Whole snake genomes from eighteen families of snakes (Serpentes: Caenophidia) and their applications to systematics.

We present genome assemblies for 18 snake species representing 18 families (Serpentes: Caenophidia): Acrochordus granulatus, Aparallactus werneri, Boaedon fuliginosus, Calamaria suluensis, Cerberus rynchops, Grayia smithii, Imantodes cenchoa, Mimophis mahfalensis, Oxyrhabdium leporinum, Pareas carinatus, Psammodynastes pulverulentus, Pseudoxenodon macrops, Pseudoxyrhopus heterurus, Sibynophis collaris, Stegonotus admiraltiensis, Toxicocalamus goodenoughensis, Trimeresurus albolabris, and Tropidonophis doriae. From these new genome assemblies, we extracted thousands of loci commonly used in systematic and phylogenomic studies on snakes, including target-capture datasets composed of ultraconserved elements (UCEs) and anchored hybrid enriched loci (AHEs), as well as traditional Sanger loci. Phylogenies inferred from the two target-capture loci datasets were identical with each other and strongly congruent with previously published snake phylogenies. To show the additional utility of these non-model genomes for investigative evolutionary research, we mined the genome assemblies of two New Guinea island endemics in our dataset (S. admiraltiensis and T. doriae) for the ATP1a3 gene, a thoroughly researched indicator of resistance to toad toxin ingestion by squamates. We find that both these snakes possess the genotype for toad toxin resistance despite their endemism to New Guinea, a region absent of any toads until the human-mediated introduction of Cane Toads in the 1930s. These species possess identical substitutions that suggest the same bufotoxin resistance as their Australian congenerics (Stegonotus australis and Tropidonophis mairii) which forage on invasive Cane Toads. Herein, we show the utility of short-read high-coverage genomes, as well as improving the deficit of available squamate genomes with associated voucher specimens.

Systematics and distribution of Lankascincus fallax (Peters, 1860) (Reptilia, Scincidae), an endemic litter-skink from Sri Lanka.

Lankascincus fallax is an endemic, but widespread species of skink distributed throughout Sri Lanka, including all bioclimatic zones (elevations from 0 to 1,200 m a.s.l.). After thoroughly comparing morphology and morphometry between populations in different bioclimatic zones, we recognize it as a single morphospecies. We revise the systematics of Lankascincus fallax based on molecular and morphological data providing a comprehensive re-description of the adult syntype collected from either Ratnapura or Trinkomalee (sic), Sri Lanka. We provide the first-ever constructed phylogeny of Lankascincus representing five species (out of nine) based on GenBank data. In addition, we examined all the type specimens of the two synonymized species, Sphenomorphus rufogulus and Lankascincus deraniyagalae. We also provide a comprehensive discussion on the distribution of L. fallax.