Saturday, December 31, 2011
Happy New Year! The Database is updated!
Check it out! All the 2011 taxa are there. I'm off to party....
Surprise! Jeholornis palmapenis isn't valid.
What's that you say? ANOTHER supposedly new Jehol basal avialan is just a junior synonym of a known species?! Shock! Gasp! This time it's none other than the armless Jeholornis palmapenis (insert priapic joke here). On the plus side, at least the description is better than others so far published, so this will help when coding Shenzhouraptor sinensis for matrices.
O'Connor et al. (2012) listed several characters supposedly distinguishing this taxon from Jeholornis prima.
The single preserved maxillary tooth and second empty alveolus contrast with IVPP V13274 (the prima holotype), V13550 and V13553 (both referred to prima), which have been reported to lack maxillary teeth. Yet jeholornithid teeth are often unpreserved due to their small size and low number, as seen by palmapenis' lack of dentary teeth (considered preservational by O'Connor et al.) and LPM 0193's (the Shenzhouraptor holotype) lack of any recognizable teeth. Even palmapenis only preserves one of the at least two maxillary teeth it had on that side. Thus the absence of maxillary teeth in other specimens may easily be preservational.
The presence of two pairs of anterior dorsal pleurocoels was listed as diagnostic (grading into a single pair posteriorly), but pleurocoel number often varies between different vertebrae and even sides of the same vertebra in theropods. Anterior pleurocoel number has not been described in any other jeholornithid specimen, but IVPP V13353 shows single pairs in dorsals nine and eleven, and three pairs in ten. Until palmapenis is shown to be consistantly unique in pleurocoel number, this character is not considered diagnostic.
The ilium is supposedly strongly convex dorsally, but it's clear the anterodorsal portion has merely been broken off, with no dorsal margin remaining anterior to the acetabular midpoint. The margin posterior to this is slightly convex as in other jeholornithid specimens. The anterior dorsal margin is preserved on the disarticulated left ilium, which forms a similar overall ilial dorsal convexity to other jeholornithids when rotated into place. Similarly, though the postacetabular process was described as strongly concave ventrally, the concavity is almost identical to that in IVPP V13353 (20% distance from line stretching from top of acetabulum to ventral postacetabular tip is 20% of ilial depth above acetabulum, compared to 19%) and other jeholornithids (the supposedly straight margin of IVPP V13274 looks slightly curved in the photo, and any difference would be insignificant in any case).
The dorsally curved ischium was also said to be diagnostic, but the distal ischium is unpreserved in the prima holotype, with the reconstructed portion being part of the tibia or fibula instead. Indeed, O'Connor et al. state ischial curvature is unclear in other Jeholornis specimens. LPM 0193 shows a dorsally curved ischium, albeit less so than in palmapenis.
In the tail, the transition point was stated to be more gradual (in central elongation) and posterior (at caudal seven instead of six) in palmapenis than IVPP V13550. Yet the transition point is also different in IVPP V13353, where the first elongated caudal is five, and IVPP V13274, where it seems to be at four (an unlabeled caudal is disarticulated adjacent to the last sacral). Differences in transition point abruptness are present as individual variation in other taxa, such as two nearly identical Microraptor specimens (CAGS 20-7-004 and 20-8-001), where the difference between lengths of caudals three and four is 9% in one and 53% in the other). Both caudal differences are thus more probably individual variation.
Finally, the diagnosis lists "elongated caudals possess chevrons with hooked articulations", but these articulations are not mentioned again and photos show normal, straight dorsal, anterior and posterior ends as in other paravians.
Of the diagnostic characters listed for prima by O'Connor et al., the ones not mentioned above are all unknown in palmapenis (except the robust dentary, which is true for all jeholornithids). In the text, the dentaries are said to appear unfused unlike the prima holotype, but they note this may be due to poor preservation. It may also be due to ontogeny, as palmapenis is smaller and has an unfused metatarsus. The text also states the ilium differs in having a bround rounded preacetabular process supposedly unlike IVPP V13274, but this is due to the latter being in medial view and not showing the ventral flange that would be lateral to the cuppedicus fossa, as seen in IVPP V13353 and LPM 0193.
So of the listed differences from prima, only the difference in maxillary dentulousness can even be plausibly considered true and not subject to individual variation. Ironically there are some valid differences not mentioned in the text. The dentary is a third deeper than the prima holotype and IVPP V13350, which is opposite the expected trend for a juvenile. The ischium slightly expands at its tip, unlike the Shenzhouraptor holotype. But since the first difference is not observable in the Shenzhouraptor type (whose anterior dentary angles beneath the skull) and the second difference is not observable in the prima type (whose distal ischium is broken off), these would form a weak differentiation from either species. As both character states are derived in Avialae, Shenzhouraptor and prima could not be united by their counterpart states. Instead, until they are shown to have a consistant variation between multiple specimens, the differences are more readily ascribed to individual variation as is found in any theropod known from large sample sizes (Allosaurus, Tyrannosaurus, Microraptor, Archaeopteryx). Jeholornis palmapenis is here made a junior synonym of Shenzhouraptor sinensis.
Referennces- Zhou and Zhang, 2003. Jeholornis compared to Archaeopteryx, with a new understanding of the earliest avian evolution. Naturwissenschaften. 90, 220-225.
O'Connor, Sun, Xu, Wang and Zhou, 2012. A new species of Jeholornis with complete caudal integument. Historical Biology. DOI: 10.1080/08912963.2011.552720
O'Connor et al. (2012) listed several characters supposedly distinguishing this taxon from Jeholornis prima.
The single preserved maxillary tooth and second empty alveolus contrast with IVPP V13274 (the prima holotype), V13550 and V13553 (both referred to prima), which have been reported to lack maxillary teeth. Yet jeholornithid teeth are often unpreserved due to their small size and low number, as seen by palmapenis' lack of dentary teeth (considered preservational by O'Connor et al.) and LPM 0193's (the Shenzhouraptor holotype) lack of any recognizable teeth. Even palmapenis only preserves one of the at least two maxillary teeth it had on that side. Thus the absence of maxillary teeth in other specimens may easily be preservational.
The presence of two pairs of anterior dorsal pleurocoels was listed as diagnostic (grading into a single pair posteriorly), but pleurocoel number often varies between different vertebrae and even sides of the same vertebra in theropods. Anterior pleurocoel number has not been described in any other jeholornithid specimen, but IVPP V13353 shows single pairs in dorsals nine and eleven, and three pairs in ten. Until palmapenis is shown to be consistantly unique in pleurocoel number, this character is not considered diagnostic.
 |
| Comparison of palmapenis ilium (top; after O'Connor et al., 2012) with prima (bottom; after Zhou and Zhang, 2003). Note the ventral edge of the postacetabular process (blue) is not significantly more concave in palmapenis. Note also the obvious breakage of the ilium (circled in red), making the dorsal border look highly convex. The upper right picture shows superimposed and flipped images of the anterior left ilium and posterior right ilium to show the dorsal margin (surrounded by green) is straight. Note that when the dorsal margins are lined up this way, the preserved posteroventral portion conveniently follows the outline of the other pubic peduncle. |
The ilium is supposedly strongly convex dorsally, but it's clear the anterodorsal portion has merely been broken off, with no dorsal margin remaining anterior to the acetabular midpoint. The margin posterior to this is slightly convex as in other jeholornithid specimens. The anterior dorsal margin is preserved on the disarticulated left ilium, which forms a similar overall ilial dorsal convexity to other jeholornithids when rotated into place. Similarly, though the postacetabular process was described as strongly concave ventrally, the concavity is almost identical to that in IVPP V13353 (20% distance from line stretching from top of acetabulum to ventral postacetabular tip is 20% of ilial depth above acetabulum, compared to 19%) and other jeholornithids (the supposedly straight margin of IVPP V13274 looks slightly curved in the photo, and any difference would be insignificant in any case).
