Despite their popularity and a wealth of good material, the origins of the Dinosauria are still somewhat murky. This is not to say that paleontologists don't know where they came from--not at all. Dinosaurs are dinosauriform ornithodirans more derived than Marasuchus. The stepwise progression from Lagerpeton to Marasuchus to Psuedolagosuchus (and maybe Silesaurus) to Dinosauria well supported and has withstood every cladistic analysis I can think of that deals with the issue of dinosaur origins.
What's not so fully understood is the most basic split between the two major dinosaur clades. On one end, the more basal Saurischia, which retained the tri-radiate pelvis of its ornithodiran ancestors, as well as the carnivorous appetite and bipedal gait of its forebearers.
On the other side, the ornithischians were slower to diversify (if Eocursor's authors are right) but that could be thanks to their much more derived skeleton. These were herbivores through and through. And while theropods were carnivores, prosauropods may have been omnivores, and sauropods were growing to enormous sizes off the ferns of Pangea, ornithischians were having a tough time finding their niche. Right off the bat, ornithischians reworked their skeleton to include a sizeable gut, quara-radiate pelvis, and a unique predentary bone which capped the lower jaw.
I have reproduced two skulls here. Eoraptor (top) after Sereno's description with bits and pieces from Paul (2003), and Lesothosaurus after The Dinosauria, 2nd Edition, which is three or four years old now. Even the basic skull structures of these two animals are strikingly different, which seems so bizarre to me, given that both are the most primitive members of their respective groups--the closest on both sides of the Dinosauria to the common ancestor*.
The most notable difference (to me) is that in the ornithischians, the quadrate articulates with the surangular, unlike the case in Eoraptor and sauropodmorphs, in which the quadrojugal is the articulating bone. Exactly how this difference affects function, I'm not sure. In Archaeopteryx, however, the quadrojugal has been reduced to a small L-shaped splint between the jugal and the quadrate, and the quadrate articulates with the surangular. Another major difference is that the general construction of Lesothosaurus' skull is far more robust than Eoraptor's. Just look at a simple bone like the jugal (light blue). In Eoraptor, it's thin, but in Lesothosaurus, it's an enormous bone. Ornithischians also quickly began closing off the antorbital fenestra--the hole between the orbit and naris. In advanced ornithischians like thyreophorans and cerapods, the hole closes off completely.
Ornithischians also developed a strange "prong" of bone off the prefrontal (I can't remember the exact name--it's always "pap" in descriptions). This prong would have sat just above and in front of the living animal's eye, giving ornithischians a sort of "eye shade." Ankylosaurs eventually lose the prong, and hadrosaurs reduce its size, but exactly what purpose an eyeshade served is beyond me. Whether any workers have published on this question, I do not know (but I'd like to! Anybody?!). The nasals are large and wide in Lesothosaurus, but not so much in Eoraptor. The nasal bones rise in importance for many later theropod groups including abelisaurs and various tetanurine lineages, but their prominance is never questioned among the cerapoda. Ceratopsians and lambeosaurine hadrosaurs put an evolutionary premium on the nasal bones.
Since there's a loss of the antorbital fenestra, the lacrimal bone is large in Lesothosaurus and serves to wall off the preorbital region of the skull. In Eoraptor and many later theropods (and some early sauropodmorphs), the lacrimal is L or T shaped and twisted along its waist.
On the mandible, theropods and sauropodmorphs kept the strong mandibular fenestrae of their ornithodiran forebearers, but this hole, like the antorbital fenestra, simply shrinks and then closes off completely in ornithischians. Ornithischian dinosaurs developed a upward flange on the surangular that I find analogous to the large flange for muscle attachment in mammal jaws. The ornithischian flange is nowhere near as large (proportionately), but the fact that the two flanges developed in essentially the same place may have to do with chewing food. Since theropods and sauropodmorphs swallowed their food whole, a flange never developed.
It is interesting that Eoraptor and Lesothosaurus both display heterodonty, although they are reversed respective to each other. Eoraptor has spade-shaped teeth in the premaxilla and more traditional slicing teeth in the maxilla, while Lesothosaurus has pointed teeth in the premaxilla and spade-shaped teeth in the maxilla. Rather than indicate omnivory in Lesothosaurus, the sharp premaxillary teeth may simply compliment the animal's predentary bone in cropping vegetation. It's entirely possible, however, that Eoraptor occassioned plant matter from time to time. Some prosauropods, including Anchisaurus, have been regarded as omnivorous given their subtle heterdont conditions.
The wealth of differences present in the skulls of Eoraptor and Lesothosaurus are somewhat disturbing, given their supposedly "primitive" conditions. One would not expect to see an animal as obviously derived as Lesothosaurus while its near-contemporary, Eoraptor, retained so many ancestral features. Furthermore, Eocursor (see previous post) suggests that the ornithischian radiation did not explode until the Triassic/Jurassic extinction event opened up herbivorous niches previously unavailable to ornithischian dinosaurs. This suggests that ornithischian evolution went through a considerable "lag" period where diversity was very low. But the contradictory evidence is Lesothosaurus, who, if a primitive ornithischian, reveals that ornithischian evolution was fast, and that these animals were able to diversify beyond the ancestral condition in only a few million years.
I suppose the question I'm dancing around is this: "are ornithischians really Dinosauria?" Is the old thinking right, and the new thinking wrong? Supposedly the Dinosauria is united by a suit of postcranial characters, but I can name two right now that have been struck from the list thanks to Eoraptor, Herrerasaurus, and Saturnalia. It's also strange to me that those three animals, while derived in their own ways, still obviously retained more primitive ornithodiran characters, and they are all closely related to each other.
Lesothosaurus, on the other hand, looks like it's been around for awhile. The pelvis and ribcage have been completely rebuilt, the skull is amazingly different, and it's got a whopping five sacral vertebrae, unlike two or three in primitive saurischians (two in Marasuchus). Plus, if ornithischian dinosaurs were having a hard time in the beginning, as Eocursor suggests, then wouldn't that pressure have been there when ornithischians were first getting started? How would the group even get so far as a quadra-radiate pelvis if aeteosaurs were keeping them down? No, it seems like Lesothosaurus alone is evidence that the ornithischians have a longer evolutionary history than we think. Unless the split between the Saurischia and the Ornithischia occured much earlier than we think it did (maybe Middle Triassic?), I think the possibility exists that Dinosauria is a paraphyletic group, and that the Ornithischia originated a bit further down the Ornithodira tree**. Perhaps, in that sense, Silesaurus really is a key figure in the Ornithischia. Instead of trying to pigeon-hole it as an early dinosaur, maybe it's just a derived ornithodir which began a great bird-hipped herbivorous lineage.
*Actually, if you consider Dzik's little-known Silesaurus to be an incredibly primitive ornithischian, like I do, then here's it's skull. White areas indicate unknown material. For simplicity's sake, I'm not going to consider Silesaurus in my discussion here, but it's an interesting animal to consider. For more on this little upstart, see this post.
**Of course, what would probably happen is that "Dinosauria" would simply be moved down a few nodes to incorporate both the Saurischia and the Ornithischia, regardless of where Silesaurus eventually winds up. The union of the two groups is at the heart, after all, of our concept of the Dinosauria.