Sunday, May 27, 2012

The Yurgovuchia analysis isn't all it's cracked up to be

When I first saw Senter et al.'s 2012 analysis for the Yurgovuchia paper, I was excited.  Senter (2007) did a better job coding than the versions of the TWG analysis leading up to it, and a better job at defining characters to be non-composite.  Senter's also gradually increased his taxonomic scope to impressive levels.  But now that I'm integrating the Yurgovuchia matrix data into the Lori matrix, things aren't as great as they seem.

First, that taxonomic scope.  Eotyrannus and microraptorian NGMC 91 are missing without explanation.  Similicaudipteryx isn't there from the Xiaotingia analysis.  Chirostenotes not only lacks Caenagnathus data (Caenagnathus was its own OTU in Senter, 2007 but was deleted from his 2010 paper to decrease computational time, something that might have been useful then since that paper was not primarily a phylogenetic analysis, but which is inexcusable now), but it also lacks data from ROM 43250, the holotype of Epichirostenotes.  Even though I don't think Epichirostenotes can be distinguished taxonomically from Chirostenotes, that would be fine if he made an OTU for Epichirostenotes too.  But no, he didn't.  So we're left with a matrix with no cranial, mandibular, presacral, caudal or pubic data for caenagnathids.  Is it any wonder they're deeply nested within oviraptorids?  For Archaeopteryx, starting in the 2010 paper Senter included "data only from the Thermopolis, Berlin, and Munich specimens. New observations (Mayr et al., 2007) have cast doubt on the conspecificity of the London specimen with those three specimens, so data that came only from the London specimen were deleted from the OTU."  But the holotype is the London specimen!  Thus Senter's OTU does not include the only specimen which is definitely Archaeopteryx.  It's also the only specimen to preserve a lot of braincase data.  Again, he didn't make a separate London OTU, so the data just isn't used.  In Dromaeosauridae, since Senter breaks down Microraptor into the holotype, the CAGS specimens described by Hwang et al. (2002), M. gui and Cryptovolans, we miss out on most cranial data from specimens with complete skulls like IVPP V13475.  He also stopped including Atrociraptor and Saurornitholestes, and deleted the data from the referred Utahraptor specimens.

Perhaps worse are the characters and coding though.  Surprisingly, this is actually coded worse than his 2007 and 2010 versions, with all members of a clade often coded identically regardless of actual variation. As an example, all oviraptorosaurs and paravians are coded as lacking prefrontals. So he recoded Deinonychus incorrectly, and left Sinornithosaurus suspiciously unknown. Or the next character, postorbital bar absent, is incorrectly recoded to give Shuvuuia a complete postorbital bar and leave Avimimus unknown.  Senter also disregards the rule of cladistic analyses to let the tree decide homoplasy.  Since 2007, he's had a pet hypothesis ornithomimosaurs lack promaxillary fenestrae and that the fenestrae below their maxillary fenestrae were not homologous.  This was somewhat defensable in 2007 since other tetanurines have fenestrae arranged horizontally instead of vertically.  But now that Tahara and Larsson (2011) found Dromiceiomimus' lower fenestra communicates with its promaxillary recess, things are unambiguous.  It IS a promaxillary fenestra, even if it was convergently evolved.  The Yurgovuchia paper notes this and addresses it as follows-

"However, the absence of that opening in basal ornithomimosaurs suggests that its appearance in advanced ornithomimosaurs is neomorphic. Therefore, the phylogenetic data matrix used here does not recognize the presence of the promaxillary fenestra in Ornithomimus and other advanced ornithomimosaurs."

But... but... by that reasoning, we might as well just code Avimimus, ornithomimids and derived troodontids as lacking an arctometatarsus, since its absence in basal relatives of those groups show it developed convergently with tyrannosaurids.  Ditto for any character with homoplasy.  By coding this way you completely destroy the point of using PAUP in the first place.  I wonder if this is also the reason for the miscodings alluded to above.  Is Shuvuuia coded as having a complete postorbital bar because it's convergent with the incomplete bar of Aves?  I certainly hope this wasn't Senter's reasoning.

