Snake evolution in Melanesia: origin of the Hydrophiinae (Serpentes, Elapidae), and the evolutionary history of the enigmatic New Guinean elapidToxicocalamus

Whip it into shape: Revision of the Demansia psammophis (Schlegel, 1837) complex (Squamata: Elapidae), with a description of a new species from central Australia

The genus Demansia Günther is the most diverse genus of Australian terrestrial elapids. A phylogenetic framework for the familiar but problematic taxa D. psammophis and D. reticulata (Gray) has been long overdue to ascertain interspecific relationships and resolve unclear taxonomic issues. Here we present an integrated molecular phylogenetic and morphological analyses to review species delineation, resulting in confirmation that both D. psammophis and D. reticulata are full species and that some populations referred to D. r. cupreiceps Storr are not distinguishable from more typical D. reticulata. We also find the widespread central Australian population (treated by most authors as part of cupreiceps) to be specifically distinct. We redescribe D. psammophis and D. reticulata to clarify morphological and geographical boundaries and describe D. cyanochasma sp. nov. based on a combination of molecular genetic markers, details of colour and pattern, adult total length and a few morphometric attributes. We also designate a lectotype for D. psammophis from the original syntype series and comment on the necessity for further taxonomic refinement of this distinctive group.

Hidden diversity in semi-fossorial Melanesian forest snakes: A revision of the Toxicocalamus loriae complex (Squamata, Elapidae) from New Guinea

With its conservative set of scalation characters, Toxicocalamus loriae is a morphologically confusing species to which a wide array of phenotypes has been assigned. Careful analysis of 224 museum specimens reveals that multiple distinct species remain hidden under the name T. loriae and that diagnostic, species-level differences are more nuanced in this group of snakes than among other members of the genus. Our taxonomic reassessment leads us to resurrect the species T. lamingtonicomb. nov., T. loennbergiicomb. nov., and T. nymanicomb. nov. from synonymy with T. loriae, retain only T. pratti as a synonym, and describe three new species. As a consequence, T. loriae is no longer recognized as ranging throughout the entire island of New Guinea but is instead restricted to the southern versant of the Papuan Peninsula, and T. lamingtoni and T. spilorhynchussp. nov. are species restricted to that same peninsula’s northern versant. Toxicocalamus loennbergii is known only from the type series taken on the Onin Peninsula in West Papua, Indonesia, Toxicocalamus atratussp. nov. is a high-elevation (800–2200 m) Central Highlands endemic, and T. vertebralissp. nov. ranges from the Central Highlands of Papua New Guinea eastward into the Wau area of Morobe Province. Toxicocalamus nymani inhabits a geologically more heterogenous region, occurring from the Central Highlands eastward to the Huon Peninsula, including Karkar Island, and adjacent areas of Madang Province as well as the northernmost reaches of the Papuan Peninsula. We expect that denser geographic sampling across New Guinea and focussed specimen collection of a few known populations will result in the recognition of additional species in this complex.

A new species of New Guinea Worm-Eating Snake (Serpentes, Elapidae, Toxicocalamus Boulenger, 1896) from Western Highlands Province, Papua New Guinea

We describe a new species of New Guinea Worm-Eating Snake (Elapidae: Toxicocalamus) from a specimen in the reptile collection of the Papua New Guinea National Museum and Art Gallery. Toxicocalamus longhagensp. nov. can be easily distinguished from other species of this genus by the presence of paired subcaudals, a preocular scale unfused from the prefrontal scale, a prefrontal distinct from the internasal scale that contacts the supralabials, a single large posterior temporal and two postocular scales. The new taxon is currently known only from one specimen, which was collected from Mt. Hagen Town in Western Highlands Province, Papua New Guinea in 1967. The new species was originally identified as T. loriae, but the unique head scalation and postfrontal bone morphology revealed through micro-computed tomography scanning easily distinguish the new species from T. loriaesensu stricto. This is the first species of this genus described from Western Highlands Province.

Australian Sea Snake Envenoming Causes Myotoxicity and Non-Specific Systemic Symptoms - Australian Snakebite Project (ASP-24)

Background: Sea snakes are venomous snakes found in the warm parts of the Indo-Pacific, including around Australia. Most sea snake envenoming causes myotoxicity, but previous Australian case reports describe neurotoxicity. We aimed to describe the epidemiology and clinical presentation of Australian sea snake envenoming and the effectiveness of antivenom.

Methods: Patients were recruited to the Australian Snakebite Project (ASP), an Australia-wide prospective observational study recruiting all patients with suspected or confirmed snakebite >2 years. Information about demographics, bite circumstances, species involved, clinical and laboratory features of envenoming, and treatment is collected and entered into a purpose-built database.

