Saturday, July 13, 2019

How to add your taxon to the Lori analysis

When designing the Lori analysis, I didn't want it to just be a single use test.  With nearly every Mesozoic maniraptoromorph included, quantified characters and a character list that's been modified to avoid any correlated or composite examples, it's the best published analysis to include your new taxon in as long as its not stemward of Ornitholestes or a member of crown Aves.  The corollary is that it's so detailed that the usual quick TNT run will not find the Most Parsimonious Trees.  Don't let that deter you though, as I'm writing this blog post to walk you through the steps of adding a new taxon and finding its most parsimonious position.

The first step is to score your new taxon.  You might notice I've included two NEXUS files at PeerJ.  This one is for scoring taxa in Nexus Data Editor (NDE).  It includes character and state descriptions to make this easy.  If your specimen is immature, I've added the option to score it 'N' for characters that are known to vary with ontogeny.  The character list indicates which characters qualify for this, but they're easy to notice in NDE too because they have a series of undefined states through state 9 before it lists state N (Figure 1).  Another advantage of NDE is that you can distinguish uncertainty polymorphies from variation polymorphies.  Uncertainty polymorphies, such as 'it either has six or seven sacrals, but I can't tell which' are indicated with a slash, as in '1/2'.  Variation polymorphies, such as 'some individuals have six sacrals and others have seven' are indicated with a plus sign, such as '1+2'.  If a feature is inapplicable, such as a tooth character for a toothless taxon, score it with a dash.  N, /,  + and - are thus great ways to keep track of how much we know about your taxon.  Contrast this with Cau's MegaMatrix, which is entirely 0s, 1s and ?s.  It contains basically the same information TNT will use, but isn't as obvious or transparent.

Figure 1. Example of a Lori matrix in NDE.

These symbols would all work fine in PAUP, but that program is far too slow for the Lori analysis.  So instead I used TNT (Goloboff and Catalano, 2016).  The problem is that TNT has a different set of symbols it recognizes.  When NDE makes a NEXUS file from your matrix, uncertainty polymorphies are displayed as curly brackets, such as '{12}'.  Variation polymorphies are displayed as normal parentheses, such as '(12)'.  TNT doesn't recognize the difference and just uses curly brackets for all polymorphies.  Similarly, TNT doesn't recognize inapplicable states and doesn't allow another symbol like 'N' to count as an unknown state.  So you'll have to copy your list of scores into a word processor and 'replace all' normal parentheses with curly brackets, capital Ns with question marks and dashes with question marks.  Now you have your entry ready for TNT.

Hesperornithoides                   ???3111??? ?????????? ?????????? ?10???01?? 0110?????? ?????????1 ?????????? ?0?{01}0?10?? ???????0(01)1 0100???1?? 1?01??000? ??1{12}1????? ?????11??1 (01)??????0?? ?????2{01}000 0??10000{01}0 00001000?? ???1?1???? ?????????? ?????????1 ?000110000 1?0000??10 0{12}0?01???? ??{01}??????? {01}1?????{12}?? ???{12}00???? ?????1???0 ???1????10 ???0?0???0 ??????1?0? 00?11???0? ??2?11???1 100001?1?? ???1??1011 00{12}?00?0?? 00???2???0 ?????1010? ?00????10{12} ??11{01}11?0? 1{23}?01?0?01 ??10???1?0 0??????1?? ?00021???? ?0??000?1? ????00???? 00?102001? ???10000?? ?????????? ??0000000? 110??????0 ?0???00??? ??0????11? ?????00?10 ?000?0?0?? ???0?????? ?????????? ??0?0????? ??0?0???10 ?????0???? ???000???? 0???01???1 -1?1000-00 ?0?1?????? ?0??00001? ?0???????? ????000{01}10 0200000?0- -00?1-?0?? ?????0??-1 01????????

becomes...

Hesperornithoides ???3111????????????????????????10???01??0110???????????????1???????????0?{01}0?10?????????0{01}10100???1??1?01??000???1{12}1??????????11??1{01}??????0???????2{01}
0000??10000{01}000001000?????1?1???????????????????????1?0001100001?0000??100{12}0?01???
???{01}???????{01}1?????{12}?????{12}00?????????1???0???1????10???0?0???0??????1?0?00?11???0???2?11???1100001?1?????1??101
100{12}?00?0??00???2?
??0?????1010??00????10{12}??11{01}11?0?1{23}?01?0?01??10???1?00??????1???00021?????0??00
0?1?????00????00?102001????10000??????????????0000000?110??????0?0???00?????0????11??????
00?10?000?0?0?????0??????????????????0?0???????0?0???10?????0???????000????0???01???1?1?10
00?00?0?1???????0??00001??0????????????000{01}100200000?0??00?1??0???????0???101????????

Now take the other NEXUS file, the one designed to run in TNT.   Change the number of taxa to add one for your new taxon under the 'ntax=' commend (Figure 2), add your new taxon with its scores to the bottom of the matrix block (Figure 3), and now the important step.  I included one saved Most Parsimonious Tree in this NEXUS file, at the bottom after 'begin trees ; tree tnt_1 = [&U]'.  If you added your taxon to the base Lori TNT file with 501 taxa, yours is number 502.  So where it says '(1,(18,((2,3),(36,('... add your taxon as '(502,(1,(18,((2,3),(36,('..., being sure to include the comma and then add another parentheses to the end of the tree description before the semicolon where it says ',(59,60)))))))))));' .

Figure 2. Where to increase taxon number.
Figure 3. Where to insert your new taxon and scores.

Now save the NEXUS file and open it in TNT.  For our example, I've added newly described scansoriopterygid Ambopteryx as taxon 502.  In TNT, select 'Trees' > 'View' and you'll see your taxon at the base of the tree and at the bottom center is the tree length as 'Len.' (Figure 4).  Here it's 12175, significantly higher than the shortest trees I found at 12123, because Ambopteryx would need a LOT of steps to place so basally.  Select 'Settings' > 'Lock trees' to unlock the cladogram, and now you can click just to the left of your new taxon's name.  When you right click a node or just to the left of another taxon's name, your new taxon will move there.  If we move Ambopteryx to the base of Scansoriopterygidae, tree length drops to 12147.  You wouldn't expect it to get back down to 12123 unless your new taxon adds no new information.  Conversely, any information it adds has the power to change the topology of closely related taxa.

Figure 4. Your new taxon added and where to see tree length.
Now you let TNT use its power to find the best topology.  After increasing the 'Max. trees' under 'Memory' in 'Settings' to 10000, run a 'New Technology search' getting trees from 'RAM' using 'Sect. Search' (with 'CSS' unchecked), 'Ratchet', 'Drift' and 'Tree fusing'. With Ambopteryx, this quickly finds 13 trees of length 12142.  One thing I've noticed is that a low amount of trees, like 13, indicates there's more work to do.  So reset 'Max. trees' to 100 and run a 'Traditional search' of 'trees from RAM'.  This gets you 100 trees of that length to work with.  Now reset it to 10000 Max. trees and run the New Technology search from RAM again.  The new result is 100 trees of length 12142, which from my experience usually means those are the shortest trees you'll find.  You can keep switching New Tech and Trad searches like this until you're satisfied, but end it with a Trad search after increasing the Max. trees to 99999 to fully sample tree space.  In the present example, the topology within Scansoriopterygidae changed, it moved to the base of Paraves (1 step longer in the original matrix) and Pedopenna moved to Archaeopterygidae (1 step longer in the original matrix) (Figure 5).

Figure 5.  Taxon successfully added.
And that's how you add a new taxon to the Lori matrix.  Later in Lori Week, I'll show you the new and better way to run a constraint analysis in a huge matrix like this, and also how to track down where taxa with multiple equally parsimonious positions can go.  Also, some diagrams for exactly what to measure for some of the potentially ambiguous quantified characters.

References- Goloboff and Catalano, 2016. TNT version 1.5, including a full implementation of
phylogenetic morphometrics. Cladistics. 32(3), 221-238. DOI: 10.1111/cla.12160

Hartman, Mortimer, Wahl, Lomax, Lippincott and Lovelace, 2019. A new paravian dinosaur from the Late Jurassic of North America supports a late acquisition of avian flight. PeerJ. 7:e7247. DOI: 10.7717/peerj.7247

Friday, July 12, 2019

Phylogeny of the Lori analysis 2 - Topology

Now that we've covered my philosophy in designing the Lori analysis, let's look at some of the basic relationships it recovered.  The details are all laid out in the paper of course, and I'll write a post on each main clade as part of this series.

