Wednesday, May 16, 2018

Testing alternative stem bird topologies in Cau, 2018

In the comments to my last post describing Cau's (2018) new paper detailing the acquisition of characters on the line to Aves, reader AOF requested a post similar to what I did six years ago with the Carrano et al. (2012) tetanurine analysis.  Namely, testing alternative topologies using constraint analyses to see how many more steps they would require.  I think these kinds of things can be illuminating.  I've often said that we shouldn't think of a new cladogram as just 'the best new hypothesis', but rather check individual components of the tree to see how likely or unlikely they are to be correct.  Cau's 2018 matrix has a reduced taxon sample, which could easily change the number of steps compared to a complete sample.  On the other hand, I think Andrea tries to include all proposed characters in his MegaMatrix, which could make this a more honest measure of comparative topology length than most studies.  I'm not sure which variable overrides the other.  Then we have score correctness, which I've never checked in a Cau matrix, so I'm taking that at face value.

Andrea sent me his NEXUS file, but whereas the paper reports 3072 MPTs of 6790 steps, I found 10872 MPTs of that length.   Eoraptor and Buriolestes aren't always sauropodomorphs, Pisanosaurus is sometimes an ornithischian, Asilisaurus, Silesaurus and Sacisaurus are an unresolved trichotomy, Enantiornithes can be paraphyletic with Zhongjianornis among them, and Fake Ornithuromorpha is less resolved, as Patagopteryx and Apsaravis can be outside Hongshanornis+Aves, Archaeornithura can be a songlingornithid, etc..  I think Andrea's philosophy would be that these things vary with taxon inclusion, so aren't a definite part of his data.  The absence of any included spinosaurids, carcharodontosaurines, parvicursorines or Avimimus unfortunately makes some weird 80s and 90s hypotheses untestable.  After six more years of experience, I've added a new category "less likely" because I think that factors like scoring accuracy and taxon inclusion can have a larger influence.  As I said in the 2012 post, the corrected TWG matrix needed 15 more steps to get a monophyletic Deinonychosauria which is the most common outcome for TWG matrices today.  I'll say the Lori matrix recovers at least one hypothesis found to be "unlikely" here, so even that's not the kiss of death.

Basically ambiguous

0 steps- Maniraptoromorph Compsognathus.

0 steps- Megaraptoran Gualicho.

1 step- Ceratosaurus closer to abelisauroids than Elaphrosaurus.

1 step- Megalosauroid piatnitzkysaurids.

1 step- Coelurosaurian Zuolong.  Ends up as a basal maniraptoromorph between Coelurus and Ornitholestes.

1 step- Coelurid Aorun, as in its original description.  It moves to Maniraptoromorpha with Coelurus.

1 step- Coelurid Tanycolagreus, as in its original description.  Coelurus moves into Tyrannosauroidea with Tanycolagreus.

1 step- Compsognathid Sinosauropteryx and/or Sinocalliopteryx.

1 step- Tyrannosauroid Sinocalliopteryx or Coelurus.

1 step- Anchiornithid or archaeopterygid Xiaotingia.

1 step- Scansoriopterygids closer to Aves than Archaeopteryx.

1 step- Sapeornis closer to Aves than Confuciusornis.

1 step- Zhongjianornis sister to Pygostylia, as in its original description.

1 step- Ichthyornis closer to Aves than Hesperornis, the consensus until the recent cranial redescription of Ichthyornis.

2 steps- Theropodan Eodromaeus.

2 steps- Chilesaurus just outside Avepoda, which was my best guess back in 2015 considering the results of its original misscored matrices and my subjective feelings of what would plausibly reverse.

2 steps- Ceratosaurian Gualicho.  It has an uncertain placement within the clade, though is excluded from Abelisauria.

2 steps- Megaraptora as coelurosaurs just outside of Tyrannoraptora.  This was my result back in 2010 after adding Benson's Neovenatoridae data to my theropod supermatrix (since superseded by the Lori analysis).  Bicentenaria is at this level too, while Guanlong and Tanycolagreus become maniraptoromorphs.

2 steps- Maniraptoran Ornitholestes.

2 steps- Hongshanornithid Parahongshanornis, as in its original description.

Cast YPM 56693 of the Mononykus olecranus holotype pes in plantar view, courtesy of Senter.

Quite likely to be true

3 steps- Saurischia.  Herrerasaurs and Eodromaeus are theropods.  Note that while some of these constraints were tested in the Ornithoscelida paper, the studies differ in both taxonomic content and characters used, so that MegaMatrix results don't necessarily correlate with Ornithoscelida paper results and should not be seen as scooping anything we find. 

3 steps- Ornithischian Daemonosaurus. Chilesaurus is sister to Averostra.

3 steps- Theropodan Herrerasaurus/Tawa/Daemonosaurus.  These each take three steps more, and other herrerasaurs follow when one is constrained.

3 steps- Dilophosaurid Liliensternus, as in Paul (1988).

3 steps- Ceratosauria sensu lato, combining Neoceratosauria and Coelophysoidea.  Chilesaurus is the most basal theropod, Elaphrosaurus plus Limusaurus are the basal neoceratosaurs, and Gualicho is the most basal tetanurine.

3 steps- Eustreptospondylus and/or Megalosaurus outside Avetheropoda.  If one is constrained, the other follows.

3 steps- Megaraptoran Eotyrannus, as in Novas et al. (2013).

3 steps- Maniraptoran Coelurus.

3 steps- Troodontid Aurornis, Anchiornis and/or Xiaotingia.

3 steps- Chongmingia sister to Ornithothoraces, as in p2 of its original description. 

4 steps- Ornithischian silesaurids.  Lewisuchus is outside Dinosauria, Saurischia exists, and Asilisaurus and Pisanosaurus form a silesaur grade to either side of Silesauridae.

4 steps- Phytodinosauria.  Eoraptor and Buriolestes are sister to Dinosauria, while herrerasaurs and Eodromaeus are theropods.

4 steps- Ornithischian Chilesaurus.  Ornithoscelida occurs.

4 steps- Theropodan EoraptorBuriolestes, herrerasaurs and Eodromaeus also theropods.

4 steps- Abelisaurid Eoabelisaurus, as in its original description.

4 steps- Metriacanthosaurids outside Allosauria (Allosaurus plus Carcharodontosaurus).  Acrocanthosaurus joins Neovenator, so this also covers carcharodontosaurid Neovenator.

4 steps- Tyrannosauroid Compsognathus, as in Olshevsky (1991).  Surprised this one is so parsimonious.  A Compsognathidae with Aorun, Bicentenaria and Sinosauropteryx are the basalmost tyrannosauroids, with Sinocalliopteryx, Coeluridae including Tanycolagreus and Guanlong successively closer to core tyrannosauroids.

4 steps- Maniraptoromorph Tanycolagreus and/or Guanlong.

4 steps- Ornithomimosaurian Gualicho.  Tested due to Rauhut (2003) finding the very similar Deltadromeus in this position.  Note that ornithomimosaurian Elaphrosaurus is 36 steps longer, so the cases aren't that similar.

4 steps- Therizinosaurian Jianchangosaurus.  Still outside Falcarius plus Beipiaosaurus, and Cau said in a comment to the last post Jianchangosaurus was still an alvarezsauroid even after adding Erlikosaurus and Shuvuuia.  I'm not revealing much by saying the Lori analysis finds Jianchangosaurus to be a therizinosaur between Falcarius and Beipiaosaurus as in its original description.  Seems fishy...

4 steps- Archaeopterygid Jinfengopteryx, as in its original description.

4 steps- Archaeopterygid Anchiornis.

4 steps- Oviraptorosaurian scansoriopterygids.  They have an uncertain position within the clade, and therizinosaurs are still sister to oviraptorosaurs.

Allosaurus fragilis holotype tooth (YPM 1930) in ?lingual view.  Courtesy of the YPM.

5 steps- Dilophosaurus/Cryolophosaurus closer to Averostra than Coelophysis.

5 steps- Non-avetheropod Compsognathus, as in Novas (1992).  Very surprised this is so easy to get.  It's even more extreme than Novas' version, where Compsognathus was at least closer to avetheropods (his Tetanurae) than Piatnitzkysaurus and Eustreptospondylus, because in the constrained trees Carnosauria still has the same content as Cau's MPTs.  Sinosauropteryx joins it.

5 steps- Maniraptoromorph Eotyrannus.  I'm surprised by this, since I figured the result in other matrices was due to a lack of tyrannosauroid characters, which I think are all in the MegaMatrix.

5 steps- Non-tyrannoraptoran Coelurus, as in Paul (1988).

5 steps- Avemetatarsalian alvarezsauroids, as in Sereno (1999).  Jianchangosaurus is still a basal alvarezsauroid.

5 steps- Haplocheirus compsognathid/coelurid grade, as in Alifanov and Saveliev (2011).  Wasn't there some analysis that recovered it here too?  I just constrained it to be outside Maniraptoriformes (including alvarezsaurids).

5 steps- Non-pennaraptoran therizinosaurs, which fall out sister to Pennaraptora like the current consensus.

5 steps- Chongmingia a basal ornithurine (sensu Gauthier) outside Shenzhouraptor and Pygostylia, as in p1 of its original description.  The Lori analysis recovers it in a different position than  p1, p2 or Cau's analysis.

