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. 

12 comments:

  1. I suspect the Turner et al. data matrix will be released with Turner's in press monograph on dromaeosaurs (grrr).

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  2. David MarjanovićOctober 21, 2011 at 8:46 PM

    Also, Jingmai O'Connor's forthcoming analysis

    *Nature editors holding big scary knife to Jingmai's throat*

    *Jingmai holding big scary knife to my throat*

    Sorry.

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  3. It'd be quite annoying if we didn't get the matrix until the (eagerly awaited) dromaeosaur monograph. Not because I'm impatient (though I am), but because the Mahakala paper claims the matrix is available online or via author request. It seems... ethically problematic to say these things when a paper's released if they aren't true until some indeterminate time afterward.

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  4. archaeopteryxa is a bird had weak keel a missing tail bone found in all dinosaurs hallux was preaching bird like modern birds dromaesaurs raptor are not dinosaurs they are flightless bird my be from arch family early dinosaurs look like reptile protoavis a bird date 225 millon years agentine modern bird foot print 210 millon years

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  5. Is it even worth replying to Anonymous' poorly worded screed? Doubtful, but here goes...

    1. Archaeopteryx lacked an ossified sternum, so didn't even have a weak keel.
    2. Archaeopteryx had the same tail bones as other dinosaurs- vertebrae and chevrons. It had less tail vertebrae than most, but there were other maniraptorans with less.
    3. Archaeopteryx's hallux was not reversed, but pointed medially, as shown by Middleton.
    4. Dromaeosaurids are dinosaurs and may have had flying ancestors, so could be considered birds under some definitions.
    5. Early dinosaurs were reptiles so of course looked like them, though birds are reptiles too.
    6. Protoavis is a mix of animals including a juvenile coelophysoid and an undescribed supposed pterosauromorph (see Atanassov's thesis), but near certainly contains no bird bones.
    7. Melchor et al.'s (2002) Santo Domingo tracks are interesting, but not enough to prove Triassic birds exist.

    Are there BANDit poes?

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  6. maniraptorans is not a dinosaurs they are birds there pelvis is close to lizard hip pelvis but its not same arms does not move like a real dinosaurs more like birds there ears is like owl and only found in a owl german archaeopteryx family had weak keel archaeopteryx had primtive perching hallux a modern bird feature and is a bird feature modern bird perching hallux bird foot print found in argentine date 210 millon years even bird to dinosaurs evo said its a bird but said they will find dinosaurs covergent to look like bird made them wishful thinking but not a fact btde paleontologist and paleontologist know trassic dinosaurs are worst case for bird evo that why btde paleontologist said it have to happen in archaoepteryx time there were no bird like dinosaurs in triassac with there heavey bones 4 to5 fingers and legs plant eating jaw and other primtive reptile feature and there tran link to bird hip pelis giant plant eaters 4 leg runners the one dinosaurs family thing yeah meat eating bipedal mothership dinosaurs coloephysis furcula was not fuse some trassic feature for you the close to bird like dinosaurs in that time archaeopteryx missing one tail bone that you find in real dinosaurs archaeopteryx furcula look like dinosaurs but it was differant and its a big deal like like lizard hip pelvis in maniraptorans that means still a bird so protoavis bones were mix up but there were bird parts in there bird brain leight weight modern bird skull and others bird to dinosaurs evo croud put down paleontologist for changing there stand about raptor i think all agree feathers are big deal find you made it a big deal there is a other way around it to be fair advance meat eating theropod dinosaurs carnotaurus date 75 years spinosaurus date 112to97 millon years carnotaurus have crocs thermoregulation bums cold blood feature if it was warm blood it would not need that fossil scale skin most of it body spinosaurus has a sailfin thermoregulation a cold blood feature its cold blood aligater tautara sailfin basilisk all have thermoregulation bums and sailfin and can take cold very well like dinosaurs modern reptile does have these feature only these 3 crocs have trouble with the cold any way they are all cold blood feral basilisk can be found in st pete florida probly could go farer mybe they are cold reptile feature on to protofeathers dinosaurs they are collagen fiber dead frill skin that are found in dolphin marine reptile flying reptile and others and are worst case for birds evo duck bill dinosaurs had it too and find allmost complete scalely skin fossil of them there is no protofeathers dinosaurs one of protofeather dinosaurs have a croc lungs and liver on to bird evo bird fingers 2,3,4, dinosaurs fingers 1,2,3, my thought on bird flight bird fly before feathers they were tree animals if they had a protocoat animal would have been success alive today and on the ground there is a protobatcoat animal alive today there is no trans link protofeathers protofeathers is all hype media hype archaeoraptor hype before the detail even btde paleontologist expert said its collagent fibers on to archaeopteryx did it had a land animal moving femur birds are knee runners because there lung will collaps dinosaurs is a cold blood reptile

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  7. And just like John Jackson at Tet Zoo, my response elicits a tsunami of BANDit nonsense. I'll tell you what- learn to use punctuation and capitalization, then we'll talk.

    In the meantime, think of what evidence would make you agree that 'birds are dinosaurs' is the better hypothesis. As for me, an extensive (character-wise and taxon-wise) and well coded cladistic analysis showing birds to be most parsimoniously placed outside Dinosauria would make me provisionally agree birds aren't dinosaurs. So it really doesn't matter if Archaeopteryx had a reversed hallux, Coelophysis lacked a furcula, birds' fingers are II-III-IV, non-maniraptorans were ectothermic or lacked feathers, etc., even though I don't agree with any of these things. In science, it's the totality of evidence that counts.

    Finally, discussing this with you isn't useful if you simply ignore points I make. You mentioned Archaeopteryx's supposed weak keel above, I noted it doesn't have an ossified sternum, then you listed it again without even trying to show why I'm wrong. Repeating assertions doesn't make them true, you need to engage the evidence contradicting your statements.

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  8. ok archaeopteryx munich specimen s6 archaeopteryx bavarica data i got was old i thought i was right so i got the anwser i wanted thanks i am only looking for the answer i was looking for more detail and i got it hahaha later the sternum turn out to be coracoid they said it may have cartilage sternum not only band i got the answer from i got it from bird to dinosaur evo and creationist on my writing style i sence a goof you are not a rookie of layback websurfer 2 answer i guest i am not in the nerd croud i am the small fish in a big pond my answer are 3 percent 97 percent are paleontologist answer the real war is band nerd paleontologist vs you i think you live that long not to throw out my answer but go to vegas with it no more goofy feeling the animal of bird ancester evo from only tree lifestyle with no ground lifestyle flight came first then the airo thing ah wishful thinking and hypothesis and facts allways was part paleontology more goof scalely foot hype bipedal hype nature was never that easy any way i guest its the paleontologist waiting game for trans link fossil fish to bird croc to bird basilisk to bird tautara to bird evo any way i am reptile fan evo fan flip flop fan first i thought dinosaurs were only scalely lizard then a bird then a bad acme only scalely cold blood lizard i am just surfing the data any way what the differant between crocs and dinosaurs

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  9. dinosaurs is a armo back turtle a primtive reptile there close reltive is the turtle tuatara aligator its a kind of a turtle it evo like that that the path it took that why these animal does not change that much they got bad airo package too bird ancester are the lizard scute free smood skin scalely animals snakes monter lizard look at the armo back reptle scute free armo back reptile the turtle its still got its shell

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