A reference genome assembly for the continentally distributed ring-necked snake, Diadophis punctatus.

Snakes in the family Colubridae include more than 2,000 currently recognized species, and comprise roughly 75% of the global snake species diversity on Earth. For such a spectacular radiation, colubrid snakes remain poorly understood ecologically and genetically. Two subfamilies, Colubrinae (788 species) and Dipsadinae (833 species), comprise the bulk of colubrid species richness. Dipsadines are a speciose and diverse group of snakes that largely inhabit Central and South America, with a handful of small-body-size genera that have invaded North America. Among them, the ring-necked snake, Diadophis punctatus, has an incredibly broad distribution with 14 subspecies. Given its continental distribution and high degree of variation in coloration, diet, feeding ecology, and behavior, the ring-necked snake is an excellent species for the study of genetic diversity and trait evolution. Within California, six subspecies form a continuously distributed "ring species" around the Central Valley, while a seventh, the regal ring-necked snake, Diadophis punctatus regalis is a disjunct outlier and Species of Special Concern in the state. Here, we report a new reference genome assembly for the San Diego ring-necked snake, D. p. similis, as part of the California Conservation Genomics Project. This assembly comprises a total of 444 scaffolds spanning 1,783 Mb and has a contig N50 of 8.0 Mb, scaffold N50 of 83 Mb, and BUSCO completeness score of 94.5%. This reference genome will be a valuable resource for studies of the taxonomy, conservation, and evolution of the ring-necked snake across its broad, continental distribution.

The Harderian gland transcriptomes of Caraiba andreae, Cubophis cantherigerus and Tretanorhinus variabilis, three colubroid snakes from Cuba.

The Harderian gland is a cephalic structure, widely distributed among vertebrates. In snakes, the Harderian gland is anatomically connected to the vomeronasal organ via the nasolacrimal duct, and in some species can be larger than the eyes. The function of the Harderian gland remains elusive, but it has been proposed to play a role in the production of saliva, pheromones, thermoregulatory lipids and growth factors, among others. Here, we have profiled the transcriptomes of the Harderian glands of three non-front-fanged colubroid snakes from Cuba: Caraiba andreae (Cuban Lesser Racer); Cubophis cantherigerus (Cuban Racer); and Tretanorhinus variabilis (Caribbean Water Snake), using Illumina HiSeq2000 100 bp paired-end. In addition to ribosomal and non-characterized proteins, the most abundant transcripts encode putative transport/binding, lipocalin/lipocalin-like, and bactericidal/permeability-increasing-like proteins. Transcripts coding for putative canonical toxins described in venomous snakes were also identified. This transcriptional profile suggests a more complex function than previously recognized for this enigmatic organ.

Ecological correlates of cranial evolution in the megaradiation of dipsadine snakes.

BACKGROUND: Dipsadine snakes represent one of the most spectacular vertebrate radiations that have occurred in any continental setting, with over 800 species in South and Central America. Their species richness is paralleled by stunning ecological diversity, ranging from arboreal snail-eating and aquatic eel-eating specialists to terrestrial generalists. Despite the ecological importance of this clade, little is known about the extent to which ecological specialization shapes broader patterns of phenotypic diversity within the group. Here, we test how habitat use and diet have influenced morphological diversification in skull shape across 160 dipsadine species using micro-CT and 3-D geometric morphometrics, and we use a phylogenetic comparative approach to test the contributions of habitat use and diet composition to variation in skull shape among species. RESULTS: We demonstrate that while both habitat use and diet are significant predictors of shape in many regions of the skull, habitat use significantly predicts shape in a greater number of skull regions when compared to diet. We also find that across ecological groupings, fossorial and aquatic behaviors result in the strongest deviations in morphospace for several skull regions. We use simulations to address the robustness of our results and describe statistical anomalies that can arise from the application of phylogenetic generalized least squares to complex shape data. CONCLUSIONS: Both habitat and dietary ecology are significantly correlated with skull shape in dipsadines; the strongest relationships involved skull shape in snakes with aquatic and fossorial lifestyles. This association between skull morphology and multiple ecological axes is consistent with a classic model of adaptive radiation and suggests that ecological factors were an important component in driving morphological diversification in the dipsadine megaradiation.

Six additional mitochondrial genomes for North American nightsnakes (Dipsadidae: Hypsiglena) and a novel gene feature for advanced snakes.

