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First
an apology for misspelling the name of Fukuivenator earlier (needed one more ‘u’). In addition, Fukuivenator now nests one node lower, closer to Ornitholestes, with which it shares a cervical series longer than the skull. Additional data enabled that correction here.
Second
We have another theropod cladogram (Hendrickx et al. 2015; Fig. 1) that more or less matches the large reptile tree (661 taxa) — from a distance. Closer in several nodes and clades differ as shown below. Phytodinosaurs are not theropods.
Figure 1. Theropod cladogram from Hendrickx et al. I colorized clades recovered by the large reptile tree. Here the phytodinosaurs do not belong. The Marasuchus clade was omitted. Other clades recovered by the large reptile tree are colored here. Only a few taxa do not nest the same in the two compared trees, but I wonder about the genera included within the suprageneric clades. Click to enlarge.
The above cladogram
(Fig. 1) pretty much says it all. The large reptile tree recovered roughly the same clades in the same order (see Fig. 2, colorized in Fig. 1), but with specific taxa, not suprageneric taxa. A few long-rostrum taxa, like Deinocheirus and Proceratosaurus nest similar spinosaurs, as shown on the color overlay. Why this was not recognized earlier is one of the few remaining mysteries of paleontology.
Figure 2. Fukuivenator nests with basal tyrannosaurs in the theropod subset of the large reptile tree.
Third
One of the reasons why Fukuivenator was difficult for the the original authors to nest was its basal position in a clade. Basal taxa don’t have a long list of clade synapomorphies built in, but are generalized in their character scores.
References
Hendrickx C, Hartman SA and Mateus O 2015. An overview of non-avian theropod discoveries and classification. PalArch’s Journal of Vertebrate Palaeontology, 12(1):1-73. ISSN 1567-2158