In phylogenetic analysis one attempts to find relationships among taxa.
Each taxon may be composed of a single specimen up to a major clade filled with billions of specimens (like the Dinosauria). It has long been recognized that employing single specimens is the ideal. Employing single species would be next to ideal. Employing a single genus as a taxon is less than ideal. Often with prehistoric animals all we have is a single specimen to represent a particular genus, so that solves that particular problem.
The large reptile tree and the large pterosaur tree employ specimens, chiefly. If a specimen doesn’t have a skull or a post-crania, then that’s a problem, but its not a deal breaker. Most taxa can still be nested even if they are known from only a few parts. So even a fraction of a specimen can represent a taxon.
Most recent studies and current paradigms mix specimens, genera and suprageneric taxa (= many to many dozens of specimens within a single clade). The problem for the viewer is always, which specimen or genus represented the suprageneric taxon in the study? Which dinosaur? Which phytosaur? Which synapsid?
Recent papers (Brusatte et al. 2010, Nesbitt 2011) have nested the Pterosauria (Eudimorphodon and Dimorphodon, two fairly good taxa hopefully based on the holotypes alone as several specimens have been attributed to each) with Scleromochlus (a good genus based on several specimens with no discernable distinctions) and the Dinosauromorpha (but which one, Silesaurus? Coelophysis?). These taxa were nested as the sisters to the Phytosauria (but which one?) + an unresolved clade of Aetosauria + Rauisuchia + Crocodylomorpha + Ornithosuchia.
Now we’re talking about a very large group of reptiles.
As you can imagine such a clade encompasses a wide variety of morphologies, quite literally a vague cloud of sizes and shapes. Somewhere in this long list of taxa we should find a sister to the Pterosauria, according to the most widely followed paradigm (Brusatte et al. 2010, Nesbitt 2011). But NONE of these clades produce ANY good candidates. Nothing comes close. Even so, most paleontologists hang their hats on this hope, and that’s all it is, a hope that somewhere, someday in the more derived Archosauria we’ll eventually find a good pterosaur ancestor.
But Wait…We Already Have Some Great Pterosaur Ancestral Taxa!!
Many established paleontologists have let it be known they’re not happy with (= they prefer to ignore) the basal lizard Huehuecuetzpalli (which has a short list of pterosaurian traits), Cosesaurus (which has a long list of pterosaurian traits), Sharovipteryx (which heads off in its own direction but has additional pterosaurian traits) or Longisquama (which is very nearly a pterosaur itself). All of these are single specimens with Huehuecuetzpalli represented by an adult and juvenile.
They’re Still Pinning Their Hopes on The Cloud
It’s really amazing to witness the resistance put up by so many paleontologists to new insights. They prefer to hope for some undiscovered specimen to sweep them off their feet when there is a perfectly good set of specimens knocking on the door with everything they would ever want. They don’t even want to look at them and they made sure papers describing them were rejected.
There’ s Always Hope
Certain phylogenetic mysteries will continue to remain mysteries through the power of the suprageneric taxon cloud of hope. If you choose to employ suprageneric taxa, by definition you will be in the cloud, able to cherry pick trait scores and thereby cheat or short change your results to suit your preconceived ideas. Worse yet, the viewer who looks only at your results, will not see the specific evolutionary pathway and the gradual accumulation of character traits that are key to understanding evolutionary processes. They, too, will be left in the cloud.
Populate your matrices with specimens. That settles all issues. And you’ll be amazed at the variation and relationships you’ll find.
Trees should be built without prejudice and exclusion. Sure that’s a lot of work in the beginning, but once clades are established by overarching studies (like the big reptile tree), then more focused studies can proceed with greater confidence that all included taxa are indeed sisters and cousins.
As always, I encourage readers to see specimens, make observations and come to your own conclusions. Test. Test. And test again.
Evidence and support in the form of nexus, pdf and jpeg files will be sent to all who request additional data.
Brusatte SL , Benton MJ , Desojo JB and Langer MC 2010. The higher-level phylogeny of Archosauria (Tetrapoda: Diapsida), Journal of Systematic Palaeontology, 8:1, 3-47.
Nesbitt SJ 2011. The early evolution of archosaurs: relationships and the origin of major clades. Bulletin of the American Museum of Natural History 352: 292 pp.