because Larry Martin died while under house arrest for his views and Alan Feduccia was kicked out of his position at the University of North Carolina, amirite?

A section on peer review follows, bemoaning the bias that can exist in the system.  The ironic thing here is that I completely agree, but what I find disturbing are all of the falsehoods that slip through peer review in Feduccia's papers.  And where are many of those published?  In The Auk, published by the American Ornithologist' Union, where Feduccia is a fellow.  And who is credited with reviewing e.g. Feduccia's (2013) "Bird origins anew" paper in that journal?  Burnham, Czerkas, James, Ruben, Lingham-Soliar, Zhou, and two I haven't heard of.  What an unbiased lot!  There's some phrase about pots and kettles that seems appropriate here...

Page 302 is where things start to get silly- the first figure in this chapter is a cartoon of The Emporer's New Clothes.  Because Prum's (2003) statement "current critics of the theropod origin of birds are not doing science" is analogous to telling Feduccia he needs to see a nonexistent item, or something.  Several figures follow using redrawn scenes from Tim Burton's Alice in Wonderland movie, with quotes changed to deride cladistics.  Well if that's not convincing, I don't know what is.  Lingham-Soliar then scolds Nature senior editor Henry Gee for a post on the vrtpaleo mailing list where he accurately criticized BAND for not using cladistics, correctly stated to be the accepted form of phylogenetic inference in the scientific community.  Little did I realize this is "pure censorship."  What's especially ironic is Lingham-Soliar's description of this as an inappropriate "outburst" with "purple prose", when Gee wrote that post in reply to Storrs Olson.  Has he ever read Olson's writing?!  I can't think of anyone in paleontology who writes less professional pieces and gets them published- cladistics was "elevated to a religion years ago", one has to "to suppress one's gag reflex" to read about living dinosaurs, the whole story of Chinese feathered dinosaurs "is essentially a hoax" and "the information has been suppressed" regarding Jehol non-theropods with filaments.  

But Lingham-Soliar is not to be outdone by Olson.  Having already implicitly compared the situation to Galileo and Nazi Germany, he now writes BADists "then state that most scientists support their view, which ironically dominates "primetime" magazines. The regime in apartheid South Africa also said that most people in the country supported its ideology - the fact that most opponents were prevented a voice seemed a tiny, insignificant detail not worth considering."  Does he really think there's some population of theropod and basal bird workers out there who believe in BAND but are being prevented from publishing that opinion?  All of the theropod workers I know must be very good actors.  He even follows Olson's penchant for referring to BAD in religious terms- "people like Dr. Padian with their reduction of science to evangelical preaching and biblical-like hell and damnation for nonbelievers."  Who knew BANDits get thrown into an eternal lake of fire?

In addition to the Peters-esque conspiracy vibe, Lingham-Soliar is similar to David in claiming his own studies as definitive evidence against Big Paleontology.  The following would fit right in on Pterosaur Heresies- "can there be at least some level of justification for Gee’s (2010) euphoric editorial, i.e., if the finding of melanosomes is correct then the filaments are indeed protofeathers? Alas, it seems not as we discovered in Chap. 6 - the notion of melanosomes in the filaments of Sinosauropteryx was shown to be "without scientific merit" (Lingham-Soliar 2011)."  Ah yes, 'we' discovered it was shown to be wrong- by me!  Also amusing is Lingham-Soliar's constant use of positive adjectives to describe those whose view he supports.  Olson is "Curator of Birds (now Emeritus Curator) at The National Museum of Natural History and one of the most eminent ornithologists in the world", while Norell is "curator of dinosaurs at the AMNH."  A bit better than a janitor, really.  The capitalization, the lack of abbreviation, it's just too good. Similarly, Lingham-Soliar has a penchant for describing his own work with superlatives- "detailed", "rigorous ... which received global attention", "the most revolutionary and explicit images of fiber microstructure in the feather."

BADistics

Lingham-Soliar writes at length about how cladistics is supposedly unfalsifiable, but that's simply untrue.  Any given phylogenetic hypothesis found via cladistic analysis can be falsified by the discovery of a different relationship once new taxa or characters are added.  Bullatosauria was popular for a while, the joining of ornithomimosaurs and troodontids recovered in analyses like Holtz (1994).  What falsified that?  The cladistic analyses of a newly discovered series of basal troodontids (e.g. Sinovenator, Mei) that were more Archaeopteryx-like, not more ornithomimosaur-like.  Indeed, we now have taxa like Anchiornis that blur the line so much that some analyses recover them as troodontids and others as birds.  The last time I checked the parsimony of alternative hypotheses in the Lori matrix, Bullatosauria was actually the least parsimonious of any previously suggested maniraptoriform topology I could think of.  

You want falsifiability?  If Lingham-Soliar is correct that the filaments of non-bird ornithodirans are collagen (and I agree in a minority of cases they are), then where are all of the fuzzy Jehol fish, frogs, lizards, choristoderes, etc.?  These all had collagen in life, so at least a few should be preserved this way if coelurosaurs, pterosaurs and small ornithischians are.  No doubt they've been suppressed as Olson claimed. :|  Or alternatively, present a repeatable method for distinguishing Jehol feathers on birds/maniraptorans from collagen on other ornithodirans.  As far as I know, neither Lingham-Soliar nor anyone else has ever tried to demonstrate Jehol bird filaments are collagen and BANDits have always interpreted them as feathers.

To continue the hyperbole, did you know that because Ernst Mayr drew attention to pitfalls in cladistics, "he was defamed by supporters of cladistics and the dinosaurian origin of birds in a manner reminiscent of Lysenkoism in the Soviet Union."  I must have been too young to remember Mayr being imprisoned in a labor camp and executed.  Similarly, "Erik Jarvik had been the butt of the attack by the cladists in the search for tetrapod ancestors" because he had lungfish closer to tetrapods than coelacanths.  "It turned out Jarvik was subsequently shown to have been right and the cladists at the time, who were highly critical of him, wrong."  So to this day, cladistic analyses of sarcopterygian relationships must be untrusted, right?  No, actually what changed the consensus were better cladistic analyses.  The more extensive cladistic analyses falsified the hypothesis found in the earlier analyses.  Astounding.  And you know what's further tested those analyses?  Cladistic molecular analyses, which used a completely different character set.

In case you're wondering, "the Achilles heel of cladistics" was discovered by Jarvik- "cladists arbitrarily pick out unreliable characters from a list without checking their reliability."  Of course!  Why don't I fire up my objective reliabilitometer more often?!  Or if only there were some method to delete and replace random characters then rerun these permutations multiple times, in order to test the strength of each node if certain characters are deleted and other characters are weighted more strongly.  But that would be as impossible as pulling yourself up by your own bootstraps!

The only good analysis is a BAND analysis

Repeating the ridiculous notion of Feduccia et al. (2005)- "To take one powerful alleged line of support for the theropod origin of birds namely Caudipteryx, Maryanska et al. (2002) in an exhaustive cladistic analysis showed that rather than a theropod dinosaur as proposed by some cladistics studies, Caudipteryx is a flightless bird. This finding remains undisputed."  Undisputed!  Except that Lingham-Soliar is blatantly lying, since Maryanska et al. placed Caudipteryx within Theropoda, even using undisputed(!) theropods such as Coelophysis and Allosaurus.  And except that the result of placing Caudipteryx closer to Aves than Archaeopteryx was disputed by Rauhut (2003), Holtz (2004), Ji et al. (2005), Choiniere et al. (2010) and its variations, Turner et al. (2012), Cau's analysis in Godefroit et al. (2013), Foth et al. (2014), all of the 60+ variants of the TWG matrix published over the last decade and a half, and even James and Pourtless' (2009) terrible BAND analysis.  Indeed, I don't think any other analysis has ever recovered that result.  As for "exhaustive", Maryanska et al. had 20 taxa and 195 characters, so 3,900 total codings.  The analysis of Godefroit et al. had a similar purview but used 101 taxa and 992 characters, resulting in 100,192 codings.  Over 25 times the size, and just to make Jarvik happy, it was reweighted two different ways to emphasize those "reliable" characters.

