Monday, July 2, 2012
Silently combining taxa
Just a brief rant today. Senter et al.'s (2012) Yurgovuchia paper includes Linheraptor codings in its Tsaagan OTU, and the fairly complete IGM 100/99 and 100/120 codings in its Parvicursor OTU. Would have been nice to at least mention this in the Methods section so that I now don't have to go back and delete those Tsaagan codings I thought were due to Senter examining it firsthand but were actually from a genus which has never even had its synonymy defended. grr...
Wednesday, June 13, 2012
Why doesn't Peters find Dinosauria or Saurischia?
Peters has defended his amniote analysis as being superior to other published analyses, since it includes numerous genus-level OTUs. And in this he is correct, though there are other measures of analysis quality too. One obvious example is the number of characters. There's no hard and fast rule regarding how many characters are needed to analyze a certain number of taxa, but you should at least include all characters previously utilized for the clade you're examining, unless some are invalid for whatever reason. Peters' analysis has a large number of areas in which it differs not only from the consensus, but from any other proposed phylogeny. One of these is his Dinosauria, which instead of the standard Ornithischia vs. Saurischia dichotomy, with the latter including Theropoda and Sauropodomorpha, has...
--Theropoda including Marasuchus, Herrerasaurus and Trialestes
--- Panphagia+Pampadromaeus
---- a clade of Pisanosaurus, poposaurs and silesaurids
----- Sauropodomorpha including Saturnalia, Thecodontosaurus and Massospondylus
------ Daemonosaurus + standard Ornithischia
Thus it has an equivalent of Phytodinosauria and includes a host of non-dinosaurian taxa. Now, Saurischia is one of those clades (like Ornithothoraces) that while near-ubiquitous in published analyses, only takes a few extra steps to negate, so I'm not biased against it a priori. And I've said half-seriously before that ornithischian-like silesaurids and theropod-like shuvosaurines and hallopodines could threaten dinosaurian monophyly. Peters no doubt thinks his results are superior to the consensus, but did he actually test the consensus? Let's see which saurischian and dinosaurian synapomorphies (based on only the unambiguous synapomorphies of Nesbitt, 2011) Peters included in his analysis.
Saurischia
Yes- (1) Subnarial foramen between the premaxilla-maxilla where the border of the foramen is present on both the maxilla and the premaxilla (12-1)*.
(12) Metacarpal IV shaft width significantly narrower than that of metacarpals I–III (261-1).
(13) Distal end of pubis expanded relative to the shaft (5 pubis boot) (283-1).
No- (2) Lacrimal folds over (5 overhangs) the posterior/posterodorsal part of the antorbital fenestra (38-1)*.
(3) Ventral ramus of the opisthotic covered by the lateralmost edge of exoccipital in posterior view (111-1). (4) Foramen in the ventral part of the splenial (165-1)*.
(5) Epipophyses present in posterior cervical vertebrae (cervicals 6–9) (187-1).
(6) Hyposphene- hypantrum accessory intervertebral articulations in the posterior cervical and/or dorsal vertebrae (195-1)*.
(7) First primordial sacral rib C-shaped in lateral view (209-1)*.
(8) Manual length accounts for more than 0.3 but less than 0.4 of the total length of humerus plus radius (247-1).
(9) Distal carpal V absent (249-1)*.
(10) Manual digit I, first phalanx (1.1) is the longest nonungual phalanx of the manus (253-1)*.
(11) Lateral distal condyle strongly distally expanded relative to medial condyle of metacarpal I (254-1). (14) Cross section of the distal portion of the ischium subtriangular (293-2).
(15) Deep groove between the lateral condyle and crista tibiofibularis on the distal surface of the femur (322-1).
(16) Posterior prong of distal tarsal 4 pointed (350-1)*.
(17) Distal tarsal 4 with a distinct medial process present in the anteroposterior middle of the element (351-1)*.
(18) Astragalus, proximal surface possesses a marked rimmed and elliptical fossa posterior to the anterior ascending process (359-1)*.
Dinosauria
Yes- (7) Fourth trochanter a sharp flange (316-1)*.
No- (1) Exoccipitals do not meet along the midline on the floor of the endocranial cavity (115-1)*. Also in Crocodylomorpha and Effigia + Shuvosaurus.
(2) Supratemporal fossa present anterior to the supratemporal fenestra (144-1).
(3) Epipophyses present in postaxial anterior cervical vertebrae (186-0)*.
(4) Apex of deltopectoral crest situated at a point corresponding to more than 30% down the length of the
humerus (230-1)*.
(5) Radius shorter than 80% of humerus length (241-1).
(6) Proximal articular surfaces of the ischium with the ilium and the pubis separated by a large concave surface (297-2)*.
(8) Fourth trochanter asymmetrical, with distal margin forming a steeper angle to the shaft (317-1).
(9) Cnemial crest arcs anterolaterally (328-2)*.
(10) Distinct proximodistally oriented ridge present on the posterior face of the distal end of the tibia (336-1)*.
(11) Proximal articular facet for fibula of the astragalus occupies less than 0.3 of the transverse width of the element (362-1).
(12) Concave articular surface for the fibula of the calcaneum (378-2).
Wow! Peters included 3 (17%) of saurischian characters and 1 (8%) of dinosaurian characters and didn't recover either clade? Who'd have thunk? In general, Peters' postcranial characters are few and usually reflect gross morphology. Wanna know the humeral characters included? Humerofemoral length and torsion. The tibial ones? Tibioilial length. Distal tarsal characters? None. Peters is fond of saying his sister taxa "look similar", and this is why- the characters reflect a general morphotype.
There's a reason making an amniote analysis is so challenging. It'd be easy enough to enter 300 taxa into Rieppel's or Mueller's analyses, but at that resolution, you need to add more characters to arrange taxa right within each subclade. Peters has not done this, but I'd bet doing so, and defining his states better, would result in a more standard topology, albeit one that may have genuine surprises.
--Theropoda including Marasuchus, Herrerasaurus and Trialestes
--- Panphagia+Pampadromaeus
---- a clade of Pisanosaurus, poposaurs and silesaurids
----- Sauropodomorpha including Saturnalia, Thecodontosaurus and Massospondylus
------ Daemonosaurus + standard Ornithischia
Thus it has an equivalent of Phytodinosauria and includes a host of non-dinosaurian taxa. Now, Saurischia is one of those clades (like Ornithothoraces) that while near-ubiquitous in published analyses, only takes a few extra steps to negate, so I'm not biased against it a priori. And I've said half-seriously before that ornithischian-like silesaurids and theropod-like shuvosaurines and hallopodines could threaten dinosaurian monophyly. Peters no doubt thinks his results are superior to the consensus, but did he actually test the consensus? Let's see which saurischian and dinosaurian synapomorphies (based on only the unambiguous synapomorphies of Nesbitt, 2011) Peters included in his analysis.
Saurischia
Yes- (1) Subnarial foramen between the premaxilla-maxilla where the border of the foramen is present on both the maxilla and the premaxilla (12-1)*.
(12) Metacarpal IV shaft width significantly narrower than that of metacarpals I–III (261-1).
(13) Distal end of pubis expanded relative to the shaft (5 pubis boot) (283-1).
No- (2) Lacrimal folds over (5 overhangs) the posterior/posterodorsal part of the antorbital fenestra (38-1)*.
(3) Ventral ramus of the opisthotic covered by the lateralmost edge of exoccipital in posterior view (111-1). (4) Foramen in the ventral part of the splenial (165-1)*.
(5) Epipophyses present in posterior cervical vertebrae (cervicals 6–9) (187-1).
(6) Hyposphene- hypantrum accessory intervertebral articulations in the posterior cervical and/or dorsal vertebrae (195-1)*.
(7) First primordial sacral rib C-shaped in lateral view (209-1)*.
(8) Manual length accounts for more than 0.3 but less than 0.4 of the total length of humerus plus radius (247-1).
(9) Distal carpal V absent (249-1)*.
(10) Manual digit I, first phalanx (1.1) is the longest nonungual phalanx of the manus (253-1)*.