The dorsally curved ischium was also said to be diagnostic, but the distal ischium is unpreserved in the prima holotype, with the reconstructed portion being part of the tibia or fibula instead. Indeed, O'Connor et al. state ischial curvature is unclear in other Jeholornis specimens. LPM 0193 shows a dorsally curved ischium, albeit less so than in palmapenis.
In the tail, the transition point was stated to be more gradual (in central elongation) and posterior (at caudal seven instead of six) in palmapenis than IVPP V13550. Yet the transition point is also different in IVPP V13353, where the first elongated caudal is five, and IVPP V13274, where it seems to be at four (an unlabeled caudal is disarticulated adjacent to the last sacral). Differences in transition point abruptness are present as individual variation in other taxa, such as two nearly identical Microraptor specimens (CAGS 20-7-004 and 20-8-001), where the difference between lengths of caudals three and four is 9% in one and 53% in the other). Both caudal differences are thus more probably individual variation.
Finally, the diagnosis lists "elongated caudals possess chevrons with hooked articulations", but these articulations are not mentioned again and photos show normal, straight dorsal, anterior and posterior ends as in other paravians.
Of the diagnostic characters listed for prima by O'Connor et al., the ones not mentioned above are all unknown in palmapenis (except the robust dentary, which is true for all jeholornithids). In the text, the dentaries are said to appear unfused unlike the prima holotype, but they note this may be due to poor preservation. It may also be due to ontogeny, as palmapenis is smaller and has an unfused metatarsus. The text also states the ilium differs in having a bround rounded preacetabular process supposedly unlike IVPP V13274, but this is due to the latter being in medial view and not showing the ventral flange that would be lateral to the cuppedicus fossa, as seen in IVPP V13353 and LPM 0193.
So of the listed differences from prima, only the difference in maxillary dentulousness can even be plausibly considered true and not subject to individual variation. Ironically there are some valid differences not mentioned in the text. The dentary is a third deeper than the prima holotype and IVPP V13350, which is opposite the expected trend for a juvenile. The ischium slightly expands at its tip, unlike the Shenzhouraptor holotype. But since the first difference is not observable in the Shenzhouraptor type (whose anterior dentary angles beneath the skull) and the second difference is not observable in the prima type (whose distal ischium is broken off), these would form a weak differentiation from either species. As both character states are derived in Avialae, Shenzhouraptor and prima could not be united by their counterpart states. Instead, until they are shown to have a consistant variation between multiple specimens, the differences are more readily ascribed to individual variation as is found in any theropod known from large sample sizes (Allosaurus, Tyrannosaurus, Microraptor, Archaeopteryx). Jeholornis palmapenis is here made a junior synonym of Shenzhouraptor sinensis.
Referennces- Zhou and Zhang, 2003. Jeholornis compared to Archaeopteryx, with a new understanding of the earliest avian evolution. Naturwissenschaften. 90, 220-225.
O'Connor, Sun, Xu, Wang and Zhou, 2012. A new species of Jeholornis with complete caudal integument. Historical Biology. DOI: 10.1080/08912963.2011.552720
Monday, December 26, 2011
Merry Christmas! It's Xu's Thesis
I received a wonderful Christmas present this year- a copy of Xu's (2002) thesis on Liaoning deinonychosaurs which I've wanted for a decade now. It's referenced in most of Xu's publications, but not in many others, and since it's not available in pdf, the info is difficult to come by. This is one of the best publications on theropods I've read, so I'll sum up the contents here.
The first section is an osteology of the holotype of Sinornithosaurus. The cranial and pedal sections have been published (as Xu and Wu, 2001 and Xu and Wang, 2000), but the axial description was most interesting to me. It preserves 21 presacral vertebrae and the first nine caudals, yet these are not easily identified in the original tabloid description, unlike the pectoral girdle, manus and pelvis, which show most of their characters in the original figures.
The second section is an osteology of Microraptor's holotype, but also a specimen otherwise unmentioned in the literature- incomplete skeleton IVPP V13475 from the Jiufotang Formation, missing only some caudal vertebrae and the left manus. This provides us with the Microraptor skull description I've been waiting for, and is what the reconstruction in Xu et al.'s (2011) paper is from, and what many of the codings for Microraptor in Xu and Zhang's (2005) matrix are from. The rest of the description is less useful now that we have Hwang et al.'s (2002), but does feature interesting details like a large coracoid fenestra as in Sinornithosaurus and a straight pubis unlike other microraptorians.
The third section is an osteology of the then-undescribed Graciliraptor, so "Graciliraptor lujiatunensis" Xu, 2002 is a nomen nudum used prior to 2004. The description is better than the published version, but not by much since it was published in a real journal, and the specimen is fragmentary to begin with.
The fourth section is my favorite- a detailed osteology of the holotype and paratype of Sinovenator. The species name is given as changae, as opposed to changii, since Li noted it was grammatically incorrect. Creisler noted this on the DML that year too, but suggested changiae. Since it's named after a woman named Chang, I think changae would be right, but as I note on the Database, the Fourth Edition of the ICZN no longer requires emendations based on this reasoning (Article 31.1.3). Nomenclature aside, the description is excellent and includes such needed things as an anterolateral view of the coracoid, posterior view of the braincase, and multiple views of presacral vertebrae. Since we really don't have any detailed published descriptions of basal troodontid anatomy, and Sinovenator is basically complete (missing most of the palate, the quadratojugal, part of the mandible, half the cervicals, the post-26 caudals, ribs, and part of the hand), this section is vital to anyone studying paravian phylogeny.
The next section is about the feathers of Liaoning dromaeosaurids, which I normally would find boring, except that among the specimens described and photographed are Microraptor gui paratypes IVPP V13477 and V13320. Of course, M. gui was a year away in 2002, so Xu refers to them as Sinornithosaurus sp. and Microraptor sp. respectively. Interestingly, IVPP V13320 has completely serrationless teeth, while most Microraptor specimens have only distally serrated (posterior) teeth, and NGMC 00-12-A has posterior dentary teeth with serrations on both carinae.
The last section is one I would normally be very excited about- the phylogenetic analysis. But it's basically the same as Xu and Zhang's (2005) with one less character and without Scansoriopteryx, Shenzhouraptor and Pedopenna (careful readers will note two mentions of Shenzhouraptor as an unnamed new bird without a pygostyle and one mention of Zuolong as an unnamed basal coelurosaur). Xu runs lots of variations (cranial only, postcranial only, only basal taxa, only derived taxa, excluding various taxa) that would have been very interesting back in 2003, but since so many new taxa are lacking, are now more of historical interest like my Evaluating Phylogenetic Analyses section. One good thing is that he describes several of the characters in depth and even provides graphs showing ratio distributions, so that they can be evaluated better than most TWG characters.
Xu ends with extensive measurement tables for the specimens described in the osteologies, but unfortunately not for the M. gui paratypes. I would have liked more illustrations, but Xu's descriptions are top notch, and are badly needed for taxa described in tabloids like Sinornithosaurus and Sinovenator. I don't know why most of this material was never published, since it's been written up for almost a decade now. Similarly, I can only hope something of this caliber is written up for Beipiaosaurus and Mei. Unfortunately, I only have a hard copy, so cannot send pdfs yet.
References- Xu and Wang, 2000. Troodontid-like pes in the dromaeosaurid Sinornithosaurus. Paleont. Soc. Korea Special Publication. 4, 179-188.
Xu and Wu, 2001. Cranial morphology of Sinornithosaurus millenii Xu et al. 1999 (Dinosauria: Theropoda: Dromaeosauridae) from the Yixian Formation of Liaoning, China. Canadian Journal of Earth Sciences. 38, 1739-1752.
