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Natural history museum collections worldwide represent a tremendous resource of information on past and present biodiversity. Fish, reptiles, amphibians and many invertebrate collections have often been preserved in ethanol for decades or centuries and our knowledge on the genomic and metagenomic research potential of such material is limited. Here, we use ancient DNA protocols, combined with shotgun sequencing to test the molecular preservation in liver, skin and bone tissue from five old (1842 to 1964) museum specimens of the common garter snake (Thamnophis sirtalis). When mapping reads to a T. sirtalis reference genome, we find that the DNA molecules are highly damaged with short average sequence lengths (38-64 bp) and high C-T deamination, ranging from 9% to 21% at the first position. Despite this, the samples displayed relatively high endogenous DNA content, ranging from 26% to 56%, revealing that genome-scale analyses are indeed possible from all specimens and tissues included here. Of the three tested types of tissue, bone shows marginally but significantly higher DNA quality in these metrics. Though at least one of the snakes had been exposed to formalin, neither the concentration nor the quality of the obtained DNA was affected. Lastly, we demonstrate that these specimens display a diverse and tissue-specific microbial genetic profile, thus offering authentic metagenomic data despite being submerged in ethanol for many years. Our results emphasize that historical museum collections continue to offer an invaluable source of information in the era of genomics.

The critically endangered leaf-scaled (Aipysurus foliosquamaI) and short-nosed (A. apraefrontalis) sea snakes are currently recognised only from Ashmore and Hibernia reefs ~600km off the northwest Australian coast. Steep population declines in both species were documented over 15 years and neither has been sighted on dedicated surveys of Ashmore and Hibernia since 2001. We examine specimens of these species that were collected from coastal northwest Australian habitats up until 2010 (A.foliosquama) and 2012 (A. apraefrontalis) and were either overlooked or treated as vagrants in conservation assessments. Morphological variation and mitochondrial sequence data confirm the assignment of these coastal specimens to A. foliosquama (Barrow Island, and offshore from Port Hedland) and A.apraefrontalis (Exmouth Gulf, and offshore from Roebourne and Broome). Collection dates, and molecular and morphological variation between coastal and offshore specimens, suggest that the coastal specimens are not vagrants as previously suspected, but instead represent separate breeding populations. The newly recognised populations present another chance for leaf-scaled and short-nosed sea snakes, but coastal habitats in northwest Australia are widely threatened by infrastructure developments and sea snakes are presently omitted from environmental impact assessments for industry. Further studies are urgently needed to assess these species' remaining distributions, population structure, and extent of occurrence in protected areas.

One of the primary goals in biogeography is to understand how different biotas have been assembled in different regions of the world. The presence of the viviparous sea snakes in the Indian Ocean (IO) poses a unique question in this regard due to their evolutionary origins in Australasia (Australia and New Guinea). Here, we examined the origins and patterns of colonization of the IO sea snake assemblage through time-calibrated molecular phylogenies and ancestral area reconstructions. We further evaluated how past and present barriers to dispersal affect genetic diversity of IO sea snakes by examining the population genetic structure of the widespread sea snake, Hydrophis curtus. Our phylogenetic analyses and ancestral area reconstructions strongly indicate that the majority of the IO sea snakes are derived from the Southeast Asian (SEA) sea snake fauna through dispersal and colonization with an in situ radiation (Hydrophis stricticollis-Hydrophis obscurus clade). Further, many species have undergone vicariant speciation events across the Sunda shelf/Indo-Pacific barrier, which formed during the low sea level periods of the Pleistocene. Population genetic analysis of H. curtus revealed a prominent genetic break between populations broadly distributed in the IO and SEA with limited recent gene flow indicating possible cryptic species. These results suggest that compared to the viviparous sea snake stem group that originated 10.6-6.5 million years ago, the IO viviparous sea snakes have a relatively long and complex evolutionary history in the IO and thus have a unique conservation value.

Marine snakes represent the most speciose group of marine reptiles and are a significant component of reef and coastal ecosystems in tropical oceans. Research on this group has historically been challenging due to the difficulty in capturing, handling, and keeping these animals for field- and lab-based research. Inexplicable declines in marine snake populations across global hotspots have highlighted the lack of basic information on this group and elevated multiple species as conservation priorities. With the increased interest in research on marine snakes, we conducted a systematic survey of experts to identify twenty key questions that can direct future research. These questions are framed across a wide array of scientific fields to produce much-needed information relevant to the conservation and management of marine snakes.

Viviparous sea snakes are the most rapidly speciating reptiles known, yet the ecological factors underlying this radiation are poorly understood. Here, we reconstructed dated trees for 75% of sea snake species and quantified body shape (forebody relative to hindbody girth), maximum body length and trophic diversity to examine how dietary specialization has influenced morphological diversification in this rapid radiation. We show that sea snake body shape and size are strongly correlated with the proportion of burrowing prey in the diet. Specialist predators of burrowing eels have convergently evolved a ‘microcephalic’ morphotype with dramatically reduced forebody relative to hindbody girth and intermediate body length. By comparison, snakes that predominantly feed on burrowing gobies are generally short-bodied and small-headed, but there is no evidence of convergent evolution. The eel specialists also exhibit faster rates of size and shape evolution compared to all other sea snakes, including those that feed on gobies. Our results suggest that trophic specialization to particular burrowing prey (eels) has invoked strong selective pressures that manifest as predictable and rapid morphological changes. Further studies are needed to examine the genetic and developmental mechanisms underlying these dramatic morphological changes and assess their role in sea snake speciation.