(11) Lateral distal condyle strongly distally expanded relative to medial condyle of metacarpal I (254-1). (14) Cross section of the distal portion of the ischium subtriangular (293-2).
(15) Deep groove between the lateral condyle and crista tibiofibularis on the distal surface of the femur (322-1).
(16) Posterior prong of distal tarsal 4 pointed (350-1)*.
(17) Distal tarsal 4 with a distinct medial process present in the anteroposterior middle of the element (351-1)*.
(18) Astragalus, proximal surface possesses a marked rimmed and elliptical fossa posterior to the anterior ascending process (359-1)*.
Dinosauria
Yes- (7) Fourth trochanter a sharp flange (316-1)*.
No- (1) Exoccipitals do not meet along the midline on the floor of the endocranial cavity (115-1)*. Also in Crocodylomorpha and Effigia + Shuvosaurus.
(2) Supratemporal fossa present anterior to the supratemporal fenestra (144-1).
(3) Epipophyses present in postaxial anterior cervical vertebrae (186-0)*.
(4) Apex of deltopectoral crest situated at a point corresponding to more than 30% down the length of the
humerus (230-1)*.
(5) Radius shorter than 80% of humerus length (241-1).
(6) Proximal articular surfaces of the ischium with the ilium and the pubis separated by a large concave surface (297-2)*.
(8) Fourth trochanter asymmetrical, with distal margin forming a steeper angle to the shaft (317-1).
(9) Cnemial crest arcs anterolaterally (328-2)*.
(10) Distinct proximodistally oriented ridge present on the posterior face of the distal end of the tibia (336-1)*.
(11) Proximal articular facet for fibula of the astragalus occupies less than 0.3 of the transverse width of the element (362-1).
(12) Concave articular surface for the fibula of the calcaneum (378-2).
Wow! Peters included 3 (17%) of saurischian characters and 1 (8%) of dinosaurian characters and didn't recover either clade? Who'd have thunk? In general, Peters' postcranial characters are few and usually reflect gross morphology. Wanna know the humeral characters included? Humerofemoral length and torsion. The tibial ones? Tibioilial length. Distal tarsal characters? None. Peters is fond of saying his sister taxa "look similar", and this is why- the characters reflect a general morphotype.
There's a reason making an amniote analysis is so challenging. It'd be easy enough to enter 300 taxa into Rieppel's or Mueller's analyses, but at that resolution, you need to add more characters to arrange taxa right within each subclade. Peters has not done this, but I'd bet doing so, and defining his states better, would result in a more standard topology, albeit one that may have genuine surprises.
Monday, June 4, 2012
Why David Peters' analysis sucks
For a while now, Peters has played the part of the outcast whose new ideas have been shunned by the outdated but stubborn establishment, locked in its consensus purely due to tradition and an unwillingness to include numerous genus-level OTUs in an analysis. And he actually has a point. Published large scale reptile analyses DO suffer from using suprageneric OTUS, are heavily miscoded, and include way too few taxa to be useful. However, Peters' analyses are even worse. One huge reason is that they include what are certainly wrong codings caused by Peters' method of running photos through his computer to "find" things people looking at the specimen missed, like the entire posterior skeleton of Longisquama, babies and crazy frills on it and various pterosaurs, teeth in toothless taxa, and anything else you can imagine. But even ignoring that, there's another level at which Peters' analysis fails, and that's when we look at the characters themselves. I asked Peters for his matrix today (and I will credit him for being so transparent as to send it to anyone who asks, despite his study not being published in peer reviewed literature), and here's what I found...
Let's just look at dental characters. Character 107 is palatal teeth present vs. absent, but character 96 covers vomer teeth being absent and character 101 covers pterygoid teeth being absent, so this is correlated right off the bat.
Character 108 is number of premaxillary teeth with the states four, more than four, one two or three, none, teeth fused and three or four plus medial. Ack, where to begin? First, no character is ordered, so while "four" should be between "1-3" and ">4", it's not. Second, multiple variables are involved here. Each character should only involve one variable. Having medial premaxillary teeth should be its own character. Having teeth fused should also be its own character. And since we don't know toothless premaxillae evolved via decreasing number of teeth, a toothless premaxilla should also be its own character. Any coding not falling within the states given should be inapplicable (e.g. Citipati for number of premaxillary teeth 1 vs. 2 vs. 3 vs. 4. vs. 5 vs. 6 vs. 7 or more). A good way to test for how well character states are defined is to see if any possible morphologies couldn't be coded. In this case, what if a taxon had six premaxillary teeth with medial teeth too? Or what if it had less than four fused teeth?
Character 109 is medial premaxillary teeth larger vs. smaller than lateral teeth. And yet all dinosaurs are coded 0, when none have medial premaxillary teeth. They should be coded inapplicable. This is the same for many derived reptiles, no doubt. I notice Thecodontosaurus is coded as derived though, when no premaxilla is known, and even Pantydraco only has lateral teeth.
Character 110 is premaxillary teeth robust vs. tiny to absent. Yet absent was already covered by character 108, and these states are never defined so that I could always know when a specimen has state 0 or 1.
Character 111 is procumbant premaxillary teeth, which is fine except needing an angle at which teeth are defined as procumbant.
No complaints about character 112- maxillary tooth length less than twice root depth (presubamly FABL).
Character 113 is canine maxillary teeth, but Peters codes taxa with toothless maxillae such as Hupehsuchus and Endennasaurus as lacking canine maxillary teeth when they should be inapplicable.
Character 114 is the position of the last maxillary tooth compared to the orbit, but is not ordered, so "mid orbit" is not between "anterior to orbit" and posterior to orbit". Furthermore, it includes a state for "toothless", which makes it correlated with the next character...
Character 115 is maxillary teeth sharp vs. blunt vs. multicusped vs. multicusped with constricted bases vs. absent vs. constricted bases. This makes 108 look formatted well. SO MANY variables are combined! Sharpness, number of cusps, constriction of base, presence. This needs to be four characters.
So yeah, that's just a sample. Can you all see why no one trusts Peters' analysis, even ignoring his coding accuracy in the first place? It's true some other analyses have some of the same issues, like Rieppel's (http://theropoddatabase.blogspot.com/2011/06/rieppels-reptile-matrix-and-turtle.html), but this doesn't make Peters' more likely to be correct. Honestly, Rieppel's, Mueller's and Peters' are all flawed. I don't trust the results of any of them. If someone wants to be the true shining light on the subpar tradition of reptile analyses, they need to understand how to construct characters well, and not put their faith in graphic artifacts created by Photoshop. Peters can accomplish the first step by posting this on his blog and adusting the characters as per my critique.
Let's just look at dental characters. Character 107 is palatal teeth present vs. absent, but character 96 covers vomer teeth being absent and character 101 covers pterygoid teeth being absent, so this is correlated right off the bat.
Character 108 is number of premaxillary teeth with the states four, more than four, one two or three, none, teeth fused and three or four plus medial. Ack, where to begin? First, no character is ordered, so while "four" should be between "1-3" and ">4", it's not. Second, multiple variables are involved here. Each character should only involve one variable. Having medial premaxillary teeth should be its own character. Having teeth fused should also be its own character. And since we don't know toothless premaxillae evolved via decreasing number of teeth, a toothless premaxilla should also be its own character. Any coding not falling within the states given should be inapplicable (e.g. Citipati for number of premaxillary teeth 1 vs. 2 vs. 3 vs. 4. vs. 5 vs. 6 vs. 7 or more). A good way to test for how well character states are defined is to see if any possible morphologies couldn't be coded. In this case, what if a taxon had six premaxillary teeth with medial teeth too? Or what if it had less than four fused teeth?
Character 109 is medial premaxillary teeth larger vs. smaller than lateral teeth. And yet all dinosaurs are coded 0, when none have medial premaxillary teeth. They should be coded inapplicable. This is the same for many derived reptiles, no doubt. I notice Thecodontosaurus is coded as derived though, when no premaxilla is known, and even Pantydraco only has lateral teeth.
