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Australia harbors the most diverse lizard assemblages on Earth, yet the biodiversity of its vast arid zone remains incompletely characterized. Recent sampling of remote regions has revealed new species with unique phenotypes and unclear evolutionary affinities. Here, we describe a new species of scincid lizard that appears to be widely distributed across the Great Victoria Desert and adjacent regions. The new species was previously overlooked among specimens of the wide-ranging desert taxon Ctenotus schomburgkii but is distinguished from it by coloration and scalation characters. Phylogenetic analyses based on mitochondrial and genome-wide nuclear loci confirmed that the new species is highly divergent from C. schomburgkii, with which it appears to be sympatric across much of its range. In addition to the new species, our survey of genetic variation within C. schomburgkii as currently recognized revealed three additional lineages that approach one another in southern and northwestern Australia, and which may also represent distinct species. These results suggest that our knowledge of the extraordinary biodiversity of arid Australia remains incomplete, with implications for the conservation and management of this unique fauna. The targeted collection of voucher specimens in undersampled regions, coupled with population genetic screening of lineage diversity, will be crucial for characterizing species boundaries and understanding the composition of Australia’s vertebrate communities. 

Synopsis Pygopodids are elongate, functionally limbless geckos found throughout Australia. The clade presents low taxonomic diversity (∼45 spp.), but a variety of cranial morphologies, habitat use, and locomotor abilities that vary between and within genera. In order to assess potential relationships between cranial morphology and ecology, computed tomography scans of 29 species were used for 3D geometric morphometric analysis. A combination of 24 static landmarks and 20 sliding semi-landmarks were subjected to Generalized Procrustes Alignment. Disparity in cranial shape was visualized through Principal Component Analysis, and a multivariate analysis of variance (MANOVA) was used to test for an association between shape, habitat, and diet. A subset of 27 species with well-resolved phylogenetic relationships was used to generate a phylomorphospace and conduct phylogeny-corrected MANOVA. Similar analyses were done solely on Aprasia taxa to explore species-level variation. Most of the variation across pygopodids was described by principal component (PC) 1(54%: cranial roof width, parabasisphenoid, and occipital length), PC2 (12%: snout elongation and braincase width), and PC3 (6%: elongation and shape of the palate and rostrum). Without phylogenetic correction, both habitat and diet were significant influencers of variation in cranial morphology. However, in the phylogeny-corrected MANOVA, habitat remained weakly significant, but not diet, which can be explained by generic-level differences in ecology rather than among species. Our results demonstrate that at higher levels, phylogeny has a strong effect on morphology, but that influence may be due to small sample size when comparing genera. However, because some closely related taxa occupy distant regions of morphospace, diverging diets, and use of fossorial habitats may contribute to variation seen in these geckos. 

Abstract Genomic‐scale datasets, sophisticated analytical techniques, and conceptual advances have disproportionately failed to resolve species boundaries in some groups relative to others. To understand the processes that underlie taxonomic intractability, we dissect the speciation history of an Australian lizard clade that arguably represents a “worst‐case” scenario for species delimitation within vertebrates: theCtenotus inornatusspecies group, a clade beset with decoupled genetic and phenotypic breaks, uncertain geographic ranges, and parallelism in purportedly diagnostic morphological characters. We sampled hundreds of localities to generate a genomic perspective on population divergence, structure, and admixture. Our results revealed rampant paraphyly of nominate taxa in the group, with lineages that are either morphologically cryptic or polytypic. Isolation‐by‐distance patterns reflect spatially continuous differentiation among certain pairs of putative species, yet genetic and geographic distances are decoupled in other pairs. Comparisons of mitochondrial and nuclear gene trees, tests of nuclear introgression, and historical demographic modelling identified gene flow between divergent candidate species. Levels of admixture are decoupled from phylogenetic relatedness; gene flow is often higher between sympatric species than between parapatric populations of the same species. Such idiosyncratic patterns of introgression contribute to species boundaries that are fuzzy while also varying in fuzziness. Our results suggest that “taxonomic disaster zones” like theC. inornatusspecies group result from spatial variation in the porosity of species boundaries and the resulting patterns of genetic and phenotypic variation. This study raises questions about the origin and persistence of hybridizing species and highlights the unique insights provided by taxa that have long eluded straightforward taxonomic categorization. 

Abstract Morphological variation among the viviparous sea snakes (Hydrophiinae), a clade of fully aquatic elapid snakes, includes an extreme “microcephalic” ecomorph that has a very small head atop a narrow forebody, while the hind body is much thicker (up to three times the forebody girth). Previous research has demonstrated that this morphology has evolved at least nine times as a consequence of dietary specialization on burrowing eels, and has also examined morphological changes to the vertebral column underlying this body shape. The question addressed in this study is what happens to the skull during this extreme evolutionary change? Here we use X-ray micro-computed tomography and geometric morphometric methods to characterize cranial shape variation in 30 species of sea snakes. We investigate ontogenetic and evolutionary patterns of cranial shape diversity to understand whether cranial shape is predicted by dietary specialization, and examine whether cranial shape of microcephalic species may be a result of heterochronic processes. We show that the diminutive cranial size of microcephalic species has a convergent shape that is correlated with trophic specialization to burrowing prey. Furthermore, their cranial shape is predictable for their size and very similar to that of juvenile individuals of closely related but non-microcephalic sea snakes. Our findings suggest that heterochronic changes (resulting in pedomorphosis) have driven cranial shape convergence in response to dietary specializations in sea snakes.