Characters themselves are often "redefined" to be worse.  The 'depth of the jugal beneath the orbit' character has gotten another state for when it tapers anteriorly, but that should be a whole new character.  The character coding for the cross section of the posterior jugal process has been redefined to code for its length and depth, but those aren't the same as cross section AND are independent of each other.  Or take this hilarious example-

"External naris an elongate oblong, with long axis diagonal in lateral view (0) or an elongate oblong with long axis subhorizontal (1) or a short oblong, with length not much greater than height, with long axis subhorizontal (2) [3].  This character replaces a previous one: “Internarial bar rounded (0) or flat (1) [5].” The internarial bar appears flat when the long axis of the external naris is subhorizontal."

Er... the flat internarial bar character refers to its cross section, not its dorsal convexity in lateral view.  A lot of characters from previous TWG analyses are now excluded without comment, so I have to retract my statement on the DML that this analysis is definitely better than prior TWG analyses, because now we have the complication that it's missing some characters.

It goes without saying that no characters are ordered and no codings are polymorphic.

All of this is such a shame, because Senter's 2007 work was such an improvement on other analyses up till that point, and he's been quite a help to me personally over the years.  I'm afraid I can't recommend the Yurgovuchia analysis for those wishing to know coelurosaur phylogeny, and hope that Senter's next version fixes these problems.

References- Senter, 2007. A new look at the phylogeny of Coelurosauria (Dinosauria: Theropoda). Journal of Systematic Palaeontology. 5(4), 429-463.

Senter, 2010. Using creation science to demonstrate evolution: application of a creationist method for visualizing gaps in the fossil record to a phylogenetic study of coelurosaurian dinosaurs. Journal of Evolutionary Biology. 23(8), 1732-1743.

Tahara and Larsson, 2011. Cranial pneumatic anatomy of Ornithomimus edmontonicus (Ornithomimidae: Theropoda). Journal of Vertebrate Paleontology. 31(1), 127143.

Senter, Kirkland, DeBlieux, Madsen and Toth, 2012. New dromaeosaurids (Dinosauria: Theropoda) from the Lower Cretaceous of Utah, and the evolution of the dromaeosaurid tail. PLoS ONE. 7(5), e36790. 

Thursday, May 17, 2012

Testing alternative tetanurine topologies in Carrano et al. 2012

In my last post, I described Carrano et al.'s superb new tetanurine analysis.  One of my biggest complaints was that very few alternative topologies were tested, so while the cladogram had plenty of novel and interesting ideas, the paper doesn't tell us just how well they're supported.  Note Carrano et al.'s reported "branch support" (Bremer?) is flawed because 1) fragmentary taxa lead to nodes collapsing easily even if the node is well supported for complete taxa in it, 2) distant taxa will often share characters (which show up as homoplasies or autapomorphies in the most parsimonious tree), so that moving a taxon across three nodes will not simply cost the number of Bremer support steps in each of those nodes added together, and 3) rearrangements change character state distributions, which will change support in adjacent nodes.

Luckily, another wonderful thing about Carrano et al.s' paper is that it comes with a fully constructed NEXUS file.  Not only that, the NEXUS includes character descriptions for NDE and even ran without error the first time.  Future authors please follow suit!  So, with this I was able to test alternbative topologies myself.  I must say I was surprised by some of the results.  What follows are the results, arranged in order of extra steps needed, with my subjective interpretation of liklihood...

Basically ambiguous

1 step- (stated in paper) Cryolophosaurus outside Neotheropoda sensu Bakker, as in Smith et al. (2007).  Though this isn't a good test without more basal taxa.

1 step- (stated in paper) Monolophosaurus as a basal megalosauroid, as in Benson (2010).

1 step- Xuanhanosaurus as a piatnitzkysaurid, as in Benson (2010).

1 step- (stated in paper) Poekilopleuron as a piatnitzkysaurid, allosaur or other kind of megalosaurid.

1 step- Eustreptospondylus sister to Magnosaurus.  This was proposed by Rauhut (2003), who made the former a species of that latter.  Magnosaurus moves out of Afrovenatorinae to join Eustreptospondylus easily.

1 step- Duriavenator as an afrovenatorine.

