Chromosome-Level Genome Assembly of the Cape Cliff Lizard (Hemicordylus capensis)

Squamates represent a highly diverse and species-rich vertebrate group that is remarkably understudied from a genomic perspective. A scarcity of genomic data is particularly evident for scincomorph lizards, which encompass over 10% of all living squamates, and for which high-quality genomic resources are currently lacking. To address this knowledge gap, we present the first chromosome-level reference genome for this group, generated from a male Cape cliff lizard (Hemicordylus capensis), using highly accurate PacBio HiFi long-read sequencing data, long-range Omni-C chromosomal conformation capture data and transcriptomic data for annotation. The rHemCap1.1 genome assembly spans 2.29 Gb, with a scaffold N50 of 359.65 Mb, and includes 25,300 protein-coding genes, with a BUSCO completeness score of 95.5% (sauropsida_odb10). We have generated the most contiguous and complete chromosome-level squamate reference genome assembly publicly available to date. Furthermore, we used short-read resequencing of 35 males and females and applied a differential coverage approach to infer the sex-determination system of the species, which was previously unknown. Our results suggest this species has XX/XY sex chromosomes, representing the first evidence of sex determination in the family Cordylidae. This reference genome will help to establish this species as an evolutionary model for studying variation in body armor, a key trait in cordylids and other squamate groups. Lastly, this is the first squamate reference genome from a continental African species and, as such, represents a valuable resource not only for further evolutionary research in cordylids but also in closely related groups.

Swimming through the sands of the Sahara and Arabian deserts: Phylogeny of sandfish skinks (Scincidae, Scincus) reveals a recent and rapid diversification

Large parts of the Sahara Desert and Arabia are covered by sand seas and sand dunes, which are inhabited by specialized animal communities. For example, many lizards have developed adaptations to life in loose sand, including sand-swimming behavior. The best-known sand swimmers of the Saharo-Arabia are the sandfish skinks (genus Scincus). Although there are currently only four Scincus species recognized, their phylogenetic relationships have not yet been addressed in detail. We use eight genetic markers (three mitochondrial, five nuclear) and a complete sampling of species to infer the relationships within the genus. We employ multiple phylogenetic approaches to reconstruct the evolutionary history of these skinks and to assess the level of reticulation at the onset of their radiation. Our results indicate the presence of five strongly supported species-level lineages, four represented by the currently recognized species and the fifth by S. scincus conirostris, which does not form a clade with S. scincus. Based on these results we elevate the Iranian and northern Arabian S. conirostris to the species level. The two Saharan species, S. albifasciatus and S. scincus, are sister in all analyses. Deeper relationships within the genus, however, remained largely unresolved despite the extensive genetic data set. This basal polytomy, together with the fact that we detected no sign of hybridization in the history of the genus, indicates that the diversification of the five Scincus species was rapid, burst-like, and not followed by secondary hybridization events. Divergence time estimations show a Middle Pliocene crown radiation of the genus (3.3 Mya). We hypothesize that the aridification of the Saharo-Arabia that began in the Late Miocene triggered the initial diversification of Scincus, and that the subsequent expansion of sand deserts enabled their dispersal over the large Saharan and Arabian range. We discuss the evolution of body form in sand swimming lizards and ponder how Scincus retained their fully limbed morphology despite being sand swimmers that are typically limbless.