Something I'd like to clarify is that some commentary I've read has been to the effect of 'the support for lots of these clades is low, so be skeptical.'  That's true in the broad sense, but my point was that TWiG analyses over the past two decades also have low support for these clades, they just hardly ever report it.  You see e.g. Deinonychosauria again and again not because it's strongly supported in any TWiG analysis, but rather because scorings are reused and each analysis weakly supports Deinonychosauria based on the same weak character evidence.  So don't think the Lori analysis has unusually weak support for these clades, but rather that previous TWiG analyses don't report their support levels so you never knew how weak they were.

In any case, here's the full topology of taxa I consider strongly supported as maniraptoromorphs...

Strict consensus tree of Maniraptoromorpha after a posteriori exclusion of 43 taxa (see Positions of maniraptoromorphs pruned a posteriori in the supplementary info) (after Hartman et al., 2019).You'll probably want to click to enlarge...
Prior to Maniraptoriformes, we have a series of compsognathid-grade taxa including compsognathids themselves.  One surprise was finding Haplocheirus in Compsognathidae instead of Alvarezsauroidea.  As far as I know, this has only been previously suggested by Alifanov and Saveliev (2011:184) without proposed evidence, and based only on the initial description.  I used Choiniere's (2010) detailed thesis description to score the taxon, so incomplete scoring isn't an issue here.  I thought adding the new Xiyunykus and Bannykus might pull it toward alvarezsaurs, but nope, although scoring them in more detail after further description might influence things.  "Eight characters used by Choiniere et al. (2010) to place it in the latter clade were not included, but it also requires nine steps to constrain there in our analysis ... This suggests neither a compsognathid nor an alvarezsauroid identification is well supported and more study is needed."

The next 'big picture' concept is a fairly standard maniraptoriform topology of ornithomimosaurs branching first, then alvarezsaurs and therizinosaurs, then Pennaraptora.  What I found interesting about this area of the tree is that it's highly unstable.  As I wrote, "only four steps are required
to get a result similar to Sereno’s (1999) where alvarezsauroids are sister to ornithomimosaurs
and therizinosaurs sister to that pair. Similarly, while we recover a pairing of alvarezsauroids
and therizinosaurs to the exclusion of pennaraptorans, placing therizinosaurs closer
to the latter clade merely needs three additional steps. Positioning alvarezsauroids sister
to Pennaraptora or putting therizinosaurs just outside Maniraptoriformes are slightly
less parsimonious at six steps each..."  So Maniraptora is not the stable clade, Pennaraptora is.  For instance, moving therizinosaurs sister to oviraptorosaurs as used to be common in the late 90s-early 00s requires 13 steps while placing alvarezsaurs as paravians takes 11 steps.

Alternative topologies for major maniraptoriform clades in the Lori matrix showing the number of extra steps needed from the most parsimonious trees.
Similarly, there are a few taxa in this non-pennaraptoran maniraptoriform grade which have 'consensus positions' that are actually very poorly supported.  Pelecanimimus and Nqwebasaurus are ornithomimosaurs, right?  Well, Nqwebasaurus seems more likely to be an alvarezsaur as it "requires six steps to be an ornithomimosaur ... [and] all but two characters recovered by Choiniere et al. (2012) as supporting an ornithomimosaurian placement were included."  Pelecanimimus is more ambiguous, although it's most parsimoniously an alvarezsaur in my trees.  "Constraining it as an ornithomimosaur only requires two additional steps, however, where it emerges just above Shenzhousaurus as in Macdonald and Currie (2018). As only two of their characters supporting an ornithomimosaurian identification were not used by us, and only one from Brusatte et al. (2014), its true position is unclear pending a detailed osteology such as Perez-Moreno’s (2004) unreleased description."  The third controversial taxon of this kind is Fukuivenator, "emerging as the first branching alvarezsauroid, but moving to a basal therizinosauroid position with only two steps. A more stemward position seems more likely than a relationship with dromaeosaurids as suggested in its original description or Cau (2018), as it can be a coelurid with only four more steps, but takes seven steps to be sister to Pennaraptora and 11 steps to be paravian."  I'd now add Lingyuansaurus to this list, though it was published after submission time.  Recall it it a supposed therizinosaur, but moves to Ornithomimosauria with just three more steps.

Whatever Hesperornithoides is, it's clearly paravian, and paravian topology proved particularly labile in my analysis.  Your initial reaction might be 'hey, Xu et al. 2011 were right, and Archaeopteryx is a basal deinonychosaur."  Maybe.  But placing archaeopterygids (including 'anchiornithines') as avialans or sister to troodontids is only a step longer each.  Add to this scansoriopterygids, which are avialans in the most parsimonious trees but move to basal paravians in a single step, and troodontids, which are deinonychosaurs but move to Avialae in a single step, and the basic topology of Paraves is uncertain.  This isn't to say all alternatives are great though, as dromaeosaurids closer to birds than troodontids takes six more steps, and archaeopterygids basal to troodontids, dromaeosaurids and avialans takes 15 more steps. Oviraptorosaurian scansoriopterygids are 12 steps longer.  So we have a subset of plausible alternatives, and that's where the research should be focusing.  Stratigraphically basal deinonychosaurian archaeopterygids and basal avialan scansoriopterygids make sense, but who knows.

Alternative topologies for major paravian clades in the Lori matrix showing the number of extra steps needed from the most parsimonious trees.
The fifth major paravian clade is Unenlagiidae, traditionally paired with dromaeosaurids but here uniquely recovered as sister to Dromaeosauridae plus Troodontidae.   This Unenlagiidae includes halszkaraptorines as in Senter et al. (2012) and Cau (2018).  One interesting point is that the position of unenlagiids varies with the position of archaeopterygids- when archaeopterygids are sister to troodontids in trees one step longer, unenlagiids are sister to dromaeosaurids.  But when archaeopterygids are avialans in trees one step longer, so are unenlagiids as in Agnolin and Novas (2013).  Besides the standard set of taxa, we recovered the Gondwanan Pyroraptor and Ornithodesmus as unenlagiines as well as Dakotaraptor.  If the latter is true, is that a situation like Titanis and Alamosaurus where a southern taxon moved into North America?  New halszkaraptorines include the Early Cretaceous Ningyuansaurus and ISMD-VP09.

Finally, let's go over the basal avialan results.  I've always recovered Balaur as an avialan as in Cau et al. (2015) and it takes 8 steps to move to Dromaeosauridae.  Surprisingly, Hesperonychus groups with Balaur instead of microraptorians.  It only takes three steps to move to Microraptoria, but the stratigraphy is a better fit by Balaur.  "The branching order of Jehol non-ornithothoracine birds has been contentious, with our matrix supporting Sapeornis branching first, followed by jeholornithids then confuciusornithiforms. Jeholornithids branching first is only three steps longer, but Sapeornis branching last as in some recent analyses requires 12 more steps."  Between confuciusornithiforms and Ornithothoraces are Chongmingia, Yandangornis and Jinguofortis.  "... Jinguofortis joins Chongmingia in only three steps. Our analysis supports the latter’s position close to Ornithothoraces as in p2 of Wang et al.’s (2016) figure 7, whereas moving it to their p1 more stemward of Jeholornis and Sapeornis requires 11 more steps."

There are hundreds of other things to say about the topology, but next time I'm going to switch gears and discuss my first successful experience with peer review.  In the mean time, if any of you have questions about taxon placements or alternative topologies, feel free to ask.

References- Sereno, 1999. The evolution of dinosaurs. Science. 284(5423), 2137-2147.
DOI: 10.1126/science.284.5423.2137

Perez-Moreno, 2004. Pelecanimimus polyodon: Anatomía, sistemática y paleobiología de un
Ornithomimosauria (Dinosauria: Theropoda) de Las Hoyas (Cretácico Inferior; Cuenca,
España). PhD thesis, Universidad Autónoma de Madrid. 149 pp.

Choiniere, 2010. Anatomy and systematics of coelurosaurian theropods from the Late Jurassic of Xinjiang, China, with comments on forelimb evolution in Theropoda. PhD thesis, George Washington University. 994 pp.

Choiniere, Xu, Clark, Forster, Guo and Han, 2010. A basal alvarezsauroid theropod from the Early Late Jurassic of Xinjiang, China. Science. 327(5965), 571-574. DOI: 10.1126/science.1182143

Alifanov and Saveliev, 2011. Brain structure and neurobiology of alvarezsaurians (Dinosauria), exemplified by Ceratonykus oculatus (Parvicursoridae) from the Late Cretaceous of Mongolia. Paleontological Journal. 45(2), 183-190. DOI: 10.1134/S0031030111020031

Choiniere, Forster and De Klerk, 2012. New information on Nqwebasaurus thwazi,
a coelurosaurian theropod from the Early Cretaceous Kirkwood Formation in South Africa.
Journal of African Earth Sciences. 71-72, 1-17. DOI: 10.1016/j.jafrearsci.2012.05.005

Senter, Kirkland, DeBlieux, Madsen and Toth, 2012. New dromaeosaurids (Dinosauria:
Theropoda) from the Lower Cretaceous of Utah, and the evolution of the dromaeosaurid tail.
PLOS ONE. 7(5), e36790. DOI: 10.1371/journal.pone.0036790.