Less likely

6 steps- Non-eusaurischian saurischian EoraptorBuriolestes follows, but herrerasaurs and Eodromaeus are theropods.

6 steps- Theropodan Guaibasaurus.  Non-dinosaurian Eoraptor and Buriolestes, and this recovers Phytodinosauria.

6 steps- Eustreptospondylus closer to Neotetanurae than Megalosaurus, as in Holtz (2000).  I'm actually surprised this is so unlikely.

6 steps- Carnosaurian Sinosauropteryx, as in Longrich (2002).  Though Longrich's phylogeny was a bit different in having megalosaurids and metriacanthosaurids outside Avetheropoda.

6 steps- Ornithomimosaurian Haplocheirus, as in the Bayesian analyses of Cau and Lee and Worthy (2011).

6 steps- Arctometatarsalian therizinosaurs, as in Sereno (1999).

6 steps- Shenzhouraptor closer to Aves than Sapeornis.  

7 steps- Sauropodomorph Staurikosaurus but not Herrerasaurus, as in pachypodosaur Staurikosaurus of Kischlat (2000).

7 steps- Megalosauroid Monolophosaurus.  Megalosauroidea remains in Carnosauria.

7 steps- Coelurosaurian Neovenator.  Not sure if this has been suggested in print before, but I noticed quite a few coelurosaur-like characters when scoring Neovenator for the Lori matrix.  It forms the most basal coelurosaur clade with Aorun and Gualicho.

7 steps- Maniraptoran Compsognathus.

7 steps- Paravian alvarezsaurids, though note the lack of parvicursorines probably affects these numbers.  They (including Jianchangosaurus and Haplocheirus) emerge as the most basal paravians.

7 steps- Basal paravian Anchiornis, Aurornis, scansoriopterygids, Serikornis and/or Xiaotingia.

7 steps- Archaeopterygid Rahonavis, as in Forster et al. (1998).

7 steps- Fake-Ornithuromorphan Confuciusornis, as in Kurochkin (2006).  I really thought this would be more difficult to achieve than enantiornithine Confuciusornis (below).

Box of Archaeornithimimus asiaticus elements from AMNH 6576, with my identifications (dc- distal caudal, dt- distal tarsal, pedal except m 1-1 and m 3-2).  Is that a proximal metatarsal I in the upper left?  Courtesy of the AMNH.

8 steps- Non-eusaurischian saurischian HerrerasaurusEodromaeus and sometimes Eoraptor become herrerasaurs and Buriolestes is one node more stemward.

8 steps- Tetanurine Cryolophosaurus, as in Carrano et al. (2002).  Dilophosaurus stays in Coelophysoidea.

8 steps- Ceratosaurian megalosaurids, as in Britt (1991).  Chilesaurus falls out in a polytomy with megalosaurids and other ceratosaurs.

8 steps- Megalosauroid piatnitzkysaurids, with Megalosauroidea outside Avetheropoda.  Since this is the Carrano et al. consensus, I thought it would take less steps.

8 steps- Monolophosaurus sister to Avetheropoda, as in Smith et al. (2007).  Megalosaurids and piatnitzkysaurids fall out as more basal tetanurines.

8 steps- Arctometatarsalian tyrannosauroids, AKA Tyrannosaurus closer to Ornithomimus than to birds as in Holtz (1994).  I'm very surprised this is so parsimonious.  Coelurus and Bicentenaria join Tyrannosauroidea, but Gualicho leaves to be a ceratosaur.

8 steps- Maniraptoran tyrannosauroids, as in Sereno (1999).  This is accomplished more by moving ornithomimosaurs (including Gualicho) stemward to be the most basal coelurosaurs except for Zuolong

Somewhat possible

9 steps- Classic late 80s to early 90s topology where Staurikosaurus is sister to Herrerasaurus plus Dinosauria.  Tawa plus Daemonosaurus are closer to dinosaurs than both, while Sanjuansaurus follows Herrerasaurus.

9 steps- Piatnitzkysaurus outside Orionides, as in Rauhut (2003).  Condorraptor follows Piatnitzkysaurus, and megalosauroids fall outside Avetheropoda.  Surprised this is so high.

9 steps- Carnosaurian Tyrannosaurus, which brings megaraptorans, Gualicho and Bicentenaria to form the sister group of Allosauroidea (including Monolophosaurus).  I bet this is more parsimonious than most readers would assume given published topologies over the past two decades.

9 steps- Avialan Caudipteryx, as in its original description.  The rest of Oviraptorosauria follows it, though troodontids are still closer to Aves.

9 steps- Avialan Microraptor, as in Agnolin and Novas (2013).  Weirdly becomes the most basal troodontid, with that family closer to Aves than scansoriopterygids and anchiornithids.

9 steps- Avialan Unenlagia, as in its original description and Agnolin and Novas (2013).  Halszkaraptorines are unenlagiids, which are outside the Troodontidae plus Ornithes clade.

9 steps- Deinonychosauria.  Scansoriopterygids are oviraptorosaurs, while Jinfengopteryx and anchiornithids are avialans.

9 steps- Archaeopterygidae sister to Troodontidae.  Anchiornithines fall out as archaeopterygids. 

10 steps- Monolophosaurus outside Orionides, as in Carrano et al. (2002).  Megalosaurids and piatnitzkysaurids form successively closer outgroups to Avetheropoda.

10 steps- Fukuivenator excluded from Alvarezsauridae plus Therizinosauria plus Pennaraptora as in its original description.  It emerges as the sister to other maniraptorans.

10 steps- Eumaniraptora excluding troodontids as in Agnolin and Novas (2013).  Scansoriopterygids are oviraptorosaurs.

10 steps- Dromaeosaurid Xiaotingia, as in Senter et al. (2012).  Falls out in Microraptoria.

10 steps- Dromaeosaurid Balaur, as in its original description.  Falls out sister to Unenalagiinae plus Halszkaraptorinae.

11 steps- Tyrannosauroid Acrocanthosaurus, as in Bakker et al. (1988).  Tyrannosauroids become carnosaurs, with Sinraptor, Acrocanthosaurus and Bicentenaria successively closer to the 'core tyrannosauroid' clade of Eotyrannus, Gualicho, megaraptorans and TyrannosaurusTanycolagreus and Guanlong are now maniraptoromorphs.

11 steps- Alvarezsauroid Nqwebasaurus.  Alvarezsauroids emerge sister to ornithomimosaurs, with Haplocheirus and Jianchangosaurus forming a basal [edit] arctometatarsalian clade.

11 steps- Mahakala outside Unenlagiinae plus Eudromaeosauria (Halszkaraptor follows), as in most TWG matrices (though Senter et al. 2012 recovered it sister to unenlagiines like Cau).


12 steps- Alvarezsauroid Chilesaurus, where it emerged in the Lori matrix back in 2015.

12 steps- Ornithuran (sensu Gauthier) oviraptorosaurs, as in Maryanska et al. (2002).  Constraining Khaan to be closer to Meleagris than Archaeopteryx results in oviraptorosaurs (including scansoriopterygids) being the first clade to diverge from the avian stem after Archaeopteryx.

12 steps- Basal paravian Jinfengopteryx, as in Foth et al. (2014). 

13 steps- Coelophysoid Elaphrosaurus, as in Paul (1988).  Ceratosauria sensu lato forms, Elaphrosaurus is outside core coelophysoids and Limusaurus and sometimes Gualicho follow.

13 steps- Compsognathid Nqwebasaurus, as in Novas et al. (2013).  Compsognathids (including Aorun) become ornithomimosaurs.

13 steps- Dromaeosaurid Rahonavis.  Emerges in the unenalgiine plus halszkaraptorine clade.

14 steps- Neovenatorid megaraptorans, though this actually moves Neovenator out of Carnosauria into Tyrannosauroidea, so isn't that similar to Benson's topology.

14 steps- Enantiornithine Confuciusornis.

15 steps- Sauropodomorphan Chilesaurus, where it emerges as the most basal member.

15 steps- Carnosaurian Ceratosaurus, as in Currie (1995).  Other ceratosaurs follow.

15 steps- Alvarezsaurids closer to Aves than dromaeosaurids or troodontids.  Haplocheirus and Jianchangosaurus remain behind as ornithomimosaurs.  Note the lack of parvicursorines probably affects this number.

15 steps- Archaeopterygid Unenlagia, as in Forster et al. (1998).  Buitreraptor remains in Dromaeosauridae.

Cladogram of archosauromorphs after Kischlat (2000).  Note saurischian Marasuchus and sauropodomorph Staurikosaurus.

16 steps- Saurischian Marasuchus, as in Kischlat (2000).  Ornithischian silesaurs result, and Lewisuchus sister to Eodromaeus plus avepods.

16 steps- Non-avetheropod Sinraptor as in Longrich (2002).  Carnosauria becomes a grade, Acrocanthosaurus joins Neovenator, and Guanlong and Tanycolagreus become maniraptoromorphs. 

18 steps- Basal paravian Archaeopteryx.  Deinonychosauria forms, and anchiornithids and scansoriopterygids are further from Eumaniraptora.

