Digging into another cladogram, pt. 2

Yesterday we opened up a cladogram
by Nesbitt et al. 2017, for examination and taxon addition.

The first driving issue here
is one we looked at earlier and even earlier: the origin of the Aetosauria. Nesbitt 2011 and Nesbitt et al. 2017 considered similarly armored Revueltosaurus the basalmost taxon in the aetosaur branch. Barely armored Ticinosuchus nests nearby, one node crown ward (Fig. 1) and 8 steps removed.

Figure 1. Reduced cladogram from Nesbitt et al. 2017

Figure 1. Reduced cladogram from Nesbitt et al. 2017

By contrast,
the large reptile tree (LRT, 1560 taxa) nests Ticinosuchus as the proximal outgroup taxon to the Aetosauria. Revueltosaurus nests with Fugusuchus and Tasmaniosaurus, together forming a previously overlooked sister clade to traditional erythrosuchids, like Erythrosuchus.

A second driving issue is the simple addition of taxa
to another, larger, character list created by someone else and published in an academic journal. This is an experiment in doing so.

A third driving issue is character scoring,
checking Nesbitt et al. 2017 for errors and omissions, and if repairable, do so. 

The MorphoBank Nesbitt character list needs a proofreader.
Several characters are not labeled and neither are their states, other than “State 0″, State 1”, etc. Those were deleted from my review of their cladogram since they contained no useful data. Before publishing, it’s best to take one last look around to see if everything is neat and tidy.

I realize that no character list is perfect,
but some in Nesbitt’s work look like they should be divided in two because a pair of dichotomies are presented. For instance:

Nasal 

  1. Does not possess a posterolateral process that envelops part of the anterior rams of the lacrimal.
  2. Possess a posterolateral process that envelops part of the anterior ramis of the lacrimal.
  3. Does not form part of the dorsal border of the antorbital fossa.
  4. Forms part of the dorsal border of the antorbital fossa.

In this case
I pretended choices 3 and 4 did not exist. I may be wrong in doing so. You decide. IMHO this one needs to go back to the shop to be split in two even though the matrix, as a whole, is still good enough to run.

A minor point, but worth mentioning:
Verbose characters with many letters tend to run off the edges of the columns provided by MacClade, even when set quite wide. Characters do this too often in Nesbitt 2017 (example above). If I may offer a suggestion? In the above example, #2 could have been stated as is (or shortened by deleting the grammatical articles), while #1 could have been shortened to: “does not.” In the LRT characters are really pared down to make them easy to read in relatively narrower MacClade columns.

For the skull of Ticinosuchus
Nesbitt and Nesbitt et al. scored very few characters, perhaps because they did not understand the roadkill-crushed skull enough make a reconstruction. This is where DGS works wonders. The addition of Ticinosuchus skull traits brought this taxon within one step of the Aetosauria, compared to its original nesting. Corrections to the post-crania shifted Ticinosuchus to the base of the Aetosauria, as in the LRT, with 9 steps needed to move it back to its Nesbitt nesting.

With its emphasis on ankle traits
and hind limb long bone end shapes, the Nesbitt et al. cladogram has its roots in a traits-based era when archosauriforms were divided according to ankle traits. This era is when the traditionally beloved, but since invalidated clade ‘Pseudosuchia‘ originated. Since the concavity or flatness of certain ankle elements cannot be determined or confirmed from published data, I had to ignore all such traits and rely on others from the list of 400 or so. The remainder still left plenty to work with.

Several characters in Nesbitt et al. 2017
are related to braincase foramina, sutures and processes. These are not employed by the LRT because they, too, are not readily visible in published data. Palatal and occipital traits, whenever visible, are scored. Unfortunately palate and occipital reconstructions for Ticinosuchus have not been generated and those for Revueltosaurus have not been published. Bottom line: omitting all the tiny and hard-to-see traits lets all the large and easy-to-see traits determine relationships resulting in a cladogram in which sister taxa indeed do like each other.

Results
The addition of Fugusuchus (still need to add Tasmaniosaurus) and the re-scoring of errors and omissions moved Revueltosaurus to the FugusuchusErythrosuchus clade away from Aetosauria. Ticinosuchus moved to the base of the Aetosauria (Fig. 2). Both of these are echoed in the LRT. Most of the rest of the Nesbitt et al. tree remains unchanged despite its difference from the LRT.  Note: Euparkeria has moved one node root-ward, as in the LRT. Further testing is planned for several other taxa.

