Now that you have the revised version up, I'll tell you no one familiar with dinosaurs is going to believe your claims that Psittacosaurus just happens to preserve consistent gastric collections by accident
By accident (lines 80–84) or deliberately e.g. for mineral supplement (lines 57–58). The presence of gastric mill in ceratopsians is poorly-supported by available evidence (e.g. lines 77–80, 84–85). In any case, ceratopsians are not considered as ancestors of birds, so they have little to do with the problem.
You don't need to tell scientists what they should think. This is not the first time that you say what the entire scientific community will think of my work because the entire world is supposed to think and must think what you think, Mickey.
that Limusaurus is a bird. That's the definition of special pleading. If you actually think Limusaurus is a bird, wouldn't that be the big story? "Late Jurassic flightless bird found in China, not a theropod." But every phylogenetic analysis including Limusaurus has recovered it as a ceratosaur. So you're just brushing off every theropod worker as an aside?
First, the phylogenetic position of Limusaurs is rather problematic for cladists (lines 63–64): “which is thought to represent a basal ceratosaur or an abelisauroid (e.g. Xu et al. 2009, Rauhut and Carrano 2016).” It is not very firmly nested within ceratosaurs.
Second, there are known so many independent cases of the loss of flight ability in Cenozoic birds... I’m not really surprised by a one more secondarily flightless bird species on the long list of flightless birds of the Mesozoic and the Cenozoic Eras. The case of Limusaurs is indeed interesting due to its Late Jurassic age. However, Limusaurus appears to be some younger than scansoriopterygids or coeval, so there already existed true flying birds which could go down from the trees. Non-theropod ancestry of Limusaurs is strongly supported by the hand anatomy (lines 65–66) if it was correctly reconstructed by Xu et al. (2009).
Similarly, at least Martin and Lingham-Soliar have claimed ornithomimosaurs are dinosaurs, not birds. So for you to claim differently because of gastroliths in Shenzhousaurus and Sinornithomimus should be pretty important news since theropods and birds are in your mind distantly related.
First, if ornithomimosaurs were feathered, they represented birds (secondarily flightless).
Second, birds and dinosaurs are CLOSELY RELATED “in my mind”, as clearly shown at the Fig. 2.
It's so similar to my discussion with Martin where I asked if he thought tyrannosaurs were birds, and he said if they evolved from an ancestor with wings, then yes, but he didn't care/know. It's putting the evolutionary cart before the horse.
This sounds like a typical “scientific answer” given by a scientist. Moreover, the answer was correct: if they evolved from an ancestor with wings, then yes.
In contrast, cladists are 100% sure about their birds are dinosaurs hypothesis.
Since I replied to your Yi preprint, let's address this.
In your first paragraph, we have an issue common to BANDits and displayed in your new preprint. Basically, you claim birds have character X that dinosaurs don't, so can't be dinosaurs. We reply this dinosaur has character X (gastric mill in psittacosaurs, closed acetabulum in ankylosaurs, etc.), so surely the same mutation could have evolved in birds from the basal dinosaurian condition too? You reply psittacosaurs don't have to do with bird origins. But that doesn't matter. The point is that biology allows the dinosaur condition to move to the bird condition. If it happened in non-birds it could happen in birds. There's no gate saying "dinosaurs can never evolve the bird trait" or even a reason why that should be infrequent. So what's your response to 'any mutation could happen anywhere'?
Re: Limusaurus, you know abelisauroids ARE ceratosaurs, right? Everyone's finding it in Ceratosauria. That you claim a ceratosaur could be a pennaraptoran is VERY unparsimonious and unheard of.
Also, Xu et al.'s analysis recovered megalosaurs, carnosaurs, tyrannosauroids and compsognathids as having Limusaurus' manual homologies, so you can't argue they found Limusaurus to have a bird hand but other averostrans to have a dinosaur hand.
Regarding figure 2, are sauropodomorphs, ornithischians and/or Marasuchus closer to theropods than birds, or between birds and crocodyles?
As for the "scientific answer", that's because that's how zoological phylogeneticists do things. If you haven't noticed 99%+ of working phylogeneticists are cladists. Nobody says "if you evolved from an ancestor with hooves, you're an ungulate." Workers don't define groups based on whether they ultimately evolved from a taxon with a character, they construct trees using that character and others and apply a model. Do you honestly think biologists are going to throw out the thousands of characters they use for cladistic analyses now and go back to a subjective model involving key characters like you seem to value?