Another DNA analysis fails to replicate LRT analysis

Earlier we talked about the failure of DNA studies to replicate or confirm morphological studies in phylogenetic analysis. A few days ago Shaffer et al. 2017 discussed turtle origins using DNA, trying to figure out when turtles diverged from archosaurs (birds + crocs) and when cryptodires diverged from pleurodires.

Figure 1. From Schaeffer et al. a graphic showing the divergence times for cryptodires and pleurodires according to their studies of molecules and morphology.

Figure 1. From Schaeffer et al. a graphic showing the divergence times for cryptodires and pleurodires according to their studies of molecules and morphology. Some titles were added for clarity. 

From the Shaffer et al. abstract
“We used our genomic data to estimate the ages of living turtle clades including a mid-late Triassic origin for crown turtles and a mid-Carboniferous split of turtles from their sister group, Archosauria. By specifically excluding several of the earliest potential crown turtle fossils and limiting the age of fossil calibration points to the unambiguous crown lineage Caribemys oxfordiensis from the Late Jurassic (Oxfordian, 163.5–157.3 Ma) we corroborate a relatively ancient age for living turtles. We also provide novel age estimates for five of the ten testudine families containing more than a single species, as well as several intrafamilial clades. Most of the diversity of crown turtles appears to date to the Paleogene, well after the Cretaceous-Paleogene mass extinction 66 mya.
By contrast 
In the large reptile tree (LRT 1042 taxa) the divergence date between soft-shell turtles (like Odontochelys) and hard-shelled domed turtles (like Meiolania or perhaps Elginia) dates back probably to, but at least to the Late Permian with Elginia. Without valid outgroups, like Elginia and Sclerosaurus, there is no way Schaeffer et al. are going to get the base of their turtle tree right. And the dominoes fall from there.
The “mid-Carboniferous split” reported by Shaffer et al. between Archosauria and turtles is more or less supported by the LRT In that analysis the Viséan (Early Carboniferous) is when we have evidence that the Lepidosauromorpha (including turtle ancestors) and Archosauromorpha (including archosaur ancestors) had split apart from its last common ancestor, Gephyrostegus at the base of the Reptilia.
But let’s be clear,
turtles are in no way related to archosaurs, except at the very base of the Reptilia.
The journal title:
‘Molecular Phylogenetics and Evolution’
 (see below) is fast becoming an oxymoron and an invalidated science except when taxa are closely related to one another. Someone please mention this to the editors. Long phylogenetic distances constantly fail to produce DNA trees that match morphology trees, as everyone acknowledges, but no one else is ready to accept at present.

Shaffer HB, McCartney-Melstad E, Near TJ, Mount GG and Spinks PQ 2017. Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines). Molecular Phylogenetics and Evolution 115: 7–15. doi:


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