Agnolin and Novas, 2013. Avian ancestors: a review of the phylogenetic relationships of the
theropods Unenlagiidae, Microraptoria, Anchiornis and Scansoriopterygidae. Netherlands:
Springer. 96 pp. DOI: 10.1007/978-94-007-5637-3_1

Brusatte, Lloyd, Wang and Norell, 2014. Gradual assembly of avian body plan
culminated in rapid rates of evolution across the dinosaur-bird transition. Current Biology.
24(20), 2386-2392. DOI: 10.1016/j.cub.2014.08.034

Cau, Brougham and Naish, 2015. The phylogenetic affinities of the bizarre Late Cretaceous
Romanian theropod Balaur bondoc (Dinosauria, Maniraptora): dromaeosaurid or flightless
bird? PeerJ. 3:e1032. DOI: 10.7717/peerj.1032

Wang, Wang, Wang and Zhou, 2016. A new basal bird from China with implications for
morphological diversity in early birds. Scientific Reports. 6:19700. DOI: 10.1038/srep19700

Cau, 2018. The assembly of the avian body plan: a 160-million-year long process. Bollettino della
Società Paleontologica Italiana. 57(1),1-25. DOI: 10.4435/BSPI.2018.01

Macdonald and Currie, 2018. Description of a partial Dromiceiomimus (Dinosauria: Theropoda)
skeleton with comments on the validity of the genus. Canadian Journal of Earth Sciences. 56(2), 129-157. DOI: 10.1139/cjes-2018-0162

Hartman, Mortimer, Wahl, Lomax, Lippincott and Lovelace, 2019. A new paravian dinosaur from the Late Jurassic of North America supports a late acquisition of avian flight. PeerJ7:e7247. DOI: 10.7717/peerj.7247

Thursday, July 11, 2019

Phylogeny of the Lori analysis 1 - Philosophy

Now that Lori is published, as Hesperornithoides, I can finally discuss the topology I recovered for its phylogenetic analysis.  But first, here's the tedious part where I describe why I did what I did.  I mean, I could have just added Lori to Brusatte et al. (2014) and Reviewer 1 would have been happy.  But no, published Theropod Working Group (TwiG) analyses are flawed, and anyone using them is going to get a flawed result.  It's a great framework to start with though, and by standing on the shoulders of giants I've published the best version to date.  For non-avian maniraptoromorphs.

My first lesson was that this analysis turned out to be as difficult to run as it was to create.  Due to the huge number of taxa (501 Operational Taxonomic Units, or OTUs) and characters (700), and the large number of polymorphic scorings caused both by variation within an OTU and partial uncertainty of incomplete remains, you can't just load up TNT on a New Technology search and get the Most Parsimonious Trees (MPTs).  Note many analyses ignore polymorphies and just score the taxon a certain state or unknown, and that Cau in particular structured his character list to be bistate only, with additional characters scoring for each additional state.  I think the large amount of homoplasy might also contribute, since one of my takeaways was that certain areas of the tree are much less well resolved than common knowledge or consensus would have one believe.  In any case, about 70 hours on my new beast of a PC will get you within 10 steps of the MPTs, then you have to run further analyses to find shorter trees, and even then I found trees a step or two shorter using constraint analyses.  I wouldn't be surprised if there are trees a step or so shorter than what I found, but this is a problem we'll need to face as analyses become ever larger.  The fact none of the peer reviewers mentioned how unwieldy the analysis is makes me think none of them tried to run it, which is a flaw in reviewing I've called out before.  Like when Baron and Barrett added Chilesaurus to their Ornithoscelida analysis but included the wrong matrix, so that Mueller et al. found it fell out as a sauropodomorph, then Baron and Barrett's "corrected" matrix deleted all the dashes denoting inapplicable characters so that it couldn't possibly be run or checked for accuracy..  *sigh*  In any case, I included a saved shortest tree in the TNT file so even those with slow computers can access the MPTs.

Geneology of Theropod Working Group analyses, with indented references being expanded from the preceding reference.  All Mesozoic maniraptoromorphs from these analyses have been used here, and each bolded reference has had its character list completely utilized.  Number of characters informative within Maniraptoromorpha yet to be analyzed in parentheses.  After Hartman et al. (2019).

I described my phylogenetic philosophy in detail in the paper, but the basic gist is to take the TWiG analysis, add all usefully scorable taxa, and redefine the characters to reflect the modern sensibilities of Jenner (2004) and Sereno (2007).  Thus, I aimed to eliminate correlated characters, composite characters, eliminate "the use of “absent” as a state in a transformational character (Sereno, 2007:582-584), character traits constructed with discontinuous quantified states (so that certain ranges of values aren’t covered by any state) and those that include a state merely scoring for any condition except those specified by the other states (Jenner, 2004:301-302). We have begun the process of resolving these issues by quantifying 163 characters, isolating 240 composite states into single variables (often using the other variables to form new characters), and excluding 36 correlated characters (see Excluded Characters in the Supplementary Information). Our character list includes details of how each character has been changed from previously published versions. When possible, newly quantified character states have been formulated to best match the taxon distribution for each originally subjective character. All characters have been rewritten in the logical structure advocated by Sereno (2007) to reduce ambiguity and variability between analyses."

The first draft limited the taxa to maniraptoromorphs, but we expanded to all neotheropods in order to test Rauhut's idea Lori could be Coelurus or Ornitholestes.  Of course the TWiG character list was not intended to sort non-coelurosaurs, so that part of the tree is rather Peters-ian in recovering some standard clades but also getting some odd results.  It's possible taxa around the compsognathid grade would organize differently given a comprehensive carnosaur and/or tyrannosauroid character list, but our concern was paravian phylogeny and that's separated by several nodes.  The same philosophy occurs in the crown clade Aves, where I didn't recover Galloanseres or the topology of recent detailed avian analyses because TWiG wasn't designed for that.  This is a concept that's very rarely articulated in published analyses- barring extraordinary circumstances, there are parts of your tree that didn't sample a comprehensive range of suggested characters for that group.  I tried to communicate this in my discussion, that certain groups like therizinosaurs, non-ornithothoracine paravians and non-avian fake-ornithuromorphs have extremely well covered character evidence, while others like ornithomimosaurs, caenagnathoids and enantiornithines should not necessarily be trusted more than recent studies concentrating on those clades.

Holotype of Dalianraptor cuhe (D2139), a probable composite of jeholornithid skull, confuciusornithiform manus and enantiornithine feet.  Due to its chimaerical nature, it was excluded from the Lori analysis (after Gao and Liu, 2005).

So what taxa did I include?  Basically everything.  I "scored almost every named Mesozoic maniraptoromorph known from more than single elements or teeth (the seven exceptions are noted under Excluded Taxa in the Supplementary Information), as well as twenty-eight unnamed specimens. Five recent examples of Aves were included, the palaeognath Struthio and the neognaths Chauna, Anas, Meleagris and Columba. The Tertiary Lithornis and Qinornis were also included as both have been suggested to be outside Aves by some authors, as were Palaeotis, Anatalavis, Presbyornis, Sylviornis, Gallinuloides, Paraortygoides and Foro as basal representatives of modern clades."  "All named Mesozoic maniraptoromorphs described through 2018 and known from more than teeth or single elements were included with few exceptions.  Testing indicated Valdoraptor, Unquillosaurus, Canadaga and Gallornis each had spurious positions due to their fragmentary remains and the current character sample, although the addition of new characters could change this in future iterations.  "Ornithomimus" minutus is only known from a paragraph of text due to loss of the holotype and absence of illustration, so that possible hyperarctometatarsaly (219:2/3) is the only scorable character.  ... Finally, the chimaerical Bagaraatan, Beipiaognathus and Dalianraptor were not included pending detailed reanalysis of their types."

And what characters did I include?  "Characters are designed to incorporate all of those previously used in matrices using the Theropod Working Group (TWiG) as their base through 2012 with the exception of Senter (2011) a baraminology paper which was recognized too late in the coding cycle to be fully incorporated.  Functionally, this led to all proposed TWiG maniraptoromorph characters through mid 2018 being used except 20 from Senter (2011), 102 from Brusatte et al. (2014) and 23 from eight other published analysis (see Fig. S1)."  83% of relevant TWiG characters isn't too bad, especially as I rechecked every one using the latest data and reformatted the characters as noted above.  As I stated, "Ten characters are parsimony-uninformative among our 389 maniraptoromorphs (excluding the possibly tyrannosauroid megaraptorans, coelurids and proceratosaurids in this and the following taxon totals, to ensure similar content). These are retained pending future expansions of the analysis, leaving 690 parsimony-informative characters among our taxon sample of maniraptoromorphs. This makes it the second largest character sample and the largest taxonomic sample in a TWiG analysis of maniraptoromorphs to date, compared to other recent iterations of each TWiG lineage- Gianechini et al. (2018) (700 parsimony-informative characters for their 135 maniraptoromorph OTUs), Foth and Rauhut (2017) (534 such characters and 120 such OTUs), Brusatte et al. (2014) (666 such characters and 127 such OTUs), Agnolin and Novas (2013) (405 such characters and 80 such OTUs) and Senter et al. (2012) (367 such characters and 98 such OTUs)."

