Saturday, April 2, 2016

Database update plus Predatory Dinosaurs of the World with phylogenetic nomenclature

Hey fellow 80s kids!  Like me, you probably grew up with Paul's (1988) Predatory Dinosaurs of the World as your first serious non-technical theropod source, along with The Dinosauria.  After raking Peters' horrific theropod phylogeny over the coals and applying current phylogenetic nomenclature for fun, I wondered how the most famous non-technical topology of our time would fare.  So here's Paul's phylogeny from his influential book using the taxonomy from The Theropod Database.  Note a number of his named groups are paraphyletic in his topology (based on overleaf 10-1, with additional details based on his comments in the taxonomic section).  Only species with entries were included.


|  |--Lagosuchus (inc. Marasuchus)
|  |--Lewisuchus

|  `--Lagerpeton

         |  |?*Alwalkeria
         |  |?-Protoavis
         |  |--Freguellisaurus
         |  `--+--Aliwalia
         |     `--Herrerasaurus
               |--Spinosauroidea (= Coelophysoidea, Spinosauridae)
               |  |?-Elaphrosaurus
               |  |--Coelophysidae
               |  |  Coelophysis
               |  |  |--rhodesiensis
               |  |  `--bauri
               |  `--Dilophosauridae
               |     |--Liliensternus
               |     `--+--Dilophosaurus
               |        `--+--Baryonychinae
               |           |  Baryonyx
               |           `--Spinosaurinae
               |              Spinosaurus
               `--Neotheropoda (= Averostra, Neoceratosauria, Abelisauroidea, Torvosauridae)
                  |--Ceratosauria (= Ceratosauridae)
                  |  |--Sarcosaurus
                  |  `--Ceratosaurus
                  |     |?-ingens
                  |     `--nasicornis
                  `--Tetanurae (= Abelisauridae, Orionides)
                     |--Megalosauroidea (= Megalosauridae)
                     |  |--+--Megalosaurus
                     |  |  |--Torvosaurus 
                     |  |  `--Poekilopleuron
                     |  `--Abelisauria
                     |     |?-Noasauridae
                     |     |  Noasaurus
                     |     |--Carnotaurinae
                     |     |  Carnotaurus
                     |     `--Abelisaurinae
                     |        Abelisaurus
                        |  Eustreptospondylus (inc. Streptospondylus)
                           |  Piatnitzkysaurus
                                    |--Metriacanthosauridae (= Sinraptoridae)
                                    |  |--Yangchuanosaurus (inc. Metriacanthosaurus? sp.)
                                    |  `--Metriacanthosaurus (assuming Sinraptor)
                                    `--Avetheropoda (= Neotetanurae, Allosauria, Tyrannoraptora)
                                       |  Compsognathus
                                       |--Tyrannosauroidea (= Carnosauria)
                                       |  |--Coeluridae
                                       |  |  |--Aristosuchus
                                       |  |  `--Coelurus
                                       |  |--Proceratosauridae
                                       |  |  |--+--Proceratosaurus
                                       |  |  |  `--Pivetaeusaurus 
                                       |  |  |--Rapator
                                       |  |  `--Ornitholestes
                                       |  `--+--Allosauridae
                                       |     |  Allosaurus fragilis (inc. A. atrox, A. amplexus)
                                       |     `--Carcharodontosauridae (= Carcharodontosauria)
                                       |        |--+--Chilantaisaurus
                                       |        |  `--Shaochilong
                                       |        `--+--+--Acrocanthosaurus
                                       |           |  `--Becklespinax
                                       |           `--+--Indosaurus
                                       |              `--+--Labocania
                                       |                 |--Erectopus
                                       |                 |--Carcharodontosaurus
                                       |                 |--Bahariasaurus
                                       |                 `--+--Aublysodontinae
                                       |                    |  |--Aublysodon
                                       |                    |  |--Shanshanosaurus
                                       |                    |  `--Stygivenator
                                       |                    `--+--Indosuchus
                                       |                       `--+--Alioramini
                                       |                          |  Alioramus
                                       |                          `--Tyrannosauridae