Hwang, Norell, Qiang and Keqin, 2002. New specimens of Microraptor zhaoianus (Theropoda: Dromaeosauridae) from northeastern China. American Museum Novitates. 3381, 1-44.
Xu, 2002. Deinonychosaurian fossils from the Jehol Group of Western Liaoning and the coelurosaurian evolution. PhD Thesis. Chinese Academy of Sciences. 325 pp.
Xu and Zhang, 2005. A new maniraptoran dinosaur from China with long feathers on the metatarsus. Naturwissenschaften. 92, 173-177.
Xu, You, Du and Han, 2011. An Archaeopteryx-like theropod from China and the origin of Avialae. Nature. 475, 465-470.
The first section is an osteology of the holotype of Sinornithosaurus. The cranial and pedal sections have been published (as Xu and Wu, 2001 and Xu and Wang, 2000), but the axial description was most interesting to me. It preserves 21 presacral vertebrae and the first nine caudals, yet these are not easily identified in the original tabloid description, unlike the pectoral girdle, manus and pelvis, which show most of their characters in the original figures.
The second section is an osteology of Microraptor's holotype, but also a specimen otherwise unmentioned in the literature- incomplete skeleton IVPP V13475 from the Jiufotang Formation, missing only some caudal vertebrae and the left manus. This provides us with the Microraptor skull description I've been waiting for, and is what the reconstruction in Xu et al.'s (2011) paper is from, and what many of the codings for Microraptor in Xu and Zhang's (2005) matrix are from. The rest of the description is less useful now that we have Hwang et al.'s (2002), but does feature interesting details like a large coracoid fenestra as in Sinornithosaurus and a straight pubis unlike other microraptorians.
The third section is an osteology of the then-undescribed Graciliraptor, so "Graciliraptor lujiatunensis" Xu, 2002 is a nomen nudum used prior to 2004. The description is better than the published version, but not by much since it was published in a real journal, and the specimen is fragmentary to begin with.
The fourth section is my favorite- a detailed osteology of the holotype and paratype of Sinovenator. The species name is given as changae, as opposed to changii, since Li noted it was grammatically incorrect. Creisler noted this on the DML that year too, but suggested changiae. Since it's named after a woman named Chang, I think changae would be right, but as I note on the Database, the Fourth Edition of the ICZN no longer requires emendations based on this reasoning (Article 31.1.3). Nomenclature aside, the description is excellent and includes such needed things as an anterolateral view of the coracoid, posterior view of the braincase, and multiple views of presacral vertebrae. Since we really don't have any detailed published descriptions of basal troodontid anatomy, and Sinovenator is basically complete (missing most of the palate, the quadratojugal, part of the mandible, half the cervicals, the post-26 caudals, ribs, and part of the hand), this section is vital to anyone studying paravian phylogeny.
The next section is about the feathers of Liaoning dromaeosaurids, which I normally would find boring, except that among the specimens described and photographed are Microraptor gui paratypes IVPP V13477 and V13320. Of course, M. gui was a year away in 2002, so Xu refers to them as Sinornithosaurus sp. and Microraptor sp. respectively. Interestingly, IVPP V13320 has completely serrationless teeth, while most Microraptor specimens have only distally serrated (posterior) teeth, and NGMC 00-12-A has posterior dentary teeth with serrations on both carinae.
The last section is one I would normally be very excited about- the phylogenetic analysis. But it's basically the same as Xu and Zhang's (2005) with one less character and without Scansoriopteryx, Shenzhouraptor and Pedopenna (careful readers will note two mentions of Shenzhouraptor as an unnamed new bird without a pygostyle and one mention of Zuolong as an unnamed basal coelurosaur). Xu runs lots of variations (cranial only, postcranial only, only basal taxa, only derived taxa, excluding various taxa) that would have been very interesting back in 2003, but since so many new taxa are lacking, are now more of historical interest like my Evaluating Phylogenetic Analyses section. One good thing is that he describes several of the characters in depth and even provides graphs showing ratio distributions, so that they can be evaluated better than most TWG characters.
Xu ends with extensive measurement tables for the specimens described in the osteologies, but unfortunately not for the M. gui paratypes. I would have liked more illustrations, but Xu's descriptions are top notch, and are badly needed for taxa described in tabloids like Sinornithosaurus and Sinovenator. I don't know why most of this material was never published, since it's been written up for almost a decade now. Similarly, I can only hope something of this caliber is written up for Beipiaosaurus and Mei. Unfortunately, I only have a hard copy, so cannot send pdfs yet.
References- Xu and Wang, 2000. Troodontid-like pes in the dromaeosaurid Sinornithosaurus. Paleont. Soc. Korea Special Publication. 4, 179-188.
Xu and Wu, 2001. Cranial morphology of Sinornithosaurus millenii Xu et al. 1999 (Dinosauria: Theropoda: Dromaeosauridae) from the Yixian Formation of Liaoning, China. Canadian Journal of Earth Sciences. 38, 1739-1752.
Hwang, Norell, Qiang and Keqin, 2002. New specimens of Microraptor zhaoianus (Theropoda: Dromaeosauridae) from northeastern China. American Museum Novitates. 3381, 1-44.
Xu, 2002. Deinonychosaurian fossils from the Jehol Group of Western Liaoning and the coelurosaurian evolution. PhD Thesis. Chinese Academy of Sciences. 325 pp.
Xu and Zhang, 2005. A new maniraptoran dinosaur from China with long feathers on the metatarsus. Naturwissenschaften. 92, 173-177.
Xu, You, Du and Han, 2011. An Archaeopteryx-like theropod from China and the origin of Avialae. Nature. 475, 465-470.
Friday, December 2, 2011
Top 10 Most Poorly Described and Illustrated Mesozoic Theropods
Look at that, I managed to skip a month between posts. The hazards of coding, illness and other such excuses. Here's a quickie that was fueled by my annoyance at any significant primary literature while coding Adasaurus. These are the theropods whose publically available information is the most paltry compared to the completeness of their remains, and have been officially described already in the literature. The relative importance of the taxon isn't a factor, and taxa whose remains are lost aren't considered due to the impossibility of their redescription.
10. Anserimimus
Anserimimus' holotype is a skeleton missing only some cervicals and the skull, but only the scapulocoracoid, manus and metatarsus were described and illustrated by Barsbold (1988). Kobayashi and Barsbold (2006) helped a bit, as does Bronowicz's (2011) fragmentary but well described specimens. But what keeps this from scoring higher is the availability of good photos of the mount (e.g. this) and Kobayashi's (2004) coding it for several matrices.
9. Tie between Cristatusaurus, Deltadromeus and Afrovenator
These taxa all have a common theme- Sereno described them (well, he described Suchomimus, which I sink into Cristatusaurus). Published by the king of the Science tabloid, featuring a Paulian skeletal and several zoomed in line drawings, these taxa have yet to be redescribed in detail. While there are photos of mounted skeletons available, these are all casts. The best source of information on these are the matrices of Rauhut (2003) and Benson (2010).
8. Aucasaurus
Basically complete, but only the proximal tail, arm and lower hindlimbs have been illustrated and briefly described. Recently, the braincase was also described, though I lack that paper so far. Ceratosaur matrices like Carrano and Sampson (2007) have some info.
7. Inosaurus
Known from quite fragmentary remains, but very poorly described and only illustrated by two partial vertebrae (apparently my tracing survives unattributed online). Is it even dinosaurian?
6. "Chilantaisaurus" zheziangensis
Dong (1979) gave this proximal tibia and partial pes a fairly useless description and illustrated two pedal digits in ventrolateral view and curving towards the viewer. :| Therizinosaurian affinities have been suggested, but it's not been examined since.