19 steps- Coelophysoid ornithischians or ornithischians sister to Neotheropoda, as in Baron (2017).  Chilesaurus is the most basal theropod.

19 steps- Basal deinonychosaur Archaeopteryx, as in Xu et al. (2011).   Anchiornis, Aurornis and Serikornis are one node closer to Dromaeosauridae plus Troodontidae.

20 steps- Monolophosaurus sister to Guanlong, as in Carr (2006) who proposed they were an adult and juvenile of the same species.  The pairing resolves as sister to Tyrannoraptora.

21 steps- Carnosaurian megaraptorans.  Er, wow.  The Carrano et al. consensus is blown out of the water.  They don't even group with Neovenator, instead (including Gualicho and Bicentenaria) being in a trichotomy with megalosaurids and an Allosauroidea including piatnitzkysaurids.

I'm drawing the line here for plausibility

22 steps- Theropodan Marasuchus, as in Olshevsky (1991). Silesaurids, Eoraptor+Buriolestes and herrerasaurians are also theropods.

23 steps- Avialan therizinosaurs, as in Maryanska et al. (2002).  One of the odder parts of the classic 'oviraptorosaurs are birds' analysis is that they recovered therizinosaurs as closer to birds than dromaeosaurids or troodontids, which was only briefly mentioned in the text, while they removed Troodontidae and Therizinosauria from their figured cladogram.  Constraining this result leads to oviraptorosaurs being dragged along, and the whole of Caenagnathiformes is sister to taxa closer to Aves like scansoriopterygids, anchiornithids, Archaeopteryx, etc..

24 steps- 'Allosaur' Ornitholestes, as in Paul (1988).   Although Paul includes Ornitholestes in his Allosauridae, he views that family as paraphyletic to tyrannosaurids and his figure 10-1 shows Allosaurus closer to tyrannosaurids than Ornitholestes.  I thus only specified Ornitholestes to be closer to Allosaurus than megalosaurids, piatnitzkysaurids, Compsognathus and birds.  The resulting tree has ornitholestiids (including Zuolong) sister to core allosauroids including Monolophosaurus (which was considered closer to Allosaurus by Paul too- pg. 307), but tyrannosauroids and compsognathids are coelurosaurs.

24 steps- Ornithuran (sensu Gauthier) alvarezsaurids.  The most crownward alvarezsaurids were ever proposed to be, closer to Aves than Archaeopteryx.  They end up just crownward of anchiornithids, and weirdly form a clade there with scansoriopterygids and oviraptorosaurs.  As usual, the absence of parvicursorines probably affects the numbers.

24 steps- Archaeopterygid Protarchaeopteryx, as in Paul (2002).  Xiaotingia and scansoriopterygids are also closer to Archaeopteryx than Aves in these trees.

25 steps- Tyrannosauroids sister to Pennaraptora, as in Sereno (1999).  Like Sereno's trees, alvarezsauroids and therizinosaurs (Beipiaosaurus) form an expanded Arctometatarsalia, though now joined by Ornitholestes, Aorun and CompsognathusCoelurus becomes a tyrannosauroid.

26 steps- Ornithischian alvarezsaurids, as in Alifanov and Barsbold (2009).  Chilesaurus emerges as an alvarezsauroid.  Note the true number is probably much higher since neither included alvarezsaurid has cranial material.

30 steps- Ceratosaurian ornithomimosaurs, as in my half-joking post.  They don't even come out by Limusaurus or Elaphrosaurus, instead Ornithomimosauria (including Zuolong and Gualicho) are sister to other ceratosaurs.  How disappointing.

35 steps- Sauropodomorphan BeipiaosaurusFalcarius stays by oviraptorosaurs, while Beipiaosaurus ends up sister to Guaibasaurus.

35 steps- Phytodinosaurian BeipiaosaurusFalcarius stays by oviraptorosaurs, while Beipiaosaurus is sister to Chilesaurus as an ornithischian.

36 steps- Ornithomimosaurian ElaphrosaurusGualicho follows, and ornithomimosaurs move stemward to be sister to Tyrannoraptora.

36 steps- Megalosaurid abelisauroids, as in Paul (1988).  Megalosaurus moves to Abelisauria.

36 steps- Dromaeosaurid Ornitholestes, as in Makovicky (1995).  Fukuivenator emerges as the most basal dromaeosaurid, and dromaeosaurids are the most basal pennaraptorans with oviraptorosaurs, scansoriopterygids, anchiornithids and troodontids successively closer to birds.  This is equivalent to my old post about getting dromaeosaurid evolution backwards.

37 steps- Bullatosauria.  This actually moves ornithomimosaurs plus alvarezsauroids into Avialae to be sister to troodontids.  I had to specify both Zanabazar and Sinornithoides as troodontids, because specifying Zanabazar alone moves it into Ornithomimosauria without the other troodontids at a lower cost of 21 steps.

37 steps- Oviraptorosaurian Sapeornis, as in Paul (2010).  Oviraptorosaurs move to just closer to Aves than Archaeopteryx, with scansoriopterygids closer to core oviraptorosaurs than Sapeornis.

Phylogram from Huene (1923) showing his idea of what were carnosaurs vs. coelurosaurs.

39 steps- Huene's (1923) Carnosauria vs. Coelurosauria dichotomy.  For such an archaic concept, this works surprisingly well.  The trick is that Huene's and Cau's Carnosauria are basically the same.  By 1923, Huene had moved Ceratosaurus to Coelurosauria and placed tyrannosaurids and Elaphrosaurus there as well.  His carnosaurs are Megalosaurus, Eustreptospondylus and Allosaurus.  Even looking at the taxa not included in Cau's analysis, most shake out right- coelurosaurian Sarcosaurus, Halticosaurus, Procompsognathus, Podokesaurus, Betasuchus, Genyodectes, Proceratosaurus and Thecocoelurus vs. carnosaurian Magnosaurus, Poekilopleuron, Spinosaurus and Metriacanthosaurus.  There's a load of non-theropods in there and Huene got Sarcosaurus? andrewsi, Dryptosaurus and Valdoraptor wrong, but still impressive.  So this basically how many steps it takes to force carnosaurs stemward of Ceratosauria sensu lato.

43 steps- Sauriurine enantiornithines, as in Martin (1983).  Basically constraining enantiornithines (Bohaiornis and Cruralispennia here) as closer to Archaeopteryx than to Aves.  Rahonavis and Balaur emerge as sauriurines, but surprisingly scansoriopterygids, Sapeornis, jeholornithids, Confuciusornis, Zhongjianornis and Protopteryx remain as closer to Aves ('Ornithurae' in BANDit terminology).

57 steps- Sauriurine enantiornithines and Confuciusornis, as in Hou et al. (1995).  This is more in line with BANDit thought, as not only enantiornithines, Archaeopteryx and Confuciusornis fall out as sauriurines, but also Protopteryx, Sapeornis, jeholornithids (Martin, 2004),  Vorona (Kurochkin, 2006), Rahonavis and Xiaotingia (those two as archaeopterygids).  Unlike the plus 43 step tree, scansoriopterygids are outside Sauriurae plus 'Ornithurae' similar to Czerkas' hypothesis.

58 steps- Abelisaurid Piatnitzkysaurus, as in Currie and Zhao (1994).  Condorraptor follows, Eoabelisaurus also becomes an abelisaurid.

75 steps- 'Carnosauria' vs. 'Oviraptorosauria' of Russell and Dong (1994).  The Alxasaurus description is my most nostalgic technical paper, because it was the first I tracked down that wasn't in Science or Nature.  The authors presented a strange new analysis of theropods, where tetanurines fell into 'Carnosauria' (Baryonyx, Yangchuanosaurus, Allosaurus, dromaeosaurids and tyrannosaurids in successive order) and 'Oviraptorosauria' (ornithomimosaurs, therizinosauroids, oviraptorosaurs and troodontids in successive order).  Needless to say, it doesn't hold up, even when topology within each clade is allowed to vary like it is here.  Birds end up in 'Oviraptorosauria', so that would be Coelurosauria under current nomenclature.

78 steps- "Pneumatocrania", Holtz's (1994) concept combining oviraptorids, 'elmisaurids', tyrannosaurids, troodontids and ornithomimosaurs to the exclusion of dromaeosaurids and birds.  Cau's matrix doesn't result in anything close to Holtz's topology for this clade, with troodontids sister to oviraptorosaurs (including scansoriopterygids), and ornithomimosaurs sister to tyrannosauroids with alvarezsauroids and therizinosaurs in a trichotomy with Tyrann+Ornithom.  As with Bullatosauria, Sinornithoides had to be specified as well.

81 steps- Arctometatarsalia sensu Holtz (1994).  This is like "Pneumatocrania" except it excludes oviraptorids.  In Cau's analysis, this results in most oviraptorosaurs (including scansoriopterygids) being maniraptorans, but 'elmisaurid' Anzu being sister to Zanabazar deep within Troodontidae.  Again unlike Holtz's topology, tyrannosauroids, ornithomimosaurs, alvarezsauroids, therizinosaurians and Fukuivenator are successively closer to troodontids.

