GENERAL COMMENTARY published: 03 December 2018 doi: 10.3389/feart.2018.00220 Response: Commentary: A Reassessment of the Taxonomic Position of Mesosaurs, and a Surprising Phylogeny of Early Amniotes Michel Laurin 1* and Graciela Piñeiro 2 1 CR2P (UMR 7207), CNRS/MNHN Sorbonne Université, “Centre de Recherches sur la Paléobiodiversité et les Paléoenvironnements”, Muséum National d’Histoire Naturelle, Paris, France, 2 Departamento de Paleontología, Facultad de Ciencias, Montevideo, Uruguay Keywords: Mesosauridae, Parareptilia, Synapsida, Sauropsida, Amniota, Paleozoic, temporal fenestration A Commentary on Commentary: A Reassessment of the Taxonomic Position of Mesosaurs, and a Surprising Phylogeny of Early Amniotes by MacDougall, M. J., Modesto, S. P., Brocklehurst, N., Verrière, A., Reisz, R. R., and Fröbisch, J. (2018). Front. Earth Sci. 6:99. doi: 10.3389/feart.2018.00099 INTRODUCTION Edited by: Corwin Sullivan, University of Alberta, Canada Mesosaurs, known from the Early Permian of southern Africa, Brazil, and Uruguay, are the oldest known amniotes with a primarily, though probably not strictly, aquatic lifestyle (Nuñez Demarco Reviewed by: et al., 2018). Despite having attracted the attention of several prominent scientists, such as Wegener Tiago Simoes, University of Alberta, Canada (1966), who used them to support his theory of continental drift, and the great anatomist and paleontologist von Huene (1941), who first suggested the presence of a lower temporal fenestra *Correspondence: Michel Laurin in Mesosaurus, several controversies still surround mesosaurs. One concerns the presence of the [email protected] lower temporal fenestra in mesosaurs, which we accept (Piñeiro et al., 2012a; Laurin and Piñeiro, 2017, p. 4), contrary to Modesto (1999, 2006) and MacDougall et al. (2018); the other concerns Specialty section: the systematic position of mesosaurs, which have been argued, in the last decades, to be either This article was submitted to the basalmost sauropsids (Laurin and Reisz, 1995; Laurin and Piñeiro, 2017), or the basalmost Paleontology, parareptiles (Gauthier et al., 1988; Modesto, 1999; MacDougall et al., 2018). Note that we adopt a section of the journal a branch-based definition of Parareptilia as Laurin and Reisz (1995) did, but use Procolophon Frontiers in Earth Science trigoniceps as an internal specifier rather than turtles, because of the controversy surrounding the Received: 26 September 2018 affinities about turtle origins. Accepted: 14 November 2018 In their recent response to our recent paper on the taxonomic position of mesosaurs, Published: 03 December 2018 MacDougall et al. (2018) make a number of problematic claims, which we wish to discuss. These Citation: claims are that we used an outdated matrix and ignored over two decades of parareptile research, Laurin M and Piñeiro G (2018) that our taxon selection was insufficient and that along with variability in temporal fenestration Response: Commentary: A in parareptiles, all these choices explain the different taxonomic position of mesosaurs that we Reassessment of the Taxonomic Position of Mesosaurs, and a obtained (as the basalmost sauropsids rather than the basalmost parareptiles). Below, we respond to Surprising Phylogeny of Early these claims by providing additional background data and by performing various analyses of their Amniotes. Front. Earth Sci. 6:220. matrix and ours that show, through taxon and character deletion among other approaches, that doi: 10.3389/feart.2018.00220 neither the omission of some taxa, nor variability in temporal fenestration explains the differences Frontiers in Earth Science | www.frontiersin.org 1 December 2018 | Volume 6 | Article 220 Laurin and Piñeiro Response: Commentary: A Taxonomic Position of Mesosaurs in topologies between our study and theirs. We also highlight two decades of parareptilian research.” These two closely related problems with their analyses and discuss why reusing phenotypic claims are factually wrong. The second point (that we ignore data matrices produced by other systematists is difficult. two decades of parareptilian research) is refuted by a simple examination of the bibliography of our paper. We did not claim to have cited all recent papers on parareptiles (given that our MATERIALS AND METHODS paper was not a review of recent studies on parareptiles), but we cited several papers published in the 1998–2018 period that The reanalyses below use a version of our data matrix (Laurin and discuss parareptile extensively (Reisz and Scott, 2002; Cisneros Piñeiro, 2017) in which we deleted characters linked to temporal et al., 2004; Müller and Tsuji, 2007; Modesto et al., 2009; Lyson fenestration, to assess the impact of this complex of characters et al., 2010, 2013; Tsuji et al., 2010, 