Combining Phylogenomics and Fossils in Higher-Level Squamate Reptile Phylogeny: Molecular Data Change the Placement of Fossil Taxa

Abstract

Molecular data offer great potential to resolve the phylogeny of living taxa but can molecular data improve our understanding of relationships of fossil taxa? Simulations suggest that this is possible, but few empirical examples have demonstrated the ability of molecular data to change the placement of fossil taxa. We offer such an example here. We analyze the placement of snakes among squamate reptiles, combining published morphological data (363 characters) and new DNA sequence data (15,794 characters, 22 nuclear loci) for 45 living and 19 fossil taxa. We find several intriguing results. First, some fossil taxa undergo major changes in their phylogenetic position when molecular data are added. Second, most fossil taxa are placed with strong support in the expected clades by the combined data Bayesian analyses, despite each having >98% missing cells and despite recent suggestions that extensive missing data are problematic for Bayesian phylogenetics. Third, morphological data can change the placement of living taxa in combined analyses, even when there is an overwhelming majority of molecular characters. Finally, we find strong but apparently misleading signal in the morphological data, seemingly associated with a burrowing lifestyle in snakes, amphisbaenians, and dibamids. Overall, our results suggest promise for an integrated and comprehensive Tree of Life by combining molecular and morphological data for living and fossil taxa.

Lizards and amphisbaenians (Reptilia, Squamata) from the late Eocene of Sossís (Catalonia, Spain)

“…Higher-level relationships within squamates are still not resolved, with a conflict between morphology based trees (e.g., Estes et al, 1988;Conrad, 2008;Gauthier et al, 2012) and those based on molecular or combined data sets (e.g., Townsend et al, 2004;Vidal and Hedges, 2005;Wiens et al, 2006Wiens et al, , 2010Wiens et al, , 2012Conrad et al, 2010;Müller et al, 2011). However, most of these analyses support the monophyly of the same major squamate groups: Iguania, Gekkota, Dibamidae, Scincoidea, Anguimorpha, Serpentes, and Lacertiformes, the latter clade encompassing Amphisbaenia in molecular (e.g., Townsend et al, 2004;Wiens et al, 2012) and combined evidence (Wiens et al, 2006(Wiens et al, , 2010Müller et al, 2011) trees, but not those derived from morphology alone (e.g., Estes et al, 1988;Conrad, 2008;Gauthier et al, 2012). Gauthier et al (2012) use the alternative name Lacertoidea for this clade but previous authors (e.g., Estes et al, 1988;Conrad, 2008) applied Lacertoidea to a larger clade that included xantusiids, a group now more often placed with scincoids (e.g., Vicario et al, 2003;Gauthier et al, 2012;Wiens et al, 2012).…”

Jaw Adductor Muscles across Lepidosaurs: A Reappraisal

“…The general homology hypotheses proposed previously using the more inclusive groups Actinistia, Dipnoi, Amphibia, Reptilia, and Mammalia have been applied in this work. The characters that were found to be the most variable were optimized in recent phylogenies for lepidosauria based on morphology using parsimony (Conrad, 2008) and molecular data with Bayesian inference (Wiens et al, 2010). Optimization was done in WinClada (Nixon, 1999) using slow and fast optimization functions.…”

“…1) have been considered part of the adductor externus mandibulae complex in previous (Conrad, 2008) and (D) multigene analysis (Wiens et al, 2010). Black circles indicate nonhomplasious changes.…”

Rhetoric vs. reality: A commentary on “Bird Origins Anew” by A. Feduccia

“…Feduccia (2013) claims that phylogenetic systematics is a nonfunctional methodology that is incapable of producing evolutionarily realistic hypotheses and points out that many morphology-based hypotheses have been overturned by molecular data (Feduccia 2013:3). While it is true that some phylogenetic hypotheses for deep relationships within living birds have been affected and sometimes overturned by the addition of molecular sequence data, the majority of morphology-based hypotheses have been substantiated by analysis of molecular data and the combination of morphological and molecular data is a valuable strategy for inferring relationships among extant and extinct organisms (e.g., Wiens 2009, Wiens et al 2010. Additionally, some molecular hypotheses for vertebrate relationships turn out to be unfounded, with either morphology or further molecular analysis providing more compelling alternatives (e.g., whales; Milinkovitch et al 1993).…”