The North American nightsnakes in the genus Hypsiglena is composed of nine named and at least two unnamed species. Here, we provide the first mt-genome of H. affinis, an additional mt-genome for H. sp. nov. 1, and four additional mt-genomes from the widespread H. jani. These mtDNA genomes were sequenced using both Illumina and Ion Torrent sequencing technologies. The resulting genomes contained the expected 13 protein coding genes, 22 tRNA genes, 2 rRNA genes, and 2 control regions typical of colubroid snakes. Two of the H. jani samples had partial tRNAIle genes upstream of CR2 which has not been previously documented in colubroid snakes. A maximum likelihood gene-tree based on these data combined with previously published sequence data recovers a well-supported phylogeny and is in concordance with previous estimates of evolutionary relationships in this group.

Cranial adaptations for feeding on snails in species of Sibynomorphus (Dipsadidae: Dipsadinae).

Neotropical "goo-eating" dipsadine snakes display a set of morphological and histo-chemical adaptations linked to the capture of their soft-bodied, viscous invertebrate prey. Within this group, species from the genus Sibynomorphus feed chiefly on snails and slugs. Here, we analyzed a series of skull and mandible characters in S. mikanii, S. neuwiedi and S. turgidus using geometric morphometrics, with the aim of assessing morphological adaptations related to slug- and snail-feeding in that genus. We further compared the results with Leptodeira annulata, a species that feeds on vertebrates. To evaluate shape differences of the skull and mandible between species we performed a multivariate analysis of variance and a linear discriminant analysis. Our results show that the narrow, elongate skull in S. mikanii may help with slug ingestion, while asymmetry in teeth number and mandibular shape in S. neuwiedi and S. turgidus are likely related to snail feeding.

Systematics of Nothopsini (Serpentes, Dipsadidae), with a new species of Synophis from the Pacific Andean slopes of southwestern Ecuador.

Within Dipsadinae, some recent authors have recognized a tribe Nothopsini containing the genera Diaphorolepis, Emmochliophis, Nothopsis, Synophis, and Xenopholis, on the basis of a number of putative morphological synapomorphies. However, molecular results suggest that Nothopsis, Synophis, and Xenopholis do not form a monophyletic group, while the remaining taxa are unsampled in recent molecular phylogenies. Here, DNA-sequence data for some Diaphorolepis and Synophis species are provided for the first time, as well as additional new sequences for Nothopsis and some Synophis species. Including these and other existing data for nothopsine species, previous studies showing that Nothopsini is not a natural group are corroborated. Nothopsini Cope, 1871 is restricted to Nothopsis. Diaphorolepidini Jenner, 1981 is resurrected and re-delimited to include only Diaphorolepis, Emmochliophis, and Synophis. Finally, Xenopholis remains Dipsadinae incertae sedis. Known material of Diaphorolepidini is reviewed to generate revised and expanded descriptions and diagnoses at the tribe, genus, and species level. Numerous cryptic species are likely present in Synophis bicolor and Synophis lasallei. Finally, a new population from the low-elevation cloud forests of SW Ecuador is reported upon, which is genetically and morphologically distinct from all other species, that is here named Synophis zaheri sp. n.

Description and phylogeny of three new species of Synophis (Colubridae, Dipsadinae) from the tropical Andes in Ecuador and Peru.

The discovery of three new species of Synophis snakes from the eastern slopes of the tropical Andes in Ecuador and Peru is reported. All previous records of Synophis bicolor from eastern Ecuador correspond to Synophis bogerti sp. n., which occurs between 1000-1750 m along a large part of the Amazonian slopes of the Ecuadorian Andes. In contrast, Synophis zamora sp. n. is restricted to southeastern Ecuador, including Cordillera del Cóndor, between 1543-1843 m. Synophis insulomontanus sp. n. is from the eastern slopes of the Andes in central and northern Peru, between 1122-1798 m, and represents the first record of Synophis from this country. All three new species share in common a large lateral spine at the base of the hemipenial body. A molecular phylogenetic tree based on three mitochondrial genes is presented, including samples of Diaphorolepis wagneri. Our tree strongly supports Synophis and Diaphorolepis as sister taxa, as well as monophyly of the three new species described here and Synophis calamitus. Inclusion of Synophis and Diaphorolepis within Dipsadinae as sister to a clade containing Imantodes, Dipsas, Ninia, Hypsiglena and Pseudoleptodeira is also supported.