1 step- Monophyletic Sinraptor.  Though the characters traditionally used to combine them are cranial ones compared to Yangchuanosaurus, and their pelves are somewhat different, so how Siamotyrannus relates really isn't obvious.

1 step- (stated in paper) Chilantaisaurus as a carcharodontosaurid sensu stricto, not a neovenatorine.

2 steps- Megalosauroidea as carnosaurs, as Huene originally proposed, and Rauhut (2003) and Cau more recently find.  This rearranges the whole tree so that megalosauroid relationships are less resolved, and Piatnitzkysauridae and Lourinhanosaurus are successively closer to sinraptorids+allosaurs than megalosauroids are.  The fact the backbone of the tree crashes down so easily is disconcerting.

2 steps- Streptospondylus as an afrovenatorine (or really Afrovenator as a streptospondyline).

2 steps- (stated in paper) Lourinhanosaurus as a basal carnosaur (as in Holtz et al., 2004) or sister to Avetheropoda.

Quite likely to be true

3 steps- "Dilophosaurus" sinensis outside Neotheropoda sensu Bakker, as in Smith et al. (2007).  Cryolophosaurus follows.  As with Cryolophosaurus above, we'd really need more basal taxa included to test this.

3 steps- Piatnitzkysaurus outside Orionides, as in Rauhut (2003). Other piatnitzkysaurids follow.

3 steps- Xuanhanosaurus outside Orionides, as in Holtz et al. (2004).  It ends up by Monolophosaurus.

3 steps- Eustreptospondylus as an afrovenatorine (or really Afrovenator as a eustreptospondyline), as in Allain (2002).

3 steps- Afrovenator as a carnosaur, as in Rauhut (2003).  Even though I constrained Afrovenator to be closer to Allosaurus than to Eustreptospondylus and Torvosaurus as in Rauhut's tree, this makes all megalosauroids carnosaurs.  The carnosaur phylogeny is (Strepto(Megalosauridae((Afro+Leshan)(Spino(Piatnitzky(Lourinhano(Sinrap,Allosauria))))))).  So megalosauroids end up being paraphyletic to carnosaurs.

4 steps- Monolophosaurus as a carnosaur, as in Sereno et al. (1996).  This also makes megalosauroids carnosaurs, with the topology (Megalosauria(Mono(Piat(Lour(Sinrap+Allo))))).

4 steps- Poekilopleuron as a sinraptorid, after Benson et al. (2010).

5 steps- Monolophosaurus sister to Avetheropoda, as in Smith et al. (2007).  Piatnitzkysaurids are even closer to avetheropods in this phylogeny.

5 steps-  Torvosaurus and/or Eustreptospondylus being closer to spinosaurids than Afrovenator is, as in Sereno et al. (1994).

5 steps- Siamotyrannus as a coelurosaur, as in Buffetaut et al. (1996).  It's closer to other coelurosaurs than Lourinhanosaurus is.

5 steps- Sinraptorids outside Avetheropoda, as in Paul (1988).  Poekilopleuron becomes a coelurosaur.

Somewhat possible

6 steps- Piatnitzkysaurus as an afrovenatorine, as in Holtz et al. (2004).  Megalosauridae gets shuffled around a lot.

6 steps- Sinraptorids and carcharodontosaurids as sister taxa, exclusive of Allosaurus, as in Allain (2002).  This also makes megalosauroids carnosaurs, with the topology (Megalosauria(Poekilo,Lour(Saurophag(Allo(Sinrap,Carch))))).

7 steps- Eustreptospondylus  closer to spinosaurids than Torvosaurus or Afrovenator are, as in Smith et al. (2007).

7 steps- Chilantaisaurus as a spinosaurid, as in Rauhut (2003).

7 steps- Neovenator as an allosaurid, as in Hutt et al. (2001).  This also makes megalosauroids carnosaurs, with the topology (Megalosauria(Piat(Lour(Sinrap+Allo)))), and neovenatorines become allosaurids.


9 steps- Cryolophosaurus as a coelophysoid, though again we'd like more basal taxa.

10 steps- "Dilophosaurus" sinensis as a coelophysoid, and same as above.

