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

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. 

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...

- 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.