                                       |                             |--Albertosaurinae
                                       |                             |  |--Alectrosaurus
                                       |                             |  `--+*-Albertosaurus
                                       |                             |     |--Nanotyrannus
                                       |                             |     `--+--Gorgosaurus
                                       |                             |        `--+--arctunguis
                                       |                             |           `--Dinotyrannus
                                       |                             `--Tyrannosaurinae
                                       |                                |--Daspletosaurus
                                       |                                `--+--Tarbosaurus
                                       |                                   `--Tyrannosaurus
                                       `--Coelurosauria (= Aviremigia, Ornithes)
                                          |--Archaeopterygidae (= Saurornithes)
                                          |  Archaeopteryx
                                             |--Dromaeosauridae (= Dromaeosaurinae)
                                             |  |--Dromaeosaurus
                                             |  `?-Adasaurus
                                             `--Eumaniraptora (= Pennaraptora, Averaptora)
                                                |--Deinonychosauria (= Velociraptorinae)
                                                |  |--Deinonychus
                                                |  `--+--Saurornitholestes
                                                |     `--Velociraptor
                                                   |?-Ornithomimosauria (= Arctometatarsalia)
                                                   |  |--Harpymimus
                                                   |  `--Ornithomiminae
                                                   |     |?-Deinocheiridae
                                                   |     |  Deinocheirus
                                                   |     |--Garudimimus
                                                   |     `--Ornithomimidae
                                                   |        |*-affinis
                                                   |        |*-Archaeornithomimus
                                                   |        `--+--Struthiomimus 
                                                   |           |?-Ornithomimus
                                                   |           |--Dromiceiomimus
                                                   |           |  |--brevitertius
                                                   |           |  `--samueli
                                                   |           `--Gallimimus
                                                   |--Oviraptorosauria (= Caenagnathiformes)
                                                   |  Caenagnathoidea
                                                   |  |--Caenagnathidae
                                                   |  |  |--Microvenator
                                                   |  |  `--+--Caenagnathinae
                                                   |  |     |  Chirostenotes
                                                   |  |     `--Elmisaurinae
                                                   |  |        Elmisaurus
                                                   |  `--Oviraptoridae
                                                   |     |--Oviraptorinae
                                                   |     |  Oviraptor (assuming Citipati)
                                                   |     `--"Ingeniinae"
                                                   |        "Ingenia"
                                                   `--Maniraptora (= Avimimidae, Paraves)
                                                      |  |--Troodon
                                                      |  |--Saurornithoides
                                                      |  |--Heptasteornis
                                                      |  `?-Bradycneme  
                                                         `--Ornithothoraces (= Avebrevicauda, Ornithopectae)
                                                            |  Iberomesornis (assuming Enantiornis)
                                                            `--+--Ichthyornithes (= Ambiortiformes)
                                                               |  |--Ambiortus
                                                               |  `--Ichthyornis
                                                                  |  Gansus
                                                                     |  Hesperornis