Skull of Sciurumimus albersdoerferi (BMMS BK 11).  This juvenile got a lot of N scores for ontogenetically variable characters, plus an entire section in the supplemnentary information.  After Rauhut et al. (2012).

Finally, "Several characters are known to vary ontogenetically among Mesozoic theropods.  These are noted under their descriptions and have been scored with 'N' in the NEXUS file if only young specimens can be coded.  This prevents juveniles from being analyzed as adults and indicates the OTU was not merely left uncoded by accident."  Thus taxa were scored rather conservatively, with e.g. Archaeopteryx scored N for pygostyle presence.  If you think any morphology reflects the adult condition, you can change the N score and test it.

Next up, the basic topology I recovered...

References- Jenner, 2004. The scientific status of metazoan cladistics: Why current research practice must change. Zoologica Scripta. 33, 293-310. DOI: 10.1111/j.0300-3256.2004.00153.x

Gao and Liu, 2005. A new avian taxon from Lower Cretaceous Jiufotang Formation of western Liaoning. Global Geology. 24(4), 313-316.

Sereno, 2007. Logical basis for morphological characters in phylogenetics. Cladistics. 23, 565-587. DOI: 10.1111/j.1096-0031.2007.00161.x

Senter, P. 2011. Using creation science to demonstrate evolution 2: Morphological continuity within Dinosauria. Journal of Evolutionary Biology, 24, 2197-2216. DOI: 10.1111/j.1420-9101.2011.02349.x

Rauhut, Foth, Tischlinger and Norell, 2012. Exceptionally preserved juvenile megalosauroid theropod dinosaur with filamentous integument from the Late Jurassic of Germany. Proceedings of the National Academy of Sciences. 109(29), 11746-11751. DOI: 10.1073/pnas.1203238109

Senter, Kirkland, DeBlieux, Madsen and Toth, 2012. New dromaeosaurids (Dinosauria: Theropoda) from the Lower Cretaceous of Utah, and the evolution of the dromaeosaurid tail. PLoS ONE. 7(5), e36790. DOI: 10.1371/journal.pone.0036790

Agnolin and Novas, 2013. Avian ancestors: A review of the phylogenetic relationships of the theropods Unenlagiidae, Microraptoria, Anchiornis and Scansoriopterygidae. Springer Netherlands. 96 pp. DOI: 10.1007/978-94-007-5637-3_1

Brusatte, S. L., Lloyd, G. T., Wang, S. C., & Norell, M. A. 2014. Gradual assembly of avian body plan culminated in rapid rates of evolution across the dinosaur-bird transition. Current Biology, 24, 2386-2392. DOI: 10.1016/j.cub.2014.08.034

Foth and Rauhut, 2017. Re-evaluation of the Haarlem Archaeopteryx and the radiation of maniraptoran theropod dinosaurs. BMC Evolutionary Biology. 17:236. DOI: 10.1186/s12862-017-1076-y

Gianechini, Makovicky, Apesteguía and Cerda, 2018. Postcranial skeletal anatomy of the holotype and referred specimens of Buitreraptor gonzalezorum Makovicky, Apesteguía and Agnolín 2005 (Theropoda, Dromaeosauridae), from the Late Cretaceous of Patagonia. PeerJ. 6:e4558. DOI: 10.7717/peerj.4558

Hartman, Mortimer, Wahl, Lomax, Lippincott and Lovelace, 2019. A new paravian dinosaur from the Late Jurassic of North America supports a late acquisition of avian flight. PeerJ. 7:e7247. DOI: 10.7717/peerj.7247

Wednesday, July 10, 2019

Lori published! Meet Hesperornithoides

This post is a long time coming.  Remember back last April when I announced the Lori paper was submitted?  Well, we could have easily been published shortly afterward if not for one dishonest jerk of a peer reviewer.  And then we got him again when we resubmitted to another journal!  But the good news for all of you is that the final published paper is MUCH better than the April 2018 version, though ironically only a bit of that is due to peer review.  Mostly its due to me getting a new incredibly beefy computer (i9 processor with 10 cores) that can actually run the Lori analysis, instead of having to depend on coworker Scott Hartman's university setup.  This let me increase the number of constraint tests on phylogenetic relationships a couple orders of magnitude, so the new paper is the best summary of our knowledge of maniraptoromorph relationships to date.  The other benefit to waiting a year was that I got to include all the 2018 data, complete the Mesozoic bird sample and add more Aves OTUs.  Full disclosure- my contribution to the paper was about half the description, the phylogenetic analysis and phylogenetic discussion, and the supplementary information.  Both my first successful experience with peer review and phylogenetic findings are also going to be future posts here.  This one is just to introduce the world to the Jurassic ?troodontid Hesperornithoides miessleri.

Hesperornithoides is one of those taxa that's been known publically for some time, largely due to Hartman et al.'s (2005) SVP abstract and poster presentation.  At the time it was most notable for being an apparent troodontid from the Jurassic, although since 2008 we've known of anchiornithines which may also be examples of such.  Unlike anchiornithines or the similarly Jurassic Archaeopteryx and scansoriopterygids though, Hesperornithoides isn't a slab specimen, but is preserved three dimensionally with little distortion.  Here's Scott's excellent skeletal reconstruction-

Figure 1. Skeletal reconstruction of Hesperornithoides miessleri showing only known material.  Gray indicates only impressions were preserved, while the posterodorsal skull is encased on matrix and cannot be resolved well due to barite inclusions. Scale equals 250 mm. After Hartman et al. (2019).

While in many ways a generic basal paravian, there are a few weird things about it.  The jugal has an extremely deep pneumatic recess anteriorly with a large funnel-shaped opening unlike any other maniraptoromorph (fig. 2).  Velociraptor has a horizontal slit on its jugal under the anterior part of the orbit (Barsbold and Osmolska, 1999: Fig. 1B) and Zanabazar has "a longitudinally elongate dorsal slit on the medial surface of the bone" (Norell et al., 2009:34), so are both quite different.  The newly described Archaeopteryx albersdoerferi has a feature in a similar position, but this seems to be only a diamond-shaped lateral fossa (Kundrat et al., 2018: Fig. 18A-B).

Figure 2. Top (A, B and C): Hesperornithoides meissleri left jugal (WYDICE-DML-001) in medial (A), lateral (B) and anterolateral oblique (C) views showing funnel-like pneumatic recess (after Hartman et al., 2019).  Bottom: Archaeopteryx albersdoerferi right jugal (SNSB BSPG VN-2010/1) in lateral view (mirrored) showing shallow recess indicted with line (modified after Kundrat et al., 2018).

Another odd feature is the paraquadrate foramen is partially enclosed by the quadrate (fig. 3) unlike any other maniraptoriforms except Falcarius (Zanno, 2010: Fig. 1G) and Deinocheirus (Lee et al., 2014: scoring for character 118).




Figure 3. Left quadrate and partial quadratojugal of Hesperornithoides miessleri (WYDICE-DML-001) in posterior view showing the quadrate (Qd) partially enclosed the paraquadrate foramen (Pqf) laterally.  After Hartman et al. (2019).







Given these characters and a few other resemblences to Morrison basal coelurosaurs Ornitholestes and Coelurus, peer reviewer Rauhut was curious about the possibility Lori was just a juvenile of one of those (it's about a third of their size- "the humerus of WYDICE-DML-001 is 29% the length of the Coelurus holotype, 17% the length of the Tanycolagreus holotype and 28% the length of the Ornitholestes holotype"). "In order to quantify the likelihood of it being a juvenile Ornitholestes, Coelurus or Tanycolagreus, we constrained trees pairing Hesperornithoides with each Morrison OTU. These were 11, 15 and 16 steps longer respectively than the most parsimonious trees, corroborating the abundant character evidence described above that Hesperornithoides is not referable to a Morrison non-maniraptoriform."  Such characters include the mesiodistally constricted tooth roots, longitudinal sulcus on the neurocentral suture of mid and distal caudals, distal chevrons that are bifid both anteriorly and posteriorly, large U-shaped furcula, distodorsal radius flange, well developed semilunate carpal, extensor flange on metacarpal I, intermetacarpal scar on metacarpal II, tapered postacetabular process, shallow brevis fossa, posteroventral lobe on postacetabular process and deep anterior intercondylar groove on tibiotarsus.  Still, its interesting we have some taxa that seem similar to both coelurid-grade coelurosaurs and basal paravians, like Caihong and Fukuivenator.

