New coffee snake species discovered in Ecuador’s cloud forests and Schmidt’s snake revalidated

Deep in the mist-drenched cloud forests of northwestern Ecuador, a small black snake with a striking white collar has been hiding in plain sight for decades. Herpetologists have now formally described it as a species new to science, Ninia guytudori, while simultaneously resurrecting a snake name that had been buried in the literature since 1862. The double discovery, published in the journal Evolutionary Systematics, rewrites the map of coffee snake diversity in western Ecuador and removes the famously variable Variable Coffee Snake, Ninia atrata, from the country’s list of reptiles altogether.

Coffee snakes of the genus Ninia are small, secretive colubrids that spend their lives prowling leaf litter across Central and South America. The Variable Coffee Snake earned its name honestly: populations once lumped under Ninia atrata show bewildering variation in coloration, scale counts, and body proportions, particularly in the shape and hue of the nuchal collar that rings the neck. For generations, that variability masked a biological reality. What field guides treated as one widespread species was, in fact, a complex of several distinct evolutionary lineages, each with its own geography and morphology.

The taxonomic confusion in Ecuador ran deep. Until 2018, only two species of Ninia were recognized in the country: N. atrata west of the Andes and N. hudsoni east of them. Two historical names, Streptophorus sebae schmidti Jan, 1862 and Ninia spilogaster Peters, 1881, had been applied to Ecuadorian specimens but were long treated as synonyms. A previous study by Angarita-Sierra demonstrated that many Ecuadorian snakes labeled N. atrata actually belonged to N. teresitae, a species from the Chocó region of Colombia. Yet the puzzle remained unsolved for populations in the cloud forests and along the transition zone between the humid Chocó rainforests and the dry Tumbesian scrub.

To close that gap, the research team undertook a systematic review combining molecular and morphological evidence. They extracted genomic DNA from ethanol-preserved tissue samples of liver, muscle, or scales, amplified fragments of four genes, the mitochondrial 16S, CYTB, and ND4 genes and the nuclear RAG1 gene, and sequenced them in both directions. In total, 49 DNA sequences were used to build a phylogenetic tree of the genus, 37 of them generated during the study and 12 downloaded from GenBank. The fragments were aligned with MAFFT, concatenated into a single matrix with ten partitions, and analyzed under Bayesian inference in MrBayes, with four independent runs of more than 6.6 million generations each to guard against converging on a misleading result.

The molecular verdict was unambiguous. Ninia atrata emerged as paraphyletic with respect to all other included species, meaning the name as currently applied does not describe a single evolutionary unit. More striking still, a species of Ninia endemic to southwestern Ecuador was recovered as the strongly supported sister taxon of a previously unrecognized lineage confined to the cloud forests of the northwest. Following an integration-by-congruence approach, the team recognized species only where multiple independent lines of evidence intersect: mitochondrial monophyly, sequence divergence exceeding three percent in a 700-base-pair fragment of the CYTB gene, diagnosability based on coloration and lepidosis, distinct hemipenial morphology, and geographic and ecological congruence.

The new species, named Ninia guytudori in honor of naturalist and scientific illustrator Guy Tudor, carries the proposed standard English name Tudor’s Coffee-Snake. Its diagnosis rests on a precise combination of characters: dorsal scales arranged in 19 keeled rows at neck, midbody, and tail base; a single loreal scale 1.6 to 1.7 times longer than high; temporal scales in a 1+2 formula; 130 to 138 ventral scales in males; and 48 to 51 subcaudal scales in males. Externally, the snake is uniformly black above, but a white nuchal collar connects to a white upper lip band, forming what taxonomists call a bridle, while the throat, chin shields, and entire ventral surface of the body remain immaculate white. The holotype, an adult female collected in July 2017 on the road to Mindo in Pichincha province at 1,676 meters elevation, anchors the description.

The revalidated species tells a different story. The name Ninia schmidti comb. nov. is now restricted to the clade of snakes inhabiting the Chocoan–Tumbesian transition area of western Ecuador, a decision grounded in the type locality of the original name: Guayaquil, where no other member of the genus is known to occur. Because the original holotype was destroyed and the holotype of N. spilogaster could not be located, the team designated a neotype, an adult female specimen ZMH R10390 housed at the Zoologisches Museum Hamburg and collected at Guayaquil between 1901 and 1902. Schmidt’s Coffee-Snake, as it is now proposed to be called, shares the black dorsal coloration of its cloud-forest relative but lacks the white nuchal collar in adults, has supralabial scales partly or entirely black or dark gray, and shows ventral surfaces heavily obscured by dark brown pigment along the posterior edge of each scale.