5. Kaijiangosaurus
Only a few vertebrae, pectoral girdle and proximal/distal metatarsal outlines have been illustrated, and the description has yet to be translated from Chinese. An online photo shows a lot more is known, but also that size differences mean more than one individual/taxon are present.
4. Conchoraptor
Ah, Conchoraptor. You might be asking how can this be obscure when there are so many skeletons casted. I've even seen two in person. The problem with Conchoraptor is that it's unsure just which specimens belong to it, besides the holotype (of which we have illustrations of the skull, and a manus and metatarsus that presumably belong to it or a paratype). None of the articulated skeletons photographed online have the right manual proportions or slender metatarsal II, and crestless skulls like ZPAL MgD-I/95 (the one described by Osmolska, 1976 and which Kundrat has recently been describing braincase details of) and the one on Witmer's lab page identified as "Ingenia" could belong to other oviraptorids. No one has ever provided a modern diagnosis, described the holotype in any detail or justified the referral of other specimens. This makes depending on matrices more risky than for other taxa listed here, since their OTU could be chimaerical for all I know.
3. Rinchenia
This has been illustrated in the literature even more seldomly than Conchoraptor, since at least ZPAL MgD-I/95 has papers dedicated to it. We only have the skull, mandible, overly schematic ilium and a single caudal vertebra illustrated. Lucky for us, Auditore was able to obtain photos of the holotype and illustrate it as detailed by Cau on his blog. As for Conchoraptor, Norell et al. (2001), Lu (2004) and Maryanska et al. (2002) all provide codings, which can be trusted more for Rinchenia since there's only the holotype (though I note a recent incorrect trend of referring IGM 100/42 to it).
2. Adasaurus
The muse for this post only gets second place. For Adasaurus we must depend on a few schematic drawings (pelvis, metatarsus, pedal digit II), since Barsbold (1988) neither described it besides noting a couple features, nor does he allow photos to be circulated. There was a photo of the holotype online which has since disappeared, but shows Barsbold's pelvis illustration is inaccurate, and to make it worse Kubota (pers. comm. to Senter, 2010) indicates the supposed small sickle claw doesn't belong. I'm just hoping Kubota plans to redescribe the taxon like Kobayashi did for Barsbold's basal ornithomimosaurs. Until then, we depend on codings from Norell et al. (2001), Senter (2007) and Longrich and Currie (2009), and a few scattered notes. Hopefully Turner et al.'s upcoming dromaeosaurid monograph has some juicy photos.
1. Chilantaisaurus? sibiricus
There are a lot of fragmentary taxa known from a tooth or a vertebra that are poorly described (usually in a useless archaic way) and illustrated in a photo from a single view.What makes sibiricus stand out is that Riabinin (1914) didn't even identify which element the holotype was, let alone try to describe its features. He just said it was hollow and belonged to the limb of a fairly large theropod, probably a megalosaurid (named as Allosaurus? sibiricus). Even worse, he didn't illustrate it, only [Edit: Chure 2000 and Benson and Xu 2008 were incorrect about the lack of illustration and brevity of description; I've since examined the taxon here http://theropoddatabase.blogspot.com/2012/11/allosauruschilantaisaurus-sibiricus-is.html] providing six measurements (proximal width 48 mm, proximal depth 39 mm, distal width 68 mm, distal depth 62 mm, cavity width 22 mm, cavity depth 17 mm). Huene (1932) identified it as a distal metatarsal IV without rationale, but said only that it did not permit exact characterization and probably belonged to an allosaurid (renamed Antrodemus? sibiricus). Molnar et al. (1990) then said it was "almost identical with that of C. tashuikouensis in form and proportions of the distal condyle", so questionably referred it to that genus. You now possess the entirity of published information on sibiricus. Makes the available information on Adasaurus seem like an overflowing feast.
10. Anserimimus
Anserimimus' holotype is a skeleton missing only some cervicals and the skull, but only the scapulocoracoid, manus and metatarsus were described and illustrated by Barsbold (1988). Kobayashi and Barsbold (2006) helped a bit, as does Bronowicz's (2011) fragmentary but well described specimens. But what keeps this from scoring higher is the availability of good photos of the mount (e.g. this) and Kobayashi's (2004) coding it for several matrices.
9. Tie between Cristatusaurus, Deltadromeus and Afrovenator
These taxa all have a common theme- Sereno described them (well, he described Suchomimus, which I sink into Cristatusaurus). Published by the king of the Science tabloid, featuring a Paulian skeletal and several zoomed in line drawings, these taxa have yet to be redescribed in detail. While there are photos of mounted skeletons available, these are all casts. The best source of information on these are the matrices of Rauhut (2003) and Benson (2010).
8. Aucasaurus
Basically complete, but only the proximal tail, arm and lower hindlimbs have been illustrated and briefly described. Recently, the braincase was also described, though I lack that paper so far. Ceratosaur matrices like Carrano and Sampson (2007) have some info.
7. Inosaurus
Known from quite fragmentary remains, but very poorly described and only illustrated by two partial vertebrae (apparently my tracing survives unattributed online). Is it even dinosaurian?
6. "Chilantaisaurus" zheziangensis
Dong (1979) gave this proximal tibia and partial pes a fairly useless description and illustrated two pedal digits in ventrolateral view and curving towards the viewer. :| Therizinosaurian affinities have been suggested, but it's not been examined since.
5. Kaijiangosaurus
Only a few vertebrae, pectoral girdle and proximal/distal metatarsal outlines have been illustrated, and the description has yet to be translated from Chinese. An online photo shows a lot more is known, but also that size differences mean more than one individual/taxon are present.
4. Conchoraptor
Ah, Conchoraptor. You might be asking how can this be obscure when there are so many skeletons casted. I've even seen two in person. The problem with Conchoraptor is that it's unsure just which specimens belong to it, besides the holotype (of which we have illustrations of the skull, and a manus and metatarsus that presumably belong to it or a paratype). None of the articulated skeletons photographed online have the right manual proportions or slender metatarsal II, and crestless skulls like ZPAL MgD-I/95 (the one described by Osmolska, 1976 and which Kundrat has recently been describing braincase details of) and the one on Witmer's lab page identified as "Ingenia" could belong to other oviraptorids. No one has ever provided a modern diagnosis, described the holotype in any detail or justified the referral of other specimens. This makes depending on matrices more risky than for other taxa listed here, since their OTU could be chimaerical for all I know.
3. Rinchenia
This has been illustrated in the literature even more seldomly than Conchoraptor, since at least ZPAL MgD-I/95 has papers dedicated to it. We only have the skull, mandible, overly schematic ilium and a single caudal vertebra illustrated. Lucky for us, Auditore was able to obtain photos of the holotype and illustrate it as detailed by Cau on his blog. As for Conchoraptor, Norell et al. (2001), Lu (2004) and Maryanska et al. (2002) all provide codings, which can be trusted more for Rinchenia since there's only the holotype (though I note a recent incorrect trend of referring IGM 100/42 to it).
2. Adasaurus
The muse for this post only gets second place. For Adasaurus we must depend on a few schematic drawings (pelvis, metatarsus, pedal digit II), since Barsbold (1988) neither described it besides noting a couple features, nor does he allow photos to be circulated. There was a photo of the holotype online which has since disappeared, but shows Barsbold's pelvis illustration is inaccurate, and to make it worse Kubota (pers. comm. to Senter, 2010) indicates the supposed small sickle claw doesn't belong. I'm just hoping Kubota plans to redescribe the taxon like Kobayashi did for Barsbold's basal ornithomimosaurs. Until then, we depend on codings from Norell et al. (2001), Senter (2007) and Longrich and Currie (2009), and a few scattered notes. Hopefully Turner et al.'s upcoming dromaeosaurid monograph has some juicy photos.