Needless to say, Lingham-Soliar's discussion of James and Pourtless' analysis is completely uncritical.  I just went over why that analysis was so bad, so no need to repeat it here.  It's ironic that he complains so often about BAD being 'verificationist' yet just accepts that James and Pourtless had valid, meaningful results despite claiming cladistics is "a discipline I am familiar with as a "working scientist" i.e. when I was involved in taxonomy."  What about that pseudosuchian nested sister to ornithomimosaurs?  You didn't notice that because the authors chose not to mention or figure it and you never examined the actual data yourself?  I see, I see...

Lingham-Soliar then complains about a rejection he got, where the reviewer wrote "The author of this paper might be taken more seriously if he did not show such contempt for all other work done on the subject, if he did not ignore all other lines of evidence that he pretends his particular investigation is overthrowing, and if he did not appear so injured by the refusal of the scientific community to recognize his genius."  Haha, that describes Theagarten to a tee.  "That this was a personal assault did not concern the referee and shamefully was wholly supported by the editor-in-chief of a notable US biological/science journal, with the words, "referees are only human." So was Jack the Ripper!"  Why, rejecting poor Lingham-Soliar's manuscript was just like serial murder!  Nazis, Stalin, the Inquisition... what evil characters are left for Lingham-Soliar to equate BADists to?  I got it!  We're the Galactic Empire and Padian is just like Emperor Palpatine, crushing rebellion and silencing dissenters with his force lightning of parsimony!

BranchingGate... no wait, Branchgazi

Alas, that guess was incorrect.  Instead, Xu, Prum and Zhao get compared to Richard Nixon and accused of fraud in the next section.  Why fraud, you ask?  Because Lingham-Soliar doesn't understand how citations work.  In the description of Sinornithosaurus' feathers (Xu et al., 2001), they state "the shorter, unbranched integumental appendages of Sinosauropteryx^2, a basal coelurosaur, are also congruent with the predicted Stage I feather morphology."  Lingham-Soliar thinks "the superscripted 2 refers to Chen et al. (1998) who they cite as making that critical description namely that feather morphology in Sinosauropteryx are "UNBRANCHED" [my emphasis] as support for their model."  And because one line of Chen et al.'s discussion calls the feathers "multibranched", and the last line in the paper suggests feathers evolved from "simpler, branched structures", the authors are "falsifying (OED, misrepresent, distort, (a fact, etc.)) another author’s work."  Here's an innocent explanation- that superscript 2 just refers to citing Sinosauropteryx's latest description, not to any particular interpretation in that description.  Why describe its feathers as unbranched?  Because Prum (1999) in the paper establishing that model wrote "From my direct observations of the two specimens of Sinosauropteryx (Chen et al., ’98), the integumentary structures appear to consist of unbranched filaments about 20 mm long."  Here again, Chen et al. is merely cited as the description, and we can see Prum has his own interpretation of the morphology.  He then says "Additional
examination of the integumental structures of Sinosauropteryx and Beipiaosaurus is required to establish: (1) whether the filaments are branched, unbranched, or hollow."  The truth is that there's still ambiguity, and even the eventual osteology (Currie and Chen, 2001) merely concluded that several features "suggest a feather-like structure with central shafts and plumulaceous barbs" and that "the evidence does favour the interpretation that each has a simple branching structure", but that there was no direct observation of such.  Notable is that Lingham-Soliar later quotes this paper in a way I would describe as misleading as it removes the caveats of uncertainty- "They stated that the integumentary structures comprise "central shafts and plumulaceous barbs" and have a "simple branching structure."  Who's lying now?


It just gets worse from here based on that one misunderstanding of what Xu et al. were citing Chen et al. for in 2001.  Xu et al. (2009) claimed Beipiaosaurus' EBFFs were the first unambiguous unbranched feather, yet they "quite astonishingly" cited the 2001 paper as evidence for prior examples being branched!  Yeah, because the 2001 paper was primarily describing branched feathers of Sinornithosaurus.  The 2001 noting of unbranched feathers in Sinosauropteryx was likely from Prum's 1999 observation, but by 2009 that had been overridden by Currie and Chen's 2001 osteology of the genus, which is indeed cited by Xu et al. in 2009 too.

But wait!  In the slightly later Zheng et al. (2009) description of Tianyulong, "Xing Xu along with his present PNAS co-author Xiaoting Zheng" wrote "In both Tianyulong and Sinosauropteryx, the filamentous structures are singular and unbranched."  Ha!  They can't keep their story straight!  Well, no again.  You see, Theagarten, coauthors sometimes disagree about details and even conclusions, and often have different responsibilities.  If we check the contributions of each paper, Xu wrote the Beipiaosaurus manuscript, and You wrote the Tianyulong one.  Maybe You thinks Sinosauropteryx's feathers are unbranched and thus disagrees with Currie and Chen but agrees with Prum?

So this whole thing is due to Lingham-Soliar not knowing how scientific papers work.  It's not fraud.  There's no massive coverup.  How surprising!

Beating a dead Yanornis-Microraptor chimaera

The next section is a tired recounting of the "Archaeoraptor" story, which Lingham-Soliar should actually be happy about.  Nature and Science both rejected manuscripts of the would-be official "Archaeoraptor" description, and the name and chimaerical misinterpretation only made it into the popular press.  He writes "Archaeoraptor" "has joined the ranks
of paleontological folklore notoriety on a par with Piltdown man", but Eoanthropus (Piltdown man) was accepted by some of the literature for years.  Lingham-Soliar further simply believes Olson's statements that Sloan "decided first, that it was appropriate for a journalist to differentiate a taxon new to science and second that evidence claiming to support the new taxon could be presented in a nonpeer reviewed magazine" and that "the name Archaeoraptor liaoningensis Sloan is now
available for purposes of zoological nomenclature."  Neither is true, as Creisler showed in 2001 on the DML.  If you're thinking citing a mailing list would be problematic, Lingham-Soliar is referencing in part a post by Olson on vrtpaleo here, so DML posts would be up for grabs too.  Next time check The Theropod Database, Theagarten!  I covered the whole story there, with references.  Yet due to his misplaced trust in Olson's accuracy, Lingham-Soliar says "one might think it would have spelt the end of Sloan’s days as an editor of NGM."  Ouch.


Apples to... um... microapples

Believe it or not, in this supposedly technical treatise of vertebrate integument, the penultimate section is "Education and Freedom in Apartheid South Africa."  That's what it's about too.  No paleontology or biology here.  Might I humbly suggest that any comparison between BAD vs. BAND and Apartheid is terribly disrespectful to the victims of the latter?

Theagarten ends the book with a chapter on freedom of press/speech and an appendix which lists the Universal Declaration of Human Rights.  If you want yet more irony, recall what I wrote above about the reviewers of Feduccia (2013).  Yet Lingham-Soliar has the gall to write "All the evidence points to the fact that in Birds are Dinosaurs only potentially favorable referees are chosen."  There's that pot and kettle again.

Actually, it turns out that's not quite how he ends this book.  You see, I didn't read ahead when writing this post.  I've been writing responses as I read the sections in Lingham-Soliar's book.  Remember above, when I guessed "what evil characters are left for Lingham-Soliar to equate BADists to?"  My first thought of a remaining evil was Islamic militants.  But that was too contemporary for me to feel comfortable joking about, so I went with Star Wars.  Yet Lingham-Soliar actually goes there with his Note in Press- "The tragic events in France concerning Charlie Hebdo and Press Freedom is a reminder of those who put their lives on the line for the rights we enjoy in democratic and secular societies - in the words of the children of Soweto [part of his Apartheid section],"the struggle continues." France’s stance against being blackmailed by totalitarian states and terrorists must be applauded lest we become like them."