84 steps- Huene's Pachypodosauria, where his carnosaurs are closer to sauropodomorphs than his coelurosaurs.  Pachypodosauria ends up containing sauropodomorphs and ceratosaurs plus Cau's expanded Carnosauria, with every other theropod a coelurosaur.

[Edit] 100 steps- Conservative BANDit topology.  Here I specified taxa with stage III or IV feathers as birds, and retained Heterodontosaurus, Plateosaurus, Herrerasaurus, Coelophysis, Majungasaurus, Megalosaurus, Allosaurus and Sinosauropteryx as dinosaurs theropodsForcing birds outside Saurischia, Dinosauria, Dracohors, Dinosauriformes, etc. is difficult as it is actually easier to get Teleocrater up in basal Coelurosauria than to break up those clades.  But just breaking up Theropoda into these two clades takes 83 steps.  Tyrannosauroids, ornithomimosaurs, alvarezsauroids and therizinosaurs group with birds.  

140 steps- Coelophysoid birds, as in Raath (1985).  Other theropods known at the time were constrained as monophyletic relative to a Coelophysoidea containing rhodesiensis, Archaeopteryx, Hesperornis, Ichthyornis and MeleagrisBicentenaria, Fukuivenator, halszkaraptorids, scansoriopterygids and paraphyletic anchiornithids end up bridging the gap between coelophysoids and birds.

Paul's (1984) cladogram of predatory dinosaurs, after Raath (1990).  It differs from Paul's actual printed cladogram where compsognathids are better interpreted as in an unresolved trichotomy between 'allosaurs' and other coelurosaurs, ornithomimids merely extend with a '?' falling between tyrannosaurids and Archaeopteryx, and oviraptorids extend with a '?' that falls on the troodontid plus bird branch.  Note this differs from the PDW phylogeny in that megalosaurids are down by Procompsognathus and tyrannosaurids are sister to Protoavia.

191+ steps- Kurochkin's (2006) diphyletic birds.  BANDit Kurochkin had a weird hypothesis that Archaeopteryx and enantiornithines were theropods, but Confuciusornis, Patagopteryx, Ichthyornis, Hesperornis and of course Aves are birds.  These diverged at the typically vague BANDit level of Archosauromorpha or Archosauria, with no comment on where crocodylians, ornithischians, sauropodomorphs, etc. go.  It's again very hard to constrain in TNT since the program doesn't let the outgroup (Euparkeria) be specified, so if you constrain the next closest taxon (Teleocrater) to be outside of dinosauromorphs on one side and 'Ornithurae' on another, it's more parsimonious for TNT to force Teleocrater into Ornithothorces than to make that basal divergence.  But even a weak version of Kurochkin's hypothesis where Coelophysis and Allosaurus are still theropods and lead to enantiornithines but are more closely related to 'Ornithurae' than Teleocrater, Lagerpeton, Marasuchus, Heterodontosaurus and Plateosaurus results in 191 more steps.  Fukuivenator, halszkaraptorids, scansoriopterygids, Balaur and Zhongjianornis end up on the 'ornithurine' line.

Ignoring maniraptoromorphs (so as not to hint at Lori's topology) I'm most surprised by the robusticity of Cau's expanded Carnosauria, the rootward mobility of compsognathid-grade taxa, how unparsimonious carnosaurian megaraptorans are, and how parsimonious ceratosaurian megalosaurids and arctometatarsalian tyrannosaurids are.  I think Gualicho is the most interesting theropod right now in terms of just what it is, since its remains are decent but it can pretty easily move between ceratosaurs, tyrannosauroids and ornithomimosaurs.  Bicentenaria also finds its way into a suprisingly large number of hypotheses, so deserves a more detailed description.

References- Huene, 1923. Carnivorous Saurischia in Europe since the Triassic. Bulletin of the Geological Society of America. 34, 449-458.

Martin, 1983. The origin and early radiation of birds. in Brush and Clark, (eds.). Perspectives in Ornithology. 291-338.

Paul, 1984. The archosaurs: A phylogenetic study. In Reif and Westphal (eds.). Third Symposium on Mesozoic Terrestrial Ecosystems, Short Papers. 175-180.

Raath, 1985. The theropod Syntarsus and its bearing on the origin of birds. In Hecht, Ostrom, Viohl and Wellnhofer (eds.). The Beginnings of Birds. Freunde des Jura-Museums Eichstätt, Eichstätt. 219-227.

Bakker, Williams and Currie, 1988. Nanotyrannus, a new genus of pygmy tyrannosaur, from the latest Cretaceous of Montana. Hunteria. 1, 1-30.

Paul, 1988. Predatory Dinosaurs of the World. Simon & Schuster, New York. 464 pp.

Raath, 1990. Morphological variation in small theropods and its meaning in systematics: Evidence from Syntarsus rhodesiensis. In Carpenter and Currie (eds.). Dinosaur Systematics: Approaches and Perspectives. Cambridge University Press, Cambridge. 91-105.

Britt, 1991. Theropods of Dry Mesa Quarry (Morrison Formation, Late Jurassic), Colorado, with emphasis on the osteology of Torvosaurus tanneri. Brigham Young University Geology Studies. 37, 1-72.

Olshevsky, 1991. A Revision of the Parainfraclass Archosauria Cope, 1869, Excluding the Advanced Crocodylia. Mesozoic Meanderings. 2, 196 pp.

Novas, 1992. La evolucion de los dinosaurios carnivoros. In Sanz and Buscalioni (eds.). Los Dinosaurios y Su Entorno Biotico: Actas del Segundo Curso de Paleontologia in Cuenca. Instituto "Juan Valdez", Cuenca, Argentina. 126-163.

Currie and Zhao, 1994. A new carnosaur (Dinosauria, Theropoda) from the Jurassic of Xinjiang, People's Republic of China. Canadian Journal of Earth Sciences. 30(10), 2037-2081.

Holtz, 1994. The phylogenetic position of the Tyrannosauridae: Implications for theropod systematics. Journal of Paleontology. 68(5), 1100-1117.

Russell and Dong, 1994. The affinities of a new theropod from the Alxa Desert, Inner Mongolia, People’s Republic of China. Canadian Journal of Earth Sciences. 30(10), 2107-2127.

Currie, 1995. Phylogeny and systematics of theropods (Dinosauria). Journal of Vertebrate Paleontology. 15(3, 25A.

Hou, Zhou, Gu and Zhang, 1995. Confuciusornis sanctus, a new Late Jurassic sauriurine bird from China. Chinese Science Bulletin. 40(18), 1545-1551.

Forster, Sampson, Chiappe and Krause, 1998. The theropod ancestry of birds: New evidence from the Late Cretaceous of Madagascar. Science. 279, 1915-1919.

Sereno, 1999. The evolution of dinosaurs. Science. 284, 2137-2147.

Holtz, 2000. A new phylogeny of the carnivorous dinosaurs. GAIA. 15, 5-61.

Kischlat, 2000. Tecodoncios: A aurora dos Arcosaurios no Triassico. in Holz and De Rose (eds.). Paleontologia do Rio Grande do Sul. 273-316.

Longrich, 2002. Systematics of Sinosauropteryx. Journal of Vertebrate Paleontology. 22(3), 80A.

Maryanska, Osmolska and Wolsan, 2002. Avialan status for Oviraptorosauria. Acta Palaeontologica Polonica. 47(1), 97-116.

Paul, 2002. Dinosaurs of the Air. The Johns Hopkins University Press, Baltimore. 460 pp.

Rauhut, 2003. The interrelationships and evolution of basal theropod dinosaurs. Special Papers in Palaeontology. 69, 1-213.

Martin, 2004. A basal archosaurian origin for birds. Acta Zoologica Sinica. 50(6), 978-990.

Carr, 2006. Is Guanlong a tyrannosauroid or a subadult Monolophosaurus? Journal of Vertebrate Paleontology. 26(3), 48A.

Kurochkin, 2006. Parallel evolution of theropod dinosaurs and birds.  Entomological Review. 86 (Supp. 1),  S45-S58.

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.

Alifanov and Barsbold, 2009. Ceratonykus oculatus gen. et sp. nov., a new dinosaur (?Theropoda, Alvarezsauria) from the Late Cretaceous of Mongolia. Paleontological Journal. 43(1), 94-106.

Paul, 2010. The Princeton Field Guide to Dinosaurs. Princeton University Press. 320 pp.

Alifanov and Saveliev, 2011. Brain structure and neurobiology of alvarezsaurians (Dinosauria), exemplified by Ceratonykus oculatus (Parvicursoridae) from the Late Cretaceous of Mongolia. Paleontological Journal. 45(2), 183-190.

Lee and Worthy, 2011. Likelihood reinstates Archaeopteryx as a primitive bird. Biology Letters. 8(2),

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

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.

Agnolin and Novas, 2013. Avian ancestors: A review of the phylogenetic relationships of the theropods Unenlagiidae, Microraptoria, Anchiornis and Scansoriopterygidae. Springer Netherlands. 96 pp.

Novas, Agnolin, Ezcurra, Porfiri and Canale, 2013. Evolution of the carnivorous dinosaurs during the Cretaceous: The evidence from Patagonia. Cretaceous Research. 45, 174-215.

Foth, Tischlinger and Rauhut, 2014. New specimen of Archaeopteryx provides insights into the evolution of pennaceous feathers. Nature. 511, 79-82.