Hemipenial anatomy provided some of the sharpest diagnostic tools. In N. schmidti, the everted and inflated organ is cylindrical, weakly bilobed, and semicalyculate, with a bifurcate sulcus spermaticus whose walls are strongly defined. The lateral and asulcate surfaces of the hemipenial body bear two to five rows of medium-sized hooked spines arranged in an inverted V pattern, dominated by one large basal hook larger than any other spine on the organ. N. teresitae, by contrast, possesses a pocket-shaped structure at the base of the hemipenial body that N. schmidti lacks, and N. guytudori differs from trans-Andean populations of N. atrata by having the sulcate surface of the hemipenial body ornamented with a large basal hooked spine. These intimate details of reproductive anatomy, invisible in life, prove decisive for separating species whose external appearance overlaps.

Ecologically, the three western Ecuadorian species partition the landscape with remarkable precision. N. teresitae remains a strictly Chocoan species. N. guytudori is endemic to an estimated 3,432 square kilometers of Pacific slope lower-montane forest between the Río Mira and Toachi valleys, recorded at elevations from 1,190 to 1,676 meters across 11 localities. N. schmidti occupies a far broader estimated range of 42,281 square kilometers along the transition zone, from 46 to 1,843 meters across eight localities. Environmental niche models built with Maxent using 19 bioclimatic variables from WorldClim confirmed these distributions, and the models themselves proved diagnostic for each clade. Crucially, the researchers found no sympatry between the sister species N. schmidti and N. guytudori, a pattern consistent with allopatric speciation driven by geographic separation.

Natural history observations add texture to the taxonomy. Tudor’s Coffee-Snake has been found active at night on leaf litter in old-growth cloud forest and hidden under rotten logs by day; when threatened, individuals flatten the body and tail. Schmidt’s Coffee-Snake prowls evergreen lowland forest and seasonally dry forests, and is reported to be common under leaf litter in humid soil and fallen trunks in Manabí province, particularly in cacao plantations. In captivity, one specimen consumed earthworms and leeches but rejected slugs and land flatworms, and laid a clutch of two eggs. Field observations suggest N. schmidti does not tolerate dry, open areas. Both species are proposed for the IUCN Near Threatened category: N. guytudori because roughly 53 percent of its forest cover remains, and N. schmidti because, despite a range exceeding the 20,000 square kilometer threshold for Vulnerable status, most of its habitat, around 80 percent, has been transformed into plantations and settlements, with only fragmented populations persisting, two of its eight known localities historical and five represented by single individuals.

The biogeographic implications extend beyond the snakes themselves. The distribution of N. schmidti mirrors that of other reptiles restricted to the transition between humid Chocó rainforests and Tumbesian dry forests, including the lizard Enyalioides touzeti and several snake species described in recent years. The researchers argue this shared pattern points to the existence of a unique biogeographical province in western Ecuador, one that deserves recognition in conservation planning. The work also leaves questions open: the paraphyly of N. atrata across its full trans-Andean range remains unresolved, the hemipenial morphology of N. guytudori has not yet been described in detail, and the relationship between Ecuadorian N. hudsoni and populations from the type locality in Guyana awaits study. The team hopes future systematic work on the N. atrata complex will include comprehensive molecular sampling across the Guianas and the Río Magdalena valley in Colombia, clarifying the evolutionary history of this charismatic group of colubrids.

Subject of Research: Taxonomic description of a new Ninia snake species from western Ecuador and revalidation of N. schmidti

Article Title: A new species of Ninia ( Serpentes , Colubridae ) from western Ecuador and revalidation of N. schmidti

Article References: Arteaga, A., & Harris, K. J. (2023). A new species of Ninia (Serpentes, Colubridae) from western Ecuador and revalidation of N. schmidti. Evolutionary Systematics, 7(2), 317-334. https://doi.org/10.3897/evolsyst.7.112476

Image Credits: AI Generated

DOI: 10.3897/evolsyst.7.112476

Keywords: Ninia, coffee snakes, Ecuador, cloud forests, taxonomy, herpetology, species discovery, Chocó, Tumbesian, revalidation, species, Serpentes