2012; Lee, 2013; Bever on the resulting topology. We also reanalyze the data matrix of et al., 2015). Note that this list does not include papers about MacDougall et al. (2018), in three versions: unmodified, modified mesosaurs, which our results suggest are not parareptiles. The by ordering characters that form morphoclines, and modified first point (that the matrix is obsolete) is equally factually further by removing the parareptile taxa not found in our matrix wrong as shown by the fact that we extensively updated the (Laurin and Piñeiro, 2017). We have not studied the scores of original matrix (Laurin and Reisz, 1995) using both the literature the cells of the data matrix of MacDougall et al. (2018) because and direct observations of specimens, especially mesosaurs, and this would be very time-consuming and would largely duplicate explained this clearly (Laurin and Piñeiro, 2017, p. 4). For a more ambitious project focusing on early amniote phylogeny instance, Owenetta, which we added to the matrix (it was not and the origin of turtles (mesosaurs are in the matrix, though in the matrix of Laurin and Reisz, 1995), was scored using the the project does not focus particularly on their affinities) initiated detailed description of Reisz and Scott (2002). We also added by one of us (ML) in January 2018 in collaboration with Ingmar one of the basalmost, best-known parareptiles (Acleistorhinus), Werneburg, Gabriel Ferreira, and Márton Rabi. to better test previous suggestions that mesosaurs are basal All phylogenetic analyses were carried out with PAUP∗ parareptiles, and made other changes to the taxon set (see below). (Swofford, 2003) version 4.0a, build 163 for Macintosh (the latest Given all these changes, we do not consider that we used an version available as of July 28, 2018), using the branch and bound outdated phylogenetic matrix. algorithm for our own data matrix, using the heuristic search MacDougall et al. (2018) object to the use of suprageneric with 50 random addition sequence replicates, holding 3 trees taxa as terminals because they claim that the resulting higher at each step, and using the tree-bisection-reconnection (TBR) rate of polymorphism can weaken support values. We think algorithm for the various versions of the matrix by MacDougall that the interpretation of support values is more complex than et al. (2018) because that matrix had too many taxa for the branch MacDougall et al. (2018) suggest because these values tend to and bound algorithm to conclude tree search in a reasonable reflect character congruence and the number of characters (or the amount of time. The branch and bound algorithm guarantees ratio between number of characters and number of OTUs). For discovery of all possible most parsimonious trees. No heuristic many taxa, various mutually incompatible phylogenies with good algorithm provides a similar guarantee, but we verified for each support values have been published, which shows that such values of our analyses that all most parsimonious islands of trees had should not be equated with reliability (Marjanovic´ and Laurin, been recovered at least three times (most were recovered far more 2018). The famous case of “The guinea-pig is not a rodent” frequently and all were found at least 4 times), allowing us to be (D’Erchia et al., 1996) illustrates this point. Furthermore, while reasonably certain that we had all the most parsimonious trees. the increased polymorphism in OTUs corresponding to large We also repeated one of these analyses (on the original version clades is unavoidable and simply reflects reality, the relationship of the matrix of MacDougall et al., 2018) using 1,000 addition between that elevated rate of polymorphism and support values sequence replicates, to ensure that our settings (in particular, use in a matrix is far more complex than suggested by MacDougall of 50 addition replicates) were appropriate; we found exactly the et al. (2018). This is illustrated by the fact that the taxa (typically same set of trees, which validated our choice. The results of these ranked as genera) that they introduced to replace the OTU analyses allow us to test the main claims made by MacDougall Synapsida yield a tree that suggests that this taxon, as currently et al. (2018). delimited, is paraphyletic! Of course, a monophyletic Synapsida Information associated with the analyses carried out in this could still be recognized in accordance with the definition of paper (modified list of characters, in which we document this clade that has been proposed under the PhyloCode (using which characters were ordered, and how the states had to be Cynognathus crateronotus as the sole internal specifier, and reordered to reflect the underlying continuous characters, and three extant sauropsids as