A new squamate phylogeny that resolves from previous problems

Estimated phylogeny of squamate reptiles from 
likelihood analysis of combined morphological 
and molecular data, after removal of four “rogue” 
fossil taxa. Red dots indicate clades with 
bootstrap values from 90–100%, black dots 
indicate values from 70–89% (values
not shown; for bootstrap values for all branches 
see. Fossil taxa are indicated with “” and green 
branches. The four abbreviated fossil taxa in 
gray at the base of the phylogeny are the four rogue 
taxa (Eichstaetisaurus, Huehuecuetzpalli
SineoamphisbaeniaAMNH FR 21444), shown in 
their phylogenetic positions as inferred in the 
combined analysis including all taxa. Photos 
include representatives of Dibamidae (Anelytropsis), 
Gekkota Carphodactylidae:Underwoodisaurus), 
Scincoidea (Scincidae: Plestiodon), Amphisbaenia
(Bipedidae:Bipes), Mosasauria (Tylosaurus), 
Serpentes (Boidae: Exiliboa), Anguimorpha 
(Xenosauridae: Xenosaurus), Polyglyphanodontia 
(Polyglyphanodon), Acrodonta (Agamidae:
 Calotes), and Pleurodonta (Phrynosomatidae: 
Sceloporus). See Acknowledgments in 
original paper for photo credits (except for 
Anelytropsis from T. M. Townsend). 

In a new paper published in PLoS, Reeder et al. (2015) note that squamate reptiles (lizards and snakes) are an important and diverse group of terrestrial vertebrates, with more than 9,000 species and that studies of squamate biology are presently hampered by uncertainty over their phylogeny.
Higher-level squamate phylogeny is currently unresolved because of conflicts between hypotheses based on separate analyses of morphological and molecular datasets. 

Most attention has focused on the placement of iguanians (including iguanas, anoles, chameleons, dragons, and relatives), which are placed at the base of the squamate tree in morphological analyses, and in a clade (called Toxicofera) with snakes and anguimorphs (including monitor and alligator lizards, the Gila monster, and relatives) in molecular analyses. The largest morphological dataset (in characters) included 189 squamate taxa (140 living and 49 fossil; plus 3 outgroup taxa) and 610 characters (~33% missing data; Gauthier et al., GEA hereafter). 

The largest molecular dataset (in terms of characters) included 161 living taxa (plus 10 outgroup taxa) for up to 44 nuclear protein-coding loci (33,717 base pairs/characters; ~20% missing data); Wiens et al., (WEA hereafter). Given the unresolved conflict between these two large datasets over the placement of Iguania, some authors have considered higher-level squamate relationships to be unresolved. Some recent, prominent studies have considered the traditional, morphological tree only, ignoring the molecular hypothesis altogether.

In this study the authors perform an integrated analyses to resolve this conflict and further elucidate the relationships of both living and fossil squamates. First, they generated an expanded morphological dataset with taxon sampling largely matching that of GEA for extant taxa, adding new data from 81 additional characters (primarily from squamation) to the mostly osteological dataset of GEA. This is a 13% increase in characters (to 691), and the largest morphological dataset for squamates. Next, they expanded the molecular dataset of WEA by including published sequences from two additional loci (nuclear c-mos; mitochondrial ND2) for closely matched species yielding up to 46 protein-coding loci and 35,673 characters for each of 161 taxa. We then performed separate and combined analyses of each dataset using likelihood, Bayesian, and parsimony approaches, and evaluated the potential causes of conflict by examining trees from subsets of the molecular and morpohological data. Combined analyses included reweighting the molecular data such that genes were treated as equivalent to morphological characters.

The results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, the authors find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia), demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. These results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement.

The combined analyses strongly suggest that the phylogenetic hypothesis for living squamates based on the molecular data is correct. Specifically, the results support the hypothesis that Iguania is placed with snakes and anguimorphs, and not at the squamate root (as suggested by morphological data alone). The conclusions are based on several lines of evidence, including: (a) combined analyses of the relevant molecular and morphological data supports the molecular placement of Iguania, even when the molecular dataset is reduced to only 63 characters, less than one tenth the size of the morphological dataset, (b) mapping morphological characters on the combined-data tree shows that there is actually hidden support for the molecular hypothesis in the morphological data (similar to the number of characters supporting the morphological hypothesis), (c) the morphological dataset is dominated by misleading phylogenetic signal associated with convergent evolution of a burrowing lifestyle and associated traits, and a similar problem associated with feeding modes may explain the morphological placement of Iguania, and (d) the morphological hypothesis is unambiguously supported by only one of six subsets of the morphological data. Conversely, we find no evidence for hidden signal supporting the morphological hypothesis among the 46 genes in the molecular dataset; no genes support this hypothesis. Further, the failure of some genes to fully support the molecular placement of iguanians in Toxicofera seems to be associated with sampling error (i.e. shorter genes).

Reeder TW, Townsend TM, Mulcahy DG, Noonan BP, Wood PL Jr, et al. (2015) Integrated Analyses Resolve Conflicts over Squamate Reptile Phylogeny and Reveal Unexpected Placements for Fossil Taxa. PLoS ONE 10(3): e0118199. doi:10.1371/journal.pone.0118199.

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