Character 110 is premaxillary teeth robust vs. tiny to absent. Yet absent was already covered by character 108, and these states are never defined so that I could always know when a specimen has state 0 or 1.
Character 111 is procumbant premaxillary teeth, which is fine except needing an angle at which teeth are defined as procumbant.
No complaints about character 112- maxillary tooth length less than twice root depth (presubamly FABL).
Character 113 is canine maxillary teeth, but Peters codes taxa with toothless maxillae such as Hupehsuchus and Endennasaurus as lacking canine maxillary teeth when they should be inapplicable.
Character 114 is the position of the last maxillary tooth compared to the orbit, but is not ordered, so "mid orbit" is not between "anterior to orbit" and posterior to orbit". Furthermore, it includes a state for "toothless", which makes it correlated with the next character...
Character 115 is maxillary teeth sharp vs. blunt vs. multicusped vs. multicusped with constricted bases vs. absent vs. constricted bases. This makes 108 look formatted well. SO MANY variables are combined! Sharpness, number of cusps, constriction of base, presence. This needs to be four characters.
So yeah, that's just a sample. Can you all see why no one trusts Peters' analysis, even ignoring his coding accuracy in the first place? It's true some other analyses have some of the same issues, like Rieppel's (http://theropoddatabase.blogspot.com/2011/06/rieppels-reptile-matrix-and-turtle.html), but this doesn't make Peters' more likely to be correct. Honestly, Rieppel's, Mueller's and Peters' are all flawed. I don't trust the results of any of them. If someone wants to be the true shining light on the subpar tradition of reptile analyses, they need to understand how to construct characters well, and not put their faith in graphic artifacts created by Photoshop. Peters can accomplish the first step by posting this on his blog and adusting the characters as per my critique.
Sunday, May 27, 2012
The Yurgovuchia analysis isn't all it's cracked up to be
When I first saw Senter et al.'s 2012 analysis for the Yurgovuchia paper, I was excited. Senter (2007) did a better job coding than the versions of the TWG analysis leading up to it, and a better job at defining characters to be non-composite. Senter's also gradually increased his taxonomic scope to impressive levels. But now that I'm integrating the Yurgovuchia matrix data into the Lori matrix, things aren't as great as they seem.
First, that taxonomic scope. Eotyrannus and microraptorian NGMC 91 are missing without explanation. Similicaudipteryx isn't there from the Xiaotingia analysis. Chirostenotes not only lacks Caenagnathus data (Caenagnathus was its own OTU in Senter, 2007 but was deleted from his 2010 paper to decrease computational time, something that might have been useful then since that paper was not primarily a phylogenetic analysis, but which is inexcusable now), but it also lacks data from ROM 43250, the holotype of Epichirostenotes. Even though I don't think Epichirostenotes can be distinguished taxonomically from Chirostenotes, that would be fine if he made an OTU for Epichirostenotes too. But no, he didn't. So we're left with a matrix with no cranial, mandibular, presacral, caudal or pubic data for caenagnathids. Is it any wonder they're deeply nested within oviraptorids? For Archaeopteryx, starting in the 2010 paper Senter included "data only from the Thermopolis, Berlin, and Munich specimens. New observations (Mayr et al., 2007) have cast doubt on the conspecificity of the London specimen with those three specimens, so data that came only from the London specimen were deleted from the OTU." But the holotype is the London specimen! Thus Senter's OTU does not include the only specimen which is definitely Archaeopteryx. It's also the only specimen to preserve a lot of braincase data. Again, he didn't make a separate London OTU, so the data just isn't used. In Dromaeosauridae, since Senter breaks down Microraptor into the holotype, the CAGS specimens described by Hwang et al. (2002), M. gui and Cryptovolans, we miss out on most cranial data from specimens with complete skulls like IVPP V13475. He also stopped including Atrociraptor and Saurornitholestes, and deleted the data from the referred Utahraptor specimens.
Perhaps worse are the characters and coding though. Surprisingly, this is actually coded worse than his 2007 and 2010 versions, with all members of a clade often coded identically regardless of actual variation. As an example, all oviraptorosaurs and paravians are coded as lacking prefrontals. So he recoded Deinonychus incorrectly, and left Sinornithosaurus suspiciously unknown. Or the next character, postorbital bar absent, is incorrectly recoded to give Shuvuuia a complete postorbital bar and leave Avimimus unknown. Senter also disregards the rule of cladistic analyses to let the tree decide homoplasy. Since 2007, he's had a pet hypothesis ornithomimosaurs lack promaxillary fenestrae and that the fenestrae below their maxillary fenestrae were not homologous. This was somewhat defensable in 2007 since other tetanurines have fenestrae arranged horizontally instead of vertically. But now that Tahara and Larsson (2011) found Dromiceiomimus' lower fenestra communicates with its promaxillary recess, things are unambiguous. It IS a promaxillary fenestra, even if it was convergently evolved. The Yurgovuchia paper notes this and addresses it as follows-
"However, the absence of that opening in basal ornithomimosaurs suggests that its appearance in advanced ornithomimosaurs is neomorphic. Therefore, the phylogenetic data matrix used here does not recognize the presence of the promaxillary fenestra in Ornithomimus and other advanced ornithomimosaurs."
But... but... by that reasoning, we might as well just code Avimimus, ornithomimids and derived troodontids as lacking an arctometatarsus, since its absence in basal relatives of those groups show it developed convergently with tyrannosaurids. Ditto for any character with homoplasy. By coding this way you completely destroy the point of using PAUP in the first place. I wonder if this is also the reason for the miscodings alluded to above. Is Shuvuuia coded as having a complete postorbital bar because it's convergent with the incomplete bar of Aves? I certainly hope this wasn't Senter's reasoning.
Characters themselves are often "redefined" to be worse. The 'depth of the jugal beneath the orbit' character has gotten another state for when it tapers anteriorly, but that should be a whole new character. The character coding for the cross section of the posterior jugal process has been redefined to code for its length and depth, but those aren't the same as cross section AND are independent of each other. Or take this hilarious example-
"External naris an elongate oblong, with long axis diagonal in lateral view (0) or an elongate oblong with long axis subhorizontal (1) or a short oblong, with length not much greater than height, with long axis subhorizontal (2) [3]. This character replaces a previous one: “Internarial bar rounded (0) or flat (1) [5].” The internarial bar appears flat when the long axis of the external naris is subhorizontal."
Er... the flat internarial bar character refers to its cross section, not its dorsal convexity in lateral view. A lot of characters from previous TWG analyses are now excluded without comment, so I have to retract my statement on the DML that this analysis is definitely better than prior TWG analyses, because now we have the complication that it's missing some characters.
It goes without saying that no characters are ordered and no codings are polymorphic.
All of this is such a shame, because Senter's 2007 work was such an improvement on other analyses up till that point, and he's been quite a help to me personally over the years. I'm afraid I can't recommend the Yurgovuchia analysis for those wishing to know coelurosaur phylogeny, and hope that Senter's next version fixes these problems.
References- Senter, 2007. A new look at the phylogeny of Coelurosauria (Dinosauria: Theropoda). Journal of Systematic Palaeontology. 5(4), 429-463.
Senter, 2010. Using creation science to demonstrate evolution: application of a creationist method for visualizing gaps in the fossil record to a phylogenetic study of coelurosaurian dinosaurs. Journal of Evolutionary Biology. 23(8), 1732-1743.
Tahara and Larsson, 2011. Cranial pneumatic anatomy of Ornithomimus edmontonicus (Ornithomimidae: Theropoda). Journal of Vertebrate Paleontology. 31(1), 127143.
Senter, Kirkland, DeBlieux, Madsen and Toth, 2012. New dromaeosaurids (Dinosauria: Theropoda) from the Lower Cretaceous of Utah, and the evolution of the dromaeosaurid tail. PLoS ONE. 7(5), e36790.
