Earlier, and on the Dinosaur Mailing List, David Marjanovic and Mickey Mortimer dismissed the phylogenetic analysis that produced the large reptile tree and the other trees (pterosaur, therapsid) due to their inclusion of purported correlated characters. I think this is short-sighted.
I’m here to tell you, it’s damn hard to avoid including correlated characters. For instance:
1. A long dorsal series of vertebrae is correlated to short to absent limbs.
2. A long canine tooth is correlated to a tall maxilla (that’s where the root is found) and often correlated to a deep dentary to protect it.
3. A large orbit is often correlated to a short rostrum, especially in taxa of relatively small overall size.
4. Unsharp, unconical teeth (they come in many shapes and sizes) are correlated to a broad or deep ribcage.
5. Wings of two sorts are correlated to a strap-like scapula and an elongated, locked-down coracoid.
6. A kinked tail is correlated to the development of flippers
7. A carapace is correlated to short fingers and toes.
8. Bipedal hind limbs and simple hinge ankle joints are correlated to reduced forelimbs, except in flying tetrapods.
9. An elongated neck is typically correlated to a small skull (with exceptions, of course).
10. A thick-boned skull is typically correlated with a thick-boned pelvis and hind limbs.
I’m sure you can think of others.
Caveat: There are exceptions to everything listed above. So don’t raise a finger immediately. I’m only asking, “how can you create a list of characters that does not include a certain amount of correlation?” Or even a lot of correlation? Evolution follows certain patterns. A dorsal fin will often appear in marine taxa. That happens. Correlation is everywhere.
Convergence in the Large Reptile Tree
The Consistency Index (CI) is a number that can be recovered in PAUP and it represents the amount of convergence in the matrix. In the large reptile tree the CI hovers near 0.1. Nearly every character finds at least two expressions somewhere on the tree. Mortimer and Marjanovic see this as a fault of the study. I see this as a fact recovered by the study. And it shows the strength of the study that the tree could separate the various convergent traits by maximizing parsimony.
Emphasizing Certain Traits
In the past, paleontologists have emphasized skull fenestrae and ankle traits in determining phylogenetic relationships. According to Mortimer and Marjanovic correlation is to be avoided because it over-emphasizes certain traits. The problem is, certain taxa are known from only a skull, so by default, skull traits are emphasized in the scoring of these taxa. Others are known from only other body parts and these are emphasized, by default. There’s nothing else you can do about it!
Like democracy, it’s not perfect, but it’s the best thing we have at present. Notably, neither Mortimer nor Marjanovic have been able to identify misnested genera within the large reptile tree without resorting to nebulous suprageneric taxa.
The large reptile tree is completely resolved and continues to be so as more taxa are added. All evolutionary pathways provide a gradual accumulation of traits, which is what we’re looking for as we attempt to model the original family tree of life.
Methods can always be faulted. There’s always a sniper in the bell tower. The results here speak for themselves. Even so, if errors are found, please bring them to my attention.