1. Chilantaisaurus? sibiricus
There are a lot of fragmentary taxa known from a tooth or a vertebra that are poorly described (usually in a useless archaic way) and illustrated in a photo from a single view.
Tuesday, October 25, 2011
Cladistics good, Aurorazhdarcho bad
Today I'm reporting on two papers, one good, one bad. Both involve cladistics, but besides that are basically unrelated.
Tom Holtz notified the DML of a new paper by Brazeau (2011). I highly recommend anyone making or examining a cladistic analysis read this work. He basically outlines many of the problems I describe in the Evaluating Phylogenetic Analyses page of my website.
- Don't make "pseudo-ordered" characters of the form "bone x absent (0); bone x lacks feature A (1); bone x has feature A (2)", because if it's unordered PAUP has no reason to know to group all taxa with bone x together. If it's ordered, it solves that problem, but has the probably undesired effect of assuming feature A is related to the loss of the bone.
- Don't have multiple characters implicitly coding for the same thing, with absence of that thing a state in addition to states coding for the presence/absence of a feature on the thing. So "bone x absent (0); bone x present (1)" and "bone x absent (0); bone x present and without feature A (1); bone x present and with feature A (2)" should not both exist. Have one character for the bones's absence/presence, and another character for each feature of the bone. Just code taxa without the bone as inapplicable for characters about that bone's feature. But be sure to set PAUP to collapse 0 length branches if you use inapplicable characters (TNT and NONA collapse them automatically).
- Don't make compound characters. Each character should code for only one variable.
- Remember that "0" does not mean "primitive". 0 has to be a distinct state just like 1, 2 or any other number. So don't make a character like "deltopectoral crest shape not described by any of the other states (0); crest round (1); crest triangular (2)", because there are lots of other shapes besides round and triangular, but PAUP could easily make state 0 synapomorphic for some clade. That could end up grouping taxa with rectangular, pentagonal, etc. crests together as having the same condition, which is clearly not justified.
- As a consequence of this, making ordered multistate characters is better than making a series of less inclusive bistate characters.
The second paper was announced today- the description of a new taxon of pterosaur. Frey et al. (2011) described Aurorazhdarcho, which is a damned cool name. Unfortunately, the paper goes downhill from there.
First, they assign Aurorazhdarcho to the new family Protazhdarchidae. Are there really people who still think you can make up a family-group name that's not eponymous with an existing genus? Without a Protazhdarcho (which doesn't exist), there can be no Protazhdarchidae. And Frey et al. can't use the excuse that Protazhdarchidae is "just a clade" since they explicitly say "nov. fam." and "we propose to erect a new family, the Protazhdarchidae..." Tim Williams brought up the possibility on the DML that maybe the genus was originally named Protazdarcho and later changed, but the family name wasn't caught in time (though barring a VERY last minute change or editorial messiness I would hope the peer reviewers would still catch it), and if that's the case I apologize to the authors for this insulting paragraph. Regardless, my insults in the next two paragraphs still apply. ;)
Second, Protazhdarchidae is monotypic, so is useless anyway. Maybe I was too hasty in dismissing Jaime's suggestion for purely monotypic theropod families in the year 2100, since apparently it's not just Ji and other Chinese workers who are stuck in the archaic typological mindset. The taxonomic world has moved beyond subjective difference being a reason to name a new clade/grade, please join the rest of us in the 21st century.
Third, Frey et al. include the highly flawed section "Problems with cladistic analysis". Note they don't actually include Aurorazhdarcho in an analysis. Why not? "The main reason is that the low wing attachment is reason enough to align the specimen with the azhdachoid construction, which separates the group from all other Pterosauria." I suppose Halloween IS a good time for Huene's ghost to rear its head, insisting on the importance of key characters. We then get this lovely gem-
"If the low position of the glenoid fossa is regarded as original tetrapod, the azhdarchoid pterosaur construction has retained the low articulation of the front limbs and thus must have separated in the early history of the Pterosauria, possibly during the Triassic. Then, the high wing articulation could have evolved several times independently within the Pterosauria. If the low wing articulation is regarded as derived, the re-development of the primitive position of the glenoid fossa has to be explained. To resolve this question, a reinvestigation of the shoulder girdle of early Pterosauria would be necessary. For now, this problem remains unresolved pending an engineering approach concerning the consequences of low wing attachment, too. Hence, the character should be dismissed because of its evident functional impetus and unclear origin (Frey et al. 2003a)."
Did anyone else hear a distinguished gentleman in a sepia photograph read the above statements? A single primitive character does not mean an entire clade is basal- we must examine the entire set of characters to determine which are more likely to be reversals or convergences. We don't have to explain why any character evolved, nor should our ability to hypothesize why one state could evolve from another affect our choice in character polarity. I'm very interested in what exactly all the characters we use were actually good for, but the analysis comes first THEN the evolutionary scenario. Frey et al. are guilty of the same thing BADists are- wanting to know the scenario first and basing the phylogeny off that. As for their last sentence, since every(?) character that's not the result of genetic drift has some functional importance (and how would we ever test that in extinct taxa?), that's not a reason to exclude them from analyses. And since origins are only made clear once you run an analysis, excluding a character due to its 'unclear origin' is just nonsensical.
The rest of their "problems" are basically of the form "character x influences character y since both are parts of some functional whole, and until we know how these influences work, we shouldn't include either character in cladistic analyses." So glenoid position influences deltopectoral crest shape and so on. Frey et al. are fundamentally wrong in their demand to know function before phylogeny, and that anatomy alone isn't enough to know when characters are strictly correlated. All you need to do is check the matrix to see if every taxon with character x also has character y, and if every taxon without x also lacks y. Now if you do find exact correlation and it's logically impossible to have a condition with x and without y and vice versa, THEN you can delete the character. Otherwise you might have a character complex like the paravian sickle claw where claw hyperextendability, size and curvature are certainly all functionally related, but should still be coded as separate characters since they're independent (e.g. Archaeopteryx lacks large size, Borogovia lacks strong curvature). Now I suppose some characters might be correlated due to combinations of osteology that are only logically impossible once soft tissues are taken into account, and not just simple muscular biomechanics as Frey et al. suggest, but even such details as involving expression of the same gene at the same time. Yet we'll never know most soft tissue anatomy for most fossil taxa (and even living taxa are poorly studied in this regard), so to rule out such correlation in our matrices is basically impossible. We can either try to determine phylogeny now while excluding the logically correlated characters, or wait forever until we have fully examined a complete living growing example of each taxon to eliminate the possibility of correlation for each character. I vote for the former.
Incidentally, given Frey et al.'s lack of a modern phylogenetic perspective, I don't trust their placement of Aurorazhdarcho in Azhdarchoidea. Maybe it is, I'm not qualified to say, but I await the results of someone using a modern approach.
References- Brazeau, 2011. Problematic character coding methods in morphology and their effects. Biological Journal of the Linnean Society. 104, 489-498.
Frey, Meyer and Tischlinger, 2011. The oldest azhdarchoid pterosaur from the Late Jurassic Solnhofen Limestone (Early Tithonian) of Southern Germany. Swiss Journal of Geosciences. DOI: 10.1007/s00015-011-0073-1
Tom Holtz notified the DML of a new paper by Brazeau (2011). I highly recommend anyone making or examining a cladistic analysis read this work. He basically outlines many of the problems I describe in the Evaluating Phylogenetic Analyses page of my website.
- Don't make "pseudo-ordered" characters of the form "bone x absent (0); bone x lacks feature A (1); bone x has feature A (2)", because if it's unordered PAUP has no reason to know to group all taxa with bone x together. If it's ordered, it solves that problem, but has the probably undesired effect of assuming feature A is related to the loss of the bone.