First, that taxonomic scope. Eotyrannus and microraptorian NGMC 91 are missing without explanation. Similicaudipteryx isn't there from the Xiaotingia analysis. Chirostenotes not only lacks Caenagnathus data (Caenagnathus was its own OTU in Senter, 2007 but was deleted from his 2010 paper to decrease computational time, something that might have been useful then since that paper was not primarily a phylogenetic analysis, but which is inexcusable now), but it also lacks data from ROM 43250, the holotype of Epichirostenotes. Even though I don't think Epichirostenotes can be distinguished taxonomically from Chirostenotes, that would be fine if he made an OTU for Epichirostenotes too. But no, he didn't. So we're left with a matrix with no cranial, mandibular, presacral, caudal or pubic data for caenagnathids. Is it any wonder they're deeply nested within oviraptorids? For Archaeopteryx, starting in the 2010 paper Senter included "data only from the Thermopolis, Berlin, and Munich specimens. New observations (Mayr et al., 2007) have cast doubt on the conspecificity of the London specimen with those three specimens, so data that came only from the London specimen were deleted from the OTU." But the holotype is the London specimen! Thus Senter's OTU does not include the only specimen which is definitely Archaeopteryx. It's also the only specimen to preserve a lot of braincase data. Again, he didn't make a separate London OTU, so the data just isn't used. In Dromaeosauridae, since Senter breaks down Microraptor into the holotype, the CAGS specimens described by Hwang et al. (2002), M. gui and Cryptovolans, we miss out on most cranial data from specimens with complete skulls like IVPP V13475. He also stopped including Atrociraptor and Saurornitholestes, and deleted the data from the referred Utahraptor specimens.
Perhaps worse are the characters and coding though. Surprisingly, this is actually coded worse than his 2007 and 2010 versions, with all members of a clade often coded identically regardless of actual variation. As an example, all oviraptorosaurs and paravians are coded as lacking prefrontals. So he recoded Deinonychus incorrectly, and left Sinornithosaurus suspiciously unknown. Or the next character, postorbital bar absent, is incorrectly recoded to give Shuvuuia a complete postorbital bar and leave Avimimus unknown. Senter also disregards the rule of cladistic analyses to let the tree decide homoplasy. Since 2007, he's had a pet hypothesis ornithomimosaurs lack promaxillary fenestrae and that the fenestrae below their maxillary fenestrae were not homologous. This was somewhat defensable in 2007 since other tetanurines have fenestrae arranged horizontally instead of vertically. But now that Tahara and Larsson (2011) found Dromiceiomimus' lower fenestra communicates with its promaxillary recess, things are unambiguous. It IS a promaxillary fenestra, even if it was convergently evolved. The Yurgovuchia paper notes this and addresses it as follows-
"However, the absence of that opening in basal ornithomimosaurs suggests that its appearance in advanced ornithomimosaurs is neomorphic. Therefore, the phylogenetic data matrix used here does not recognize the presence of the promaxillary fenestra in Ornithomimus and other advanced ornithomimosaurs."
But... but... by that reasoning, we might as well just code Avimimus, ornithomimids and derived troodontids as lacking an arctometatarsus, since its absence in basal relatives of those groups show it developed convergently with tyrannosaurids. Ditto for any character with homoplasy. By coding this way you completely destroy the point of using PAUP in the first place. I wonder if this is also the reason for the miscodings alluded to above. Is Shuvuuia coded as having a complete postorbital bar because it's convergent with the incomplete bar of Aves? I certainly hope this wasn't Senter's reasoning.
Characters themselves are often "redefined" to be worse. The 'depth of the jugal beneath the orbit' character has gotten another state for when it tapers anteriorly, but that should be a whole new character. The character coding for the cross section of the posterior jugal process has been redefined to code for its length and depth, but those aren't the same as cross section AND are independent of each other. Or take this hilarious example-
"External naris an elongate oblong, with long axis diagonal in lateral view (0) or an elongate oblong with long axis subhorizontal (1) or a short oblong, with length not much greater than height, with long axis subhorizontal (2) [3]. This character replaces a previous one: “Internarial bar rounded (0) or flat (1) [5].” The internarial bar appears flat when the long axis of the external naris is subhorizontal."
Er... the flat internarial bar character refers to its cross section, not its dorsal convexity in lateral view. A lot of characters from previous TWG analyses are now excluded without comment, so I have to retract my statement on the DML that this analysis is definitely better than prior TWG analyses, because now we have the complication that it's missing some characters.
It goes without saying that no characters are ordered and no codings are polymorphic.
All of this is such a shame, because Senter's 2007 work was such an improvement on other analyses up till that point, and he's been quite a help to me personally over the years. I'm afraid I can't recommend the Yurgovuchia analysis for those wishing to know coelurosaur phylogeny, and hope that Senter's next version fixes these problems.
References- Senter, 2007. A new look at the phylogeny of Coelurosauria (Dinosauria: Theropoda). Journal of Systematic Palaeontology. 5(4), 429-463.
Senter, 2010. Using creation science to demonstrate evolution: application of a creationist method for visualizing gaps in the fossil record to a phylogenetic study of coelurosaurian dinosaurs. Journal of Evolutionary Biology. 23(8), 1732-1743.
Tahara and Larsson, 2011. Cranial pneumatic anatomy of Ornithomimus edmontonicus (Ornithomimidae: Theropoda). Journal of Vertebrate Paleontology. 31(1), 127143.
Senter, Kirkland, DeBlieux, Madsen and Toth, 2012. New dromaeosaurids (Dinosauria: Theropoda) from the Lower Cretaceous of Utah, and the evolution of the dromaeosaurid tail. PLoS ONE. 7(5), e36790.
Thursday, May 17, 2012
Testing alternative tetanurine topologies in Carrano et al. 2012
In my last post, I described Carrano et al.'s superb new tetanurine analysis. One of my biggest complaints was that very few alternative topologies were tested, so while the cladogram had plenty of novel and interesting ideas, the paper doesn't tell us just how well they're supported. Note Carrano et al.'s reported "branch support" (Bremer?) is flawed because 1) fragmentary taxa lead to nodes collapsing easily even if the node is well supported for complete taxa in it, 2) distant taxa will often share characters (which show up as homoplasies or autapomorphies in the most parsimonious tree), so that moving a taxon across three nodes will not simply cost the number of Bremer support steps in each of those nodes added together, and 3) rearrangements change character state distributions, which will change support in adjacent nodes.
Luckily, another wonderful thing about Carrano et al.s' paper is that it comes with a fully constructed NEXUS file. Not only that, the NEXUS includes character descriptions for NDE and even ran without error the first time. Future authors please follow suit! So, with this I was able to test alternbative topologies myself. I must say I was surprised by some of the results. What follows are the results, arranged in order of extra steps needed, with my subjective interpretation of liklihood...
Basically ambiguous
1 step- (stated in paper) Cryolophosaurus outside Neotheropoda sensu Bakker, as in Smith et al. (2007). Though this isn't a good test without more basal taxa.
1 step- (stated in paper) Monolophosaurus as a basal megalosauroid, as in Benson (2010).
1 step- Xuanhanosaurus as a piatnitzkysaurid, as in Benson (2010).
1 step- (stated in paper) Poekilopleuron as a piatnitzkysaurid, allosaur or other kind of megalosaurid.
1 step- Eustreptospondylus sister to Magnosaurus. This was proposed by Rauhut (2003), who made the former a species of that latter. Magnosaurus moves out of Afrovenatorinae to join Eustreptospondylus easily.
1 step- Duriavenator as an afrovenatorine.
1 step- Monophyletic Sinraptor. Though the characters traditionally used to combine them are cranial ones compared to Yangchuanosaurus, and their pelves are somewhat different, so how Siamotyrannus relates really isn't obvious.
1 step- (stated in paper) Chilantaisaurus as a carcharodontosaurid sensu stricto, not a neovenatorine.
2 steps- Megalosauroidea as carnosaurs, as Huene originally proposed, and Rauhut (2003) and Cau more recently find. This rearranges the whole tree so that megalosauroid relationships are less resolved, and Piatnitzkysauridae and Lourinhanosaurus are successively closer to sinraptorids+allosaurs than megalosauroids are. The fact the backbone of the tree crashes down so easily is disconcerting.