So how does it fare?  Pretty well, though Herrerasauridae, Megalosauria, Spinosauridae and Tyrannosauridae have definitions that fail.  There are some uncertainties based on the unclear position of ornithomimosaurs, and due to the date there are no taxa between Archaeopteryx and ornithothoracines.  But overall, not bad. 

Among the "Theropod Odds and Ends", Taquet's (1984) taxon has yet to be redescribed but seems to be a coelophysoid, "Labrosaurus" ferox is agreed to be an allosaurid/Allosaurus specimen and maybe a portion of the A. fragilis neotype.  (Magnosaurus) nethercombensis is a megalosauroid, possibly afrovenatorine.  (Duriavenator) hesperis is a megalosaurid.  Xuanhanosaurus seems to be a metriacanthosaurid.  Iliosuchus may be a basal tyrannosauroid or other basal coelurosaurian, which is debated for taxa known from far more than only ilia.  Stokesosaurus is universally agreed to be a basal tyrannosauroid.  Finally, Segisaurus is agreed to be a coelophysoid closer to Coelophysis than Dilophosaurus.

Twenty-third (II) and twenty-second (III) dentary tooth of holotype of Segnosaurus galbinensis (IGM 10/80), after Zanno et al. (2016). Note the weird lingual carina (lc).
Oh, and I updated the Database this month, but less than usual due to coding more in the Lori matrix.  Besides the last sauropodomorph entry  (Ignavusaurus ?= Massospondylus), a couple braincases were added to the Bissekty tyrannosauroid(s?) and named Timurlengia.  Wonder where this falls out in the new tyrannosauroid matrix of Brusatte and Carr (2016).  The Pierre Shale hesperornithoids of Manitoba were clarified by Aotsuka and Sato (2016), with the description of a new species.  Segnosaurus' mandible was also redescribed (Zanno et al., 2016), which I hope is the first of many therizinosaurian redescriptions from them.  It's quite an odd specimen, exhibiting a coronoid process like oviraptorosaurs, no posterior surangular ridge or foramen and TRIcarinate posterior dentary teeth.  Yes, unlike (?)any other theropod, Segnosaurus has a lingual carina with serrations (see above).

References- Taquet, 1984. Two new Jurassic specimens of coelurosaurs (Dinosauria). In Hecht, Ostrom, Viohl and Wellnhofer (eds.). The Beginnings of Birds: Proceedings of the International Archaeopteryx Conference, Eichstaett. 229-232.

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

Aotsuka and Sato, 2016. Hesperornithiformes (Aves: Ornithurae) from the Upper Cretaceous Pierre Shale, southern Manitoba, Canada. Cretaceous Research. doi: 10.1016/j.cretres.2016.03.003.

Brusatte and Carr, 2016. The phylogeny and evolutionary history of tyrannosauroid dinosaurs. Scientific Reports. 6, 20252.

Zanno, Tsogtbaatar, Chinzorig and Gates, 2016. Specializations of the mandibular anatomy and dentition of Segnosaurus galbinensis (Theropoda: Therizinosauria). PeerJ. 4:e1885.

Saturday, March 26, 2016

Peters' theropod craziness

So David Peters, whose analyses I have thoroughly trashed on this blog before, has branched out into theropods.  In my prior foray into his basal dinosaurian phylogeny, I was surprised by how poorly coded (~30% miscoded) taxa were for his tiny and badly formed analysis.  Now that he's trying to interpret MY turf, it's just sad.  Or laughable.  Or laughably sad, take your pick.  Even in the best of circumstances, taking 228 characters designed for amniote phylogeny and coding theropods for them is likely to give you a terrible result.  But add Peters' DGS to the mix, where he takes photos and discovers missing bones in a slab or traces his own outlines, and you have hilarious fiction.  Peters might know pterosaurs, but when he tries tracing theropods, it's obvious he does NOT know theropods.  He mixes bone outlines, identifies random sediment texture or feathers as bones, and based on his results just has no idea how theropods look.  I commented on this on his Archaeornithura skull post last week (see last figure below), but Peters deleted the comment and changed his reconstruction to be wrong in different ways (new ways include that the pubis is the ischium, the ischium has a huge obturator process, the manus has a complete digit, as does the fifth pedal digit(!)).

Reconstructions of Sinosauropteryx prima by me (top), and Peters (bottom), scaled to same femoral length.
As an example, here's Sinosauropteryx as reconstructed by him vs. by me.  Now, Peters is no doubt the more experienced artist, and my reconstruction isn't perfect.  I made it back in 2005, and if I were to redraw it today, I'd give the tibia and fibula less generic shapes (e.g. larger cnemial crest, flatter distal tibia, expanded proximal fibula), orient the humerus to not be in posterior view, and get rid of the post-obturator notch in the ischium, which was later found to be erroneous.  But compare that to Peters' monstrosity.  The squamosal is just a triangular plate, lacking any posterior process so that the quadrate head is impossibly just floating freely posterior to it.  The quadrate has a narrow orbital/pterygoid process unlike anything but derived birds.  There are twenty-five presacral vertebrae unlike (?)all non-maniraptoran avepods, the caudals vary randomly in length by large degrees unlike any theropod, and the chevrons are all short as if it were a derived paravian.  In the pectoral girdle, there's some huge crescent where the sternum would be, but Sinosauropteryx lacks an ossified sternum.  The ilium is just wacky- tiny postacetabular process and concave dorsal margin.  The ischium is a thick blob with nary an obturator process.  Perhaps most sadly, Peters can't even draw the tibia as longer than the femur, which is (?)universal in small theropods, stated even in the crappy original Chinese description and is character 195 in Peters' analysis.