Wow.

Conclusion

The sad part here is that Lingham-Soliar actually has a very good point about how crappy many peer reviews are.  You don't have to look further than this blog to find examples of miscoding, not coding, poor procedure, etc..  It's in desperate need of revision.  But this is hardly unique to BAD.  Just look at my recent posts- James and Pourtless' paper is sympathetic to BAND and has terrible flaws, Xu et al.'s 2015 defense of a dromaeosaurid species' validity was conceptually flawed and didn't involve birds, Carrano et al.'s ICZN petition seems shady but is about an actual basal theropod with no bearing on bird origins, Norman's 2014 paper with poor understanding and utilization of phylogenetic nomenclature was about ornithischians, etc..  It's not even unique to dinosaurs.  In a manuscript I wrote with David Marjanovic criticizing papers that don't code taxa for characters that are known for those taxa, I wrote about dinosaurian examples, and he wrote about basal tetrapod examples.  I would bet the issue pervades all of science.  Peer reviewers are unpaid, busy themselves, and often not specialists in what they're reviewing.  So they don't check some important things, often don't know what to check for, and are probably often too trusting the author's 'done the work.'  It's a problem.

But what an unhelpful way to present this problem!  It proposes a bias in the rigor of peer review, but any BAD supporter who has read a paper by a BANDit would laugh.  Even ignoring any methodological problems with BANDits, they simply don't know much about dinosaurs.  As a brief example, here are a couple statements made by Feduccia et al. (2005)- which had Lingham-Soliar as a coauthor.  "To illustrate the difficulty of defining the various dinosaur groups, Carroll (1988, p. 290) pointed out that "The 'carnosaur' families may each have evolved separately from different groups that have been classified as coelurosaurs."" "Like the term "thecodont," a collective term to describe Triassic basal archosaurs, coelurosaur and carnosaur describe, respectively, small and large theropod dinosaurs."  Did you realize, Theagarten, that these concepts are so obsolete that no one in the 90s, let alone the 2000s, would take them seriously?  Carroll's cited work is a general vertebrate paleontology textbook written 17(!) years earlier.  Who would ever think that's a valid source for contemporary taxonomy?!  Past the 80s, Coelurosauria has basically always been recognized as the clade of theropods closer to birds than to carnosaurs, including Compsognathus, Ornitholestes, ornithomimosaurs, oviraptorosaurs, dromaeosaurids and troodontids.  Even if you dispute birds belong there, the concept of the group has remained consistent.  The idea that carnosaurs are big theropods and coelurosaurs are small theropods is the kind of simplification of 1920-1970s phylogeny that you read in old childrens books.  So how did such a blatant misrepresentation make it through peer review into your paper?  And there are endless examples like this in BANDit works.  I could say that you and Feduccia are maliciously misrepresenting how well established the consensus of dinosaur phylogeny/taxonomy is.  The same paper also says "the question of whether birds are derived from dinosaurs depends on what one defines as dinosaur, or the Dinosauromorpha", even though the concept of Dinosauromorpha has never been controversial, nor is contingent on the definition of Dinosauria, which itself hasn't been controversial since dinosaur monophyly was established in the 70s.  Is this because the BANDits have peer reviewers that are in cahoots to let bad information through?  No.  It's just that peer reviews are sometimes poor and that you and Feduccia don't know much about dinosaurs.  "Basal dinosaur" Sinosauropteryx... "undisputed" Maryanska et al. 2002...

Next up is your mischaracterization of Prum's (2003) "not doing science" critique as being focused on cladistics.  Far from it.  Prum was criticizing Feduccia for- not explicitly proposing an alternative phylogenetic position for birds (e.g. why or why not are they in Avemetatarsalia, or Archosauria, or Archosauriformes); ignoring how character evidence works together to support or refute hypotheses, instead only taking single characters and disputing their homology, stating a single character is homoplasious, and ignoring the fact convergence can only be shown if the majority of characters support the real relationship; and most importantly for completely contradicting all of his previous work which disputed similarity between dromaeosaurids and birds without any sort of explanation for how he got things so wrong before, and why we should trust his methods now that they've been disproven.  Was your mischaracterization malicious or merely ignorant?

Your paper has continual complaints about free speech, free press, censorship!  But BANDits get tons of media presence.  If we look at everything since Gee's 1999 "censorship" mailing list post, Feduccia's gotten published on the topic of bird origins...
- a 2000 American Zoologist article. 
- a 2001 Journal of Ornithology article.
- a 2001 rebuttal in TREE.
- a 2002 Auk article. 
- a 2002 Naturwissenschaften article.
- a 2003 TREE letter.
- a 2003 Auk book review.
- a 2005 Journal of Morphology article.
- a 2007 Auk article.
- a 2007 Proceedings B article.
- a 2013 Auk article.
- a 2014 Journal of Ornithology Article.
And more, no doubt.  There is an article published almost every year.  He also wrote the book "Riddle of the Feathered Dragons: Hidden Birds of China" from New Yale University Press.  How is Feduccia being prevented from airing his views?  That's not an outlier either.  Martin got plenty of publications, as did Czerkas.  And just look at yourself, Theagarten.  You've had numerous articles published disputing BAD interpretations.  Some were rejected, but EVERYONE gets many manuscripts rejected.  And you got this entire present volume published!  You got to air your accusatory views of a conspiracy in science, via a scholarly publisher.  How is this being censored?  Freedom of speech means you're allowed to say what you want without being a criminal, freedom of press means you're allowed to publish what you want without being a criminal.  Neither means any particular platform, e.g. Nature, has to host your views.


You want to accuse BADists of fraud, but in this very volume you frame the Sinosauropteryx media rush in 1996 as if it preceded  its description ("Soon after [in 1996], without any scientific investigation, a pen-and-ink sketch of the sensational specimen appeared on the front page of The New York Times, as support for the theory.  In 1998, a description of Sinosauropteryx appeared in the journal Nature (Chen et al. 1998).").  You know Sinosauropteryx was officially described, as feathered, in 1996 by Ji and Ji, right?  You falsely state Maryanska et al. (2002) did not recover Caudipteryx as a theropod, and that its results are undisputed more than a decade later.  You conveniently cut out reference to pterosaurs in Xu et al.'s (2009) quote.  You repeat Olson's incorrect allegations "Archaeoraptor" was intended to be established by Sloan in National Geographic and that his article was valid under the ICZN.  Should I accuse you of fraud, or are you just very ignorant of dinosaur research, and never bothered to look up Sinosauropteryx's Chinese description, don't follow theropod phylogenetics papers, didn't bother researching "Archaeoraptor" past what Olson said, etc.?

Finally, it turns out I was wrong.  I wrote in reference to Olson that "I can't think of anyone in paleontology who writes less professional pieces and gets them published."  That was before I read the rest of this document.  Feduccia and Martin display gross ignorance of dinosaur knowledge, Olson has a sharp tongue and tedious fondness for religious analogies, but it's only you, Theagarten, who has compared BAD researchers to the Inquisition, Nazis, Apartheid, Stalin and Al-Qaeda.  That's beyond the pale and completely unprofessional.  Even if everything you wrote were true and there was some massive conspiracy to only allow BAD ideas into Nature/Science/PNAS and the popular media, that would be insignificant compared to the evil of those parties.  Shame on you.  And a hearty **** you on behalf of Xu, Prum and Zhao who you directly accuse of fraud.  Grow up and get serious.

Reference- Lingham-Soliar, 2015. The Vertebrate Integument Volume 2: Structure, Design and Function. Springer, Heidelberg New York Dordrecht London. 348 pp.