2 steps- Streptospondylus as an afrovenatorine (or really Afrovenator as a streptospondyline).
2 steps- (stated in paper) Lourinhanosaurus as a basal carnosaur (as in Holtz et al., 2004) or sister to Avetheropoda.
Quite likely to be true
3 steps- "Dilophosaurus" sinensis outside Neotheropoda sensu Bakker, as in Smith et al. (2007). Cryolophosaurus follows. As with Cryolophosaurus above, we'd really need more basal taxa included to test this.
3 steps- Piatnitzkysaurus outside Orionides, as in Rauhut (2003). Other piatnitzkysaurids follow.
3 steps- Xuanhanosaurus outside Orionides, as in Holtz et al. (2004). It ends up by Monolophosaurus.
3 steps- Eustreptospondylus as an afrovenatorine (or really Afrovenator as a eustreptospondyline), as in Allain (2002).
3 steps- Afrovenator as a carnosaur, as in Rauhut (2003). Even though I constrained Afrovenator to be closer to Allosaurus than to Eustreptospondylus and Torvosaurus as in Rauhut's tree, this makes all megalosauroids carnosaurs. The carnosaur phylogeny is (Strepto(Megalosauridae((Afro+Leshan)(Spino(Piatnitzky(Lourinhano(Sinrap,Allosauria))))))). So megalosauroids end up being paraphyletic to carnosaurs.
4 steps- Monolophosaurus as a carnosaur, as in Sereno et al. (1996). This also makes megalosauroids carnosaurs, with the topology (Megalosauria(Mono(Piat(Lour(Sinrap+Allo))))).
4 steps- Poekilopleuron as a sinraptorid, after Benson et al. (2010).
5 steps- Monolophosaurus sister to Avetheropoda, as in Smith et al. (2007). Piatnitzkysaurids are even closer to avetheropods in this phylogeny.
5 steps- Torvosaurus and/or Eustreptospondylus being closer to spinosaurids than Afrovenator is, as in Sereno et al. (1994).
5 steps- Siamotyrannus as a coelurosaur, as in Buffetaut et al. (1996). It's closer to other coelurosaurs than Lourinhanosaurus is.
5 steps- Sinraptorids outside Avetheropoda, as in Paul (1988). Poekilopleuron becomes a coelurosaur.
Somewhat possible
6 steps- Piatnitzkysaurus as an afrovenatorine, as in Holtz et al. (2004). Megalosauridae gets shuffled around a lot.
6 steps- Sinraptorids and carcharodontosaurids as sister taxa, exclusive of Allosaurus, as in Allain (2002). This also makes megalosauroids carnosaurs, with the topology (Megalosauria(Poekilo,Lour(Saurophag(Allo(Sinrap,Carch))))).
7 steps- Eustreptospondylus closer to spinosaurids than Torvosaurus or Afrovenator are, as in Smith et al. (2007).
7 steps- Chilantaisaurus as a spinosaurid, as in Rauhut (2003).
7 steps- Neovenator as an allosaurid, as in Hutt et al. (2001). This also makes megalosauroids carnosaurs, with the topology (Megalosauria(Piat(Lour(Sinrap+Allo)))), and neovenatorines become allosaurids.
Unlikely-
9 steps- Cryolophosaurus as a coelophysoid, though again we'd like more basal taxa.
10 steps- "Dilophosaurus" sinensis as a coelophysoid, and same as above.
11 steps- "Szechuanosaurus" zigongensis outside Orionides, as in Rauhut (2003). It ends up by Monolophosaurus. Odd that so many more basic rearrangements are more likely, as described above.
11 steps- Siamotyrannus and Fukuiraptor as sister taxa, as in Holtz et al. (2004). The pair end up sister to Allosauria.
12 steps- Megaraptor as a carcharodontosaurine, as in Smith et al. (2007).
12 steps- Acrocanthosaurus as an allosaurid, as in Stovall and Langston (1950). This really changes things. It makes megalosauroids carnosaurs, with the topology (Megalosauria(Piat(Lour(Sinrap(Conca(Carch(Eocarch((Acro+Poek)(Neoven(Allo,Saurophag)))))))))). Again, surprising.
15 steps- Megaraptor as a megalosauroid, as in Calvo et al. (2004). Ends up sister to Megalosauria.
15 steps- Megaraptora as coelurosaurs, my pet hypothesis (but also partially Longrich 2001 and Novas et al. 2008). Oh noes! Even "worse", it's more like in this topology, "coelurosaurs become neovenatorids". But as I said in my last post, the analysis needs more coelurosaurs. Also remember the corrected TWG matrix needed 15 more steps to get a monophyletic Deinonychosauria, and that's standard now. So any of the above hypotheses may end up being true. Forcing megaraptorans to be coelurosaurs, but carnosaurs to be monophyletic otherwise needs 21 more steps, btw. So it's on par with Bullatosauria. Er.. *cough*
I guess the take home message is tetanurine basic relationships are highly uncertain.
Luckily, another wonderful thing about Carrano et al.s' paper is that it comes with a fully constructed NEXUS file. Not only that, the NEXUS includes character descriptions for NDE and even ran without error the first time. Future authors please follow suit! So, with this I was able to test alternbative topologies myself. I must say I was surprised by some of the results. What follows are the results, arranged in order of extra steps needed, with my subjective interpretation of liklihood...
Basically ambiguous
1 step- (stated in paper) Cryolophosaurus outside Neotheropoda sensu Bakker, as in Smith et al. (2007). Though this isn't a good test without more basal taxa.
1 step- (stated in paper) Monolophosaurus as a basal megalosauroid, as in Benson (2010).
1 step- Xuanhanosaurus as a piatnitzkysaurid, as in Benson (2010).
1 step- (stated in paper) Poekilopleuron as a piatnitzkysaurid, allosaur or other kind of megalosaurid.
1 step- Eustreptospondylus sister to Magnosaurus. This was proposed by Rauhut (2003), who made the former a species of that latter. Magnosaurus moves out of Afrovenatorinae to join Eustreptospondylus easily.
1 step- Duriavenator as an afrovenatorine.
1 step- Monophyletic Sinraptor. Though the characters traditionally used to combine them are cranial ones compared to Yangchuanosaurus, and their pelves are somewhat different, so how Siamotyrannus relates really isn't obvious.
1 step- (stated in paper) Chilantaisaurus as a carcharodontosaurid sensu stricto, not a neovenatorine.
2 steps- Megalosauroidea as carnosaurs, as Huene originally proposed, and Rauhut (2003) and Cau more recently find. This rearranges the whole tree so that megalosauroid relationships are less resolved, and Piatnitzkysauridae and Lourinhanosaurus are successively closer to sinraptorids+allosaurs than megalosauroids are. The fact the backbone of the tree crashes down so easily is disconcerting.
2 steps- Streptospondylus as an afrovenatorine (or really Afrovenator as a streptospondyline).
2 steps- (stated in paper) Lourinhanosaurus as a basal carnosaur (as in Holtz et al., 2004) or sister to Avetheropoda.
Quite likely to be true
3 steps- "Dilophosaurus" sinensis outside Neotheropoda sensu Bakker, as in Smith et al. (2007). Cryolophosaurus follows. As with Cryolophosaurus above, we'd really need more basal taxa included to test this.
3 steps- Piatnitzkysaurus outside Orionides, as in Rauhut (2003). Other piatnitzkysaurids follow.
3 steps- Xuanhanosaurus outside Orionides, as in Holtz et al. (2004). It ends up by Monolophosaurus.
3 steps- Eustreptospondylus as an afrovenatorine (or really Afrovenator as a eustreptospondyline), as in Allain (2002).
3 steps- Afrovenator as a carnosaur, as in Rauhut (2003). Even though I constrained Afrovenator to be closer to Allosaurus than to Eustreptospondylus and Torvosaurus as in Rauhut's tree, this makes all megalosauroids carnosaurs. The carnosaur phylogeny is (Strepto(Megalosauridae((Afro+Leshan)(Spino(Piatnitzky(Lourinhano(Sinrap,Allosauria))))))). So megalosauroids end up being paraphyletic to carnosaurs.