With his reconstructions being more or less fictional animals, it's no surprise the cladograms based on them will be equally unrealistic.  And lo, they are!  For fun, I give his cladogram from March 14th and applied phylogenetic nomenclature to see how it fares.  I listed the assumed position of taxa not yet included, as they are specifiers of various clades.  I also list where family-level taxa would have to be renamed due to ICZN rules.

   |  `--+--Segisaurus
   |     `--+--Guaibasaurus
   |        `--+--Marasuchus
   |           `--Procompsognathus
      |  |--Dracoraptor
      |  `--+--Coelophysidae
      |     |  Coelophysis
      |     `--Dilophosauridae
      |        Dilophosaurus
      `--Neotheropoda (= Orionides, Avetheropoda, Neotetanurae)
         |--Ceratosauria (= Spinosauroidea, Carnosauria, Deinocheiridae)
         |  Megalosauria
         |  |--Spinosauridae (= Proceratosauridae)
         |  |  |--Proceratosaurus
         |  |  `--+--Deinocheirus
         |  |     `--+--Xiongguanlong
         |  |        `--+--Sinocalliopteryx
         |  |           `--+--Suchomimus
         |  |              `--Spinosaurus
         |  `--+--+--Dilong
         |     |  `--Guanlong
         |     `--Allosauroidea (= Neoceratosauria) (would need to be renamed Megalosauroidea)
         |        |--Abelisauroidea (= Metriacanthosauridae)
         |        |  |--Yutyrannus
         |        |  `--+--Sinraptor (assuming Metriacanthosaurus)
         |        |     `--Abelisauridae
         |        |        Majungasaurus (assuming Abelisaurus)
         |        `--Ceratosauridae (would need to be renamed Megalosauridae)
         |           Allosauria
         |           |--Allosauridae
         |           |  Allosaurus
         |           `--Megalosauridae (= Megalosauroidea, Carcharodontosauridae)
         |              |--+--Sinosaurus
         |              |  `--Monolophosaurus
         |              `--+--Acrocanthosaurus (assuming Carcharodontosaurus)
         |                 `--+--Eustreptospondylus (assuming Megalosaurus)
         |                    `--Ceratosaurus
         `--Coelurosauria (= Tetanurae)
            Maniraptoriformes (= Aviremigia, Tyrannoraptora, Bullatosauria)
            |--Compsognathidae (= Tyrannosauroidea, Arctometatarsalia, Microraptoria)
            |  |--Ornithomimosauria
            |  |  |--Compsognathus
            |  |  `--Struthiomimus (assuming Ornithomimus)
            |  `--+--+--Ornitholestes
            |     |  `--+--Microraptor
            |     |     `--Sinornithosaurus
            |     `--+--Fukuivenator
            |        `--+--Tianyuraptor
            |           `--+--Zhenyuanlong
            |              `--+--Alioramini
            |                 |  Alioramus
            |                 `--Tyrannosauridae
            |                    |--Gorgosaurus
            |                    `--Tyrannosauridae
               Pennaraptora (= Chuniaoae)
               |--Caenagnathiformes (= Oviraptoriformes)
               |  |--Therizinosauria
               |  |  |--Falcarius
               |  |  `--+--Jianchangosaurus (assuming Therizinosaurus)
               |  |     `--Rahonavis
               |  `--Oviraptorosauria
               |     |--+--Juravenator
               |     |  `--Sinosauropteryx
               |     `--+--Limusaurus
               |        `--Khaan (assuming Caenagnathus and Oviraptor)
                  |  |--Tanycolagreus (assuming Coelurus)
                  |  `--Eotyrannus
                  `--Metornithes (= Eumaniraptora)
                     |--Dromaeosauridae (= Alvarezsauroidea, Alvarezsauria, Deinonychosauria)
                     |  |--+--Haplocheirus
                     |  |  `--Shuvuuia (assuming Alvarezsaurus)
                     |  `--+--Velociraptor (assuming Dromaeosaurus and Deinonychus)
                     |     `--Balaur
                     `--Avialae (= Averaptora)
                        |--Sinornithoides (assuming Troodon)
                           |  Jinfengopteryx
                              |  |--Anchiornis
                              |  `--+--Aurornis
                              |     `--Buitreraptor (assuming Unenlagia)
                                    |  `--Xiaotingia
                                    `--+--Thermopolis "Archaeopteryx"
                                       `--Ornithothoraces (= Ornithes, Ornithopectae)
                                          |--Archaeopterygidae (= Saurornithes, Enantiornithes)
                                          |  |--Archaeornis
                                          |  `--+--+--Archaeopteryx
                                          |     |  `--Yixian embryo IVPP V14238
                                          |     `--+--Protopteryx
                                          |        `--+--Cathayornis (assuming Iberomesornis and Enantiornis)
                                          |           `--+--Pengornis
                                          |              `--Sulcavis
                                             |  |--"Archaeopteryx" bavarica
                                             |  `--+--Mei
                                             |     `--Scansoriopterygidae
                                             |        |--Scansoriopteryx
                                             |        `--+--Yi
                                             |           `--+--Epidexipteryx
                                             |              `--Omnivoropteryx
                                                      |  |--Wellnhoferia
                                                      |  `--Confuciusornis
                                                                     `--Gallus (assuming Passer)

