Mark J. MacDougall, Sean P. Modesto, Neil Brocklehurst, Antoine Verrière, Robert R. Reisz & Jörg Fröbisch (2018)
Response: A Reassessment of the Taxonomic Position of Mesosaurs, and a Surprising Phylogeny of Early Amniotes
Frontiers in Earth Sciences 6: Article 99 (6 pp.)
I see this work as the first step toward an investigation of amniote phylogeny that will be up to current standards.
Interesting results: 1) The mesosaurs go back to their more common place, as the sister-group of all other "parareptiles"; 2) Synapsida falls apart (without strong support) – the caseo- and edaphosaurs might not be amniotes. Check out the position of Archaeothyris
in fig. 1, which is not mentioned in the text (Archaeovenator
, in the same polytomy, are varanopids and mentioned that way).
Questionable statement about methods in phylogenetics: The use of composite OTUs is criticized because it introduces polymorphic scores, which decrease support values. Composite OTUs should indeed be avoided in general, because their monophyly and (if they're monophyletic...) their ancestral character states have to be assumed and cannot tested within the analysis; but there's nothing inherently bad about polymorphic scores. Quite the opposite – failure to score observed polymorphism as such can seriously mess trees up:
Akinobu Watanabe (2015, printed and given final page numbers 2016)
The impact of poor sampling of polymorphism on cladistic analysis
Cladistics 32: 337–334