Figure 4. Top (A, B and C) holotype tooth of Koparion douglassi (DINO 3353) in side (A) and mesial (B) views with closeup of distal serrations (C); (D, E and F) maxillary tooth of Hesperornithoides meissleri (WYDICE-DML-001) in labial (D) and dentary tooth in mesial (E) views with closeup of distal serrations (F) (after Hartman et al., 2019).  Bottom (a-d) left distal radius of "Paleopteryx thomsoni" (BYU 2022) in posterior (a), medial (b), anterior (c) and lateral (d) views and (D, E) proximal femur of deinonychosaur (BYU 2023) possibly referrable to Hesperornithoides in lateral (D) and anterior (E) views (after Jensen, 1981).

What about previously known Morrison paravians?  Could Hesperornithoides be the same taxon?  In the case of Koparion, definitely not.  The teeth are extremely different (fig. 4, top).  As we write, Koparion "differs from Hesperornithoides teeth in being more recurved, labiolingually wide (Basal Width / FABL ~.72 compared to ~.45), possessing large serrations as in derived troodontids, exhibiting mesial serrations that extend to within two serration lengths of the crown base, and possessing blood pits..."  While I didn't include tooth-based taxa in my analysis, I wouldn't be surprised if Koparion was something that evolved large serrations convergently with troodontines since serration development is highly homoplasic in my paravian tree.  "Paleopteryx" is a distal radius (BYU 2022) that I thought was similar to microraptorians back in 2007 (fig. 4, bottom left), which could certainly use a reexamination given all the new paravians described since then.  While its not mentioned in the paper, Scott informed me the distal radius "is a bit squished and under-prepped" in Hesperornithoides, so we couldn't compare the two usefully although both have a pennaraptoran-like dorsal flange.  Finally, there's proximal femur BYU 2023 that was first referred to Archaeopteryx by Jensen (1981) and Maniraptora indet. by Jensen and Padian (1989) (fig. 4, bottom right).  I actually included this as an OTU but it "only overlaps with WYDICE-DML-001 at midshaft where it also lacks a fourth trochanter. Our analysis recovered BYU 2023 as a deinonychosaur that could belong to a troodontid or dromaeosaurid Hesperornithoides without an increase in tree length (see Positions of taxa pruned a posteriori in the supplementary information), but further comparison is limited."  So a referral to Hesperornithoides is a distinct possibility that future discoveries might corroborate.

Maniraptoromorph section of my Lori analysis after a posteriori deletion of taxa causing excess polytomies (see supp info for details).  Hesperornithoides highlighted. Modified after Hartman et al. (2019).

Finally, what is Hesperornithoides?  Definitely a member of the deinonychosaur-avialan clade, as even placing it on the paravian stem takes 15 more steps.  Beyond that, it's pretty uncertain.  My final analysis recovered it as a troodontid, as in Hartman et al. (2005).  Specifically in an intermediate clade closer to troodontines than sinovenatorines and 'jinfengopterygines' but not as close as Sinornithoides, Byronosaurus or Gobivenator.  Other members of this clade include Daliansaurus, Xixiasaurus and Sinusonasus.  But the analysis used in our first submission and 2018 SVP presentation found it to be a basal dromaeosaurid, along with Caihong, Tianyuraptor and Zhenyuanlong.  Characters like the dorsally displaced maxillary fenestra, posteroventral maxillary fossa (like Zhenyuanlong and microraptorians), mesial serrations and large lateral teeth could support this, and it's only two steps longer in the final analysis too.  But it could also be the first branching avialan, or an archaeopterygid (due to its similarity to Caihong which now falls in that family), or its troodontid clade can move to be the most stemward troodontids, all in two steps each.  I've said before that I view phylogenetic results more as a set of probabilities than a final tree, and I like to think both drafts of the paper reflect that.  I didn't go into this analysis with an agenda to place Lori in any particular position, and I found the other Jurassic paravians to have similarly uncertain relationships so I'm not surprised.

And with that, welcome to Lori Week!  We'll be discussing my phylogenetic analysis and results, what I thought of peer review, how to add your own taxon to the Lori matrix and how to check constraint trees of alternative topologies, what ideas I snuck in the paper, and so much more.  Hold on tight, I'm in the peer-reviewed literature...

References- Jensen, 1981. Another look at Archaeopteryx as the worlds oldest bird. Encyclia, The Journal of the Utah Academy of Sciences, Arts, and Letters. 58, 109-128.

Jensen and Padian, 1989. Small pterosaurs and dinosaurs from the Uncomphagre fauna (Brushy Basin Member, Morrison Formation: ?Tithonian), Late Jurassic, western Colorado. Journal of Paleontology. 63(3), 364-373. DOI: 10.1017/S0022336000019533

Barsbold and Osmólska, 1999. The skull of Velociraptor (Theropoda) from the Late Cretaceous of Mongolia. Acta Palaeontologica Polonica. 44(2), 189-219.

Hartman, Lovelace and Wahl, 2005. Phylogenetic assessment of a maniraptoran from the Morrison Formation. Journal of Vertebrate Paleontology. 25(3), 67A-68A. DOI: 10.1080/02724634.2005.10009942

Norell, Makovicky, Bever, Balanoff, Clark, Barsbold and Rowe, 2009. A review of the Mongolian Cretaceous dinosaur Saurornithoides (Troodontidae: Theropoda). American Museum Novitates. 3654, 63 pp. DOI: 10.1206/648.1

Zanno, 2010. Osteology of Falcarius utahensis: Characterizing the anatomy of basal therizinosaurs. Zoological Journal of the Linnaean Society. 158, 196-230. DOI: 10.1371/journal.pone.0198155

Lee, Barsbold, Currie, Kobayashi, Lee, Godefroit, Escuillie and Tsogtbaatar, 2014. Resolving the long-standing enigmas of a giant ornithomimosaur Deinocheirus mirificus. Nature. 515, 257-260. DOI: 10.1038/nature13874

Kundrat, Nudds, Kear, Lü and Ahlberg, 2018. The first specimen of Archaeopteryx from the Upper Jurassic Mörnsheim Formation of Germany. Historical Biology. 31(1), 3-63. DOI: 10.1080/08912963.2018.1518443

Hartman, Mortimer, Wahl, Lomax, Lippincott and Lovelace, 2019. A new paravian dinosaur from the Late Jurassic of North America supports a late acquisition of avian flight. PeerJ. 7:e7247. DOI: 10.7717/peerj.7247

Saturday, April 13, 2019

Imperobator the second named Antarctic Mesozoic theropod

Hi all.  Today we got the accepted manuscript version of Ely and Case's redescription of of the Naze dromaeosaur, initially briefly reported by Case et al. (2007).  The authors name it Imperobator and recover it as a paravian using Gianechini et al.'s (2018) version of Brusatte's TWiG analysis.

Despite the paper being titled "Phylogeny of a new gigantic paravian (Theropoda; Coelurosauria; Maniraptora) from the Upper Cretaceous of James Ross Island, Antarctica", the only hint at the size besides scale bars is "The approximate length of the pedal ungual of digit II in Utahraptor is 10 cm (approximate measurement made by one of the authors based on illustrations provided by Kirkland et al., 1993), and although the distal half of the pedal ungual in Imperobator is missing, an estimate for its total length would be 4-5 cm."  Their figure 7C suggests pedal phalanx IV-1 is 61 mm long, compared to 44.7 mm in Deinonychus specimen AMNH 3015, which would scale to 4.18 m using Paul's (1988) estimate.  For another comparison, the distal tibia is 60 mm wide according to figure 5A, while AMNH 3015's is 63.3 mm.  This would be 2.90 m if scaled to Paul's estimated length.  So Imperobator was ~3-4 meters long as far as I can tell.  Is that gigantic?

Reconstruction of the pes of Imperobator antarcticus (UCMP 276000) after Ely and Case (2019).

As regards the anatomy, I feel the authors missed an opportunity to fully figure this taxon known from multiple three dimensionally preserved fragments.  The initial paper just had a single photo of the reconstructed pes in anterior view, and this one has single perspectives for all but one of the fragments (distal mtIII is shown in anterior and posterior views).  Case et al. stated

"The dentition is poorly preserved except for two teeth that were preserved in a fragment of concretion. The teeth and the associated fragments all indicate long, narrow biconvex teeth. This shape suggests that both anterior and posterior carina were present; however, no serrations were noted on the carina, thus it is impossible to determine if serrations were present or absent. The teeth are incipiently laterally compressed, but retain a rounded outline, particularly anteriorly. The shape is indicative of teeth from the anterior region of the jaw."