Saturday, January 24, 2015

BANDit cladogram evaluated - James and Pourtless 2009

Besides Hou et al. (1996), the only BANDit (Birds Are Not Dinosaurs) cladistic analysis has been that of James and Pourtless (2009).  Little has been said about this paper, with most of the commentary noting the backwards philosophy the authors had in coding characters with supposedly controversial homology as unknown instead of letting phylogenetic analysis establish homology.  Well I finally looked at it in a little detail, and found a far larger issue.

First, let's go over the basic tests and conclusions of James and Pourtless' study.  After making the almost correct observation that no published cladistic analysis has tested whether birds are dinosaurs (Senter 2004 did, but while the authors cite it they don't comment on it in that regard), James and Pourtless aim to correct this by constructing their own dataset with alternative proposed bird ancestors included.  With basal archosauriforms as the outgroup, the authors also include crocodylomorphs,  Longisquama, a few other pseudosuchians and numerous theropods.  Running their dataset of 242 characters and 79 taxa, they recover a large number of MPTs.  These are only ever illustrated as majority rule bootstrap trees after a posteriori pruning of taxa, and each alternative tree is basically a well supported Archosauria with a massive polytomy between crocodylomorphs, numerous theropod lineages and birds.  Longisquama weakly (55% bootstrap) groups with birds if 21 "controversially homologous" characters (which are only coded for non-dinosaurs) are excluded and non-bird maniraptorans are pruned away.  Statistical tests were done, seemingly showing the 'basal archosaur' (= Longisquama), crocodylomorph and dinosaur hypotheses of bird origins aren't any worse than each other.

Figure 12 of James and Pourtless (2009), showing majority rule bootstrap tree with numerous taxa including all maniraptorans pruned away a posteriori.  *Gasp* It looks like birds are closer to non-dinosaur Longisquama and that even crocs could be as close to birds as dinosaurs.  Were BANDits right all along? (Spoiler- NO)
How to explain this?  First, I should note that when you run their data, the resulting MPTs are pretty standard.  As shown in my typed cladogram below, while there are plenty of weird details going on in Theropoda, the basic structure of birds within Pennaraptora within Maniraptora within Coelurosauria within Theropoda within Saurischia within Archosauria is present.  The only odd relevant aspects are Effigia is an ornithomimosaur and Longisquama is deeply embedded in Pennaraptora.  Note there's no way of knowing Effigia groups with ornithomimosaurs by reading the paper, as its exact results aren't mentioned and it's always pruned out of the figured trees.  I find this suspicious.  In any case, Longisquama being sister to ornithines is discussed since this is the current favored alternative of BANDits.  Besides the paltry literature, the authors depended on photos at the KU for their coding of the genus, and present a cranial reconstruction.  This reconstruction looks as if it was done assuming a theropodan morphology for the taxon.  For example, there's a T-shaped structure at the anterodorsal corner of the orbit, interpreted as a lacrimal by the authors.  But it would also compare well to a prefrontal in a basal diapsid like Coelurosauravus, where the lacrimal is reduced.  Similarly, the strip under the supposed supraorbital ridge (yellow) would match the posterodorsal strip of the lacrimal/prefrontal in Coelurosauavus.  Or the wedge just behind this, while unidentified by the authors, would match the postfrontal of Coelurosauravus.  The supposed antorbital fossa (red) matches the external naris of Coelurosauravus well, and even the big posterodorsal hole ("?" in their figure) would match Coelurosauravus' if it's a supratemporal fenestra as identified by most previous authors.  This isn't to say that Longisquama is a close relative of Coelurosauravus (as Senter 2004 recovered), merely that the lens you view a fossil like Longisquama through based on photos can affect your identifications.  The controversial aspects of Longisquama's anatomy are similarly all coded as theropod-like- thecodont teeth, antorbital fenestra with maxillary fenestra, furcula, etc..

Longisquama skull (counterslab of PIN 2584/4) and interpretation of James and Pourtless (2009) on top.  Coelurosauravus skull reconstruction at bottom after Evans and Haubold (1987), modified so that the entire spiked temporal element is the squamosal after Schaumberg et al. (2007).  I see the supposed antorbital fossa (afo in red), but don't think its obviously a fossa, as opposed to a fenestra (e.g. the naris) or bone process itself.  Similarly, the entire ventral edge of the supposed antorbital fenestra (aof) looks like a crack to me, including the supposed dorsal process of the maxilla (dpm), supposedly there to support an interfenestral bar.  I don't see any posterior edge of the antorbital fenestra either, so that that whole area could be a solid maxilla.  The ventral process (vp) is apparent, but if anything seems separated from the nasal by a suture (shown by the green space).
As for the matrix, there are of course lots of miscodings (e.g. character 5 is for dermal armor, which is coded unknown for almost all theropods and Effigia, plus coded absent in Ceratosaurus, the one theropod that actually has it).  Some of the characters are formed terribly while others are partitioned in a way that weights them (e.g. each dentigerous element has its own character for tooth serrations, each a three state ordered character of the form '0- all serrated; 1- some serrated; 2- none serrated'; thus any taxon leading from serrated to unserrated teeth needs six steps to do so).  The 21 "controversially homologous" characters include every manual character due to the I-II-III vs. II-III-IV issue, though oddly these aren't even coded for dinosaurs with five digits like Herrerasaurus.  There's also a huge imbalance of taxa, with a whopping 45 non-avian theropods plus 16 birds, only 9 pseudosuchians, 3 non-archosaurs, Eoraptor, Marasuchus and Scleromochlus.  These are all issues, but not the most important one.

|--Proterosuchus
`--+--Euparkeria
...`--+--Erythrosuchus
......`--+--Pseudosuchia(Ornithosuchus,Postosuchus,Crocodylotarsi)
.........|--Scleromochlus
.........|--Marasuchus
.........`--+--Eoraptor
............`--+--Herrerasaurus
...............|--Carnosauria("Syntarsus",Dilopho,Cerato,Sinraptor,Allo,Tyranno)
...............`--+--Juravenator
..................|--Sinosauropteryx
..................|--Compsognathus+Huaxiagnathus
..................|--Guanlong+Dilong
..................|--Effigia+Ornithomimosauria
..................|--Microvenator
..................`--+--Coelurus
.....................|--Ornitholestes
.....................|--Falcarius
.....................`--+--Therizinosauroidea
........................`--+--Oviraptorosauria+Dromaeosauridae
...........................`--+--Troodontidae
..............................`--+--Pelecanimimus+Avimimus+Parvicursorinae
.................................`--+--Caudipteryx
....................................`--+--Longisquama
.......................................`--Ornithes


Actual strict consensus of James and Pourtless' data, simplified so that genera which form monophyletic clades are represented by their clade names.  Note no dinosaurs were coded for manual characters, Effigia is an ornithomimosaur, and Longisquama is deeply nested in Theropoda.

