The effect of missing data on coalescent species delimitation and a taxonomic revision of whipsnakes (Colubridae: Masticophis).

A stable alpha taxonomy is essential to understanding evolutionary processes and achieving effective conservation aims. Taxonomy depends on the identification of independently evolving lineages, and the delimitation of these lineages based on multiple lines of evidence. Coalescent species delimitation within an integrative framework has increased the rigor of the delimitation process. Here we use genome-wide SNP data and coalescent species delimitation to explore lineage relationships within several North American whipsnake species, test the species status of several lineages, and test the effect of missing data on species delimitation. We find support for the elevation of several previously recognized subspecies to full species status, and formally elevate two species. This study demonstrates the power of molecular data and model-based delimitation methods to identify evolutionary relationships, and finds that missing data have little impact on the outcome of delimitation analyses.

Geographical features are the predominant driver of molecular diversification in widely distributed North American whipsnakes.

Allopatric divergence following the formation of geographical features has been implicated as a major driver of evolutionary diversification. Widespread species complexes provide opportunities to examine allopatric divergence across varying degrees of isolation in both time and space. In North America, several geographical features may play such a role in diversification, including the Mississippi River, Pecos River, Rocky Mountains, Cochise Filter Barrier, Gulf of California and Isthmus of Tehuantepec. We used thousands of nuclear single nucleotide polymorphisms (SNPs) and mitochondrial DNA from several species of whipsnakes (genera Masticophis and Coluber) distributed across North and Central America to investigate the role that these geographical features have played on lineage divergence. We hypothesize that these features restrict gene flow and separate whipsnakes into diagnosable genomic clusters. We performed genomic clustering and phylogenetic reconstructions at the species and population levels using Bayesian and likelihood analyses and quantified migration levels across geographical features to assess the degree of genetic isolation due to allopatry. Our analyses suggest that (i) major genetic divisions are often consistent with isolation by geographical features, (ii) migration rates between clusters are asymmetrical across major geographical features, and (iii) areas that receive proportionally more migrants possess higher levels of genetic diversity. Collectively, our findings suggest that multiple features of the North American landscape contributed to allopatric divergence in this widely distributed snake group.

Snake co-occurrence patterns are best explained by habitat and hypothesized effects of interspecific interactions.

Snakes often occur in species-rich assemblages, and sympatry is thought to be facilitated primarily by low diet overlap, not interspecific interactions. We selected, a priori, three species pairs consisting of species that are morphologically and taxonomically similar and may therefore be likely to engage in interspecific, consumptive competition. We then examined a large-scale database of snake detection/nondetection data and used occupancy modelling to determine whether these species occur together more or less frequently than expected by chance while accounting for variation in detection probability among species and incorporating important habitat categories in the models. For some snakes, we obtained evidence that the probabilities that habitat patches are used are influenced by the presence of potentially competing congeneric species. Specifically, timber rattlesnakes (Crotalus horridus) were less likely than expected by chance to use areas that also contained eastern diamond-backed rattlesnakes (Crotalus adamanteus) when the proportion of evergreen forest was relatively high. Otherwise, they occurred together more often than expected by chance. Complex relationships were revealed between habitat use, detection probabilities and occupancy probabilities of North American racers (Coluber constrictor) and coachwhips (Coluber flagellum) that indicated the probability of competitive exclusion increased with increasing area of grassland habitat, although there was some model uncertainty. Cornsnakes (Pantherophis guttatus or Pantherophis slowinskii) and ratsnakes (Pantherophis alleghaniensis, Pantherophis spiloides, or Pantherophis obsoletus) exhibited differences in habitat selection, but we obtained no evidence that patterns of use for this species pair were influenced by current interspecific interactions. Overall, our results are consistent with the hypothesis that competitive interactions influence snake assemblage composition; the strength of these effects was affected by landscape-scale habitat features. Furthermore, we suggest that current interspecific interactions may influence snake occupancy, challenging the paradigm that contemporary patterns of snake co-occurrence are largely a function of diet partitioning that arose over evolutionary time.

The taxonomic status of grass snake, Natrix natrix (Linnaeus, 1758 (Squamata: Colubridae), with designation of a neotype.

As part of an investigation into the status of the near threatened Gotland grass snake, Natrix natrix gotlandica Nilson Andrén, 1981, endemic to the island of Gotland, we discovered that Linnaeus' type series of the common grass snake, Natrix natrix (Linnaeus, 1758), is comprised of specimens from three different currently recognized species.                To stabilize the usage of the name Coluber natrix, we investigate Linnaeus' type series, and a specimen which Linnaeus in 1741 examined west of the Swedish city of Nyköping is designated lectotype. The lectotype has since been lost, and a newly collected specimen from the same locality is designated neotype for Coluber natrix. The neotype is deposited in the herpetology collection of the Swedish Museum of Natural History in Stockholm, Sweden, catalog number NRM 8260.

Additions to the phylogeny of colubrine snakes in Southwestern Asia, with description of a new genus and species (Serpentes: Colubridae: Colubrinae).