Baron, 2017. Pisanosaurus mertii and the Triassic ornithischian crisis: Could phylogeny offer a solution? Historical Biology. DOI: 10.1080/08912963.2017.1410705 

Cau, 2018. The assembly of the avian body plan: A 160-million-year long process. Bollettino della Società Paleontologica Italiana. 57(1), 1-25.

Tuesday, May 8, 2018

Cau's 2018 theropod tree

Hi all.  Work's been rapid on the Ornithoscelida project, which has improved due to David Marjanovic's request that I provide a citation for each character state we think was inaccurately coded by Baron et al..  It's time consuming, but has revealed several times where I was mistaken in my scoring, and forces you to really evaluate whether you think the evidence is good enough to truly call someone's character state choice wrong.  As tedious as it is, this should really become the standard for scoring justification in any analysis (and no, I didn't do that for the Lori analysis, though I have the preliminary steps for a far future offshoot of it).

Speaking of the Ornithoscelida paper, coauthor and fellow theropod blogger Andrea Cau just got a big new paper published using his MegaMatrix character list.  So congrats!  It's a summary of theropod evolution focusing on the path from Teleocrater to Meleagris, detailing the changes in each node from Pan-Aves (well, technically that's a stem) to Aves, and using that data to examine the trends and rates of change along that line.  We get two new clade names as well.  Dracohors is (Megalosaurus bucklandii < - Marasuchus lilloensis), so covers silesaurs and dinosaurs.  The use of a stem instead of a node like Silesaurus+Megalosaurus was wise considering some analyses (especially those recovering ornithischian silesaurids) recover Lewisuchus and such at an uncertain position relative to Silesauridae, but it's always closer to dinosaurs than Marasuchus.  But come on, 'Dracohors'?  Dragonian prostitutes?  Did no one learn from Ascendonanus?!  Oh, and the plural is 'dracohorsians', which sounds like a hybrid race from My Little Pony.  Maniraptoromorpha is (Vultur gryphus < - Tyrannosaurus rex) and is a sorely needed name that I could have used in the Lori paper, since we ended up limiting the taxon sample to maniraptoromorphs.  Recall that the results of TWG characters get worse as you get further from Norell et al.'s (2001) or Clarke's (2002) original scopes, and I didn't want to be Petersian and tackle e.g. the Megaraptora problem without the Carrano et al. (2012) or Novas et al. (2013) characters while using a batch of maniraptoromorph characters.  The name Maniraptoromorpha also fits the -morpha > -formes > basic clade pattern, which I like.

Sacrum of the maniraptoromorph Bambiraptor feinbergi (holotype AMNH 30556) in ventral view, anterior to left (courtesy of the AMNH).
Cau's analysis itself has positives and negatives.  What everyone knows about the MegaMatrix is that it's HUGE.  I'm talking 1781 characters.  That's more than all Mesozoic theropod analyses except the poorly coded Livezey and Zusi (2007), which used 2954 characters and focused on living birds though technically included 30 non-avian theropods too.  But if you look at the matrix, the size is a tiny bit misleading because Cau doesn't use any multistate characters.  So instead of a single character of "Premaxilla - number of teeth - three or less (0); four (1); five (2); six (3); seven or more (4)", he has-
"14): Premaxilla, fifth alveolus: absent (0); present (1). ...
1717): Premaxilla, sixth alveolus: absent (0); present (1).
1718): Premaxilla, seventh alveolus: absent (0); present (1).
1759): Premaxilla, fourth alveolus: absent (0); present (1)."
Or instead of "Sacral vertebrae - number - two or less (0); three (1); four (2); five (3); six (4); seven (5); eight (6); nine (7); ten (8); eleven or more (9)", he has-
"343): Third sacral vertebra: absent (0); present (1). ...
1707): Fourth sacral vertebra: absent (0); present (1).
1708): Fifth sacral vertebra: absent (0); present (1).
1709): Sixth sacral vertebra: absent (0); present (1).
1710): Seventh sacral vertebra: absent (0); present (1).
1711): Eight sacral vertebra: absent (0); present (1).
1712): Ninth sacral vertebra: absent (0); present (1).
1713): Tenth sacral vertebra: absent (0); present (1).
1714): Eleventh sacral vertebra: absent (0); present (1)."
Now this is largely fine, as both ordered and unordered multistate characters can generally be scored this way using certain procedures to avoid weighting.  Cau does it to make Bayesian analyses easier (pers. comm.).  But the Lori character list would be 25% longer (875 non-zero states in my 700 characters) using this method, for instance.  Of course the MegaMatrix was designed for a larger taxonomic scope, so will necessarily have more characters, those meant for carnosaurs, ceratosaurs, basal dinosauromorph phylogeny, etc..  Limiting the taxon sample to maniraptoromorphs finds 1170 parsimony-informative characters in Cau's dataset.  There are also 14 parsimony-uninformative characters in the Lori dataset, since some TWG characters were designed for tyrannosauroids or positioning outgroups like Dilophosaurus, Monolophosaurus, etc.. This would leave 861 Cau-style characters in the Lori analysis, so 74% as many as the MegaMatrix.  Not so bad...

It also doesn't use any polymorphic scoring, so there are no 0+1 scores in Cau's matrix.  I'm not sure if this matters analytically, since I assume he scores a polymorphic taxon unknown, and I don't know how TNT treats polymorphies when it's making trees.  Not that the standard method is without its problems, since TNT is stupider than PAUP in treating uncertainty polymorphies (could have either four or five teeth) the same as actual polymorphies (some have four teeth, others five).  He also doesn't differentiate inapplicable (-) and unknown (?) scorings, which is fine functionally as I believe TNT treats them the same, but this and the lack of polymorphic scores do make the matrix itself more opaque to users since a lot of question marks there aren't technically unknown.  For the Lori matrix, we're providing both a TNT and a NEXUS file, with the latter showing uncertainty polymorphies vs. actual polymorphies, plus when taxa can but shouldn't be scored due to ontogeny (e.g. a juvenile with unfused bones, when adults are unknown).

Cranial elements of the maniraptoromorph Microvenator celer (holotype AMNH 3041), with supposed right lacrimal of Makovicky and Sues in lateral view (upper left, anterior to right), dentary in dorsal view (lower right, anterior to top) and unidentified elements (scale bar in cm) (courtesy of the AMNH).
The taxon sample is interesting because it is very reduced compared to the Halszkaraptor analysis (Cau et al., 2017) that used the same character list (plus eight new characters; though among maniraptoromorphs, Jianianhualong and Chongmingia were added).  Alvarezsaurids are only represented by Alvarezsaurus and Patagonykus, caenagnathoids by Anzu and Khaan, therizinosaurs by Beipiaosaurus and Falcarius (and Jianchangosaurus... see below), etc..  Which still leaves it as the best large scale Mesozoic theropod analysis published, but without e.g. undisputed alvarezsaur skulls (since Haplocheirus finds itself elsewhere in some analyses), it's bound to get things wrong.  And it does differ from Cau et al.'s 2017 trees which focused on maniraptoromorphs.  Zuolong is outside Neotetanurae instead of a coelurosaur, Coelurus is a maniraptoromorph [see how useful this clade name is!] instead of a tyrannosauroid, Jianchangosaurus is an alvarezsaur(!), therizinosaurs are caenagnathiforms instead of outside Pennaraptora, Fukuivenator is a paravian instead of a therizinosaur, halszkaraptorines are unenlagiines, Xiaotingia is a scansoriopterygid instead of an anchiornithid, scansoriopterygids are further from Aves than Archaeopteryx, and Zhongjianornis is in Fake Ornithuromorpha instead of sister to Pygostylia.  Cau states on page 4 that taxon choice was based on a subjective (or at least not objectively justified) "balanced series of criteria" and I get that the point of the paper is trends leading to Aves, but having the quite complete Jianchangosaurus as the first branching of four alvarezsaurs, and eliminating a major step by placing therizinosaurs sister to oviraptorosaurs, seem like problems.  I'm sure the main trends are only very minorly affected, but still.  I think if I needed a reduced taxon sample (which was a real concern during part of the Lori process...) and was being subjective anyway, I would fiddle with the sample until I got a topology that matched the full analysis.  Or maybe Jianianhualong, Chongmingia and/or the added eight characters changed the topology, and this whole paragraph is misled.  Or maybe the reduced outgroup in the Halszkaraptor matrix affected the topology (only eight non-maniraptoromorphs compared to 58 here), which would be problematic for coelurosaur analyses since most have just been using 2-5 of the same outgroup taxa (Sinraptor dongi, Allosaurus, Monolophosaurus, Dilophosaurus, and/or Coelophysis...)..