No, the biggest problem with James and Pourtless' analysis is that its matrix consists mostly of characters designed to diagnose coelurosaur clades (e.g. 96 from Clark et al.'s 2002 TWG analysis; 26 from Chiappe's 2002 bird analysis) plus those suggested by BANDits to group Longisquama and crocs with birds.  So what happens when you analyze Longisquama in a coelurosaur/bird matrix after reconstructing its skull with theropod presumptions and pretending no dinosaur preserves hands?  Given it doesn't preserve sacrum, pelvis, hindlimbs or tail, and that the vertebrae are basically uncodable, it emerges as a coelurosaur.  When chatting with Nick Gardner about this I joked "I bet if you coded e.g. Coelurosauravus' front half into the matrix, it would be coelurosaurian too."  So I coded Coelurosauravus' front half, the same parts preserved for Longisquama, and lo...

|--Proterosuchus
`--+--Euparkeria
...`--+--Erythrosuchus
......`--+--Pseudosuchia(Sclero,Ornithosu,Posto,Crocodylo)
.........`--+--Marasuchus
............`--+--Eoraptor
...............`--+--Herrerasaurus
..................`--+--Carnosauria("Syntarsus",Dilopho,Cerato,Sin,Allo,Tyranno)
.....................`--+--Compsognathidae
........................`--+--Guanlong+Dilong
...........................`--+--Microvenator
..............................`--+--Ornitholestes
.................................`--+--+--Coelurosauravus
....................................|..`--+--Effigia
....................................|.....`--Ornithomimo (inc. Pele,Longisquama)
....................................`--+--Coelurus
.......................................`--+--Falcarius
..........................................`--+--Therizinosauroidea
.............................................`--+--Ovirapt(inc.Caudi)+Dromaeo
................................................`--+--+--Troodontidae
...................................................|..`--Avimimus+Parvicursorinae
...................................................`--+--Sinovenator
......................................................`--Ornithes


I won my own bet.  Interestingly, this tree also has a lot more resolution and details which agree with the consensus (e.g. Pelecanimimus in Ornithomimosauria, Caudipteryx in Oviraptorosauria), and Longisquama is moved from Avialae to Ornithomimosauria.  Note Coelurosauravus is not thought by anyone to have anything to do with dinosaurs or birds, but still ends up as a maniraptoriform in James and Pourtless' matrix.  This fairly neatly proves my idea that Longisquama could be a far more basal diapsid and still emerge as a coelurosaur.  Note too that Longisquama is also an ornithomimosaur once the front half of Coelurosauravus is included, perhaps suggesting more signal between them than between Longisquama and birds.

So my conclusion is that very few characters were included that would support e.g. Tetanurae, Avepoda, Theropoda, Saurischia, Dinosauromorpha.  Just enough are included to get a basically consensus phylogeny even without manual characters, though not enough to properly place Effigia or the front half of Coelurosauravus.  The latter plus the theropodan assumptions in Longisquama's anatomy makes placement of thus genus particularly untrustworthy.  Certainly, not enough characters were included to survive bootstrap analysis, where random characters are deleted or repeated and the analysis is rerun.  It doesn't mean that "both the "early-archosaur" and "crocodylomorph" hypotheses are at least as well supported as the BMT [BAD] hypothesis", it means that James and Pourtless made a crappy analysis.

References-  Evans and Haubold, 1987. A review of the Upper Permian genera Coelurosauravus, Weigeltisaurus and Gracilisaurus (Reptilia: Diapsida). Zoological Journal of the Linnean Society. 90(3), 275-303.

Hou, Martin, Zhou and Feduccia, 1996. Early adaptive radiation of birds: Evidence from fossils from Northeastern China. Science. 274, 1164-1167.

Senter, 2004. Phylogeny of the Drepanosauridae (Reptilia: Diapsida). Journal of Systematic Palaeontology. 2, 257-268.

Schaumberg, Unwin and Brandt, 2007. New information on the anatomy of the Late Permian gliding reptile Coelurosauravus. Palaontologische Zeitschrift. 81(2), 160-173.

James and Pourtless, 2009. Cladistics and the origin of birds: A review and two new analyses. Ornithological Monographs. 66, 78 pp.

Thursday, January 15, 2015

Is Linheraptor a synonym of Tsaagan?

One of the first theropod papers of 2015 is Xu et al.'s defending Linheraptor as being distinct from Tsaagan, after they were synonymized by Senter (2011) and Turner et al. (2012).  I provisionally synonymized them on the Database because Turner's arguments seemed sound, though I haven't actually studied the problem myself.  One interesting aspect here is that this paper is basically a criticism of the details and methods of Turner et al., which was basically a published version of part of Turner's (2008) thesis.  Yet Norell is a coauthor, who was not only a coauthor of Turner et al., but also Turner's advisor for his thesis. 

Unfortunately, after reading Xu et al.'s arguments, my conclusion is that a LOT of work went into arguing a point no one disputes- the holotypes are not identical.  The authors make a huge point of the number of characters they found which differ between the holotypes- sixty-one.  Also that many of these are found in some dromaeosaurids, but not others.

Xu et al. correctly state "Proposals of synonymy are usually based on a judgment that putative diagnostic differences between the taxa in question are individual, ontogenetic, or sexually dimorphic variations rather than taxonomic ones, making one of the new taxa invalid. Taxonomically informative variations can sometimes be distinguished from intraspecific ones if a sample large enough to provide a basis for rigorous investigation of patterns of variation is available."  They then say "In the present case, Evans et al. (2013), Senter et al. (2012) and Turner et al. (2012) attributed the proposed diagnostic features distinguishing L. exquisitus from T. mangas to individual intraspecific variation, but avenues for testing this hypothesis are limited because each species is currently represented only by a single individual."

Well, no.  You don't need the exact species under consideration to study the extent of individual variation, you can use relatives.  Turner himself had the right idea to use the multiple known skulls of the closely related Velociraptor mongoliensis as the basis for judging differences between Tsaagan and Linheraptor.  Xu et al.'s response to this is rather comical- "a comprehensive taxonomic review [of Velociraptor] has yet to be published to determine how observed morphological variations relate to inter- or possibly intraspecific factors. This can be addressed by including all Velociraptor specimens in a specimen-level phylogenetic analysis, by using morphometric methods to quantify the variation present and by deepening our understanding of the biological significance of the variations observed. Until this work has been completed it is in our view that noticeable variations between L. exquisitus and T. mangas are grounds for taxonomic separation."

So until we perform these studies which have been published so far for zero (specimen-level phylogenetic analysis), ?five (using morphometric methods to quantify the variation present) and ?zero (deepening our understanding of the biological significance of the variations observed) Mesozoic theropods on Velociraptor, we can't treat multiple specimens of it as one taxon?  That's a bit of a far goalpost, don't you think?  The morphometric studies done on other theropods haven't even resolved their taxonomy (e.g. Allosaurus, Archaeopteryx), so I'm skeptical a similar study on Velociraptor would yield useful results either.  If we were to extend Xu et al.'s demands to other taxa, we'd basically have to say we know nothing yet of intraspecific variation in Mesozoic theropods.

Differences between the Tsaagan (first and third rows) and Linheraptor (second and fourth rows) holotypes. After Xu et al. (2015).
Xu et al. include extensive comparisons to other dromaeosaurid taxa for each difference noted.  They say "Taken together, the distributions of these features among dromaeosaurids not only demonstrate that L. exquisitus is a valid taxon distinct from T. mangas but also provide important information on dromaeosaurid interrelationships."  Yet in almost every case, there's only one skull known for each other taxon as well.  Thus if e.g. Tsaagan shares a character with the Dromaeosaurus holotype not found in Linheraptor, yes it could mean that's a phylogenetically useful character uniting the first two genera, but it could also mean it's an individually variable character that the one preserved specimen of Dromaeosaurus happens to share with the only specimen of Tsaagan and not the only specimen of Linheraptor.

You'd have to see how the character distribution worked out in total, as if e.g. Tsaagan and Dromaeosaurus shared a lot of derived characters not found in Linheraptor, that would be increasingly good evidence for a phylogenetic signal (or sexual dimorphism or ontogenetic change, I suppose) instead of coincidence.  Needless to say, Xu et al. do not do this and indeed find even more characters shared between Tsaagan and Linheraptor.

My basic response to Xu et al. is "Could I find 61 comparable differences between two skulls and necks of specimens near universally agreed to be Tyrannosaurus rex? Yes I could."  Indeed, in every example I've looked into, from Allosaurus to Microraptor to Archaeopteryx, every specimen differs in numerous other ways from every other.  Importantly, the differences never sort themselves into mutually exclusive pools, so that instead of Morph A having traits ABCD and Morph B having traits 1234, we instead get a specimen with 1B34, one with 123D, one with A2C4, one with 12C4, etc..  So either every known relatively complete and described Mesozoic theropod individual is its own species, or Mesozoic theropods had significant individual variation, just like living organisms.  I know which option I choose.

