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Abstract 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. 

Abstract Sunda-Papuan keelback snakes (Serpentes: Natricidae: Tropidonophis Jan 1863) include 20 species distributed from the Philippines south-east through the Moluccas to New Guinea and Australia. Diversity of this insular snake lineage peaks on the island of New Guinea. Previous phylogenetic studies incorporating Tropidonophis have been limited to multi-locus Sanger-sequenced datasets with broad squamate or family-level focus. We used a targeted-sequence capture approach to sequence thousands of nuclear ultraconserved elements (UCEs) to construct the most comprehensive sequence-based phylogenetic hypothesis for this genus and estimate ancestral biogeography. Phylogenies indicate the genus is monophyletic given recent taxonomic reassignment of Rhabdophis spilogaster to Tropidonophis. All UCE phylogenies recovered a monophyletic Tropidonophis with reciprocally monophyletic Philippine and New Guinean clades. Divergence dating and ancestral range estimation suggest dispersal to New Guinea from the Philippines to have occurred during the Mid-Miocene via the Oceanic Arc Terranes. From Late Miocene into the Pliocene the genus experienced rapid diversification from orogeny of the New Guinean Central Cordillera from Oceanic Arc Terrane accretion on the northern boundary of the Sahul Shelf. Future collecting of missing taxa from the Moluccas and Indonesian Papua will better the understanding of non-volant faunal biogeography and diversification in this tectonically complex Pacific arena. 

Abstract 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. 

Abstract Snake venoms are complex mixtures of toxic proteins that hold significant medical, pharmacological and evolutionary interest. To better understand the genetic diversity underlying snake venoms, we developed VenomCap, a novel exon‐capture probe set targeting toxin‐coding genes from a wide range of elapid snakes, with a particular focus on the ecologically diverse and medically important subfamily Hydrophiinae. We tested the capture success of VenomCap across 24 species, representing all major elapid lineages. We included snake phylogenomic probes in the VenomCap capture set, allowing us to compare capture performance between venom and phylogenomic loci and to infer elapid phylogenetic relationships. We demonstrated VenomCap's ability to recover exons from ~1500 target markers, representing a total of 24 known venom gene families, which includes the dominant gene families found in elapid venoms. We find that VenomCap's capture results are robust across all elapids sampled, and especially among hydrophiines, with respect to measures of target capture success (target loci matched, sensitivity, specificity and missing data). As a cost‐effective and efficient alternative to full genome sequencing, VenomCap can dramatically accelerate the sequencing and analysis of venom gene families. Overall, our tool offers a model for genomic studies on snake venom gene diversity and evolution that can be expanded for comprehensive comparisons across the other families of venomous snakes. 

ContextSkinks comprise the dominant component of the terrestrial vertebrate fauna in Oceania, New Guinea, and Eastern Wallacea (ONGEW). However, knowledge of their diversity is incomplete, and their conservation needs are poorly understood. AimsTo explore the diversity and threat status of the skinks of ONGEW and identify knowledge gaps and conservation needs. MethodsWe compiled a list of all skink species occurring in the region and their threat categories designated by the International Union for Conservation of Nature. We used available genetic sequences deposited in the National Center for Biotechnology Information’s GenBank to generate a phylogeny of the region’s skinks. We then assessed their diversity within geographical sub-divisions and compared to other reptile taxa in the region. Key resultsApproximately 300 species of skinks occur in ONGEW, making it the second largest global hotspot of skink diversity following Australia. Many phylogenetic relationships remain unresolved, and many species and genera are in need of taxonomic revision. One in five species are threatened with extinction, a higher proportion than almost all reptile families in the region. ConclusionsONGEW contain a large proportion of global skink diversity on <1% of the Earth’s landmass. Many are endemic and face risks such as habitat loss and invasive predators. Yet, little is known about them, and many species require taxonomic revision and threat level re-assessment. ImplicationsThe skinks of ONGEW are a diverse yet underexplored group of terrestrial vertebrates, with many species likely facing extreme risks in the near future. Further research is needed to understand the threats they face and how to protect them. 

ABSTRACT AimWe assess the systematic relationships and historical biogeographic patterns in the subfamily Scincinae, a group of lizards that primarily inhabits the Afro‐Madagascan and Saharo‐Arabian regions with isolated lineages in Europe, North America, East Asia, India and Sri Lanka. The contemporary distribution of these lineages on the historical Laurasian and Gondwanan landmasses make scincines an ideal system to study the roles of vicariance and dispersal on a geologic scale of tens of millions of years. LocationGlobal. TaxonSubfamily Scincinae (Family Scincidae). MethodsWe conducted biogeographic analyses on a reconstructed, time‐calibrated species tree of scincine genera, including members of the other Scincidae subfamilies, using seven nuclear loci (~6 k base pairs). We also constructed a lineage‐through‐time plot to assess the timing of diversification within scincines. ResultsOur analysis estimated strong support for the monophyly of Scincinae that is further comprised a strongly‐supported Gondwanan clade nested within a broader Laurasian group. While most of the extant, genus‐level diversity within the Gondwanan clade was accrued post‐Eocene, the majority of the Laurasian lineages diverged during the Palaeocene or earlier, suggesting large‐scale extinctions on continents of Laurasian origin. Counterintuitively, scincines from India and Sri Lanka have distinct biogeographical origins despite a long tectonic association between these landmasses, suggesting at least two independent, long‐distance, trans‐oceanic dispersal events into the subcontinent. Our biogeographic analyses suggest that scincines likely originated in East and Southeast Asia during the late Cretaceous (ca. 70 Ma), and eventually dispersed westwards to Africa and Madagascar, where their greatest current‐day species richness occurs. Main ConclusionsOur study demonstrates the concomitant roles of dispersal and extinction in shaping modern‐day assemblages of ancient clades such as scincine lizards. Our range evolution analysis shows that despite the greater diversity observed in the Afro‐Madagascan region, the origin of scincines can be traced back to Southeast Asia and East Asia, followed by westward dispersals. These dispersals may have been followed by significant extinctions in tropical East Asia, resulting in relatively lower diversity of scincines in these regions. Notably, our analysis reveals that Sri Lankan and Peninsular Indian scincines have distinct evolutionary origins.