... but here no teeth are even mentioned.  If they couldn't be definitely associated with the hindlimb, this should have at least been stated.  Their figure 4 showing the reconstructed pes is humorously bad as someone seemingly traced a photograph with no concern for theropod phalangeal proportions, so that digit III is shortest and phalanx IV-1 is three times longer than other phalanges in that digit.  I mean, if you have a decade to make a paper you can draw a realistic theropod foot.  If the figure's accurate, phalanx IV-1 is extremely robust, bringing to mind Austroraptor.  Contra the caption for figure 7 (which is wrong, as C is "Proximal phalanx of pedal digit IV in dorsal view" and E is "Distal articular surface of a phalanx possibly pertaining to digit III (?)"), no phalangeal part shown is likely to be from pedal digit I as all are about equal in width to digits III/IV.  This makes their statement

"Potential material from digit I may be present (Fig. 7D). It is distinguished by what may be a prominent flexor heel on the proximoventral surface, morphologically similar to that of the dromaeosaurid (avialan?) Balaur bondoc (Csiki et al. 2010)."

... confusing, as 7D seems to be the proximal half of a non-ungual phalanx positioned as III-1 in Case et al. (2007).  In the materials list, Ely and Case also state "material from metatarsal I, and even metatarsal V may be preserved", but we get no description or illustration of these.  Note contra line 428, fibular fusion is absent in Buitreraptor and Graciliraptor.

Holotype of Imperobator antarcticus (UCMP 276000) as photographed by Case et al. (2007).  Distal phalanges of digits III and IV not described by Ely and Case (2019), and distal metatarsal IV and phalanx IV-1 missing.

As regards the phylogeny, Ely and Case find Imperobator to fall out in Paraves in a polytomy with eudromaeosaurian and anchiornithine OTUs.  They reran this as a Bayesian analysis which favored placing it among anchiornithines, although exclusion from Dromaeosauridae was just barely supported at 50%.  While the authors seem to favor a basal position, as in their 2016 SVP abstract where it emerged as a basal deinonychosaur, their analyses suggests an anchiornithine troodontid or eudromaeosaurian dromaeosaurid placement are about equally supported. 

Imperobator was included in the Lori analysis (as the 'Naze dromaeosaur') and had a highly unstable position.  Rescoring it given the new paper and assuming the teeth cannot be assigned to the taxon, it now emerges as a halszkaraptorine.  Interesting.

References- Paul, 1988. Predatory Dinosaurs of the World. Simon and Schuster. 464 pp.

Case, Martin and Reguero, 2007. A dromaeosaur from the Maastrichtian of James Ross Island and the Late Cretaceous Antarctic dinosaur fauna. in Cooper and Raymond (eds). Antarctica: A Keystone in a Changing World – Online Proceedings of the 10th ISAES X. USGS Open-File Report 2007-1047, Short Research Paper 083, 4 pp. DOI: 10.3133/ofr20071047SRP083

Gianechini, Makovicky, Apesteguía and Cerda, 2018. Postcranial skeletal anatomy of the holotype and referred specimens of Buitreraptor gonzalezorum Makovicky, Apesteguía and Agnolín 2005 (Theropoda, Dromaeosauridae), from the Late Cretaceous of Patagonia. PeerJ. 6:e4558. DOI: 10.7717/peerj.4558

Ely and Case, 2019. Phylogeny of a new gigantic paravian (Theropoda; Coelurosauria; Maniraptora) from the Upper Cretaceous of James Ross Island, Antarctica. Cretaceous Research. DOI: 10.1016/j.cretres.2019.04.003

Monday, March 25, 2019

What is Lingyuanosaurus?

A quick one here.  I've had the flu for the past week, so haven't felt up to doing any professional work, but we did get the description of a new fragmentary theropod taxon- Lingyuanosaurus sihedangensis (Yao et al., 2019).  It's from the same beds as Iteravis, which I think are Jiufotang because Ikrandraco is known from both there and another Jiufotang locality (Lamadong).  The holotype is four mostly partial vertebrae, some ribs, a proximal and distal humerus, two manual unguals, ilium, possible proximal ischium, femur, distal tibia and astragalus exposed proximally.  With a femoral length of 200 mm, it's about the same size as Jianchangosaurus (206 mm) and was run by its authors in a version of Zanno's (2010b) TWiG analysis.  They recovered it as a therizinosaur closer to therizinosaurids than Falcarius, Jianchangosaurus and Beipiaosaurus but less than Alxasaurus.

While my first lumping thought was "are we sure this isn't just a fragmentary Beipiaosaurus?", the more I scored it for the Lori matrix's 700 characters, the weirder it seemed.  Unlike any therizinosaur, there's only a "longitudinal depression, which may represent a pneumatic fossa" in the cervical (scored as unknown for presacral pneumatization by Yao et al.), the dorsal's parapophysis is centrally placed, the proximal caudal's complete transverse process is distally tapered (contra Yao et al., this is not true in the illustrated specimen of Falcarius- Zanno, 2010a: Fig. 9E), the humeral bicipital crest is barely projected (also in Erlikosaurus; scored unknown by Yao et al.), the distal humerus is expanded less than twice of shaft width, the ilial cuppedicus fossa is overhung laterally, the proximal femur has a lateral longitudinal ridge (scored unknown by Yao et al.), and the femoral ectocondylar tuber is medially positioned (not used by Yao et al.).  The dorsal parapophyseal position is rare outside enantiornithines so is near certainly an autapomorphy, and the cervical pneumatization may be present but difficult to see externally as in some ornithomimosaurs, but the other characters would be odd for a therizinosaur, especially the undeveloped and narrow humerus.

Lingyuanosaurus sihedangensis holotype humeri (IVPP V23589)- left proximal humerus in medial view (a), right distal humerus in posterior (b) and anterior (c) views. Scale = 30 mm. After Yao et al., 2019.

So I ran it in the Lori matrix, and it emerged... as an oviraptorosaur.  Makes more sense of the distal humerus, cuppedicus fossa and femur, and the manual ungual and ilial shape still work out.  Constraining it as a therizinosaur is only one step longer though, so maybe it really is one.  But note that of the supposedly therizinosaurian characters listed by Yao et al. (2019:9), Zanno's "dorsal vertebrae with a complex laminar structure" refers to mid-dorsals ("anterior dorsals" in Zanno's nomenclature) which are not preserved in Lingyuanosaurus and nor was that character (their 274) scored for the taxon, and oviraptorosaurs can have both "laterally flattened manual unguals with dorsally positioned collateral grooves" (e.g. Currie and Russell, 1988: Fig. 4b, mu I) and "a highly modified ilium with a deep preacetabular process, a reduced postacetabular process, a preacetabular process whose ventral margin is dorsally displaced relative to the acetabulum" (e.g. Funston et al., 2017: Fig. 9C).  The slender pubic peduncle is therizinosaur-like, however.

Interestingly, only four steps are needed to place it in Ornithomimosauria, where it emerges by the Jehol Hexing which also has a reduced humerus and highly curved manual unguals.  A further thought was that the proximal humerus and manual unguals were rather like the mysterious Yixianosaurus, but the two are otherwise incomparable.  Enforcing them to be synonymous leads to trees eight steps longer (the pair emerge as oviraptorosaurs), which isn't bad either but not as parsimonious as letting Yixianosaurus' complete pectoral girdle and arms go elsewhere.  Still, we know from compartmentalization studies that analyzing different body areas leads to different cladograms, so maybe Yixianosaurus/Lingyuanosaurus falls within the expected homoplasy range of an oviraptorosaur with arms a bit more similar to another clade?

In any case, Yao et al. modified several of Zanno's TWiG characters, but four of these are done in a way that create composite characters that hide potential homology.  For the classic character on hyposphene morphology, in addition to the original two states "0: abutting one another above neural canal, opposite hyposphenes meet to form lamina" and "1: placed lateral to neural canal and separated by groove for interspinous ligaments, hyposphenes separated", the authors add a third state for Lingyuanosaurus' supposedly autapomorphic condition "2: abutting one another above neural canal, opposite hyposphenes meet ventrally and form a transversely expanded intumescence."  But that's just another form of state 0, as the character's variable condition is abutting versus separated.  Ditto for character 158 ("Postacetabular ala of ilium in lateral view 0: squared 1: acuminate 2: reduced, iliac blade terminates at rectangular end just posterior to level of acetabulum") where new state 2 is still squared like state 0, regardless of how small the process is, and 209 ("Neural spines on caudal dorsal vertebrae in lateral view 0: rectangular or square 1: fan-shaped, with craniocaudally expanded dorsal ends 2: dorsal borders curved, but not craniocaudally expanded") where new state 2 is still unexpanded like state 0 and there should be another character for curvature.  The final example is their 310 ("Pubic peduncle of ilium 0: straight 1: anterior margin straight, posterior margin curved, articular surface ventrally directed 2: anterior margin straight, posterior margin curved, articular surface caudoventrally directed 3: anterior and posterior margins both curved, articular surface caudoventrally directed").  See if you can figure out the issue(s) with that one.

