Root causes of phylogenetic incongruence observed within basal sauropodomorph interrelationships

Abstract

The relationships among basal sauropodomorphs are controversial. Results of cladistic analyses vary from a fully paraphyletic assemblage to a monophyletic core‐prosauropod. We apply the comparative cladistics method to three published cladistic analyses of sauropodomorph dinosaurs, in order to identify root causes for differences between phylogenetic results. Except for three taxa (Saturnalia, Thecodontosaurus, and Efraasia) and one clade (Gravisauria), the remaining genera are recovered with conflicting positions. The comparative method is based on indices that allow for the quantification of the degree of similarity in characters and character states among analyses. A comparison of primary data, character selection, and scoring highlights significant discrepancies in data sets. Our results suggest that one character out of two varies from one analysis to the other. These are the root causes for the phylogenetic incongruence observed. The hurdle of the phylogenetic definition of the clade Sauropoda, which has been defined in four different ways, is also treated. We concur with several recent papers following the first node‐based definition of Sauropoda. © 2015 The Linnean Society of London

Rapid transformation in the braincase of sauropod dinosaurs: integrated evolution of the braincase and neck in early sauropods?

“…Based on the discussion in Peyre de Fabrègues et al . (), we opted to follow the definition of Salgado et al . () for Sauropoda (the least inclusive clade containing Vulcanodon and Eusauropoda) instead of any of the alternative definitions for this clade (e.g.…”

Should the terms 'basal taxon' and 'transitional taxon' be extinguished from cladistic studies with extinct organisms?

“…'Prosauropoda' was once thought to be a monophyletic group encompassing Late Triassic and Early to Middle Jurassic sauropodomorphs, and the sister group of Sauropoda (Galton and Upchurch, 2004). However, more recent studies have pointed out that the most likely scenario concerning the evolution of the Sauropodomorpha lineage is that the classical 'prosauropods' represent a paraphyletic assemblage of taxa in relation to Sauropoda (see Peyre de Fabrègues et al, 2015 for historical discussion on this issue). This paraphyletic condition of 'Prosauropoda' is the root cause of the association of the term 'basal' sauropodomorph to refer to sauropodomorph taxa that fall outside of the main Sauropoda clade (Otero and Salgado, 2015).…”

Overlap Indices: Tools to quantify the amount of anatomical overlap among groups of incomplete terminal taxa in phylogenetic analyses

“…With the widespread use of phylogenetic analysis, comparative cladistics becomes an increasingly important issue (Peyre de Fabrègues, Allain, & Barriel, 2015;Sereno, 2009;Whitlock & Wilson, 2013). In particular in well-studied taxa, where numerous research groups develop distinct phylogenetic matrices to support their cladograms, conflicting tree topologies are sometimes difficult to resolve.…”

“…In cases of extensive missing data, specific OTUs might not have any morphological character for which both could be scored. In the dawn of comparative cladistics (Sereno, 2009), where comparison of basic data underlying phylogenetic hypotheses becomes crucial (Peyre de Fabrègues et al, 2015;Whitlock & Wilson, 2013), indices like the proposed Overlap Index are increasingly important. Tschopp et al (2015) therefore introduced a so-called Overlap Index, quantifying the amount of anatomical overlap within a particular clade, and thus indicating how much of the anatomy could actually be compared directly.…”

“…Tschopp et al (2015) therefore introduced a so-called Overlap Index, quantifying the amount of anatomical overlap within a particular clade, and thus indicating how much of the anatomy could actually be compared directly. In the dawn of comparative cladistics (Sereno, 2009), where comparison of basic data underlying phylogenetic hypotheses becomes crucial (Peyre de Fabrègues et al, 2015;Whitlock & Wilson, 2013), indices like the proposed Overlap Index are increasingly important. Herein, we explain in detail how to calculate the two proposed versions of the Overlap Index and explore their potential uses in comparative cladistics.…”