Parsimony-based strict consensus of Cau (2018)with clade names along the bird lineage and Decay Indices > 1 (after Cau, 2018).
What of the phylogenetic results themselves?  Eodromaeus and herrerasaurs are in an unresolved polytomy with sauropodomorphs and ornithoscelidans, which matches their increasingly uncertain position now that people are using large taxon samples for more than Nesbitt-derived matrices and Sereno's non-testing 'analyses' from the 90s are fading into history.  Ornithoscelida itself is recovered, but with only Heterodontosaurus and Tianyulong representing Ornithischia, I don't give that much credit regardless of the character count.  Heterodontosaurids are very theropody in some ways few other ornithischians are and generally fall out as the first branching clade in analyses (now that Pisanosaurus is a silesaurid, which Cau also recovers) and ignoring Chilesaurus for the moment.  But I'm co-writing a whole paper on that, so let's move on to theropods.  Cryolophosaurus is a dilophosaurid coelophysoid, which is counter the recent consensus of finding it closer to averostrans or even a tetanurine itself.  As stated above, Zuolong is outside Neotetanurae, which is weird since it generally falls out as a basal coelurosaur.  Chilesaurus is also here, matching its authors' conclusion, but I think the poor ornithischian sample keeps this analysis from adequately dismissing an ornithischian identity.  But I'm co-writing a paper on that and etc. etc..  Back to theropods.  Cau recovers a Rauhut-like Carnosauria including megalosaurids, piatnitzkysaurids, Monolophosaurus and allosaurs.  Neovenator is sister to Allosaurus and Sinraptor sister to Acrocanthosaurus among the latter, which harkens back to late 90s phylogenies.  Megaraptorans (including Gualicho) are tyrannosauroids closer to Tyrannosaurus than Eotyrannus, matching Novas et al. (2013).  The tree is untraditional in placing compsognathid-grade taxa outside Tyrannoraptora, though Novas had that opinion back in the early 1990s.  As stated above, the maniraptoran section has the out of vogue caenagnathiform therizinosaurs and the very weird alvarezsauroid Jianchangosaurus, but those might be glitches due to the taxon sample.  Fukuivenator is sometimes a dromaeosaurid and sometimes the basalmost paravian, which its authors recovered with the addition of three steps.  Cau finds avialan troodontids, standard for his published analyses.  Like his Halszkaraptor version, Rahonavis is close to jeholornithids and Protopteryx can be outside Ornithothoraces (it always is in the 2017 trees).  The latter is funny because I had that idea way back in 2000 on the DML ("My analysis of 31 characters and 6 taxa resulted in a single most parsimonious teee (CI .81, HI .19, RI .78)" ... how quaint), so if it turns out to be true that would be something.  Finally, presumably due to excluding fragmentary taxa like Teviornis, the huge ornithuromorph polytomy of the 2017 paper is resolved and Patagopteryx falls out by Apsaravis, Ichthyornis and Hesperornis+Aves.  Wha?

Interestingly, Cau also performed a Bayesian analysis.  In these, herrerasaurs are sister to Dinosauria like Baron and Williams (2018), but Eodromaeus is a basal ornithoscelidan.  Allosauroid relationships now match the Carrano et al. consensus, and Zuolong is a basal coelurosaur but Chilesaurus follows it.  Gualicho is now closer to tyrannosaurids than to megaraptorans.  Jianchangosaurus is back to being a therizinosaur, but Ornitholestes and Haplocheirus are basal ornithomimosaurs.  Weird.  Therizinosaurs are no longer sister to oviraptorosaurs, and actually move down an extra node to be stemward of alvarezsaurids too.  Especially interesting is that scansoriopterygids move way down from being avialans to being basal oviraptorosaurs.  Are they the missing Jurassic oviraptorosaurs?  This lets Xiaotingia go back to Anchiornithidae.  Rahonavis is now sister to Jeholornithidae instead of a couple nodes stemward of it, and Sapeornis is a confuciusornithiform.  Protopteryx is always an enantiornithine (aw...), but Patagopteryx is still way crownward, though now Vorona joins it (basal fake ornithuromorph in the parsimony analysis).  Well, that does match their Late Cretaceous age at least.  Considering all of these changes, I like a few things better about the parsimony version and a few things better about the Bayesian version.

How does Cau's Maniraptoromorpha topology compare to Lori's?  Quite different on both a broad level and with regard to the detailed relationships within the clades, although there are a few things that aren't common but popped up in both.  I'm dying to say more, but that post has got to wait.  Congrats again to Andrea.

References- Norell, Clark and Makovicky, 2001. Phylogenetic relationships among coelurosaurian theropods. In Gauthier and Gall (eds.). New Perspectives on the Origin and Early Evolution of Birds: Proceedings of the International Symposium in Honor of John H. Ostrom. 49-67.

Clarke, 2002. The morphology and systematic position of Ichthyornis Marsh and the phylogenetic relationships of basal Ornithurae. PhD thesis, Yale University. 532 pp.

Livezey and Zusi, 2007. Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion. Zoological Journal of the Linnean Society. 149. 1-95.

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

Novas, Agnolin, Ezcurra, Porfiri and Canale, 2013. Evolution of the carnivorous dinosaurs during the Cretaceous: The evidence from Patagonia. Cretaceous Research. 45, 174-215.

Cau, Beyrand, Voeten, Fernandez, Tafforeau, Stein, Barsbold, Tsogtbaatar, Currie and Godefroit, 2017. Synchrotron scanning reveals amphibious ecomorphology in a new clade of bird-like dinosaurs. Nature. 552, 395-399.

Baron and Williams, 2018. A re-evaluation of the enigmatic dinosauriform Caseosaurus crosbyensis from the Late Triassic of Texas, USA and its implications for early dinosaur evolution. Acta Palaeontologica Polonica. 63(1), 129-145.

Cau, 2018. The assembly of the avian body plan: A 160-million-year long process. Bollettino della Società Paleontologica Italiana. 57(1), 1-25.

Saturday, April 28, 2018

Lori paper submitted

Hi all.  With that juicy tagline, I'd like to restart regular blog posts here.  It took almost seven years to complete after I joined the Lori team (5-13-2011), but we submitted the manuscript a couple weeks ago and now it's in review.  I'd love to say more, but it's probably more professional to hold back until publication.  But man, did I get some interesting results.

In theropod news, Wang et al. (2018) published a new specimen of Iteravis, and agree with me that the genus is synonymous with Gansus zheni, but missed the whole ZooBank issue that gives zheni precedence over huchzermeyeri.  Does zheni clade with Gansus in the Lori analysis?  You gotta wait to see, though it is somewhat surprisingly the best basal Passer < - Enantiornis clade analysis yet, as it incorporates all of the Clarke bird characters and every Mesozoic taxon known from more than one element (except Gallornis... *cough*).

Also, Elzanowski et al. (2018) did an amazing job redescribing the skull of Confuciusornis, interpreting the supposed maxillary fenestra as a nasolacrimal foramen ('fl' in figure below).  Mayr is a coauthor, and his expertise with extant birds and crushed Messel specimens clearly helped, as the cranial reconstruction makes so much sense when you compare other confuciusornithiform skulls.  It's probably the most realistic Mesozoic bird skull drawing I've seen.  One frustrating consequence of their description and 2017 paper on temporal fenestrae in modern birds is that fusion in the absence of developmental data makes it difficult to impossible to homologize features with ancestral theropod elements and processes.  So we can't really say anything about the quadratojugal in Confuciusornis for instance.  With things like this and the Rauhut et al. (2018) Archaeopteryx paper describing a prefrontal in that genus, I wonder how much 'standard knowledge' of anatomy in a given genus would be exposed as uncertain to false given enough scrutiny by other experts.

Cranial reconstruction of Confuciusornis sanctus in lateral view (A) with mandible in medial view (B) after Elzanowski et al. (2018).

Finally, a description of the Citipati Big Auntie specimen IGM 100/1004 was just published this week (Norell et al., 2018).  It's so similar in completeness and preservation to Big Mamma specimen IGM 100/978 that I thought the details on Conchoraptor and the Citipati holotype were most interesting, and am really looking forward to the AMNH papers on those specimens.  The Oviraptor info is also good to have in the literature, but isn't new to me since I saw it in 2009.  Well, the apparent baby oviraptorid hindlimb associated with the specimen is, but from my review of photos I took and those Senter took of a cast of the holotype before the manual elements were removed, I don't see where the juvenile tibia and metatarsals are in the holotype.

Dorsal vertebrae of Oviraptor philoceratops holotype AMNH 6517 (anterior to left) with proximal ribs, scapula in lower right.  Courtesy of the AMNH.

Let's try to make this blog a weekly thing again, if only in commentary.

References- Elzanowski and Mayr, 2017. Multiple origins of secondary temporal fenestrae and orbitozygomatic junctions in birds. Journal of Zoological Systematics and Evolutionary Research. 56(2), 248-269.

Elzanowski, Peters and Mayr, 2018. Cranial morphology of the Early Cretaceous bird Confuciusornis. Journal of Vertebrate Paleontology. e1439832.

Norell, Balanoff, Barta a nd Erickson, 2018. A second specimen of Citipati osmolskae associated with a nest of eggs from Ukhaa Tolgod, Omnogov Aimag, Mongolia. American Museum Novitates. 3899, 1-44.

Rauhut, Foth and Tischlinger, 2018. The oldest Archaeopteryx (Theropoda: Avialiae): A new specimen from the Kimmeridgian/Tithonian boundary of Schamhaupten, Bavaria. PeerJ. 6:e4191.