Reptiles are still being described worldwide at a pace of hundreds of species a year. While many discoveries are from remote tropical areas, biodiverse arid regions still harbor many novel taxa. Here, we present an updated phylogeny of colubrid snakes from the Western Palearctic by analyzing a supermatrix of all available global snake species with molecular data and report on the discovery of a new genus and species of colubrine snake from southeastern Iran. The new taxon, named Persiophis fahimii Gen. et sp. nov., is nested within a clade containing Middle Eastern and South Asian ground racers (Lytorhynchus, Rhynchocalamus, Wallaceophis, and Wallophis). This species has a derived morphology including an edentulous pterygoid and occurrence of short and blunt teeth on the palatine, maxillae and dentary bones, an elongated snout and a relatively trihedral first supralabial scale that is slightly bigger than the second, and elongated toward the tip of rostral. We also report on the osteology and phylogenetic placement of several poorly studied colubrines: Hierophis andreanus (reassigned to Dolichophis) and Muhtarophis barani.

Coluber Constrictor Bite to the Eye: A Novel Case Report of a Wild Snake Bite to the Eye in North America and Review of Literature.

Snake bites involving the eye are an uncommon cause of ocular trauma; herein, we present one of the few known instances of a snake bite directly to the globe, specifically by the way of a Coluber constrictor, also known as the "Black Racer." In this case report, we describe a nine-year-old girl who presented immediately following a snake bite to the right eye. The patient's vision was unaffected despite visualized puncture wounds through the conjunctiva with associated near-total subconjunctival hemorrhage. The patient was taken to the operating room emergently for globe exploration. Circumferential peritomy and direct view to the sclera did not reveal any lacerations or puncture and subconjunctival vancomycin, gentamycin, and dexamethasone were administered intraoperatively. Post-operatively, the patient was discharged on a regimen of oral Cephalexin. Throughout multiple follow-ups, she continued to maintain excellent vision without sequelae. Trauma to the globe via snake bite is an exceedingly rare occurrence. Upon literature review, three out of three cases involving venomous snakes resulted in "No Light Perception" vision despite anti-venom. While nonvenomous snake bites may lend a better visual outcome, if not treated properly they may also yield poor final visual potential. Methods of treatment include oral or subconjunctival antibiotic administration with or without a steroid or cycloplegic agent. All reported cases of nonvenomous cases ultimately resulted in excellent visual potential (20/40 or better) and no reports of endophthalmitis. As such, it is evident that identifying the species of snake is of the utmost importance when considering visual prognosis. Due to very few reported incidences of globe trauma via snake bite, there is no mainstay therapy for either the venomous or nonvenomous snake bite variety. Despite this, we encourage careful pursuance of the appropriate therapy on a case-by-case basis, considering operative treatment, antivenom (if necessary), and antibiotic coverage with possible cycloplegia and steroid administration.

Convergence in reduced body size, head size, and blood glucose in three island reptiles.

Many oceanic islands harbor diverse species that differ markedly from their mainland relatives with respect to morphology, behavior, and physiology. A particularly common morphological change exhibited by a wide range of species on islands worldwide involves either a reduction in body size, termed island dwarfism, or an increase in body size, termed island gigantism. While numerous instances of dwarfism and gigantism have been well documented, documentation of other morphological changes on islands remains limited. Furthermore, we lack a basic understanding of the physiological mechanisms that underlie these changes, and whether they are convergent. A major hypothesis for the repeated evolution of dwarfism posits selection for smaller, more efficient body sizes in the context of low resource availability. Under this hypothesis, we would expect the physiological mechanisms known to be downregulated in model organisms exhibiting small body sizes due to dietary restriction or artificial selection would also be downregulated in wild species exhibiting dwarfism on islands. We measured body size, relative head size, and circulating blood glucose in three species of reptiles-two snakes and one lizard-in the California Channel Islands relative to mainland populations. Collating data from 6 years of study, we found that relative to mainland population the island populations had smaller body size (i.e., island dwarfism), smaller head sizes relative to body size, and lower levels of blood glucose, although with some variation by sex and year. These findings suggest that the island populations of these three species have independently evolved convergent physiological changes (lower glucose set point) corresponding to convergent changes in morphology that are consistent with a scenario of reduced resource availability and/or changes in prey size on the islands. This provides a powerful system to further investigate ecological, physiological, and genetic variables to elucidate the mechanisms underlying convergent changes in life history on islands.

A new coccidian parasite (Apicomplexa: Eimeriidae: Eimeria) from the southern black racer, Coluber constrictor priapus (Reptilia: Ophidia: Colubridae) from Arkansas, USA.

Between April 2012 and October 2017, 18 southern black racers, Coluber constrictor priapus, were collected from nine counties of Arkansas (n = 13) and McCurtain County, Oklahoma (n = 5) and their faeces examined for coccidian parasites. One of 18 (6%) C. c. priapus harboured an eimerian that we describe here as new. Oocysts of Eimeria dunni sp. nov. were subspheroidal with a lightly pitted bi-layered wall measuring L × W 24.0 × 21.1 and L/W ratio of 1.2. A micropyle was absent but an oocyst residuum and polar granule were present. Sporocysts were ovoidal and measured 11.9 × 8.1 with L/W of 1.5. A Stieda body was present but substieda and parastieda bodies were absent. The sporocyst residuum was composed of medium-sized granules aligned along perimeter of sporocyst or in a dispersed mass. This represents the first valid eimerian reported from the southern black racer.