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...|
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.|
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.|
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.
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