For now, I'm considering Lingyuanosaurus one of several maniraptoriform taxa that belong to a non-pennaraptoran clade but can't be securely placed given the analyzed data.

References- Currie and Russell, 1988. Osteology and relationships of Chirostenotes pergracilis (Saurischia, Theropoda) from the Judith River (Oldman) Formation of Alberta, Canada. Canadian Journal of Earth Sciences. 25(7), 972-986. DOI: 10.1139/e88-097

Zanno, 2010a. Osteology of Falcarius utahensis: Characterizing the anatomy of basal therizinosaurs. Zoological Journal of the Linnaean Society. 158, 196-230. DOI: 10.1371/journal.pone.0198155

Zanno, 2010b. A taxonomic and phylogenetic re-evaluation of Therizinosauria (Dinosauria: Maniraptora). Journal of Systematic Palaeontology. 8(4), 503-543. DOI: 10.1080/14772019.2010.488045

Funston, Mendonca, Currie and Barsbold, 2017. Oviraptorosaur anatomy, diversity and ecology in the Nemegt Basin. Palaeogeography, Palaeoclimatology, Palaeoecology. 494, 101-120. DOI: 10.1016/j.palaeo.2017.10.023

Yao, Liao, Sullivan and Xu, 2019. A new transitional therizinosaurian theropod from the Early Cretaceous Jehol Biota of China. Scientific Reports. 9:5026. DOI: 10.1038/s41598-019-41560-z

Wednesday, June 27, 2018

Etrigansauria, the unnecessary demon

For this week's post, we have a new paper on ceratosaurs by Delcourt (2018).  The paper discusses anatomy, behavior and such (and provides some good photos of Limusaurus), but here I only want to deal with the phylogenetic taxonomy proposed.  Delcourt uses the topology of Analyses 1 and 2 of Wang et al. (2016) from the Limusaurus ontogeny paper, which seems to have been well done from what I've seen.  Tons of taxa, tons of characters, and some sage commentary on OTUs and anatomy.  It's a shame the full tree is never presented in the paper, and I hope that analysis or a derivative is used for a stand alone phylogeny paper in the future.  Wang et al. interestingly find noasaurids to group with Elaphrosaurus, Limusaurus, Spinostropheus and Deltadromeus in a clade outside ceratosaurids plus abelisaurids, which is also what the Lori analysis found weirdly enough.

Ceratosaur portion of Analysis 1 and 2 of Wang et al. (2016).  Numbers are GC jacknife supports from Analysis A (above branches) and B (below branches).  After Wang et al., 2016.

So I have no issue with the phylogeny, but Delcourt's proposed phylogenetic taxonomy is... bad.  Let's start with his new taxon- Etrigansauria, named after DC Comics character Etrigan who is a demon bound to the human Jason Blood.  Now I love the DC Animated Universe as much as the next person, but what's the phylogenetic definition of Etrigansauria? "The most inclusive clade containing Carnotaurus sastrei and Ceratosaurus nasicornis but not Noasaurus leali."  But wait a second, we already have a Carnotaurus plus Ceratosaurus node-based clade- Neoceratosauria from Novas 1991, most recently refined by Hendrickx et al. (2015) as "The least inclusive clade containing Ceratosaurus nasicornis and Carnotaurus sastrei."  So if we have a standard topology with abelisauroid noasaurids, Etrigansauria self destructs, and if we have a Wang et al. style topology then Etrigansauria is just a junior synonym of Neoceratosauria.  [Edit: I noticed when commenting on the journal's website that the definitions are slightly different in that Etrigansauria is stem-based, so that there could be non-neoceratosaurian etrigansaurs under a Wang et al. style topology.  But the only such taxon in Wang et al.'s trees that were used is the skull-less Berberosaurus, which falls out other places in their other analyses- elaphrosaurid, stem-ceratosaur, etc..  Indeed, I doubt Delcourt had this distinction in mind because his figure 1 actually places Etrigansauria at the neoceratosaur node, not the stem containing Berberosaurus as his definition would have it.]  The word "neoceratosaur" only appears once in Delcourt's paper, as a brief mention- "In some analyses, Berberosaurus is considered as a basal ceratosaurian, a neoceratosaurian, ...".  This seems weird, and I urge everyone not to forget Novas's decades of work on these animals, and use Neoceratosauria instead of Etrigansauria published twenty-seven years later.

I don't know why everyone has such a hard time with Phylocode Article 11.7, which reads in part "when a clade name is converted from a preexisting typified name or is a new or converted name derived from the stem of a typified name, the definition of the clade name must use the type species of that preexisting typified name or of the genus name from which it is derived (or the type specimen of that species) as an internal specifier."  Let's keep that rule in mind as we look at the rest of the definitions...

Delcourt's other big blunder is with Abelisauroidea versus Ceratosauroidea.  Delcourt uses Wilson et al.'s (2003) definition of Abelisauroidea which is (Carnotaurus sastrei + Noasaurus leali).  That's a bad definition since it doesn't include Abelisaurus as a specifier, but we'll ignore that for the moment.  He also uses Wilson et al.'s definition for Abelisauridae- (Carnotaurus sastrei < - Noasaurus leali).  Which is also bad in not including Abelisaurus, but whatever.  Using these bad definitions in Wang et al.'s phylogeny gets us the bad result of making Ceratosaurus an abelisaurid abelisauroid.  Which Delcourt correctly notes it can't be, because Ceratosauridae/oidea has priority over Abelisauridae/oidea.  Delcourt's weird solution is to instead use Wilson et al.'s Abelisauroidea definition for Ceratosauroidea, so that Ceratosauroidea is now Carnotaurus plus Noasaurus. Ack!

Okay, first of all, that doesn't work because Ceratosaurus nasicornis needs to be an internal specifier of Ceratosauroidea (Phylocode Article 11.7!).  Second, we have much earlier and better definitions to use than Wilson et al.'s.  Holtz (1994) defined Abelisauroidea as taxa closer to abelisaurids than Ceratosaurus, which can be easily modified to (Abelisaurus comahuensis < - Ceratosaurus nasicornis).  See, that's a good definition that follows Article 11.7, maps correctly on to Novas' (1991) topology when he created the taxon, and never includes Ceratosaurus to avoid that whole kerfuffle.  In Wang et al.'s topology, noasaurids aren't abelisauroids, simple as that.  What is Ceratosauroidea?  It's only ever been defined before this as an alternative to Neoceratosauria when that clade was thought to be sister to coelophysoids, so those definitions make it a junior synonym of Neotheropoda sensu Bakker.  Given current taxonomy, it doesn't seem like a useful clade to redefine unless what we call Ceratosauridae now expands a LOT.

Ceratosauria in a version of the Lori analysis.  I'd ignore Kayentavenator and bissektensis as flukes based on their very fragmentary holotypes.  Not bad for analyzing ceratosaurs using maniraptoromorph characters...

The rest of Delcourt's definitions aren't any better.

Ceratosauria: Most inclusive clade containing Ceratosaurus but not Neornithes

That's the standard ever since Rowe (1989) so is fine.

Noasauridae: Most inclusive clade containing Noasaurus but not Carnotaurus

That's the original definition from Wilson et al. (2003), and is fine.

Elaphrosaurinae: Most inclusive clade containing Elaphrosaurus but not Noasaurus

This is attributed to Rauhut and Carrano (2016), but that's wrong.  Those authors used the better definition "all noasaurids that are more closely related to Elaphrosaurus than to Noasaurus, Abelisaurus, Ceratosaurus, or Allosaurus" to cover alternative topologies so that we don't get stupid results like abelisaurid Ceratosaurus.

Noasaurinae: Most inclusive clade containing Noasaurus but not Elaphrosaurus

Ditto here. Delcourt falsely attributes that definition to Rauhut and Carrano, but they actually used the much better "all noasaurids that are more closely related to Noasaurus than to Elaphrosaurus, Abelisaurus, Ceratosaurus, or Allosaurus."  As an obvious illustration of why Delcourt's definition is bad, in a standard topology where Noasaurus is an abelisauroid but Elaphrosaurus is not (e.g. Carrano and Sampson, 2008), Ceratosaurus and abelisaurids are all noasaurines.

Ceratosauridae: (new definition) the most inclusive clade containing Ceratosaurus but not Carnotaurus.