Wang, Huang, Hu, Liu, Peteya and Clarke, 2018. The earliest evidence for a supraorbital salt gland in dinosaurs in new Early Cretaceous ornithurines. Scientific Reports. 8:3969.

Monday, February 5, 2018

Is Eogranivora's pelvis misinterpreted?

We have another new Jehol bird, this one previously misidentified as Hongshanornis by Zheng et al. (2011).  Zheng et al. (2018) describe it as Eogranivora, and while it's one of those split through the slab specimens with almost no external detail, I do wonder about their pelvic interpretation.

The holotype preserves the pelvis in dorsolateral/ventrolateral perspective, with one lower pubic bone pair curving inward to touch at the tips, or nearly do so.  Zheng et al. think these are the pubes, which seems okay at first although they note "A dorsal or dorsomedially oriented bluntly triangular process is present one-third from the proximal end of the pubes."  I can't recall any examples of this in other Mesozoic birds.  Also, there's really nowhere for the ischia to go, with the posterior edge between the postacetabular process and supposed pubis being as well defined as most edges get in this fossil.  Plus the peduncles of the pubis-ilium junction would need to be unusually long.

Pelvis of Eogranivora edentulata holotype counterslab (STM 35-3) in dorsolateral view as drawn by Zheng et al. (2018) (left), interpreted by them (center left) and interpreted by myself (right).  Pelvis of Apsaravis ukhaana (IGM 100/1017) after Clarke and Norell (2002) (center right).  Ilium is blue, pubis is red, ischium is green and mid-dorsal ischial process is yellow [edited with new label for far right].

But if these long bones were ischia instead, that clean posterior edge makes sense.  Also, Mesozoic ornithuromorph ischia almost always have a mid-dorsal process that would match that in Eogranivora.  Finally, the area where the pubis would attach in this case is fragmented and unpreserved ventrally.  I've compared it to Apsaravis above, which has a very subtle mid-dorsal process compared to most.  Apsaravis also lacks pedal digit I as in Eogranivora but no other Mesozoic birds, so I wonder if that, the short caudal transverse processes, fused dentary symphysis (I'm skeptical of this in Apsaravis though) and the slender and elongate ischia indicate a close relationship.

References- Clarke and Norell, 2002. The morphology and phylogenetic position of Apsaravis ukhaana from the Late Cretaceous of Mongolia. American Museum Novitates. 3387, 1-46.

Zheng, Martin, Zhou, Burnham, Zhang and Miao, 2011. Fossil evidence of avian crops from the Early Cretaceous of China. Proceedings of the National Academy of Sciences of the United States of America. 108, 15904-15907.

Zheng, O'Connor, Wang, Wang and Zhou, 2018. Reinterpretation of a previously described Jehol bird clarifies early trophic evolution in the Ornithuromorpha.  Proceedings of the Royal Society of London B. 285, 20172494.

Sunday, December 31, 2017

Happy New Years and sorry for the hiatus

So 2018 is upon us, and this blog and the Database have been bereft of updates since Summer.  What gives?  Well, I've finally been doing what so many of you have urged me to all these years- working on publishable papers.  Because of this, there won't be the annual Database update today of all new described taxa.  Those entries take a lot of time and I successfully fought the urge to write them.  They will be done eventually of course.  Similarly, I've wanted to write some blog entries such as one on my acquisition of an original copy of Wild's (1973) Tanystropheus monograph, but that will have to wait.

The good news is that both publishable projects are near completion and could very well be submitted in January.  For the Lori project, I just have to check several characters for the maniraptoran OTUs and run the final analysis, then send it to Hartman.  These were characters that I refined or quantified, and a few that replaced bad characters.  Every taxon that can be usefully resolved is in there, even Halszkaraptor and Almas (which was already included as IGM 100/1323, that I studied at the AMNH).  The former doesn't resolve as a basal deinonychosaur and the latter doesn't group with IGM 100/1128, contrary to the only published results for either.  Btw, if anyone can write macros for TNT or get me in contact with J. Salvador Arias of the Universidad Nacional de Tucumán, it'd be greatly appreciated.

For the Ornithoscelida project, my team (Cau, Gardner, Deccechi and Marjanovic) and I basically have to provide references for some scores (which I'm responsible for as I did the scoring, and so am the one causing the holdup), complete the bibliography and finish the conclusions.  And create figures.  I was briefly disheartened by the publication of Langer et al. (2017), but our paper is so much more extensive and explicit that I feel it will significantly add to the conversation, and Langer et al. messed up quite a bit too.  For instance, remember how Baron et al. (2017) scored 30 taxa that lack preserved integument as lacking filaments?  Langer et al. only changed nine of those scores to unknown despite perhaps being the most obvious error in the matrix.  We detail some of their errors in the paper as well.

See you all in 2018!

References- Wild, 1973. Die Triasfauna der Tessiner Kalkalpen. XXIII. Tanystropheus longobardicus (Bassani) (Neue Ergebnisse). Schweizerische Palaontologische Abhandlungen. 95, 1-162.

Baron, Norman and Barrett, 2017. A new hypothesis of dinosaur relationships and early dinosaur evolution. Nature. 543, 501-506.

Langer, Ezcurra, Rauhut, Benton, Knoll, McPhee, Novas, Pol and Brusatte, 2017. Untangling the dinosaur family tree. Nature. 551, E1-E3.

Monday, July 24, 2017

Theropod Database pilfered again? Teihivenator edition

Back when I was sorting through obscure theropod species, I noticed the case of "Laelaps" macropus.  Ignored for almost a century, I examined the syntypes at the AMNH and wrote the first substantive comparison and diagnosis on The Theropod Database back in 2009.  Eight years later, and I see Yun (2017) has published a paper on the specimen and named it Teihivenator.  Well, it's good someone finally did something with the taxon, except....

My proposed diagnosis- "lateral tibial malleolus at same level as medial malleolus; paired proximoventral processes on pedal phalanges II-1 and III-2."
Yun's last two characters in his diagnosis- "lateral malleolus is at same level as medial malleolus; paired ventral processes proximally on all preserved pedal phalanges."

My materials list- "... distal tibia (100 mm wide)
....(AMNH 2551) phalanx II-1 (109 mm), phalanges III-2 (93, 96 mm)"
Yun's discussion- "and distal ends of a tibia (Fig. 1A, C), about 100 mm wide.
... Phalanx II-1 is about 109 mm long, and each phalanges III-2 are about 93, 96 mm long."
And no, these aren't measurements from the literature, they're from my photos with scale bar taken at the AMNH. Hmm...

My discussion- "The material is tyrannosauroid based on the anterior process of the lateral tibial condyle..."
Yun's- "the material clearly belongs to tyrannosauroid based on the presence of the anterior process on the lateral tibial condyle.
Me- "All phalanges are ... more robust than similar-sized ornithomimids (e.g. Gallimimus' holotype)."
Yun- "Also, preserved pedal phalanges are much more robust than similarly sized ornithomimosaurs..."
Me- "The proximal metatarsal is II, and has a sharper posterior corner, more rounded anteromedial corner and shallower lateral notch than Alectrosaurus, Appalachiosaurus and Tyrannosaurus."
Yun- "The posterior corner is more narrow and triangular compared to other derived tyrannosauroids, and the medial corner is more rounded. The notch for metatarsal III is much shallower than most tyrannosauroids."

Some syntypes of "Teihivenator" macropus.  Top left- proximal metatarsal II AMNH 2553. Top right- distal metatarsal IV AMNH 2552. Bottom- proximal and distal tibiae AMNH 2550.  Courtesy of the AMNH.

I want to make clear that this isn't a hack job like Easter's "Ajancingenia" copy-paste nonsense.  Yun came up with quite a few features of his own and his own conclusion, that macropus is closer to tyrannosaurids than Dryptosaurus and thus deserves a new genus name.  But I think it's inarguable Yun used the Database for information, but did not cite it or myself in the Acknowledgements.

There's "good" news though!   As noted by Marjanovic on the DML, the name is not valid because there was no physical publication or ZooBank registration.  So here's my proposal to Yun- Add me as a second author for a brief follow-up paper, we can correct a few things like -venator being Latin as opposed to Greek, add my high res photos from the AMNH to give the genus a proper illustrative debut, and with a ZooBank registration make it official.  Deal?

[Edit- When I wrote this, I was unaware of Brownstein's preprint placed online today arguing macropus is a chimaera of tyrannosaur and ornithomimosaur specimens.  While I haven't had a chance to study the chimaera issue, Brownstein does provide detailed descriptions and high resolution photographs, so that I don't think any further contribution by myself is necessary.  So, uh, proposal retracted.  Though if Yun does publish a corrective paper with ZooBank registry, I would like to be in the acknowledgements.  Man, that story changed fast.

Brownstein, 2017. Theropod specimens from the Navesink Formation and their implications for the diversity and biogeography of ornithomimosaurs and tyrannosauroids on Appalachia. PeerJ Preprints. 5:e3105v1.]

[Edit #2- News continues to fly in.  As McCabe commented on below, Yun has left feedback on another preprint of Brownstein's indicating he thought the macropus syntypes were lost, though he really should have mentioned this in his paper.  Creisler also informed me via the DML that Yun registered the genus on ZooBank, but without a mention of this in the paper itself it still violates ICZN Article 8.5.3 (a name must "be registered in the Official Register of Zoological Nomenclature (ZooBank) (see Article 78.2.4) and contain evidence in the work itself that such registration has occurred.").  Thus a corrigendum is still necessary, which Yun's been informed of.  Whew.  This is going to be a messy Database entry to write...]