4 steps- Monolophosaurus as a carnosaur, as in Sereno et al. (1996). This also makes megalosauroids carnosaurs, with the topology (Megalosauria(Mono(Piat(Lour(Sinrap+Allo))))).
4 steps- Poekilopleuron as a sinraptorid, after Benson et al. (2010).
5 steps- Monolophosaurus sister to Avetheropoda, as in Smith et al. (2007). Piatnitzkysaurids are even closer to avetheropods in this phylogeny.
5 steps- Torvosaurus and/or Eustreptospondylus being closer to spinosaurids than Afrovenator is, as in Sereno et al. (1994).
5 steps- Siamotyrannus as a coelurosaur, as in Buffetaut et al. (1996). It's closer to other coelurosaurs than Lourinhanosaurus is.
5 steps- Sinraptorids outside Avetheropoda, as in Paul (1988). Poekilopleuron becomes a coelurosaur.
Somewhat possible
6 steps- Piatnitzkysaurus as an afrovenatorine, as in Holtz et al. (2004). Megalosauridae gets shuffled around a lot.
6 steps- Sinraptorids and carcharodontosaurids as sister taxa, exclusive of Allosaurus, as in Allain (2002). This also makes megalosauroids carnosaurs, with the topology (Megalosauria(Poekilo,Lour(Saurophag(Allo(Sinrap,Carch))))).
7 steps- Eustreptospondylus closer to spinosaurids than Torvosaurus or Afrovenator are, as in Smith et al. (2007).
7 steps- Chilantaisaurus as a spinosaurid, as in Rauhut (2003).
7 steps- Neovenator as an allosaurid, as in Hutt et al. (2001). This also makes megalosauroids carnosaurs, with the topology (Megalosauria(Piat(Lour(Sinrap+Allo)))), and neovenatorines become allosaurids.
Unlikely-
9 steps- Cryolophosaurus as a coelophysoid, though again we'd like more basal taxa.
10 steps- "Dilophosaurus" sinensis as a coelophysoid, and same as above.
11 steps- "Szechuanosaurus" zigongensis outside Orionides, as in Rauhut (2003). It ends up by Monolophosaurus. Odd that so many more basic rearrangements are more likely, as described above.
11 steps- Siamotyrannus and Fukuiraptor as sister taxa, as in Holtz et al. (2004). The pair end up sister to Allosauria.
12 steps- Megaraptor as a carcharodontosaurine, as in Smith et al. (2007).
12 steps- Acrocanthosaurus as an allosaurid, as in Stovall and Langston (1950). This really changes things. It makes megalosauroids carnosaurs, with the topology (Megalosauria(Piat(Lour(Sinrap(Conca(Carch(Eocarch((Acro+Poek)(Neoven(Allo,Saurophag)))))))))). Again, surprising.
15 steps- Megaraptor as a megalosauroid, as in Calvo et al. (2004). Ends up sister to Megalosauria.
15 steps- Megaraptora as coelurosaurs, my pet hypothesis (but also partially Longrich 2001 and Novas et al. 2008). Oh noes! Even "worse", it's more like in this topology, "coelurosaurs become neovenatorids". But as I said in my last post, the analysis needs more coelurosaurs. Also remember the corrected TWG matrix needed 15 more steps to get a monophyletic Deinonychosauria, and that's standard now. So any of the above hypotheses may end up being true. Forcing megaraptorans to be coelurosaurs, but carnosaurs to be monophyletic otherwise needs 21 more steps, btw. So it's on par with Bullatosauria. Er.. *cough*
I guess the take home message is tetanurine basic relationships are highly uncertain.
Amazing new tetanurine paper
Carrano et al. just published an excellent new paper on tetanurine phylogeny, with perhaps the most new information on varied theropod taxa to be released in one place in the last decade. Not only does it cover almost every basal tetanurine known at the time it was submitted (giving revised diagnoses for many taxa), it accomplishes several things that have been long in coming. Piatnitzkysauridae (including Marshosaurus and Condorraptor) is named, though it's found to be megalosauroidean here instead of outside Orionides. What's Orionides? The megalosauroid+avetheropod group we've been needing a name for since 2003 (that's right- Avetheropoda is used instead of Neotetanurae, another win for the paper). I'm SO glad someone finally analyzed more metriacanthosaurids than Sinraptor dongi. The authors first get my applause for ressurrecting Metriacanthosauridae since it was named earlier than Sinraptoridae. My next applause is due to including Yangchuanosaurus, which has been well described since 1983 but almost always ignored since. Not only that, they tested sinraptorid ingroup relationships by coding dongi and hepingensis separately. We also get names for the megalosaurid+spinosaurid node (Megalosauria) and the allosaurid+carcharodontosaurid node (Allosauria).
I'm glad the authors excluded Sigilmassasaurus from their Carcharodontosaurus OTU, though I would have been interested to see where the genus went when coded separately. Carrano et al. recognize the referred Chuandongocoelurus specimen is Elaphrosaurus-like, which I first determined back in 2001. Like me, they keep "yandonensis" and zigongensis separate. Interestingly, both are close to Yangchuanosaurus, and indeed the authors use the combination Yangchuanosaurus zigongensis. I finally learn why the "Dilophosaurus" sinensis skull I saw at the RTMP doesn't look like the illustration in Hu's paper- there are two sinensis specimens! Young Dilophosaurus specimen TMM 43646 differs from the other specimens, so may be a new species. We learn that new specimens confirm the snout elements are correctly referred to Marshosaurus. Turns out the type of Allosaurus? sibiricus is metatarsal II, not IV. Erectopus is stated to be a non-carcharodontosaurid carnosaur, though this isn't tested. Oddly though stated to be possibly metriacanthosaurid, it's placed above allosaurids in their phylogram. Gasosaurus lacks a proximally extensive anterior trochanter and is being restudied (cited as Hone pers. comm.). Carrano et al. retain "Poekilopleuron" schmidti's identification as a theropod humerus, but I disagree. Unquillosaurus' pubis is correctly flipped so that the supposed medial side is lateral, something which Headden and I found in 2002. They think it's possibly carcharodontosaurid, which is interesting because back then I said it resembled Acrocanthosaurus most in anterior view. The pelvis of Kryptops is carcharodontosaurid, probably belonging to Eocarcharia.
The phylogeny is interesting in several ways. Since Carrano and Benson have done good cladistic work in the past, I'm betting all codable characters are coded and with few miscodings, unlike several other recent tetanurine phylogenies (Holtz et al. 2004 Smith et al. 2007 *cough cough*). I will note all characters are unordered though, which should be fixed. One of the coolest things is supplementary table 1, which shows what prior analyses have used each character and how they phrased it.
Cryolophosaurus and "Dilophosaurus" sinensis are not only not coelophysoids, they're basal tetanurines. This has happened sometimes in my saurischian supermatrix as well, but I always figured it was due to not all characters being coded for all taxa.
Eustreptospondylus is a basal megalosaurid, and Streptospondylus may be related, but can go anywhere in Megalosauria outside Baryonychinae+Spinosaurinae and Megalosaurinae+Afrovenatorinae. The latter clade is another new name, since it turns out Dubreuillosaurus, Magnosaurus and Afrovenator aren't closely related to Streptospondylus or Eustreptospondylus (countering Rauhut's synonymization of the latter with Magnosaurus) after all. Other afrovenatorines are Leshansaurus (which Cau correctly placed in Megalosauridae), Poekilopleuron and Piveteausaurus. Duriavenator and Torvosaurus are megalosaurines.