11 steps- "Szechuanosaurus" zigongensis outside Orionides, as in Rauhut (2003).  It ends up by Monolophosaurus.  Odd that so many more basic rearrangements are more likely, as described above.

11 steps- Siamotyrannus and Fukuiraptor as sister taxa, as in Holtz et al. (2004).  The pair end up sister to Allosauria.

12 steps- Megaraptor as a carcharodontosaurine, as in Smith et al. (2007).

12 steps- Acrocanthosaurus as an allosaurid, as in Stovall and Langston (1950).  This really changes things.  It makes megalosauroids carnosaurs, with the topology (Megalosauria(Piat(Lour(Sinrap(Conca(Carch(Eocarch((Acro+Poek)(Neoven(Allo,Saurophag)))))))))).  Again, surprising.

15 steps- Megaraptor as a megalosauroid, as in Calvo et al. (2004).  Ends up sister to Megalosauria.

15 steps- Megaraptora as coelurosaurs, my pet hypothesis (but also partially Longrich 2001 and Novas et al. 2008).  Oh noes!  Even "worse", it's more like in this topology, "coelurosaurs become neovenatorids".  But as I said in my last post, the analysis needs more coelurosaurs.  Also remember the corrected TWG matrix needed 15 more steps to get a monophyletic Deinonychosauria, and that's standard now.  So any of the above hypotheses may end up being true.  Forcing megaraptorans to be coelurosaurs, but carnosaurs to be monophyletic otherwise needs 21 more steps, btw.  So it's on par with Bullatosauria.  Er.. *cough*

I guess the take home message is tetanurine basic relationships are highly uncertain.

Amazing new tetanurine paper

Carrano et al. just published an excellent new paper on tetanurine phylogeny, with perhaps the most new information on varied theropod taxa to be released in one place in the last decade.  Not only does it cover almost every basal tetanurine known at the time it was submitted (giving revised diagnoses for many taxa), it accomplishes several things that have been long in coming. Piatnitzkysauridae (including Marshosaurus and Condorraptor) is named, though it's found to be megalosauroidean here instead of outside Orionides.  What's Orionides?  The megalosauroid+avetheropod group we've been needing a name for since 2003 (that's right- Avetheropoda is used instead of Neotetanurae, another win for the paper).  I'm SO glad someone finally analyzed more metriacanthosaurids than Sinraptor dongi.  The authors first get my applause for ressurrecting Metriacanthosauridae since it was named earlier than Sinraptoridae.  My next applause is due to including Yangchuanosaurus, which has been well described since 1983 but almost always ignored since.  Not only that, they tested sinraptorid ingroup relationships by coding dongi and hepingensis separately.  We also get names for the megalosaurid+spinosaurid node (Megalosauria) and the allosaurid+carcharodontosaurid node (Allosauria). 

I'm glad the authors excluded Sigilmassasaurus from their Carcharodontosaurus OTU, though I would have been interested to see where the genus went when coded separately.  Carrano et al. recognize the referred Chuandongocoelurus specimen is Elaphrosaurus-like, which I first determined back in 2001.  Like me, they keep "yandonensis" and zigongensis separate.  Interestingly, both are close to Yangchuanosaurus, and indeed the authors use the combination Yangchuanosaurus zigongensis.  I finally learn why the "Dilophosaurus" sinensis skull I saw at the RTMP doesn't look like the illustration in Hu's paper- there are two sinensis specimens!  Young Dilophosaurus specimen TMM 43646 differs from the other specimens, so may be a new species.  We learn that new specimens confirm the snout elements are correctly referred to Marshosaurus. Turns out the type of Allosaurus? sibiricus is metatarsal II, not IV.  Erectopus is stated to be a non-carcharodontosaurid carnosaur, though this isn't tested.  Oddly though stated to be possibly metriacanthosaurid, it's placed above allosaurids in their phylogram.  Gasosaurus lacks a proximally extensive anterior trochanter and is being restudied (cited as Hone pers. comm.).  Carrano et al. retain "Poekilopleuron" schmidti's identification as a theropod humerus, but I disagreeUnquillosaurus' pubis is correctly flipped so that the supposed medial side is lateral, something which Headden and I found in 2002.  They think it's possibly carcharodontosaurid, which is interesting because back then I said it resembled Acrocanthosaurus most in anterior view. The pelvis of Kryptops is carcharodontosaurid, probably belonging to Eocarcharia.

