Fossil identifications made in a phylogenetic framework are beholden to specific tree hypotheses. Without phylogenetic consensus, the systematic provenance of any given fossil can be volatile. Paleobiogeographic and divergence time hypotheses are contingent on the accurate systematic placement of fossils. Thus, fossil diagnoses should consider multiple topologies when phylogenetic resolution or clear apomorphies are lacking. However, such analyses are infrequently performed. Pleurodonta (Squamata: Iguania) is an ancient and frequently-studied lizard clade for which phylogenetic resolution is notoriously elusive. I describe a skull fossil of a new pleurodontan lizard taxon from the Eocene deposits of the Willwood Formation, Wyoming, and use the new taxon as a case-study to explore the effects of phylogenetic uncertainty on fossil identification. The relationships of the new taxon differ considerably among analyses, and resulting interpretations are correspondingly disparate. These results illustrate generalizable and severe issues with fossil interpretations made without consideration of alternative phylogenetic hypotheses.

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We provide the first description of the skull, osteoderms, and hyoid apparatus of the poorly known alligator lizard Elgaria panamintina, and compare the cranial osteology of that species to the widespread and well-studied taxon Elgaria multicarinata. Patterns of morphological variation resulting from ontogenetic transformations and pathology are discussed. We employed x-ray computed tomography (CT) scans to examine two adult specimens of Elgaria panamintina and two adult specimens of Elgaria multicarinata, in addition to examining multiple traditionally prepared skeletal specimens of the latter species. CT scans provide simultaneous study of both articulated and disarticulated elements, allowing us to describe and document the morphology of the skull with exceptional precision and detail. The description of the skull of Elgaria panamintina serves as a generalization for all Elgaria; here we provide the first complete description of the skull of this genus for future uses in morphological and phylogenetic studies of both extant species and fossils.

Genomic datasets generated by next-generation sequencing are increasingly prevalent in phylogenetics, but morphological data are required to phylogenetically place fossils, corroborate molecular hypotheses and date phylogenies. Combined-evidence analyses provide an integrative assessment of tree topology. However, no attempt has been made to simultaneously analyse next-generation genomic datasets and morphological data, and the future of morphology in the context of genomic data is uncertain. I conducted combined-evidence analyses that include genomic and morphological datasets, specifically, with ultraconserved elements and two morphological matrices. In unweighted maximum-likelihood and Bayesian combined-evidence analyses, morphological signal was dwarfed by the ultraconserved elements, and some node support values were reduced relative to ultraconserved element-only analyses. Increasing the weight of morphological characters allowed those data to influence the tree, but weighting subjectivity should be considered in future analyses. More attempts should be made to simultaneously analyse genomic and morphological datasets.

Background Fossil evidence suggests that extant North American lizard genera (north of Mexico) evolved during the Miocene. Although fossils of the clade Phrynosomatidae (spiny lizards and sand lizards) have been reported, there have been no previously described fossils of the fringe-toed sand lizards ( Uma ). In the extant biota, Uma inhabit arid deserts, and members of the western clade of Uma are restricted to sand dunes or other habitats containing fine-grained sand. Results I describe the first known fossil of Uma and refer the fossil to the total clade of Uma with an apomorphy-based diagnosis. The fossil is a partial premaxilla that was found in the Miocene strata of the Dove Spring Formation of southern California, dating to 8.77 Ma. The paleoenvironment of the Dove Spring Formation was semiarid and contained ephemeral streams that facilitated deposition, and there is no evidence of sand dune deposits in the strata containing the locality from which the Uma fossil was found. Divergence time analyses of a concatenated molecular dataset with four fossil calibrations support a Neogene origin of the total clade of Uma and of the crown clade of Uma . Those analyses also estimated a Neogene divergence between Uma scoparia and the Uma notata complex. Multispecies coalescent analyses with one fossil calibration inferred a Paleogene origin for the total clade of Uma and a Pliocene or Pleistocene divergence between Uma scoparia and the Uma notata complex. The fossil and the total and crown clades of Uma precede the evolution of modern desert ecosystems in the southwestern United States and northern Mexico by millions of years. Conclusions The total clade and the crown clade of Uma were not restricted to arid deserts throughout their evolutionary histories. I demonstrate that an apomorphy-based diagnosis can be used to identify fossils of isolated skeletal elements for at least one clade of phrynosomatid lizard, and suggest exercising caution when using environmental tolerances of extant taxa to hypothesize paleoecological reconstructions. Electronic supplementary material The online version of this article (10.1186/s12862-019-1501-5) contains supplementary material, which is available to authorized users.