Metriacanthosauridae turns out to be huge, with Yangchuanosaurus most basal, then a Metriacanthosaurinae structured as follows- (Shidaisaurus (Metriacanthosaurus, hepingensis (Sinraptor, Siamotyrannus). So Sinraptor is not monophyletic. Xuanhanosaurus is also a metriacanthosaurid, but not a member of the Metriacanthosaurus+Sinraptor clade. Saurophaganax's allosaurid position is finally tested and confirmed. Concavenator is a basal carcharodontosaurid by Eocarcharia. Lourinhanosaurus oddly emerges as a basal coelurosaur.
We get a "new" theropod taxon- "Saurocephalus" monasterii Muenster, 1836. As they say, it's "based on a recurved, serrated tooth from the Oxfordian Korallenkalk of the Lindner Berge, Hanover, Germany. Windolf (1997) transferred the taxon to Megalosaurus but Muenster’s tooth cannot be identified past the level of Theropoda indet."
There are a few things I disagree with or that could use work though. One is that additional basal and derived taxa are necessary to confirm some relationships. Placing Cryolophosaurus and sinensis in Tetanurae might be caused by excluding Sarcosaurus, Dracovenator and/or Zupaysaurus, for instance. And three coelurosaurs (Proceratosaurus, Compsognathus and Ornitholestes) are way too few to tell if megaraptorans are really carcharodontosaurids. I'd want Zuolong, Coelurus and/or Tanycolagreus, Guanlong, Dilong, Stokesosaurus, Eotyrannus and Huaxiagnathus included too. That might also reposition Lourinhanosaurus, as it is a basal carnosaur or sister to Avetheropoda with two more steps.
Also, alternative topologies are barely tested, except that making megalosauroids carnosaurs takes seven more steps (so not that unlikely, really) and several genera are stated to move to other places with one more step (Monolophosaurus a basal megalosauroid instead of non-orionidan; Poekilopleuron elsewhere in Megalosauroidea or in Allosauria; Cryolophosaurus outside Neotheropoda; etc.). I'd like to know how many more steps are needed for alternatives- non-orionidan piatnitzkysaurids or Xuanhanosaurus, coelophysoid Cryolophosaurus and/or sinensis, non-neotheropod sinensis, carnosaurian Monolophosaurus, 'afrovenatorine' Eustreptospondylus and/or Streptospondylus, Eustreptospondylus sister to Magnosaurus, afrovenatorine Duriavenator, monophyletic Sinraptor, coelurosaurian Siamotyrannus or megaraptorans, allosaurids sister to metriacanthosaurids+carcharodontosaurids, allosaurid Acrocanthosaurus and/or Neovenator, allosaurians sister to coelurosaurs, etc..
Megalosauria and Allosauria are never explicitly defined. Metriacanthosaurinae is listed as a new name, but Paul (1988) named it. It's odd they missed that, since the family is correctly attributed to him. I don't like their use of Averostra (for the cerato+tet node, when promaxillary fenestrae evolved before that), Neotheropoda (for the coelophysoid+ node instead of the cerato+tet node) or Allosauroidea (instead of Carnosauria). Though Carrano et al. agree Suchomimus is probably Cristatusaurus, they incorrectly call the latter indeterminate. Megalosaurus? "dapukaensis" and "tibetensis" are wrongly cited as Zhao 1986 instead of 1985. I would have liked matrix entries for the more complete taxa not included, like Erectopus, Kaijiangosaurus, Kelmayisaurus and Cruxicheiros. Finally, while the completeness of their taxon review is commendable, their analysis of tooth-based taxa is weak, since most are just bypassed as Theropoda indet. instead of examining dental features that vary between theropod clades.
These caveats aside, Carrano et al. (2012) is good enough that everyone should cut out the Basal Tetanurae chapter in their copy of The Dinosauria 2nd Ed. and put this there instead.
References- Muenster, 1836. Ueber die Korallenkalk das Linder Berges bei Hanover vorkommenden Ueberreste von Fischen, mit Beschreibung und Abbildung einiger neuen Arten. in Muenster and Wissman (eds.). Beitrage zur Petrefacten-Kunde. 7, 36-50.
Windolf, 1997. Theropoden-Zahne aus dem Oberen Jura Niedersachsens. in Sachs, Rauhut and Weigert (eds.). 1. Treffen der deutschsprachigen Palaoherpetologen, Terra Nostra, Extended Abstracts. Dusseldorf, Germany. 33-34.
Carrano, Benson and Sampson, 2012. The phylogeny of Tetanurae (Dinosauria: Theropoda). Journal of Systematic Palaeontology. 10(2), 211-300.
I'm glad the authors excluded Sigilmassasaurus from their Carcharodontosaurus OTU, though I would have been interested to see where the genus went when coded separately. Carrano et al. recognize the referred Chuandongocoelurus specimen is Elaphrosaurus-like, which I first determined back in 2001. Like me, they keep "yandonensis" and zigongensis separate. Interestingly, both are close to Yangchuanosaurus, and indeed the authors use the combination Yangchuanosaurus zigongensis. I finally learn why the "Dilophosaurus" sinensis skull I saw at the RTMP doesn't look like the illustration in Hu's paper- there are two sinensis specimens! Young Dilophosaurus specimen TMM 43646 differs from the other specimens, so may be a new species. We learn that new specimens confirm the snout elements are correctly referred to Marshosaurus. Turns out the type of Allosaurus? sibiricus is metatarsal II, not IV. Erectopus is stated to be a non-carcharodontosaurid carnosaur, though this isn't tested. Oddly though stated to be possibly metriacanthosaurid, it's placed above allosaurids in their phylogram. Gasosaurus lacks a proximally extensive anterior trochanter and is being restudied (cited as Hone pers. comm.). Carrano et al. retain "Poekilopleuron" schmidti's identification as a theropod humerus, but I disagree. Unquillosaurus' pubis is correctly flipped so that the supposed medial side is lateral, something which Headden and I found in 2002. They think it's possibly carcharodontosaurid, which is interesting because back then I said it resembled Acrocanthosaurus most in anterior view. The pelvis of Kryptops is carcharodontosaurid, probably belonging to Eocarcharia.
 |
| Phylogeny from Carrano et al. (2012) taken from their figure 7A. Numbers to the left of nodes are unambiguous character support and numbers to the right are branch support. |
The phylogeny is interesting in several ways. Since Carrano and Benson have done good cladistic work in the past, I'm betting all codable characters are coded and with few miscodings, unlike several other recent tetanurine phylogenies (Holtz et al. 2004 Smith et al. 2007 *cough cough*). I will note all characters are unordered though, which should be fixed. One of the coolest things is supplementary table 1, which shows what prior analyses have used each character and how they phrased it.
Cryolophosaurus and "Dilophosaurus" sinensis are not only not coelophysoids, they're basal tetanurines. This has happened sometimes in my saurischian supermatrix as well, but I always figured it was due to not all characters being coded for all taxa.
Eustreptospondylus is a basal megalosaurid, and Streptospondylus may be related, but can go anywhere in Megalosauria outside Baryonychinae+Spinosaurinae and Megalosaurinae+Afrovenatorinae. The latter clade is another new name, since it turns out Dubreuillosaurus, Magnosaurus and Afrovenator aren't closely related to Streptospondylus or Eustreptospondylus (countering Rauhut's synonymization of the latter with Magnosaurus) after all. Other afrovenatorines are Leshansaurus (which Cau correctly placed in Megalosauridae), Poekilopleuron and Piveteausaurus. Duriavenator and Torvosaurus are megalosaurines.
Metriacanthosauridae turns out to be huge, with Yangchuanosaurus most basal, then a Metriacanthosaurinae structured as follows- (Shidaisaurus (Metriacanthosaurus, hepingensis (Sinraptor, Siamotyrannus). So Sinraptor is not monophyletic. Xuanhanosaurus is also a metriacanthosaurid, but not a member of the Metriacanthosaurus+Sinraptor clade. Saurophaganax's allosaurid position is finally tested and confirmed. Concavenator is a basal carcharodontosaurid by Eocarcharia. Lourinhanosaurus oddly emerges as a basal coelurosaur.