Phylogeny from Carrano et al. (2012) taken from their figure 7A.  Numbers to the left of nodes are unambiguous character support and numbers to the right are branch support.

The phylogeny is interesting in several ways.  Since Carrano and Benson have done good cladistic work in the past, I'm betting all codable characters are coded and with few miscodings, unlike several other recent tetanurine phylogenies (Holtz et al. 2004 Smith et al. 2007 *cough cough*).   I will note all characters are unordered though, which should be fixed.  One of the coolest things is supplementary table 1, which shows what prior analyses have used each character and how they phrased it.

Cryolophosaurus and "Dilophosaurus" sinensis are not only not coelophysoids, they're basal tetanurines.  This has happened sometimes in my saurischian supermatrix as well, but I always figured it was due to not all characters being coded for all taxa.   

Eustreptospondylus is a basal megalosaurid, and Streptospondylus may be related, but can go anywhere in Megalosauria outside Baryonychinae+Spinosaurinae and Megalosaurinae+Afrovenatorinae.  The latter clade is another new name, since it turns out Dubreuillosaurus, Magnosaurus and Afrovenator aren't closely related to Streptospondylus or Eustreptospondylus (countering Rauhut's synonymization of the latter with Magnosaurus) after all.  Other afrovenatorines are Leshansaurus (which Cau correctly placed in Megalosauridae), Poekilopleuron and Piveteausaurus. Duriavenator and Torvosaurus are megalosaurines. 

Metriacanthosauridae turns out to be huge, with Yangchuanosaurus most basal, then a Metriacanthosaurinae structured as follows- (Shidaisaurus (Metriacanthosaurus, hepingensis (Sinraptor, Siamotyrannus).  So Sinraptor is not monophyletic.  Xuanhanosaurus is also a metriacanthosaurid, but not a member of the Metriacanthosaurus+Sinraptor clade.  Saurophaganax's allosaurid position is finally tested and confirmed. Concavenator is a basal carcharodontosaurid by EocarchariaLourinhanosaurus oddly emerges as a basal coelurosaur.

We get a "new" theropod taxon- "Saurocephalus" monasterii Muenster, 1836.  As they say, it's "based on a recurved, serrated tooth from the Oxfordian Korallenkalk of the Lindner Berge, Hanover, Germany. Windolf (1997) transferred the taxon to Megalosaurus but Muenster’s tooth cannot be identified past the level of Theropoda indet."

There are a few things I disagree with or that could use work though.  One is that additional basal and derived taxa are necessary to confirm some relationships.  Placing Cryolophosaurus and sinensis in Tetanurae might be caused by excluding Sarcosaurus, Dracovenator and/or Zupaysaurus, for instance.  And three coelurosaurs (Proceratosaurus, Compsognathus and Ornitholestes) are way too few to tell if megaraptorans are really carcharodontosaurids.  I'd want Zuolong, Coelurus and/or Tanycolagreus, Guanlong, Dilong, Stokesosaurus, Eotyrannus and Huaxiagnathus included too.  That might also reposition Lourinhanosaurus, as it is a basal carnosaur or sister to Avetheropoda with two more steps.

Also, alternative topologies are barely tested, except that making megalosauroids carnosaurs takes seven more steps (so not that unlikely, really) and several genera are stated to move to other places with one more step (Monolophosaurus a basal megalosauroid instead of non-orionidan; Poekilopleuron elsewhere in Megalosauroidea or in Allosauria; Cryolophosaurus outside Neotheropoda; etc.).  I'd like to know how many more steps are needed for alternatives- non-orionidan piatnitzkysaurids or Xuanhanosaurus, coelophysoid Cryolophosaurus and/or sinensis, non-neotheropod sinensis, carnosaurian Monolophosaurus, 'afrovenatorine' Eustreptospondylus and/or Streptospondylus, Eustreptospondylus sister to Magnosaurus, afrovenatorine Duriavenator, monophyletic Sinraptor, coelurosaurian Siamotyrannus or megaraptorans, allosaurids sister to metriacanthosaurids+carcharodontosaurids, allosaurid Acrocanthosaurus and/or Neovenator, allosaurians sister to coelurosaurs, etc..