Variation in three Velociraptor mongoliensis skulls. Top- holotype AMNH 6515, middle IGM 100/25 (fighting specimen), bottom IGM 100/982.  Note the numerous differences (anterior premaxillary angle in holotype, maxillary fenestra shape in top two, anterior antorbital fenestra shape, ventral lacrimal process angle in 982, posterior jugal outline in holotype, etc.).  After Norell et al. (2006).


To finish up the criticisms, I find Xu et al.'s statement that "In some taxonomic studies, some taxonomic indicators have been based on superficial rather than detailed morphological comparisons" to be based on problematic examples.  They say "Saurornitholestes and Deinonychus have been regarded as junior synonyms of Velociraptor based on overall similarities (Paul, 1988), although both are now widely accepted as valid taxa (e.g., Turner et al., 2012)."  But Paul never advocated those as being the same species, merely different species in one genus.  That's a completely different issue, since genera are (more) subjective and Turner's analysis even finds these to be monophyletic to the exclusion of Dromaeosaurus, the only other decently described dromaeosaurid Paul knew of (Paul questioningly includes Adasaurus as a dromaeosaurine but notes "not enough has been published for us to be certain of anything").  If the authors wanted an example of bad Paul synonymization, they had the easy target of his 2010 synonymization of Tsaagan with Velociraptor, but not Deinonychus or Saurornitholestes.

"Similarly, the basal tyrannosauroid Guanlong has been suggested to be a sub-adult individual of the basal tetanuran Monolophosaurus based on the fact that the two taxa are both characterized by a cranial crest and several other superficially similar features (Carr, 2006), though this proposal has received little acceptance (Brusatte et al., 2010, 2012)."  Well, Carr's argument was only an SVP abstract, so it hasn't had a chance to be detailed yet.  Seems like a low blow.

"In addition to considering L. exquisitus to be a synonym of T. mangas, Turner et al. (2012) scored some character states for [Sinornithosaurus] millenii based on IVPP V 169041). However, V 16904 is not referable to S. millenii for two key reasons. First, V 16904 is inferred to be more ontogenetically advanced than the holotype specimen of S. millenii (V 12811) based on fusion features (the neurocentral sutures are fully closed in the preserved vertebrae of V 16904 but are evident in at least some vertebrae of V 12811, the proximal tarsals are fused to the tibia in V 16904 but remain separate in V 12811), but is significantly smaller than the latter specimen; and second, V 16904 differs from the holotype of S. millenii in some important morphological features, such as the fact that all of the teeth lack denticles in the former specimen but have denticles in the latter."  Here we have a brief example of the splitter mindset- differences equal taxonomic separation.  For just a few counter-examples- the Mei referred specimen has a tibiotarsus and fused presacral neurocentral sutures but is 80% the size of the holotype that doesn't; the Sinovenator paratype has a tibiotarsus but is 89% the size of the holotype that doesn't; Microraptor specimens can have serrations on both carinae (NGMC 00-12-A), only distal serrations (holotype) or no serrations (IVPP V13320).  Again, either we have a ton of unrecognized coexisting species, or species exhibit variation.

As far as good points go, besides more details and gorgeous photos of the amazingly complete Linheraptor skull (e.g. both scleral rings are articulated and in place), Xu et al. are right to criticize some sloppiness in Turner's work.  But they missed out on the least justified problem Turner had regarding Linheraptor- if he viewed it as synonymous with Tsaagan, WHY didn't he code the basically complete Linheraptor specimen for Tsaagan's OTU?!

In conclusion, Xu et al. state "... the contrast between our own perception of L. exquisitus as a valid taxon with many distinguishing features and the view that L. exquisitus is a junior synonym of T. mangas (Evans et al., 2013; Senter et al., 2012; Turner et al., 2012) presents an example of the principle that “similarity lies in the eyes of the beholder” (Clark, 1992)."  As seven of the eight authors of this paper were authors of the Linheraptor description, I might be forgiven for wondering if "similarity lies in the eyes of the namer" has some relevance as well. :)

References- Norell, Clark, Turner, Makovicky, Barsbold and Rowe, 2006. A new dromaeosaurid theropod from Ukhaa Tolgod (Omnogov, Mongolia). American Museum Novitates. 3545, 51 pp.

Turner, 2008. Phylogenetic relationships of paravian Theropods. PhD Thesis. Columbia University. 666 pp.

Senter, 2011. Using creation science to demonstrate evolution 2: Morphological continuity within Dinosauria. Journal of Evolutionary Biology. 24, 2197-2216.

Turner, Makovicky and Norell, 2012. A review of dromaeosaurid systematics and paravian phylogeny. Bulletin of the American Museum of Natural History. 371, 1-206. 

Xu, Pittman, Sullivan, Choiniere, Tan, Clark, Norell and Wang, 2015. The taxonomic status of the Late Cretaceous dromaeosaurid Linheraptor exquisitus and its implications for dromaeosaurid systematics. Vertebrata PalAsiatica. 53(1), 29-62.

Saturday, January 10, 2015

Big "New Years" Theropod Database update

Happy only over a week from New Years everyone!  Time for a Theropod Database update.  Besides all of the new taxa, there's a huge revising of Morrison allosaurids and Baharija taxa (check out the tetanurine Bahariasaurus).  Enjoy all of the updates.

Thursday, January 8, 2015

"Madsenius" and "Wyomingraptor"

As part of the huge Allosaurus rehaul coming in my annual "New Years" (*cough* it's already January 8th *cough*) Database update, I looked over all proposed Morrison allosaurs.  Two of the most mysterious are the nomina nuda "Madsenius" and "Wyomingraptor", but I think I have them figured out.  Enjoy.

"Wyomingraptor"

Tithonian, Late Jurassic
Brushy Basin Member of the Morrison Formation, Wyoming, US
(Nail Quarry)
(TATE 542) (adult) tooth (36 mm) (Bakker, 1997)
(TATE 543) (adult) tooth (20 mm) (Bakker, 1997)
(TATE 544) (adult) tooth (9.9 mm) (Bakker, 1997)
(TATE 550) (juvenile) tooth (6.6 mm) (Bakker, 1997)
(TATE coll.; material of "Wyomingraptor") 138 juvenile to adult teeth, three adult individuals including distal caudal vertebrae, forelimb, pubes and ischia (Bakker, 1997)

Cast of "Wyomingraptor" forelimb (TATE coll.) (originally hosted on Tate Geological Museum website).
This name was published in the column 'Dr. Bob's Dinofacts' in response to a question from a reader (Anonymous, 1997). The author (possibly Bakker himself) suggested it for a Tate Geological Museum specimen currently labeled Allosaurus. From 1997 until 2006, the Tate Museum included a "Wyomingraptor" section in its exhibits page, stating Bakker has proposed that name for a new genus of allosaur found at Como Bluff including a photographed forelimb. In the PaleoWorld episode "Killer Raptors" (episode 7 of season 4) aired in 1997, Bakker claims the only theropod preserved in Nail Quarry is "Wyomingraptor" (though note this is untrue, as the "Brontoraptor" material was also found there). The material (three adults and numerous juvenile to adult teeth) was detailed in Bakker (1997) where he simply calls them Allosaurus. Hartman (DML, 2000) wrote that Bakker has been "attempting to erect a new genus of allosaur, which he dubs "Wyomingraptor." He has been using this name for some time, but recently has found a specimen he thinks is different enough from the type(s) to warrant generic distinction." Given Bakker's notoriety as a splitter, the Nail specimens are likely to just be Allosaurus fragilis in any case. The photographed forelimb is similar to A. fragilis USNM 4734 except for being more robust, at least in metacarpal I, phalanx II-1 and II-2. Indeed, the robust first metacarpal is similar Torvosaurus, though the elongate phalanx I-1, radius and ulna are not. The forelimb is stated to be a cast, so it's not certain how much is based on real Nail fossils. It's possible some elements were scaled incorrectly from other specimens or are complete fabrications. It's also possible some material such as metacarpal I actually comes from the "Brontoraptor" individuals and that the forelimb is a chimaera. Further evaluation awaits description of the Nail material, which has yet to be distinguished from Saurophaganax either.

