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.
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Perez-Moreno, 2004. Pelecanimimus polyodon: Anatomía, sistemática y paleobiología de un
Ornithomimosauria (Dinosauria: Theropoda) de Las Hoyas (Cretácico Inferior; Cuenca,
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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

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Brusatte, Lloyd, Wang and Norell, 2014. Gradual assembly of avian body plan
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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