Reference- Yun, 2017. Teihivenator gen. nov., a new generic name for the tyrannosauroid dinosaur "Laelaps" macropus (Cope, 1868; preoccupied by Koch, 1836). Journal of Zoological and Bioscience Research. 4(2), 7-13.

Tuesday, March 28, 2017

Ornithoscelida Tested- Adding taxa and checking characters

So the last post reported on Baron et al.'s (2017) new paper that recovered a theropod-ornithischian clade excluding sauropodomorphs, which they inaccurately resurrected the name Ornithoscelida for.  Now that I've been able to construct a TNT file from their matrix and have coded a few relevant taxa for it, we can explore it in further depth.

First, recall I questioned the authors' method of constraining Saurischia- "They tested this in an IMO un-ideal way, by constraining all 42 saurischians to be in an exclusive clade.  Would have been better to just use a backbone of e.g. (Euparkeria, Lesothosaurus (Plateosaurus, Coelophysis), in case e.g. herrerasaurids aren't dinosaurs."  So I did the latter (replacing Euparkeria with Postosuchus due to how TNT works) and found Saurischia is actually only 15 steps longer, not 20.  Herrerasaurids are still sauropodomorphs, and Saltopus and silesaurids are still in a trichotomy with Dinosauria.  I also wondered how many steps were needed to move Eoraptor to Sauropodomorpha.  The answer is 22(!).  Hmm.  And ornithischian silesaurids?  28 more steps, which results in Saurischia.

But one aspect I didn't initially notice is that Daemonosaurus is missing from Baron et al.'s analysis.  This genus has a skull which is rather odd for a supposed basal theropod- short-snouted with pronounced heterodonty.  It also didn't include weird theropod-ornithischian cross Chilesaurus or theropod-like supposed basal sauropodomorph Buriolestes.  So I added these three taxa to Baron et al.'s matrix.

Phylogeny of the Baron et al. 2017 dataset after adding Buriolestes, Daemonosaurus and Chilesaurus (highlighted).

What happens?  Ornithoscelida is still a thing, but herrerasaurids move to outside Dinosauria.  Buriolestes is the most basal sauropodomorph and  Daemonosaurus is a theropod sister to Tawa, which are normal placements for these taxa.  Chilesaurus is an ornithischian sister to Pisanosaurus at the base of the clade, which is interesting.  Both are South American...  Though note Chilesaurus' proposed avepod relatives (basal tetanurines) aren't in the matrix.

This makes Saurischia only ten steps longer than Ornithoscelida, with Buriolestes as the basalmost theropod and herrerasaurids still basal sauropodomorphs in that case.  A sauropodomorph Eoraptor is now 16 steps longer.  21 more steps are needed for ornithischian silesaurids, with Buriolestes again a theropod and Chilesaurus remaining sister to Pisanosaurus

Unfortunately, coding these taxa exposed a ton of problems with Baron et al.'s matrix.  First it doesn't really have 458 characters.  Weirdly enough, 6 characters are coded the same for every taxon and another 47(!) are only coded as different in one taxon.  Which makes them useless for resolving relationships, or "parsimony uninformative" in the technical jargon.  Taking into account the fake character zero that's only there because of how TNT works, the matrix actually only has 404 characters that are doing anything.  Still big, but not so much bigger than Nesbitt et al.'s 315.

Also, some of the characters are badly formed at a Petersian level. 
Check out 167- "Dentition: 0, homodont; 1, slightly heterodont, with small observable changes across tooth rows; 2, markedly heterodont, clearly distinct types of teeth present (modified from Parrish, 1993; Nesbitt, 2011). ORDERED."  This ignores the fact that heterodonty can exist in numerous ways that aren't necessarily homologous at all.  The anterior peg teeth, big canines and crushing cheek teeth of heterodontosaurids (coded 2) aren't just a further development of Eoraptor's (coded 1) anterior leaf shaped teeth which grade into posterior generalized carnivorous teeth, for instance.  The direction of gradation to herbivorous teeth is even different there.
Or how about character 139- "Foramen located on the dorsal (and sometimes lateral) face of the surangular (surangular foramen): 0, present; 1, absent. NEW."  This codes for whether an anterior or a posterior surangular foramen (or both) are present, with the next character coding for which one (or both) exist- "Surangular foramen: 0, both foramen (anterior, dorsally positioned and posterior, laterally positioned) remain open; 1 only the foramen on the dorsal surface of the surangular, anterior to or at the point of maximum mandibular depth remains open; 2, only the foramen located laterally, posterior to the point of maximum mandibular depth remains open. NEW."  But the very fact both foramina can exist in the same element shows they are not homologous with each other, so a taxon with only a posterior foramen shouldn't be counted as having the same state in character 139 as a taxon with only an anterior foramen (e.g. Coelophysis and Eocursor in the matrix), but they are.
Or character 274- "Metacarpals I and V: 0, both substantially shorter in length than metacarpal III; 1, only metacarpal I longer than or subequal to metacarpal III; 2, only metacarpal V longer than or subequal to metacarpal III; 3, both are longer than or subequal to metacarpal III (modified from Butler et al., 2008)."  This just provides all the permutations of mcI and mcV length relative to mcIII.  But the fact you need all four permutations shows mcI and mcV length don't covary, so shouldn't be covered by the same character in the first place.  This kind of coding also hides homology, since e.g. the metacarpal V reduction in states 0 and 1 won't be counted as more similar to each other by TNT.  If you're wondering which dinosauromorphs have only mcV longer or subequal to mcIII, the matrix says it's Dilophosaurus.  Which is untrue, as Dilophosaurus' mcV is a tiny nub.  Character 434 does the same thing, but for shaft widths of mtI and mtV.

Metacarpus of Dilophosaurus wetherilli (UCMP 37303?) showing metacarpal V (outlined and arrowed).  I wouldn't assign that the state "only metacarpal V longer than or subequal to metacarpal III"... (after Xu et al., 2009).

There are also a lot of correlated characters- 2 and 3; 7, 9 and 10; 21 and 24; 139 and 140; 147 and 149; 167 vs. 168, 171 and 180; 215, 221, 222 and 225; 244 and 245 (but nothing is coded 0 for 245 though Postosuchus should be...); 252 and 253; 260 and 261; 279 and 278; 292, 306 and 308; 293, 294, 296, 307 and 326; 295 and 297; 314 and 316; 328 vs. 323 and 324; 344 and 345; 378 and 380; 411 and 412; 435, 436 and 446.  These seem to happen when the authors took characters from different sources but didn't realize they cover the same ground.  So for example, 215 codes for sacral number (from Butler et al.), 221 codes for a vertebra inserted between ancestral sacrals 1 and 2 (from Nesbitt et al.), 222 codes for the number of dorsosacrals (from Gauthier) and 225 for the number of caudosacrals (supposedly new).  And now sacral number is weighted more than it should be in the matrix.

Similarly, while Baron et al. did order a number of characters, many more should have been- 10, 11, 52, 58, 80, 92, 107, 129, 151, 154, 155, 179, 194, 306, 320, 324, 329, 336, 341, 354, 358 and 403.  They also ordered 333 in the wrong way- "Shaft of pubis (postpubis), shape in cross-section: 0, blade-shaped; 1, rod-like; 2, rod-like, but with a tapering medial margin (tear-drop shaped) (modified from Butler et al., 2008)."  This should have states 1 and 2 flipped, since tear-drop shaped is the intermediate shape.

The authors didn't take ontogeny into account when coding fusion characters (351, 422, 438 and 445), so that taxa known only from young individuals (e.g. Tawa, Pantydraco, Panguraptor, Liliensternus) are coded as if they are adults.

A final minor note that doesn't affect the analysis itself is there are way too many characters credited as "NEW" which are anything but.  I don't expect every other matrix to be scoured, but there are some basic characters credited as new here- nasolacrimal crests (48); deep basisphenoid recess (100); posterior exposure of basiphenoid recess/plate (108); dorsal expansion of the anterior dentary (125); fan-shaped dorsal neural spines (211); fused sacral neural spines (219); presence of a caudosacral vertebra (225); metacarpal V absence (278); highly reduced ischial peduncle of ilium (316); obturator and pubic foramen presence (338); distal notch between pubes (348); pelvic fusion (351), etc., etc..

Overall, even if it was coded correctly, I don't think I'd trust this analysis within the 15 steps needed to dump Ornithoscelida.  So consider my earlier support withdrawn.  So disappointing.  And that's not even getting to the coding accuracy, which is coming next time...

References- Xu, Clark, Mo, Choiniere, Forster, Erickson, Hone, Sullivan, Eberth, Nesbitt, Zhao, Hernandez, Jia, Han and Guo, 2009. A Jurassic ceratosaur from China helps clarify avian digital homologies. Nature. 459, 940-944.

Baron, Norman and Barrett, 2017. A new hypothesis of dinosaur relationships and early dinosaur evolution. Nature. 543, 5601-506.