"Madsenius"

Tithonian, Late Jurassic
Brushy Basin Member of the Morrison Formation, Utah, US
(Cleveland-Lloyd quarry)
(DINO 2560, = UUVP 6000; probable intended holotype of "Madsenius trux") (7.9 m, 1.32 tons) complete skull (845 mm), nearly complete skeleton (lacking first caudal vertebra, chevrons, forearms, several pedal phalanges) including femora (880, 850 mm), tibiae (730, 745 mm), astragalus and metatarsals III (375, 372 mm) (Madsen, 1976)

Figure from Bakker (2000), which I think demonstrates his concept of "Madsenius trux", represented by the lower 'creosaur' skull of DINO 2560 (= UUVP 6000).
This name was orginally reported in a children's book (Lambert, 1990) as "a proposed new allosaurid theropod to be formally named and described." Olshevsky (1991) listed it under Allosauridae as a taxon "to be described from the Morrison Formation by R. T. Bakker; based on distinctive skull material and other remains previously referred to Allosaurus and Creosaurus." Williams (online, 2004) mentioned the combination "Madsenius trux", leading Olshevsky (online, 2004) to say "trux" "was to have been Bakker's original type species epithet for the as-yet-unpublished genus Madsenius. According to him, it fits Madsen as appropriately as it fits Madsenius" [etymology- Latin trux means "fierce, rough, savage, wild"].

While nothing else unique has been written regarding "Madsenius", I believe clues in the literature point to its probable identity. Since at least 1988, Bakker has proposed two kinds of Morrison allosaur, the classic short-snouted fragilis vs. long-snouted 'atrox' dichotomy. Bakker (2000) cited the latter species as "The creosaur-type allosaurid (unfortunately, the type of Creosaurus MARSH is, by itself, indeterminate): Dinosaur National Monument skeleton University of Utah UUVP 6000 ..." as opposed to "True Allosaurus MARSH: specimens from the type locality of Allosaurus fragilis MARSH - the skeleton United States National Museum USNM 4734 ..." In that paper, he stated "These two types of skulls are easy to tell apart from the quadrate, lower temporal fenestra, and depth of the mandible; however, I find it impossible to separate the two taxa from isolated snout bones or post-crania." This matches the "distinctive skull material" noted by Olshevsky, and the 'long-snouted' skulls have been referred to both Allosaurus and Creosaurus by different workers, also matching Olshevsky's comment. Furthermore, UUVP 6000 (later recatalogued as DINO 2560) was the basis of Madsen's (1976) classic Allosaurus monograph and "Madsenius" clearly refers to Madsen. Putting everything together, I think it's apparent "Madsenius" was to be Bakker's name for creosaur-type allosaurs when he realized the Creosaurus holotype couldn't be assigned to either variety. UUVP 6000 was probably supposed to be the holotype.

If we accept this explanation, Bakker's characters supporting "Madsenius" can be evaluated. Bakker states the ventral quadrate angles posteriorly in DINO 2560, forming a deeply concave posterior edge to the element unlike A. fragilis AMNH 600. The posterior angle formed by the dorsal and ventral quadrate edges is 24 degrees in AMNH 600 compared to 30 degrees in the UUVP coll. quadrate illustrated by Madsen and 27 degrees in his cranial reconstruction of DINO 2560. Bakker's DINO 2560 illustration shows an unprecedented angle of 52 degrees. Angles in other specimens are 18 (AMNH 30798), about 44 (BYU 571/8901), 30 (DINO 11541), 43 (MOR 693), 15 (SMA 005/02) and 34 degrees (USNM 4734). For the laterotemporal fenestra, Bakker states the restriction caused by the ventral squamosal process is greater in A. fragilis AMNH 600 (least anteroposterior length of fenestra 15% of dorsoventral height) than DINO 2560 (26% in Madsen's reconstruction, 28% in Bakker's). Measurements in other specimens are about 25% (AMNH 666), 31% (AMNH 30798), < 24% (BYU 571/8901), 38% (DINO 11541), 20% (ML 415), 40% (MOR 693), 38% (SMA 005/02) and 16% (USNM 4734). Mandibular depth is 19% of length in Bakker's DINO 2560 (similar to 19% in Madsen's reconstruction) and 24% in his A. fragilis illustration, though the latter is a composite between AMNH 666 (which has only a partial surangular) and 5753 (which does not include mandibular elements). So even this minor 5% difference cannot be determined. Values in other specimens are  about 19% (AMNH 30798), about 21% (BYU 571/8901), 17% (DINO 11541), 19% (MOR 693) and 20% (SMA 005/02). The above comparison suggests mandibular depth is fairly constant in known allosaurids, though quadrate angling and laterotemporal fenestra proportions vary widely. Yet importantly, the latter conditions both exhibit intermediates instead of two distinct clusters, and do not covary- AMNH 30798 and SMA 00/02 have low quadrate angles but wide laterotemporal fenestrae, while USNM 4734 has a high angle but restricted fenestra. Note neither of these conditions vary with stratigraphy either, and indeed the A. fragilis types and DINO 2560 are both from the Brushy Basin Member. Nor does it vary geographically, with Wyoming specimens encompassing almost the entirity of the variation. Based on this study then, "Madsenius" can be considered a synonym of Allosaurus fragilis and another example of Bakker's notorious splitting.

References-  Madsen, 1976. Allosaurus fragilis: A revised osteology. Utah Geological and Mineral Survey Bulletin. 109, 1-163.

Lambert, 1990. The Dinosaur Data Book. New York, Avon Books. 320 pp.

Olshevsky, 1991. A revision of the parainfraclass Archosauria Cope, 1869, excluding the advanced Crocodylia. Mesozoic Meanderings. 2, 196 pp.

Anonymous, 1997. Dr. Bob's dinofacts. Tate Geological Times. 5(2), 3.

Bakker, 1997. Raptor family values: Allosaur parents brought great carcasses into their lair to feed their young. In Wolberg, Sump and Rosenberg (eds). Dinofest International, Proceedings of a Symposium, Academy of Natural Sciences. 51-63.

Bakker, 2000. Brontosaur killers: Late Jurassic allosaurids as sabre-tooth cat analogues. Gaia. 15, 145-158.

Hartman, DML 2000. http://dml.cmnh.org/2000Oct/msg00066.html

Olshevsky, 2004 online. https://groups.yahoo.com/neo/groups/paleo_bio_dinosaur_ontology/conversations/messages/6655

Williams, 2004 online. https://groups.yahoo.com/neo/groups/paleo_bio_dinosaur_ontology/conversations/messages/6646

Wednesday, December 31, 2014

Neotyping past a diagnostic syntype - Majungasaurus edition

One of my pet peeves is the recent trend to petition the ICZN to designate a more complete specimen the neotype of a taxon when the fragmentary holotype hasn't even been shown to be undiagnostic.  A recent example is Paul and Carpenter's (2010) Allosaurus petition when the holotype hasn't even been well described outside a thesis or ever compared to the other accepted allosaurid genus (Saurophaganax).  Generally thoughts about which specimens are diagnostic varies, so regardless of how much laziness is involved in these petitions, there's excusable subjectivity too.  But while researching Allosaurus' case for the big New Years Theropod Database update, I found a Majungasaurus petition I hadn't heard about, and it's a weird one.