Figure 2. Reduced and partly rescored cladogram from Nesbitt et al. 2017. Colors focus on taxa discussed in today's blog post.

Figure 2. Reduced and partly rescored cladogram from Nesbitt et al. 2017. Colors focus on taxa discussed in today’s blog post. Revueltosaurus moves to Fugusuchus with one extra step.

The resulting .nex file is available now by request,
but I would postpone asking for it until more housecleaning has been done to it.


References
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.
Nesbitt S et al. 2017. The anatomy of Teleocrater Rhadinus, an early avemetatarsalian from the lower portion of the Lifua Member of the Manda Beds (Middle Triassic). Journal of Vertebrate Paleontology 142-177. https://doi.org/10.1080/02724634.2017.1396539

 

 

8 thoughts on “Digging into another cladogram, pt. 2

  1. ” I may be wrong in doing so.”

    You are. All of these states express the posterior morphology of the nasal. These states are not independent of each other and should not be separated as separate characters.

    • Chris, there are two dichotomies here. 1) process envelops or does not. 2) Process forms border or does not.

      When I said “I may be wrong”, I was being facetious and you bit. Disappointed.

      • Dave, the supposed single nasal character you listed actually is divided into 2.

        The posterolateral process states are character 36, and the antorbital fossa states are character 37.

        I’m wondering whether you bother to score Fugusuchus for braincase characters, which were discussed (and photographed) for the taxon in detail by Gower & Sennikov, 1996 (https://www.palass.org/sites/default/files/media/publications/palaeontology/volume_39/vol39_part4_pp883-906.pdf)

        I want to see your file, to analyze your “revisions”. If the file is not fully “revised”, just give me a list of all the changes you’ve made.

      • Thank you, Neil. I downloaded the paper and will add the Fugusuchus traits as the character list allows. With regard to the division or non-division of the character state labeled, ‘nasal’ I cannot imagine how they represent two traits, since they were numbered 0, 1, 2 and 3 when I got the file.

      • If not mutually independent, then perhaps the character could have been stated without the two dichotomies? This appears to be a case of unnecessary confusion.

  2. Character 36 has 4 state descriptions in the NEXUS file, even though only the first 2 are intended to be there (and only they are used in the character matrix). Likewise, character 37 has 2 states, but its state descriptions were accidentally put in the character 36 segment, leaving only placeholder descriptions. It’s a typographical error that occurs in the character descriptions more than once but does not have any repercussions on the character matrix, which does not care about descriptions.

    You’ve attempted to deal with the problem by deleting character 37 (and others) and rescoring character 36 (and others) based on the extra states, though this does more harm then good because, as you said, the state dichotomies should be independent characters. And they are, in the character matrix and TNT file, just not in the nexus file character descriptions due to transcription errors.

    I personally use the original file for Nesbitt (2011) to understand the characters he uses, since it goes into detail and does not have the same typos as the plain and simple nexus file.

    I’ll stay in touch with you on my overview of your “revisions”, which so far look to be much less accurate than Nesbitt’s original scores. I’ll send discussions to you in chunks, starting with premaxilla characters. Once I have a good understanding of the score changes you have used to justify your clades, I’ll be able to talk about the scores and their issues in the clades’ corresponding posts.

    • Your job now is not to correct my corrections (I thanked you for your suggestions and followed SOME of your corrections in private correspondence earlier), but to score your own matrix as you see the data. The transcription of certain characters is only one of several problems with the matrix of Nesbitt et al. One should not have to go to an earlier version to find fewer setup errors. If anyone reading this is interested, the corrections involved interpretation of the character. As I followed NP’s suggestions the resulting cladogram changed. It became closer to the LRT. As currently rescored, the reduced cladogram of Nesbitt et al. is nearly fully resolved (2 trees) vs. several hundred as originally scored with a gradual accumulation of traits documented between all included sisters. So taxon inclusion was not the issue here, but correct and complete scoring. Checking the scores of matrices is an onerous job. No wonder professionals traditionally avoid it… especially if they follow their own rule of seeing all the material first hand.

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