Turtles are closer to archosaurs? Please confirm.

A new paper
claims turtles are closer to archosaurs based on miRNA molecules.

From the abstract:
“Understanding the phylogenetic position of crown turtles (Testudines) among amniotes has been a source of particular contention. Recentmorphological analyses suggest that turtles are sister to all other reptiles, whereas the vast majority of gene sequence analyses support turtles as being inside Diapsida, and usually as sister to crown Archosauria (birds and crocodilians). Previously, a study using miRNAs (miRNAs) placed turtles inside diapsids, but as sister to lepidosaurs (lizards and Sphenodon) rather than archosaurs. Here, we test this hypothesis with an expanded miRNA presence/absence dataset, and employ more rigorous criteria for miRNA annotation. Significantly, we find no support for a turtle + lepidosaur sister-relationship; instead, we recover strong support for turtles sharing a more recent common ancestor with archosaurs. We further test this result by analyzing a super-alignment of precursor miRNA sequences for every miRNA inferred to have been present in the most recent common ancestor of tetrapods. This analysis yields a topology that is fully congruent with our presence/absence analysis; our results are therefore in accordance with most gene sequence studies, providing strong, consilient molecular evidence from diverse independent datasets regarding the phylogenetic position of turtles.”

Turtles are diapsids?
Then take the next step: go find turtles among the diapsids. Show us the morphological sisters. Show us the turtle-like traits in one or more diapsids. If you can’t, then go back to the drawing board. And for that matter, which diapsids? There are two convergent diapsid lineages, because the entire Reptilia is diphyletic.

Turtles are closer to archosaurs?
Then take the next step: go find turtles among the archosaurs. Show us the morphological sisters. Show us the turtle-like traits in one or more archosaurs. If you can’t, then go back to the drawing board.

Something must be off withe the miRNA. 
The large reptile tree finds maximum parsimony with millerettids and pareiasaurs, and among them, an ignored taxon, Stephanospondylus. The Field et al. (2014) tree (Fig. 1) was unable to resolve turtles from chickens from alligators. That’s an embarrassing result that tells me there’s a red flag here. Perhaps the secondary losses that are noted in lepidosaurs and mammals also have story to tell. A stronger tree would have had fewer secondary losses. What that tells me is what turtles and archosaurs share may be plesiomorphic genes secondarily lost in lepidosaurs and mammals.

I know nothing about miRNA or cellular biochemistry. But I can read a chart. If I need a lesson here, please provide it. This can be a discussion, not a lecture.

Figure 1. From Field et al. Here the secondary losses )red triangles) appear to tell the tale.  With so many secondary losses among mammals and lepidosaurs, the three genes that link turles to archosaurs basally, and the others that link them within their nodes could be a secondarily lost in lepidosaurs and mammals. A stronger tree would have had fewer secondary losses.

Figure 1. From Field et al. Here the secondary losses )red triangles) appear to tell the tale. With so many secondary losses among mammals and lepidosaurs, the three genes that link turles to archosaurs basally, and the others that link them within their nodes could be a secondarily lost in lepidosaurs and mammals. A stronger tree would have had fewer secondary losses. Most telling, perhaps, is the lack of resolution between alligators, chickens and turtles. To me, that’s a red flag.

Reference
Field DJ, Gauthier JA, King BL, Pisani D, Lyson TR, and Peterson KJ 2014. Toward consilience in reptile phylogeny: miRNAs support an archosaur, not lepidosaur, affinity for turtles. Evolution & Development (advance online publication)
DOI: 10.1111/ede.12081 http://onlinelibrary.wiley.com/doi/10.1111/ede.12081/abstract

free pdf:
http://danieljfield.com/Home/Publications.html

http://news.yale.edu/2014/05/05/study-finds-turtles-are-closer-kin-birds-crocodiles-lizards-snakes

3 thoughts on “Turtles are closer to archosaurs? Please confirm.

  1. As far as I am aware, only one study has provided evidence for turtles not being archosauromorphs, and Field et al.’s study was specifically focused on challenging that study. Pretty much every other molecular study has found turtles to be closer to crocodiles and birds than to lizards. Clearly, there is a strong phylogenetic signal supporting the topology of (Mammalia + (Lepidosauria + (Testudines + Crocodilia + Aves))).

    In the absence of a very well-documented transition that shows otherwise, the molecular evidence is much more compelling than morphological evidence, which is subjective and more easily influenced by convergent evolution.

    I would be curious to see what happens to the large reptile tree if it was constrained to match the molecular evidence.

    • This is one of the biggest question marks in all of paleontology. Unfortunately, no molecular paleontologist has advanced any archosauromorph or series of same that even remotely resembles turtles (other than placodonts and those are definitely convergent). If you have one, please let us know. Meanwhile, there’s a nice sequence starting with Icthyostega and leading through proto-lepidosauromorphs that leads nicely to Proganochelys. I wish I (or anybody) could resolve this problem. Morphological evidence, by the way, may not be as subjective as you think. After all, a trait either is or isn’t present.

      • While individual characters can be objective, the choice of what characters to use, and how to define states in some cases, is not. I am sure that you, of all people, are aware of how different character lists can be.

        You are right, though, that the lack of a clear archosauromorph precursor to turtles is curious. However, the fossil record is not complete, and we may not have looked in the right place yet. The absence of evidence is not necessarily evidence of absence, especially in a field so vulnerable to bias and chance as paleontology.

        You are certainly right that research must be done to bring together molecular data and the fossil record, and as I said before, I am curious to see what is uncovered if a large-scale amniote phylogeny is constrained to the molecular results.

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