That's pretty funny.  Nomenclature fails in Allosauroidea and Compsognathidae, due to the weird topologies there where taxa not seen as closely related enough to need their neighbors as external specifiers suffer.  Ditto for dromaeosaurids vs. alvarezsaurs.  Also for archaeopterygids vs. enantiornithines, which no BAD analysis has ever recovered. 

As for the topology, there's that sister clade to avepods, whose oldest family name would be Procompsognathidae, though none of the members have phylogenetic definitions attached to them.  The division in neotheropods is sort of like Rauhut (2003), who had a huge Carnosauria.  The most basal megalosaurians are all actually basal tyrannosauroids.  Ornithomimids plus tyrannosaurids is a classic clade from Huene to Holtz, and Compsognathus being there reminds me of Olshevsky (1995) having it as a tyrannosaur.  Funny how Peters recovered Enigmosauria, though no doubt for completely different reasons than the dinosaur community, given the inclusion of compsognathids, Limusaurus and Rahonavis.  Troodontids and unenlagiines being avialans has been more popular recently (e.g. Agnolin and Novas, 2013), and the Archaeopteryx plus Enantiornithes pairing hearkens back to the BANDits' Sauriurae.  Similarly, Confuciusornis being closer to Aves than enants reminds me of Kurochkin's (2006) ideas.  And those are the only parallels I can make between Peters' non-consensus phylogeny and science.  My head's full of non-traditional phylogenetic proposals, but Deinocheirus as a spinosaur, or microraptorans as basal tyrannosaurs while Velociraptor is by alvarezsaurs?  That's just nuts.

So David, first I'd say you should start using the names Archaeornis, Jurapteryx and Wellnhoferia if you find these taxa away from the Archaeopteryx holotype.  But also, I think it would be amusing if you added the following- Megalosaurus, Hexing, Nothronychus/Erlikosaurus, Caudipteryx, Achillobator, Dromaeosaurus and Patagopteryx.

Peters' reconstruction of Archaeornithura meemannae from 3-26-16, preserved in case it's deleted like the first was (though Peters to his partial credit does say "Updated March 16, 2016 with new images. The beak, if present, is ephemeral, questionable. Only two scores changed.").

References- Olshevsky, 1995. The origin and evolution of the tyrannosaurids. Kyoryugaku Saizensen. 9, 92-119 (part 1); 10, 75-99 (part 2).

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

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

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