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

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

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

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