- Don't have multiple characters implicitly coding for the same thing, with absence of that thing a state in addition to states coding for the presence/absence of a feature on the thing. So "bone x absent (0); bone x present (1)" and "bone x absent (0); bone x present and without feature A (1); bone x present and with feature A (2)" should not both exist. Have one character for the bones's absence/presence, and another character for each feature of the bone. Just code taxa without the bone as inapplicable for characters about that bone's feature. But be sure to set PAUP to collapse 0 length branches if you use inapplicable characters (TNT and NONA collapse them automatically).
- Don't make compound characters. Each character should code for only one variable.
- Remember that "0" does not mean "primitive". 0 has to be a distinct state just like 1, 2 or any other number. So don't make a character like "deltopectoral crest shape not described by any of the other states (0); crest round (1); crest triangular (2)", because there are lots of other shapes besides round and triangular, but PAUP could easily make state 0 synapomorphic for some clade. That could end up grouping taxa with rectangular, pentagonal, etc. crests together as having the same condition, which is clearly not justified.
- As a consequence of this, making ordered multistate characters is better than making a series of less inclusive bistate characters.
The second paper was announced today- the description of a new taxon of pterosaur. Frey et al. (2011) described Aurorazhdarcho, which is a damned cool name. Unfortunately, the paper goes downhill from there.
First, they assign Aurorazhdarcho to the new family Protazhdarchidae. Are there really people who still think you can make up a family-group name that's not eponymous with an existing genus? Without a Protazhdarcho (which doesn't exist), there can be no Protazhdarchidae. And Frey et al. can't use the excuse that Protazhdarchidae is "just a clade" since they explicitly say "nov. fam." and "we propose to erect a new family, the Protazhdarchidae..." Tim Williams brought up the possibility on the DML that maybe the genus was originally named Protazdarcho and later changed, but the family name wasn't caught in time (though barring a VERY last minute change or editorial messiness I would hope the peer reviewers would still catch it), and if that's the case I apologize to the authors for this insulting paragraph. Regardless, my insults in the next two paragraphs still apply. ;)
Second, Protazhdarchidae is monotypic, so is useless anyway. Maybe I was too hasty in dismissing Jaime's suggestion for purely monotypic theropod families in the year 2100, since apparently it's not just Ji and other Chinese workers who are stuck in the archaic typological mindset. The taxonomic world has moved beyond subjective difference being a reason to name a new clade/grade, please join the rest of us in the 21st century.
Third, Frey et al. include the highly flawed section "Problems with cladistic analysis". Note they don't actually include Aurorazhdarcho in an analysis. Why not? "The main reason is that the low wing attachment is reason enough to align the specimen with the azhdachoid construction, which separates the group from all other Pterosauria." I suppose Halloween IS a good time for Huene's ghost to rear its head, insisting on the importance of key characters. We then get this lovely gem-
"If the low position of the glenoid fossa is regarded as original tetrapod, the azhdarchoid pterosaur construction has retained the low articulation of the front limbs and thus must have separated in the early history of the Pterosauria, possibly during the Triassic. Then, the high wing articulation could have evolved several times independently within the Pterosauria. If the low wing articulation is regarded as derived, the re-development of the primitive position of the glenoid fossa has to be explained. To resolve this question, a reinvestigation of the shoulder girdle of early Pterosauria would be necessary. For now, this problem remains unresolved pending an engineering approach concerning the consequences of low wing attachment, too. Hence, the character should be dismissed because of its evident functional impetus and unclear origin (Frey et al. 2003a)."
Did anyone else hear a distinguished gentleman in a sepia photograph read the above statements? A single primitive character does not mean an entire clade is basal- we must examine the entire set of characters to determine which are more likely to be reversals or convergences. We don't have to explain why any character evolved, nor should our ability to hypothesize why one state could evolve from another affect our choice in character polarity. I'm very interested in what exactly all the characters we use were actually good for, but the analysis comes first THEN the evolutionary scenario. Frey et al. are guilty of the same thing BADists are- wanting to know the scenario first and basing the phylogeny off that. As for their last sentence, since every(?) character that's not the result of genetic drift has some functional importance (and how would we ever test that in extinct taxa?), that's not a reason to exclude them from analyses. And since origins are only made clear once you run an analysis, excluding a character due to its 'unclear origin' is just nonsensical.
The rest of their "problems" are basically of the form "character x influences character y since both are parts of some functional whole, and until we know how these influences work, we shouldn't include either character in cladistic analyses." So glenoid position influences deltopectoral crest shape and so on. Frey et al. are fundamentally wrong in their demand to know function before phylogeny, and that anatomy alone isn't enough to know when characters are strictly correlated. All you need to do is check the matrix to see if every taxon with character x also has character y, and if every taxon without x also lacks y. Now if you do find exact correlation and it's logically impossible to have a condition with x and without y and vice versa, THEN you can delete the character. Otherwise you might have a character complex like the paravian sickle claw where claw hyperextendability, size and curvature are certainly all functionally related, but should still be coded as separate characters since they're independent (e.g. Archaeopteryx lacks large size, Borogovia lacks strong curvature). Now I suppose some characters might be correlated due to combinations of osteology that are only logically impossible once soft tissues are taken into account, and not just simple muscular biomechanics as Frey et al. suggest, but even such details as involving expression of the same gene at the same time. Yet we'll never know most soft tissue anatomy for most fossil taxa (and even living taxa are poorly studied in this regard), so to rule out such correlation in our matrices is basically impossible. We can either try to determine phylogeny now while excluding the logically correlated characters, or wait forever until we have fully examined a complete living growing example of each taxon to eliminate the possibility of correlation for each character. I vote for the former.
Incidentally, given Frey et al.'s lack of a modern phylogenetic perspective, I don't trust their placement of Aurorazhdarcho in Azhdarchoidea. Maybe it is, I'm not qualified to say, but I await the results of someone using a modern approach.
References- Brazeau, 2011. Problematic character coding methods in morphology and their effects. Biological Journal of the Linnean Society. 104, 489-498.
Frey, Meyer and Tischlinger, 2011. The oldest azhdarchoid pterosaur from the Late Jurassic Solnhofen Limestone (Early Tithonian) of Southern Germany. Swiss Journal of Geosciences. DOI: 10.1007/s00015-011-0073-1
Friday, October 21, 2011
Xiaotingia commentary, is Archaeopteryx a deinonychosaur?
I just wrote this for the DML and figured it could be useful to post here.
The majority view, as in the conclusion found by almost every cladistic analysis which has tackled the problem, is that Archaeopteryx is a basal avialan. The recent controversy has been over the analysis in Xu et al.'s (2011) description of Xiaotingia. This is a version of the Theropod Working Group analysis which goes back to Norell et al. (2001). Specifically Xu et al. (2011) added a few taxa and several characters to...
- Zhang et al.'s (2008) analysis which added Epidexipteryx and a few characters to...
- Senter's (2007) analysis which completely recoded and added many characters and taxa to...
- Kirkland et al.'s (2005) analysis which added several characters and a few therizinosaurs to...
- Hwang et al.'s (2004), which is based on Xu et al.'s (2002), which is based on more analyses still all the way back to Norell et al. (2001).
So it's a re-re-re-re-re-analysis of a huge dataset. Running this dataset with Xiaotingia results in Archaeopteryx being a basal deinonychosaur instead of a basal avialan. Note this isn't a big move, since Deinonychosauria and Avialae are sister groups. It just moves from the base of one group to the base of the other. Note also that despite what the hype would indicate, this result isn't very well supported. Forcing Archaeopteryx back to its normal position as a basal avialan only takes TWO more evolutionary steps. That's not significant at all, and furthermore the analysis itself is flawed as detailed below.