Results: Between January 2002 and August 2020, 13 patients with suspected sea snake bite were recruited to ASP, 11 were male; median age was 30 years. Bites occurred in Queensland and Western Australia. All patients were in or around, coastal waters at the time of bite. The species involved was identified in two cases (both Hydrophis zweifeli). Local effects occurred in 9 patients: pain (5), swelling (5), bleeding (2), bruising (1). Envenoming occurred in eight patients and was characterised by non-specific systemic features (6) and myotoxicity (2). Myotoxicity was severe (peak CK 28200 and 48100 U/L) and rapid in onset (time to peak CK 13.5 and 15.1 h) in these two patients. Non-specific systemic features included nausea (6), headache (6), abdominal pain (3), and diaphoresis (2). Leukocytosis, neutrophilia, and lymphopenia occurred in both patients with myotoxicity and was evident on the first blood test. No patients developed neurotoxicity or coagulopathy. Early Seqirus antivenom therapy was associated with a lower peak creatine kinase.

Conclusion: While relatively rare, sea snake envenoming is associated with significant morbidity and risk of mortality. Early antivenom appears to have a role in preventing severe myotoxicity and should be a goal of therapy.

Revision of the montane New Guinean skink genus Lobulia (Squamata: Scincidae), with the description of four new genera and nine new species

The skink genus Lobulia is endemic to New Guinea, the largest and highest tropical island in the world. Lobulia and its related genera represent an important component of the montane herpetofauna of New Guinea, but it remains understudied and poorly known. We here provide the first, large-scale, systematic revision of Lobulia, using molecular phylogenetic and morphological comparisons to assess the monophyly of the genus and the diversity of species within it. We find that Lobulia, as currently defined, is polyphyletic. The eight species currently assigned to it form three clades. Furthermore, many specimens from New Guinea of unknown specific affinity are genetically and morphologically distinct from each other. Based on these data, we re-diagnose Lobulia and two of its closely related genera, Prasinohaema and Papuascincus. We erect four new genera (Alpinoscincus gen. nov., Nubeoscincus gen. nov., Ornithuroscincus gen. nov. and Palaia gen. nov.) to address the problem of polyphyly and describe nine new species Lobulia fortis sp. nov., Lobulia huonensis sp. nov., Loublia marmorata sp. nov., Lobulia vogelkopensis sp. nov., Ornithuroscincus bengaun sp. nov., Ornithuroscincus inornatus sp. nov., Ornithuroscincus pterophilus sp. nov., Ornithuroscincus shearmani sp. nov. and Ornithuroscincus viridis sp. nov. We supplement this taxonomic revision by investigating the biogeographic history of Lobulia s.l. and find evidence for a large radiation in the accreted terranes of New Guinea, with multiple independent colonizations of montane habitats and subsequent recolonization of lowland habitats. Our study reinforces the uniqueness and richness of the montane herpetofauna of New Guinea and the importance of mountains to biodiversity in the Tropics.

Repeated dietary shifts in elapid snakes (Squamata: Elapidae) revealed by ancestral state reconstruction

Identifying the traits of ancestral organisms can reveal patterns and drivers of organismal diversification. Unfortunately, reconstructing complex multistate traits (such as diet) remains challenging. Adopting a ‘reconstruct, then aggregate’ approach in a maximum likelihood framework, we reconstructed ancestral diets for 298 species of elapid snakes. We tested whether different prey types were correlated with one another, tested for one-way contingency between prey type pairs, and examined the relationship between snake body size and dietary composition. We demonstrate that the evolution of diet was characterized by niche conservation punctuated by repeated dietary shifts. The ancestor of elapids most likely fed on reptiles and possibly amphibians, with deviations from this ancestral diet occurring repeatedly due to shifts into marine environments and changes in body size. Moreover, we demonstrate important patterns of prey use, including one-way dependency—most obviously the inclusion of eggs being dependent on a diet that already included the producers of those eggs. Despite imperfect dietary data, our approach produced a robust overview of dietary evolution. Given the paucity of natural history information for many organisms, our approach has the potential to increase the number of lineages to which ancestral state reconstructions of multistate traits can be robustly applied.