The applicable ICZN Article is 75.5- "When an author considers that the taxonomic identity of a nominal species-group taxon cannot be determined from its existing name-bearing type (i.e. its name is a nomen dubium), and stability or universality are threatened thereby, the author may request the Commission to set aside under its plenary power [Art. 81] the existing name-bearing type and designate a neotype."

Most of the original syntypes of Megalosaurus crenatissimus- A. Fourth premaxillary tooth FSL 92.306b (left) and posterior dentary tooth FSL 92.306a (right) in lateral view. B. Pedal ungual FSL 92.290 in side view. C. Distal caudal vertebra FSL 92.289 in lateral view. D. sacral centrum FSL 92.343 in lateral view. Scale equals 10 mm for A, and 30 mm for B-D.  After Krause et al., 2007.
A brief history of Megalosaurus/Majungasaurus crenatissimus is as follows.  Deperet (1896) described crenatissimus based on five unassociated elements- two teeth, two partial vertebrae, and a partial pedal ungual.  Lavocat (1955) later described a dentary he referred to crenatissimus, based on dental similarity.  More complete skulls and skeletons were described in the 90s and 00s.  Krause et al. (2007) tried to make the dentary the type specimen, but this can't be done without an ICZN petition, as I said at the time.  So they did the right thing in a way, and petitioned the ICZN (Carrano et al., 2009).

Neotype of Majungasaurus crenatissimus, dentary MNHN.MAJ 1 in A. lateral, B. dorsal, and C. medial views.  Scale equals 30 mm. After Krause et al., 2007.
The problem here is that for Article 75.5 to work, the type must be a nomen dubium.  Carrano et al. state "As several authors have confirmed (Sampson et al., 1996, 1998; Krause et al., 2007), the original Depret type specimens are indeed indeterminate as to genus and species, although they can be identified as belonging to the family ABELISAURIDAE. Thus the taxonomic identity of the species Megalosaurus crenatissimus as a nominal species-group taxon cannot be determined from the existing name-bearing type materials."  Sampson et al. (1996) never says this, and indeed refers a premaxilla to crenatissimus based on similarity to Deperet's syntype teeth.  Sampson et al. (1998) did support this position (merely via the statement "none of the specimens appear to be diagnostic to the generic level" that was not supported by any data), which is why they called the new more complete specimens Majungatholus atopus, a name based on a skull roof described in the 70s.

Most importantly though, Krause et al. (2007) say the opposite of what Carrano et al. claim they did.  Krause et al. state "Furthermore, detailed examination of the teeth preserved in MNHN.MAJ 1 [the dentary] by Smith (this volume) reveals that they fall within the same size and shape parameters as the two isolated teeth (FSL 92.306a-b) described by Depéret (1896a, b), those preserved in the gnathic elements of adult individuals described by Sampson and Witmer (this volume; e.g., FMNH PR 2008, 2100; UA 8709, 8716, and 8717), and the thousands of isolated teeth recovered from the Maevarano Formation by Mahajanga Basin Project personnel and others. The teeth of the Malagasy abelisaurid most closely resemble those of AMNH 1753, 1955, and 1960 from the Late Cretaceous of India (referred to Indosuchus raptorius by Chatterjee, 1978) but, importantly, the Malagasy taxon possesses weakly developed interdenticular sulci whereas the Indian specimens lack them (Smith, this volume)."

If we go to Smith's paper in Sampson and Krause's edited volume, we read- "The morphology of FSL 92.306a is basically as Depéret (1896) described it (Krause et al., this volume:fig. 4A), except that the distal curvature profile is less strongly curved. Overall, the crown is very similar in morphology to the distal dentary teeth of Majungasaurus discovered subsequently (Fig. 21). The DFA classified FSL 92.306a as Majungasaurus (26.74 D2, p .001; Table 2), supporting the hypothesis that the tooth is morphologically congruent with dental material of this animal. I am thus confident in referring this crown to Majungasaurus."

So the authors of the petition claim their own work supports Deperet's syntypes as undiagnostic, but their own cited work actually says the reverse- that one of Deperet's teeth is identical to those in more complete specimens AND that these Malagasy teeth can be distinguished from the most similar taxon.  Now we can argue about whether the tooth actually is diagnostic, but I think the more important issue here is that Carrano et al. seem to have misrepresented the conclusions of their own work as evidence in their petition.  Even if they changed their minds between 2007 and 2009, it would still be wrong to cite their older work for supporting a position it didn't.  So of course given the lack of Comments, the Commission would assume Carrano et al. are citing their own work correctly and pass the motion, as they think the work has verified Deperet's syntypes are undiagnostic, thus fulfilling Article 75.5.  And that's what they did, declaring the dentary to be the neotype in 2011.  But if they knew the cited work actually argued a syntype tooth was diagnostic, they might not have.  Though I can't recall a petition being rejected, so who knows.

It's history now, and the dentary will be the neotype unless another is petitioned into existence in the future, but what should have happened is for Krause et al. to make FSL 92.306a the lectotype of crenatissimus without the need of the ICZN, then if later studies found another taxon with identical teeth, the ICZN could be petitioned for a neotype.  Ah well, dentary it is.

References- Deperet, 1896. Note on the sauropod and theropod dinosaurs from the Upper Cretaceous of Madagascar. Bulletin de la Societe Geologique de France, 3rd series. 24, 176.

Lavocat, 1955. Sur une portion de mandibule de Théropode provenant du Crétacé supérieur de Madagascar. Bulletin du Muséum National d’Histoire Naturelle à Paris. 27, 256-259.

Sampson, Krause, Dodson and Forster, 1996. The premaxilla of Majungasaurus (Dinosauria: Theropoda) with implications for Gondwanan Paleobiography. Journal of Vertebrate Paleontology. 16(4), 601-605.

Sampson, Witmer, Forster, Krause, O'Connor, Dodson and Ravoavy, 1998. Predatory dinosaur remains from Madagascar: Implications for the Cretaceous biogeography of Gondwana. Science, 280, 1048-1051.

Krause, Sampson, Carrano and O'Connor, 2007. Overview of the history of discovery, taxonomy, phylogeny, and biogeography of Majungasaurus crenatissumus (Theropoda: Abelisauridae) form the Late Cretaceous of Madagascar. In Sampson and Krause (eds.). Majungasaurus crenatissimus (Theropoda: Abelisauridae) from the Late Cretaceous of Madagascar. SVP Memoir 8, 1-20.

Smith, 2007. Dental morphology and variation in Majungasaurus crenatissimus (Theropoda: Abelisauridae) from the Late Cretaceous of Madagascar. In Sampson and Krause (eds.). Majungasaurus crenatissimus (Theropoda: Abelisauridae) from the Late Cretaceous of Madagascar. SVP Memoir 8, 103-126.

Carrano, Krause, O'Connor and Sampson, 2009. Case 3487 Megalosaurus crenatissimus Depéret, 1896 (currently Majungasaurus crenatissimus; Dinosauria, Theropoda): Proposed replacement of the holotype by a neotype. Bulletin of Zoological Nomenclature. 66(3), 261-264.

Paul and Carpenter, 2010. Allosaurus Marsh, 1877 (Dinosauria, Theropoda): Proposed conservation of usage by designation of a neotype for its type species Allosaurus fragilis Marsh, 1877. Bulletin of Zoological Nomenclature. 67(1), 53-56.

ICZN, 2011. Opinion 2269 (Case 3487) Megalosaurus crenatissimus Depéret, 1896 (currently Majungasaurus crenatissimus; Dinosauria, Theropoda): Designation of a neotype. Bulletin of Zoological Nomenclature. 68(1), 89-90.