When you run an analysis like this, certain characters need to be "ordered". So that for instance, taxa with six sacral vertebrae are seen as intermediate between taxa with five and taxa with seven sacrals. If you don't order the character, "six sacrals" is counted as a character that has no definite relationship to other numbers of sacral vertebrae, so you'd get weird results like grouping Rahonavis and Shenzhouraptor together to the exclusion of more derived birds because of their shared primitive sacral number. Also, ordering changes the amount of steps a character takes to evolve, since if it's unordered, you can go from five to nine sacrals as easily as you can go from five to six sacrals. When we try to find out if Xu et al. ordered their characters, we have to follow the lineage of analyses all the way back to Kirkland et al.'s (2005) version, which only says one character was ordered but doesn't say which. Xu et al. seem to ignore that anyway, since I get their results by running their analysis unordered. Running Xu et al.'s analysis with all characters ordered adds over 100 steps, which of course completely overpowers our two step difference we noted above. While not every character should be ordered, many should be. Importantly, when characters are ordered, Archaeopteryx comes out as a bird.
So how much of Xu et al.'s result is due to not having the right characters ordered? We don't know unless someone goes through the tedious steps of looking through all the characters and choosing which should be ordered. You can see how this could be important for Archaeopteryx, since any intermediate state it has between birds and deinonychosaurs will be counted as equally different from both instead of being a bit closer to birds (assuming the deinonychosaurian condition is primitive).
Another problem is that Xu et al.'s analysis doesn't include all of the relevent taxa and characters that other versions of the analysis do. Senter's newest (2010) analysis (which is a modification of his 2007 one) includes most of the same taxa but has many new codings and takes seven more steps to place Archaeopteryx in Deinonychosauria. Zanno et al.'s (2009) analysis (which has a rather different lineage going back to Hwang et al. 2004 and so doesn't include any of Senter's numerous modifications) contains a different mix of characters, adds Mahakala and Shanag, but lacks scansoriopterygids, Sapeornis, Protopteryx, NGMC 91 and Bambiraptor. Forcing deinonychosaurian Archaeopteryx is six steps longer in it. Makovicky et al.'s (2010) analysis (which is more similar to Zanno et al.'s) includes yet a different mix of characters and taxa needs eight more steps. Most recently, Turner et al. (2011) have a TWG-based analysis centered on deinonychosaurs and birds, including taxa not found in the Xiaotingia analysis like Hesperonychus, Graciliraptor, Tianyuraptor, Austroraptor, Mahakala, Jinfengopteryx, two undescribed basal troodontids, Jixiangornis and a lot of birds. Based on their taxon sample I bet they also included the numerous bird-related characters of Clarke's analyses. And this analysis found Archaeopteryx to be a bird, though I can't say how well supported that is since they haven't released their data matrix yet (grrr).
So we can see that most analyses find Archaeopteryx to be 6-8 steps more likely to be a bird, while Xu et al. found it to be 2 steps more likely to be a deinonychosaur. Each analysis includes some data others don't, and all have miscodings. Until someone combines the information (which I'm finishing up), we won't know if say adding Xiaotingia to Turner et al.'s analysis would make Archaeopteryx a deinonychosaur, or if adding Jinfengopteryx to Xu et al.'s analysis would make Archaeopteryx a bird.
Until that time, I'd say it could be either, but that both the number of analyses and the strength of support in those analyses slightly favor it being a bird.
The majority view, as in the conclusion found by almost every cladistic analysis which has tackled the problem, is that Archaeopteryx is a basal avialan. The recent controversy has been over the analysis in Xu et al.'s (2011) description of Xiaotingia. This is a version of the Theropod Working Group analysis which goes back to Norell et al. (2001). Specifically Xu et al. (2011) added a few taxa and several characters to...
- Zhang et al.'s (2008) analysis which added Epidexipteryx and a few characters to...
- Senter's (2007) analysis which completely recoded and added many characters and taxa to...
- Kirkland et al.'s (2005) analysis which added several characters and a few therizinosaurs to...
- Hwang et al.'s (2004), which is based on Xu et al.'s (2002), which is based on more analyses still all the way back to Norell et al. (2001).
So it's a re-re-re-re-re-analysis of a huge dataset. Running this dataset with Xiaotingia results in Archaeopteryx being a basal deinonychosaur instead of a basal avialan. Note this isn't a big move, since Deinonychosauria and Avialae are sister groups. It just moves from the base of one group to the base of the other. Note also that despite what the hype would indicate, this result isn't very well supported. Forcing Archaeopteryx back to its normal position as a basal avialan only takes TWO more evolutionary steps. That's not significant at all, and furthermore the analysis itself is flawed as detailed below.
When you run an analysis like this, certain characters need to be "ordered". So that for instance, taxa with six sacral vertebrae are seen as intermediate between taxa with five and taxa with seven sacrals. If you don't order the character, "six sacrals" is counted as a character that has no definite relationship to other numbers of sacral vertebrae, so you'd get weird results like grouping Rahonavis and Shenzhouraptor together to the exclusion of more derived birds because of their shared primitive sacral number. Also, ordering changes the amount of steps a character takes to evolve, since if it's unordered, you can go from five to nine sacrals as easily as you can go from five to six sacrals. When we try to find out if Xu et al. ordered their characters, we have to follow the lineage of analyses all the way back to Kirkland et al.'s (2005) version, which only says one character was ordered but doesn't say which. Xu et al. seem to ignore that anyway, since I get their results by running their analysis unordered. Running Xu et al.'s analysis with all characters ordered adds over 100 steps, which of course completely overpowers our two step difference we noted above. While not every character should be ordered, many should be. Importantly, when characters are ordered, Archaeopteryx comes out as a bird.
So how much of Xu et al.'s result is due to not having the right characters ordered? We don't know unless someone goes through the tedious steps of looking through all the characters and choosing which should be ordered. You can see how this could be important for Archaeopteryx, since any intermediate state it has between birds and deinonychosaurs will be counted as equally different from both instead of being a bit closer to birds (assuming the deinonychosaurian condition is primitive).
Another problem is that Xu et al.'s analysis doesn't include all of the relevent taxa and characters that other versions of the analysis do. Senter's newest (2010) analysis (which is a modification of his 2007 one) includes most of the same taxa but has many new codings and takes seven more steps to place Archaeopteryx in Deinonychosauria. Zanno et al.'s (2009) analysis (which has a rather different lineage going back to Hwang et al. 2004 and so doesn't include any of Senter's numerous modifications) contains a different mix of characters, adds Mahakala and Shanag, but lacks scansoriopterygids, Sapeornis, Protopteryx, NGMC 91 and Bambiraptor. Forcing deinonychosaurian Archaeopteryx is six steps longer in it. Makovicky et al.'s (2010) analysis (which is more similar to Zanno et al.'s) includes yet a different mix of characters and taxa needs eight more steps. Most recently, Turner et al. (2011) have a TWG-based analysis centered on deinonychosaurs and birds, including taxa not found in the Xiaotingia analysis like Hesperonychus, Graciliraptor, Tianyuraptor, Austroraptor, Mahakala, Jinfengopteryx, two undescribed basal troodontids, Jixiangornis and a lot of birds. Based on their taxon sample I bet they also included the numerous bird-related characters of Clarke's analyses. And this analysis found Archaeopteryx to be a bird, though I can't say how well supported that is since they haven't released their data matrix yet (grrr).