We get a "new" theropod taxon- "Saurocephalus" monasterii Muenster, 1836. As they say, it's "based on a recurved, serrated tooth from the Oxfordian Korallenkalk of the Lindner Berge, Hanover, Germany. Windolf (1997) transferred the taxon to Megalosaurus but Muenster’s tooth cannot be identified past the level of Theropoda indet."
There are a few things I disagree with or that could use work though. One is that additional basal and derived taxa are necessary to confirm some relationships. Placing Cryolophosaurus and sinensis in Tetanurae might be caused by excluding Sarcosaurus, Dracovenator and/or Zupaysaurus, for instance. And three coelurosaurs (Proceratosaurus, Compsognathus and Ornitholestes) are way too few to tell if megaraptorans are really carcharodontosaurids. I'd want Zuolong, Coelurus and/or Tanycolagreus, Guanlong, Dilong, Stokesosaurus, Eotyrannus and Huaxiagnathus included too. That might also reposition Lourinhanosaurus, as it is a basal carnosaur or sister to Avetheropoda with two more steps.
Also, alternative topologies are barely tested, except that making megalosauroids carnosaurs takes seven more steps (so not that unlikely, really) and several genera are stated to move to other places with one more step (Monolophosaurus a basal megalosauroid instead of non-orionidan; Poekilopleuron elsewhere in Megalosauroidea or in Allosauria; Cryolophosaurus outside Neotheropoda; etc.). I'd like to know how many more steps are needed for alternatives- non-orionidan piatnitzkysaurids or Xuanhanosaurus, coelophysoid Cryolophosaurus and/or sinensis, non-neotheropod sinensis, carnosaurian Monolophosaurus, 'afrovenatorine' Eustreptospondylus and/or Streptospondylus, Eustreptospondylus sister to Magnosaurus, afrovenatorine Duriavenator, monophyletic Sinraptor, coelurosaurian Siamotyrannus or megaraptorans, allosaurids sister to metriacanthosaurids+carcharodontosaurids, allosaurid Acrocanthosaurus and/or Neovenator, allosaurians sister to coelurosaurs, etc..
Megalosauria and Allosauria are never explicitly defined. Metriacanthosaurinae is listed as a new name, but Paul (1988) named it. It's odd they missed that, since the family is correctly attributed to him. I don't like their use of Averostra (for the cerato+tet node, when promaxillary fenestrae evolved before that), Neotheropoda (for the coelophysoid+ node instead of the cerato+tet node) or Allosauroidea (instead of Carnosauria). Though Carrano et al. agree Suchomimus is probably Cristatusaurus, they incorrectly call the latter indeterminate. Megalosaurus? "dapukaensis" and "tibetensis" are wrongly cited as Zhao 1986 instead of 1985. I would have liked matrix entries for the more complete taxa not included, like Erectopus, Kaijiangosaurus, Kelmayisaurus and Cruxicheiros. Finally, while the completeness of their taxon review is commendable, their analysis of tooth-based taxa is weak, since most are just bypassed as Theropoda indet. instead of examining dental features that vary between theropod clades.
These caveats aside, Carrano et al. (2012) is good enough that everyone should cut out the Basal Tetanurae chapter in their copy of The Dinosauria 2nd Ed. and put this there instead.
References- Muenster, 1836. Ueber die Korallenkalk das Linder Berges bei Hanover vorkommenden Ueberreste von Fischen, mit Beschreibung und Abbildung einiger neuen Arten. in Muenster and Wissman (eds.). Beitrage zur Petrefacten-Kunde. 7, 36-50.
Windolf, 1997. Theropoden-Zahne aus dem Oberen Jura Niedersachsens. in Sachs, Rauhut and Weigert (eds.). 1. Treffen der deutschsprachigen Palaoherpetologen, Terra Nostra, Extended Abstracts. Dusseldorf, Germany. 33-34.
Carrano, Benson and Sampson, 2012. The phylogeny of Tetanurae (Dinosauria: Theropoda). Journal of Systematic Palaeontology. 10(2), 211-300.
Tuesday, May 15, 2012
New dromaeosaurid Yurgovuchia
So a new dromaeosaurid was described today by Senter et al. (2012), whose description is free at PLoS ONE.
Interesting that the authors sink Linheraptor into Tsaagan. No evidence is given, and they commit a pet peeve of mine, in sinking a species into a genus, so Linheraptor exquisitus becomes Tsaagan sp.. Which not only is improper, as you can't just destroy species, but unecessary since Linheraptor only has one named species.
The phylogenetic analysis is Senter et al.'s (2010), with several taxa added. One of these is Xiaotingia, which makes this a partial test to see if Archaeopteryx stays a deinonychosaur when paravians Senter didn't include are added. The authors importantly add Sinusonasus (from Senter, 2010), Austroraptor, Mahakala, Shanag and Tianyuraptor, which leads to Archaeopteryx being an avialan as usual. See what I meant about waiting for other analyses to confirm Xu et al.'s finding before accepting it? Also contra Xu et al., Anchiornis and Xiaotingia aren't archaeopterygids and don't form a clade, with the former remaining a troodontid as in Senter (2010) and the latter being a basal dromaeosaurid. Still not included are Balaur, Pedopenna, Jinfengopteryx, IGM 100/1128, Jixiangornis, Dalianraptor or Yandangornis among important basal paravians. What will the Lori analysis say? We'll have to see...
References- Senter, 2010. Using creation science to demonstrate evolution: application of a creationist method for visualizing gaps in the fossil record to a phylogenetic study of coelurosaurian dinosaurs. Journal of Evolutionary Biology. 23(8), 1732-1743.
Senter, Kirkland, Bird and Bartlett, 2010. A new troodontid theropod dinosaur from the Lower Cretaceous of Utah. PLoS ONE. 5(12), e14329.
Xu, You, Du and Han, 2011. An Archaeopteryx-like theropod from China and the origin of Avialae. Nature. 475, 465-470.
Senter, Kirkland, DeBlieux, Madsen and Toth, 2012. New dromaeosaurids (Dinosauria: Theropoda) from the Lower Cretaceous of Utah, and the evolution of the dromaeosaurid tail. PLoS ONE. 7(5), e36790.
Interesting that the authors sink Linheraptor into Tsaagan. No evidence is given, and they commit a pet peeve of mine, in sinking a species into a genus, so Linheraptor exquisitus becomes Tsaagan sp.. Which not only is improper, as you can't just destroy species, but unecessary since Linheraptor only has one named species.
The phylogenetic analysis is Senter et al.'s (2010), with several taxa added. One of these is Xiaotingia, which makes this a partial test to see if Archaeopteryx stays a deinonychosaur when paravians Senter didn't include are added. The authors importantly add Sinusonasus (from Senter, 2010), Austroraptor, Mahakala, Shanag and Tianyuraptor, which leads to Archaeopteryx being an avialan as usual. See what I meant about waiting for other analyses to confirm Xu et al.'s finding before accepting it? Also contra Xu et al., Anchiornis and Xiaotingia aren't archaeopterygids and don't form a clade, with the former remaining a troodontid as in Senter (2010) and the latter being a basal dromaeosaurid. Still not included are Balaur, Pedopenna, Jinfengopteryx, IGM 100/1128, Jixiangornis, Dalianraptor or Yandangornis among important basal paravians. What will the Lori analysis say? We'll have to see...
References- Senter, 2010. Using creation science to demonstrate evolution: application of a creationist method for visualizing gaps in the fossil record to a phylogenetic study of coelurosaurian dinosaurs. Journal of Evolutionary Biology. 23(8), 1732-1743.
Senter, Kirkland, Bird and Bartlett, 2010. A new troodontid theropod dinosaur from the Lower Cretaceous of Utah. PLoS ONE. 5(12), e14329.
Xu, You, Du and Han, 2011. An Archaeopteryx-like theropod from China and the origin of Avialae. Nature. 475, 465-470.
Senter, Kirkland, DeBlieux, Madsen and Toth, 2012. New dromaeosaurids (Dinosauria: Theropoda) from the Lower Cretaceous of Utah, and the evolution of the dromaeosaurid tail. PLoS ONE. 7(5), e36790.
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