ResumenSe reporta el descubrimiento de tres especies nuevas de serpientes Synophis de las estribaciones orientales de los Andes tropicales en Ecuador y Perú. Todos los registros previos de Synophis bogerti del oriente ecuatoriano corresponden a Synophis bogertisp. n., la cual ocurre entre 1000­1750 m a lo largo de gran parte de las estribaciones amazónicas de los Andes ecuatorianos. En contraste, Synophis zamorasp. n. se restringe al suroriente de Ecuador, incluyendo la Cordillera del Cóndor, entre 1543­1843 m. Synophis insulomontanussp. n. es de las estribaciones orientales de los Andes del centro y norte del Perú, entre 1122­1798 m, y representa el primer registro de Synophis para este país. Todas las tres especies nuevas comparten en común una espina lateral larga en la base del cuerpo del hemipene. Un árbol molecular filogenético, basado en tres genes mitocondriales es presentado, incluyendo muestras de Diaphorolepis wagneri. Nuestro árbol apoya fuertemente a Synophis y Diaphorolepis como taxa hermanos, así como la monofilia de las tres especies descritas y de Synophis calamitus. La inclusión de Synophis y Diaphorolepis dentro de Dipsadinae, como hermanas a un clado que contiene a Imantodes, Dipsas, Ninia, Hypsiglena y Pseudoleptodeira también es apoyada.

Prevalencia de endoparásitos gastrointestinales y ectoparásitos en serpientes ex situ en Barranquilla, Colombia / Prevalence of gastrointestinal endoparasites and ectoparasites in ex situ snakes in Barranquilla, Colombia

RESUMEN Objetivo. Identificar la prevalencia de endoparásitos y ectoparásitos en serpientes ex situ en la Fundación Botánica y Zoológica de Barranquilla "Barranquilla Zoo". Materiales y métodos. Para esto se analizaron muestras de materia fecal y ectoparásitos de 2 colúbridos (Leptophis ahaetulla y Spilotes pullatus), 2 dipsadinos (Oxybelys aeneus y Thamnodynastes paraguanae) y 13 boidos (9 individuos de la especie Boa constrictor, 2 de Epicrates maurus y 2 de Eunectes murinus) utilizando los métodos de flotación en solución saturada de azúcar y observación directa. Resultados. Los resultados obtenidos mostraron que el 65% (11/17) de los animales evaluados fueron positivos a la presencia de parásitos, de los cuales el 91% (10/11) de los ejemplares pertenece a la familia Boidae presentando en su mayoría nematodos, mientras que en los dipsadinos se observaron principalmente protozoarios y los colúbridos resultaron negativos. Finamente como ectoparásitos se identificaron 2 especies de garrapatas (Amblyomma dissimile y Ornothodoros turicata) halladas en ejemplares de Boa constrictor, Epicrates maurus y Spilotes pullatus. Conclusiones. La identificación de las formas parasitarias en este trabajo representa una contribución para el conocimiento de los parásitos en serpientes ex situ en Colombia. Provee información para desarrollar medidas profilácticas y permite comparar los datos sobre las formas parasitarias encontradas con muestreos de estas especies en vida silvestre y bajo cuidados humanos.

ABSTRACT Objective. Identify the prevalence of internal and external parasites in ex situ snakes at the Fundación Botánica y Zoológica de Barranquilla "Barranquilla Zoo". Materials and methods. Stool samples and ectoparasites of 2 colubrids (Leptophis ahaetulla and Spilotes pullatus), 2 diapsids (Oxybelys aeneus and Thamnodynastes paraguanae) and 13 boids (9 individuals of Boa constrictor, 2 of Epicrates maurus and 2 Eunectes murinus) were analyzed using flotation method in saturated sugar solution and direct observation. Results. The results showed that 65% (11/17) of the population was positive to the presence of parasites. In relation to the positive specimens, 91% (10/11) belong to the Boidae family, presenting mostly nematodes, in the dipsadid's samples mainly protozoans were observed and the colubrid's samples were negative. Regarding ectoparasites, 2 species of ticks (Amblyomma dissimile and Ornothodoros turicata) were found in specimens of Boa constrictor, Epicrates maurus and Spilotes pullatus. Conclusions. The identification of parasitic forms in this paper represents a contribution to the knowledge of parasites in snakes ex situ in Colombia. It provides information to develop prophylactic measures against these pathological agents and also allows comparing the data about the parasitic forms found with other researches in the wild and in captivity.

A new species of blunt-headed vine snake (Colubridae, Imantodes) from the Chocó region of Ecuador.

We describe a new species of Imantodes from the Chocó region of northwestern Ecuador. The new species differs most significantly from all other congeners in lacking a loreal scale. We analyze the phylogenetic relationships among species of Imantodes based on two mitochondrial genes, and postulate that the new species and Imantodes lentiferus are sister taxa. A key to the species of Imantodes from Ecuador is presented.