Megalosauria and Allosauria are never explicitly defined.  Metriacanthosaurinae is listed as a new name, but Paul (1988) named it.  It's odd they missed that, since the family is correctly attributed to him.  I don't like their use of Averostra (for the cerato+tet node, when promaxillary fenestrae evolved before that), Neotheropoda (for the coelophysoid+ node instead of the cerato+tet node) or Allosauroidea (instead of Carnosauria).  Though Carrano et al. agree Suchomimus is probably Cristatusaurus, they incorrectly call the latter indeterminate.  Megalosaurus? "dapukaensis" and "tibetensis" are wrongly cited as Zhao 1986 instead of 1985.  I would have liked matrix entries for the more complete taxa not included, like Erectopus, Kaijiangosaurus, Kelmayisaurus and Cruxicheiros.  Finally, while the completeness of their taxon review is commendable, their analysis of tooth-based taxa is weak, since most are just bypassed as Theropoda indet. instead of examining dental features that vary between theropod clades.

These caveats aside, Carrano et al. (2012) is good enough that everyone should cut out the Basal Tetanurae chapter in their copy of The Dinosauria 2nd Ed. and put this there instead.

References- Muenster, 1836. Ueber die Korallenkalk das Linder Berges bei Hanover vorkommenden Ueberreste von Fischen, mit Beschreibung und Abbildung einiger neuen Arten. in Muenster and Wissman (eds.). Beitrage zur Petrefacten-Kunde. 7, 36-50.

Windolf, 1997. Theropoden-Zahne aus dem Oberen Jura Niedersachsens. in Sachs, Rauhut and Weigert (eds.). 1. Treffen der deutschsprachigen Palaoherpetologen, Terra Nostra, Extended Abstracts. Dusseldorf, Germany. 33-34.

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

Tuesday, May 15, 2012

New dromaeosaurid Yurgovuchia

So a new dromaeosaurid was described today by Senter et al. (2012), whose description is free at PLoS ONE.

Interesting that the authors sink Linheraptor into Tsaagan.  No evidence is given, and they commit a pet peeve of mine, in sinking a species into a genus, so Linheraptor exquisitus becomes Tsaagan sp..  Which not only is improper, as you can't just destroy species, but unecessary since Linheraptor only has one named species.

The phylogenetic analysis is Senter et al.'s (2010), with several taxa added.  One of these is Xiaotingia, which makes this a partial test to see if Archaeopteryx stays a deinonychosaur when paravians Senter didn't include are added.  The authors importantly add Sinusonasus (from Senter, 2010), Austroraptor, Mahakala, Shanag and Tianyuraptor, which leads to Archaeopteryx being an avialan as usual.  See what I meant about waiting for other analyses to confirm Xu et al.'s finding before accepting it?  Also contra Xu et al., Anchiornis and Xiaotingia aren't archaeopterygids and don't form a clade, with the former remaining a troodontid as in Senter (2010) and the latter being a basal dromaeosaurid.  Still not included are Balaur, Pedopenna, Jinfengopteryx, IGM 100/1128, Jixiangornis, Dalianraptor or Yandangornis among important basal paravians.  What will the Lori analysis say?  We'll have to see...

References- Senter, 2010. Using creation science to demonstrate evolution: application of a creationist method for visualizing gaps in the fossil record to a phylogenetic study of coelurosaurian dinosaurs. Journal of Evolutionary Biology. 23(8), 1732-1743.

Senter, Kirkland, Bird and Bartlett, 2010. A new troodontid theropod dinosaur from the Lower Cretaceous of Utah. PLoS ONE. 5(12), e14329.

Xu, You, Du and Han, 2011. An Archaeopteryx-like theropod from China and the origin of Avialae. Nature. 475, 465-470.

Senter, Kirkland, DeBlieux, Madsen and Toth, 2012. New dromaeosaurids (Dinosauria: Theropoda) from the Lower Cretaceous of Utah, and the evolution of the dromaeosaurid tail. PLoS ONE. 7(5), e36790.