So we can see that most analyses find Archaeopteryx to be 6-8 steps more likely to be a bird, while Xu et al. found it to be 2 steps more likely to be a deinonychosaur. Each analysis includes some data others don't, and all have miscodings. Until someone combines the information (which I'm finishing up), we won't know if say adding Xiaotingia to Turner et al.'s analysis would make Archaeopteryx a deinonychosaur, or if adding Jinfengopteryx to Xu et al.'s analysis would make Archaeopteryx a bird.
Until that time, I'd say it could be either, but that both the number of analyses and the strength of support in those analyses slightly favor it being a bird.
Saturday, October 15, 2011
Theropoda in the Amazing Year 2100
One of my pet peeves is the cavalier attitude many dinosaur paleontologists have recently in regard to the priority and validity of old taxa. Whether it's lazy dismissal of genera as nomina dubia without an analysis showing this is true, dumping family-level names based on supposed nomina dubia despite the ICZN having no rules about this, making up new definitions for established clades, or just plain old replacement of clade names because the eponymous genus isn't as complete or deeply nested as another. If this trend continues, we may face the following horrifying vision of the future...
Theropoda
- Coelophysoidea (based on a complete neotype for Coelophysis bauri, the only known material for the first 66 years having been ignored as archosaur scrap; IT'S ALREADY TRUE!)
- Sinodilophosauridae (people still refuse to use Dilophosauridae, but the describers of what was originally Dilophosaurus sinensis came up with their own name for this clade)
- Averostra (because enough people misused Bakker's Neotheropoda so that they forgot he created it for this node and started using a term published 16 years later instead)
-- Ceratosauria
--- Majungasauroidea (Abelisaurus was deemed too fragmentary, and Carnotaurus is still only known from one specimen. Majungasaurus itself is now based on a complete neotype found in 2068)
---- Masiakasauridae
---- Majungasauridae
-- Tetanuriformes (someone finally got enough followers after redefining Tetanurae to be less inclusive, thus Tetanurae has different meanings depending on what year a paper was published)
--- Suchomimia
---- Tayntonsauridae (after a incomplete articulated megalosaur was found in Megalosaurus' type beds, it was named to 'solve' the confusion surrounding Megalosaurus' association. All Megalosaurus remains were then referred to Tayntonsaurus)
---- Suchomimidae (Yes, ignoring Spinosauridae, Baryonychidae, Irritatoridae and Cristatusaurus)
--- Tetanurae
----Sinraptoroidea (after Allosaurus fragilis was shown to be a nomen dubium, people incorrectly said a family level name couldn't be based on it)
----- Sinraptoridae (no comment needed)
----- Neoallosauridae (people declared Allosaurus, Labrosaurus, Creosaurus and Epanterias to be undiagnostic in a footnote of the paper describing Big Al as Neoallosaurus in 2035)
----- Carcharodontosauria
------ Neovenatoridae
------ Acrocanthosauridae
------ Shaochilongidae
------ Tyrannotitanidae
------ Carcharodontosauridae (ignoring the stable stem-based definition of Carcharodontosauridae, people kept redefining it to be less and less inclusive)
---- Tyrannosauroidea (despite including the following two families, both named prior to Tyrannosauridae...)
----- Coeluridae
----- Compsognathidae
----- Tyrannosauridae
---- Avesternes (someone named it in 2019 and people started to ignore Maniraptoriformes)
----- Ornithomimosauria (based on a neotype for Ornithomimus edmontonicus, even though O. velox was the type species and brevitertius has priority over edmontonicus)
----- Eunothronychia (Therizinosauria was defeated the same way it gained usage, once graffami was given its own genus)
----- Citipatia (Oviraptor was too fragmentary, so the clade was renamed once Citipati's holotype was fully described in 2023. IGM 100/42 remains undescribed and called the Zamyn Kondt oviraptorid as of 2100)
----- Bimedicamentodontidae (Troodon is a long forgotten name, and no the family hasn't been subdivided yet despite there being 73 described diagnostic genera)
----- Dromaeosauridae (miraculously unaffected, but Barsbold's estate owns Adasaurus, which no one is allowed to circulate holograms of)
----- Shuvuuiformes (because of... well, you get the drift by now)
----- Birdia (we finally got sick of the semantic arguments)
Only you can prevent this terrifying prediction from becoming reality. Support priority, follow the ICZN until another code is viable (the Phylocode remains unofficial as of 2100, but rumors are Phylonyms is almost complete and that it will start as of 1-1-21xx), and remember a named taxon is valid until shown otherwise by a detailed redescription and comparison.
Theropoda
- Coelophysoidea (based on a complete neotype for Coelophysis bauri, the only known material for the first 66 years having been ignored as archosaur scrap; IT'S ALREADY TRUE!)
- Sinodilophosauridae (people still refuse to use Dilophosauridae, but the describers of what was originally Dilophosaurus sinensis came up with their own name for this clade)
- Averostra (because enough people misused Bakker's Neotheropoda so that they forgot he created it for this node and started using a term published 16 years later instead)
-- Ceratosauria
--- Majungasauroidea (Abelisaurus was deemed too fragmentary, and Carnotaurus is still only known from one specimen. Majungasaurus itself is now based on a complete neotype found in 2068)
---- Masiakasauridae
---- Majungasauridae
-- Tetanuriformes (someone finally got enough followers after redefining Tetanurae to be less inclusive, thus Tetanurae has different meanings depending on what year a paper was published)
--- Suchomimia
---- Tayntonsauridae (after a incomplete articulated megalosaur was found in Megalosaurus' type beds, it was named to 'solve' the confusion surrounding Megalosaurus' association. All Megalosaurus remains were then referred to Tayntonsaurus)
---- Suchomimidae (Yes, ignoring Spinosauridae, Baryonychidae, Irritatoridae and Cristatusaurus)
--- Tetanurae
----Sinraptoroidea (after Allosaurus fragilis was shown to be a nomen dubium, people incorrectly said a family level name couldn't be based on it)
----- Sinraptoridae (no comment needed)
----- Neoallosauridae (people declared Allosaurus, Labrosaurus, Creosaurus and Epanterias to be undiagnostic in a footnote of the paper describing Big Al as Neoallosaurus in 2035)
----- Carcharodontosauria
------ Neovenatoridae
------ Acrocanthosauridae
------ Shaochilongidae
------ Tyrannotitanidae
------ Carcharodontosauridae (ignoring the stable stem-based definition of Carcharodontosauridae, people kept redefining it to be less and less inclusive)
---- Tyrannosauroidea (despite including the following two families, both named prior to Tyrannosauridae...)
----- Coeluridae
----- Compsognathidae
----- Tyrannosauridae
---- Avesternes (someone named it in 2019 and people started to ignore Maniraptoriformes)
----- Ornithomimosauria (based on a neotype for Ornithomimus edmontonicus, even though O. velox was the type species and brevitertius has priority over edmontonicus)
----- Eunothronychia (Therizinosauria was defeated the same way it gained usage, once graffami was given its own genus)
----- Citipatia (Oviraptor was too fragmentary, so the clade was renamed once Citipati's holotype was fully described in 2023. IGM 100/42 remains undescribed and called the Zamyn Kondt oviraptorid as of 2100)
----- Bimedicamentodontidae (Troodon is a long forgotten name, and no the family hasn't been subdivided yet despite there being 73 described diagnostic genera)
----- Dromaeosauridae (miraculously unaffected, but Barsbold's estate owns Adasaurus, which no one is allowed to circulate holograms of)
----- Shuvuuiformes (because of... well, you get the drift by now)
----- Birdia (we finally got sick of the semantic arguments)
Only you can prevent this terrifying prediction from becoming reality. Support priority, follow the ICZN until another code is viable (the Phylocode remains unofficial as of 2100, but rumors are Phylonyms is almost complete and that it will start as of 1-1-21xx), and remember a named taxon is valid until shown otherwise by a detailed redescription and comparison.
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