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New Guinea and surrounding islands are home to some of the richest assemblages of insular biodiversity in the world. The key geological drivers of species richness in this region are largely considered to be mountain uplift and development of offshore archipelagos—some of which have accreted onto New Guinea—with the role of mountain uplift and elevational gradients receiving more attention than the role of isolation on islands. Here, we examine the distribution of lineage richness and body-size diversity in a radiation of Melanesian lizards that is almost entirely absent from montane habitats but closely associated with islands—the geckos of the genusNactus. Our data indicate that eastern New Guinea—centred on the East Papuan Composite Terrane (EPCT)—shows particularly high levels of endemism and body-size diversity and is also inferred to be a source area for multiple independent colonisations elsewhere in New Guinea, the Pacific and Australia. TwoNactuslineages in Australia have closest relatives occurring to the north of New Guinea’s Central Cordillera, suggesting dispersal through this area in the mid-Miocene, possibly via seaways that would have isolated the islands to the east and west of the proto-Papuan region. Syntopic species tend to differ in body length; however, at a phylogenetic scale, this trait appears to be conservative, with small-sized and large-sized species clustered into separate lineages. These data suggest that species richness in MelanesianNactusis in part explained by morphological diversification enabling the presence of sympatric communities to exist, but to a greater extent by multiple instances of dispersal and extensive allopatric and parapatric speciation, especially in and around the islands of the EPCT.

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.

Museum specimens provide a wealth of information to biologists, but obtaining genetic data from formalin‐fixed and fluid‐preserved specimens remains challenging. WhileDNAsequences have been recovered from such specimens, most approaches are time‐consuming and produce low data quality and quantity. Here, we use a modifiedDNAextraction protocol combined with high‐throughput sequencing to recoverDNAfrom formalin‐fixed and fluid‐preserved snakes that were collected over a century ago and for which little or no modern genetic materials exist in public collections. We successfully extractedDNAand sequenced ultraconserved elements ( = 2318 loci) from 10 fluid‐preserved snakes and included them in a phylogeny with modern samples. This phylogeny demonstrates the general use of such specimens in phylogenomic studies and provides evidence for the placement of enigmatic snakes, such as the rare and never‐before sequenced IndianXylophis stenorhynchus. Our study emphasizes the relevance of museum collections in modern research and simultaneously provides a protocol that may prove useful for specimens that have been previously intractable forDNAsequencing.