We actually already have an equivalent definition for this family- Rauhut (2004) wrote "the name is used here for a clade containing all ceratosaurs that are more closely related to Ceratosaurus than to abelisaurids." But even if one disputed that because Rauhut stated "it is premature to give such a formal definition at present", Hendrickx et al. (2015) defined it as "The most inclusive clade containing Ceratosaurus nasicornis but not Carnotaurus sastrei and Noasaurus leali." 

Abelisauridae: (new definition) the most inclusive clade containing Carnotaurus but not Ceratosaurus.

Article 11.7!  Abelisaurus comahuensis needs to be an internal specifier for Abelisauridae, again why is this so hard?  No argument for using Carnotaurus makes any sense.  Sure it's more complete, and may be more deeply nested, but if Abelisaurus somehow ends up not closer to Carnotaurus than Ceratosaurus, you're not going to be calling the Carnotaurus group Abelisauridae anyway.  The sad part is that we actually do need a new good definition for Abelisauridae.  Novas' (1997) definition is a node including the fragmentary Xenotarsosaurus which has an unstable position in recent analyses.  Rowe et al.'s (1997), Wilson et al.'s (2003) and Sereno's (perpetually in press) definitions all use Carnotaurus.  Sereno's (1998) is a node using Abelisaurus and Carnotaurus that would work (except for Rugops) in Wang et al.'s topology, but exclude all taxa except the two specifiers and Aucasaurus in Filippi et al.'s (2016) topology, for instance.  Plus none of the stem-based definitions exclude Ceratosaurus.  Delcourt's definition is bad because if noasaurids are abelisauroids as in most topologies, noasaurids are abelisaurids.  Here's what a good definition of Abelisauridae looks like- All taxa more closely related to Abelisaurus comahuensis than to Ceratosaurus nasicornis, Noasaurus leali, Elaphrosaurus bambergi or Allosaurus fragilis.  Someone publish that.

Ceratosauria phylogeny from Filippi et al. (2016), after Filippi et al. (2016).

Carnotaurinae: Most inclusive clade containing Carnotaurus but not Abelisaurus

That's fine and classic, taken from Sereno (1998) who named the clade.  Honestly, I think this and Abelisaurinae have proven to be pretty useless due to the varying position of Abelisaurus and should probably be ignored by future authors.  In Filippi et al.'s trees, Carnotaurus is the only carnotaurine, but in Wang et al.'s trees all abelisaurids except Abelisaurus and Rugops are.  Instead of abelisaurines vs. carnotaurines, the more useful split seems to be between majungasaurs and brachyrostrans (in the Lori trees too, incidentally).  It would be great to have a name for the Majungasaurus plus Carnotaurus node too, so we could easily refer to "basal" abelisaurids like Rugops, Abelisaurus and Ilokelesia in Wang et al.'s trees, Kryptops and Rugops in Filippi et al.'s trees, or Rugops, Genusaurus and Eoabelisaurus in the Lori tree.

Majungasaurini: Most inclusive clade containing Majungasaurus but not Carnotaurus

Here, Delcourt correctly notes that in Wang et al.'s topology, Majungasaurinae as originally defined falls out inside Carnotaurinae.  So it's yet another case where the Phylocode clashes with the ICZN.  Which is a fair observation, but I think the better solution would be to propose Majungasauria for that clade, which could go in either position and work fine. 

Brachyrostra: Most inclusive clade containing Carnotaurus but not Majungasaurus

The original definition, so that's fine.

Furileusauria: Most inclusive clade containing Carnotaurus but not Skorpiovenator.

This is credited to Filippi et al. (2016), but those authors actually had Ilokelesia and Majungasaurus as external specifiers too.  Since those two are also outside Furileusauria in Wang et al.'s trees, I don't see why the change was made.  I'm also not sure how useful the clade Furileusauria is yet.  It obviously works in Filippi et al.'s phylogeny, but has uncertain content in Wang et al.'s since Carnotaurus and Skorpiovenator are part of a polytomy.  I should note here that it's not at all certain whether Wang et al.'s or Filippi et al.'s trees are better supported.  Filippi et al. includes 6-8 more ceratosaur taxa and 416 characters with just a few outgroups, while Wang et al. have 744 characters but also densely sample and test coelophysoids and have quite a lot of tetanurines, so many of those characters are probably not parsimony-informative for ceratosaurs.

So that's Delcourt's (2018) phylogenetic taxonomy.  I honestly don't see how Neoceratosauria was never brought up in peer review.  It's also ironic that Delcourt goes through hoops to try to adjust Wilson et al.'s bad definitions because they only work in Wilson et al.'s topology, only to propose new definitions that only work in Wang et al.'s topologies.  I don't know about the other portions of the paper, but the phylogenetic taxonomy section is an utter failure of peer review in my opinion.  If people start using Etrigansauria and this butchered Ceratosauroidea... *cringe*

Look, if you were tasked with making good definitions for Ceratosauria, it's easy-
Ceratosauria- (Ceratosaurus nasicornis < - Passer domesticus)
Noasauridae- (Noasaurus leali < - Abelisaurus comahuensis)
Elaphrosaurinae- (Elaphrosaurus bambergi < - Noasaurus leali, Abelisaurus comahuensis, Ceratosaurus nasicornis, Allosaurus fragilis)
Noasaurinae- (Noasaurus leali < - Elaphrosaurus bambergi, Abelisaurus comahuensis, Ceratosaurus nasicornis, Allosaurus fragilis)
Neoceratosauria- (Ceratosaurus nasicornis + Abelisaurus comahuensis)
Ceratosauridae- (Ceratosaurus nasicornis < - Abelisaurus comehuensis)
Abelisauroidea- (Abelisaurus comehuensis < - Ceratosaurus nasicornis)
Abelisauridae - (Abelisaurus comahuensis < - Ceratosaurus nasicornis, Noasaurus leali, Elaphrosaurus bambergi, Allosaurus fragilis)
NEW CLADE- (Majungasaurus crenatissimus + Carnotaurus sastrei)
Majungasauria- (Majungasaurus crenatissimus < - Carnotaurus sastrei)
Brachyrostra- (Carnotaurus sastrei < - Majungasaurus crenatissimus)

Follows Article 11.7, works in everyone's topologies, ta da. 

References- Rowe, 1989. A new species of the theropod dinosaur Syntarsus from the Early Jurassic Kayenta Formation of Arizona. Journal of Vertebrate Paleontology. 9(2), 125-136.

Novas, 1991. Phylogenetic relationships of ceratosaurian theropod dinosaurs. Ameghiniana. 28, 401.

Holtz, 1994. The phylogenetic position of the Tyrannosauridae: Implications for theropod systematics. Journal of Paleontology. 68(5), 1100-1117.

Novas, 1997. Abelisauridae. In Currie and Padian (eds.). Encyclopedia of Dinosaurs. Elsevier Inc. 1-2.

Rowe, Tykoski and Hutchinson, 1997. Ceratosauria. In Currie and Padian (eds.). Encyclopedia of Dinosaurs. Elsevier Inc. 106-110.

Sereno, 1998. A rationale for phylogenetic definitions, with application to the higher-level taxonomy of Dinosauria. Neues Jahrbuch für Geologie und Paläontologie Abhandlungen. 210(1), 41-83.

Wilson, Sereno, Srivastava, Bhatt, Khosla and Sahni, 2003. A new abelisaurid (Dinosauria, Theropoda) from the Lameta Formation (Cretaceous, Maastrichtian) of India. Contributions from the Museum of Paleontology. 31(1), 1-42.

Rauhut, 2004. Provenance and anatomy of Genyodectes serus, a large-toothed ceratosaur (Dinosauria: Theropoda) from Patagonia. Journal of Vertebrate Paleontology. 24(4), 894-902. 

Carrano and Sampson, 2008. The phylogeny of Ceratosauria (Dinosauria: Theropoda). Journal of Systematic Palaeontology. 6, 183-236. 

Hendrickx, Hartman and Mateus, 2015. An overview of non-avian theropod discoveries and classification. PalArch's Journal of Vertebrate Palaeontology. 12(1), 1-73.

Filippi, Mendez, Juarez Valieri and Garrido, 2016. A new brachyrostran with hypertrophied axial structures reveals an unexpected radiation of latest Cretaceous abelisaurids. Cretaceous Research. 61, 209-219. 

Rauhut and Carrano, 2016. The theropod dinosaur Elaphrosaurus bambergi Janensch, 1920, from the Late Jurassic of Tendaguru, Tanzania. Zoological Journal of the Linnean Society. 178(3), 546-610.

Wang, Stiegler, Amiot, Wang, Du, Clark and Xu, 2016. Extreme ontogenetic changes in a ceratosaurian theropod. Current Biology. 27(1), 144-148.

Delcourt, 2018. Ceratosaur palaeobiology: New insights on evolution and ecology of the southern rulers. Scientific Reports. 8:9730.