Two reference-quality sea snake genomes reveal their divergent evolution of adaptive traits and venom systems

True sea snakes (Hydrophiini) are among the last and most successful clades of vertebrates that show secondary marine adaptation, exhibiting diverse phenotypic traits and lethal venom systems. To better understand their evolution, we generated the first chromosome-level genomes of two representative Hydrophiini snakes, Hydrophis cyanocinctus and H. curtus. Through comparative genomics we identified a great expansion of the underwater olfaction-related V2R gene family, consisting of more than 1,000 copies in both snakes. A series of chromosome rearrangements and genomic structural variations were recognized, including large inversions longer than 30 megabase (Mb) on sex chromosomes which potentially affect key functional genes associated with differentiated phenotypes between the two species. By integrating multiomics we found a significant loss of the major weapon for elapid predation, three-finger toxin genes, which displayed a dosage effect in H. curtus. These genetic changes may imply mechanisms that drove the divergent evolution of adaptive traits including prey preferences between the two closely related snakes. Our reference-quality sea snake genomes also enrich the repositories for addressing important issues on the evolution of marine tetrapods, and provide a resource for discovering marine-derived biological products.

A molecular phylogeny for the Pacific monitor lizards (Varanus subgenus Euprepiosaurus) reveals a recent and rapid radiation with high levels of cryptic diversity

We provide a geographically well-sampled, time-calibrated molecular phylogeny for the Pacific monitor lizards (Varanus: subgenus Euprepiosaurus) based on ND4 and 16S rRNA mitochondrial DNA sequences. Three well-supported clades, or species groups, are retrieved: the Varanus doreanus Group, the V. jobiensis Group and the V. indicus Group. The subgenus is estimated to have originated in the Mid-Miocene, but extant lineage diversification dates from the Late Miocene and Pliocene. A rapid and widespread radiation of the V. indicus Group into the South-West Pacific islands has occurred in the Pleistocene, but colonization onto these islands did not occur in a linear, stepping-stone fashion. Genetically distinct populations – by tradition classified as V. indicus, but seemingly representing distinct species – occur scattered on Tanimbar, several of the Solomon Islands, the Admiralty Islands, the Louisiade Archipelago, Palau and Guam. Our analyses indicate that Varanus jobiensis is a species complex with several divergent lineages that started to separate in the Pliocene and continued in the Pleistocene, the former coinciding with the uplift of the Central Dividing Range on New Guinea. We find that sympatry among species of Euprepiosaurus has not occurred until divergence times of 4.7–5.8 Myr have accrued.

Lizards of the lost arcs: mid-Cenozoic diversification, persistence and ecological marginalization in the West Pacific

Regions with complex geological histories often have diverse and highly endemic biotas, yet inferring the ecological and historical processes shaping this relationship remains challenging. Here, in the context of the taxon cycle model of insular community assembly, we investigate patterns of lineage diversity and habitat usage in a newly characterized vertebrate radiation centred upon the world's most geologically complex insular region: island arcs spanning from the Philippines to Fiji. On island arcs taxa are ecologically widespread, and provide evidence to support one key prediction of the taxon cycle, specifically that interior habitats (lowland rainforests, montane habitats) are home to a greater number of older or relictual lineages than are peripheral habitats (coastal and open forests). On continental fringes, however, the clade shows a disjunct distribution away from lowland rainforest, occurring in coastal, open or montane habitats. These results are consistent with a role for biotic interactions in shaping disjunct distributions (a central tenant of the taxon cycle), but we find this pattern most strongly on continental fringes not islands. Our results also suggest that peripheral habitats on islands, and especially island arcs, may be important for persistence and diversification, not just dispersal and colonization. Finally, new phylogenetic evidence for subaerial island archipelagos (with an associated biota) east of present-day Wallace's Line since the Oligocene has important implications for understanding long-term biotic interchange and assembly across Asia and Australia.

A Review and Database of Snake Venom Proteomes

Advances in the last decade combining transcriptomics with established proteomics methods have made possible rapid identification and quantification of protein families in snake venoms. Although over 100 studies have been published, the value of this information is increased when it is collated, allowing rapid assimilation and evaluation of evolutionary trends, geographical variation, and possible medical implications. This review brings together all compositional studies of snake venom proteomes published in the last decade. Compositional studies were identified for 132 snake species: 42 from 360 (12%) Elapidae (elapids), 20 from 101 (20%) Viperinae (true vipers), 65 from 239 (27%) Crotalinae (pit vipers), and five species of non-front-fanged snakes. Approximately 90% of their total venom composition consisted of eight protein families for elapids, 11 protein families for viperines and ten protein families for crotalines. There were four dominant protein families: phospholipase A₂s (the most common across all front-fanged snakes), metalloproteases, serine proteases and three-finger toxins. There were six secondary protein families: cysteine-rich secretory proteins, l-amino acid oxidases, kunitz peptides, C-type lectins/snaclecs, disintegrins and natriuretic peptides. Elapid venoms contained mostly three-finger toxins and phospholipase A₂s and viper venoms metalloproteases, phospholipase A₂s and serine proteases. Although 63 protein families were identified, more than half were present in <5% of snake species studied and always in low abundance. The importance of these minor component proteins remains unknown.