Sunday, September 28, 2014

New genera of homalopsid snakes

Until recently these two snakes were both in the genus Enhydris.
Both are adults, both have smooth scales and their internasals in
contact. Yet they have different ancestors within the family 
homalopsidae as suggested by their dramatically different body 
shapes. JCM
The colubroid snake family Homalopsidae also known as the Australasian rear-fanged water snakes contained 10 genera and 34 species of rear-fanged semi-aquatic and aquatic snakes in 1970 with the publication of Ko Ko Gyi’s monograph. In 2007 Murphy updated Gyi’s work and the family held the same 10 genera with 37 species plus two genera of uncertain status (Anoplohydrus, Brachyorrhos). Molecular studies published in the first decade of the 21st century demonstrated that while the Homalopsidae is monophyletic, the species-rich genus Enhydris is polyphyletic. Molecular analysis also found Brachyorrhos to be the most basal member of the clade, confirming an earlier hypothesis that it was a fangless homalopsid. Subsequently, two other fangless genera (Calamophis and Karnsophis) of homalopsids were discovered.

In a newly published paper Murphy and Voris (2014) revalidate the genera for the polyphyletic genus Enhydris: Homalophis Peters, Hypsiscopus Fitzinger, Miralia Reuss, Phytolopsis Gray, and Raclitia Gray. They also describe five new genera for species lacking available names: Gyiophis, Kualatahan, Mintonophis, Sumatranus, and Subsessor. The new arrangement for homalopsid names resolves the problem of the formerly polyphyletic genus Enhydris. See tree below.

Gyi (as well as Boulenger and Gunther) placed snakes in the genus Enhydris because they shared smooth dorsal scales and internasals that were in contact. These characters do not necessarily suggest ancestry and many other traits seen in these snakes in fact suggested they were not closely related. Consider the small headed, gracile Enhydris enhydris and the largest known homalopsid, Subsessor (formerly Enhydris) bocourti with a massive body and head (see photo). Placing these snakes in the same genus implies they share a close common ancestor, a hypothesis not supported by morphology or DNA.

With this checklist the family now contains 53 species in 28 genera. Molecular studies suggest homalopsids are old, perhaps separating from their most recent common ancestor with the Lamprophiidae 53 million years ago.

Red lines indicate species considered Enhydris by Gyi. Names at the end of the red lines are current genera.
Recent evidence suggests homalopsids show high levels of endemism and cryptic speciation so it is likely that many more species, and likely more genera will be discovered in the future.

CitationMurphy JC and Voris HK. 2014. A Checklist and key to the homalopsid snakes (Reptilia, Squamata, Serpentes), with the description of new genera. Fieldiana Life and Earth Sciences 8:1-43. doi:

A new high altitude pit viper from Sumatra

Top. Trimeresurus gunaleni. Below its habitat
Vogel et al. (2014) investigated morphological variation in 126 specimens from at least 67 populations of Trimeresurus sumatranus. They found two distinct taxa: Trimeresurus sumatranus (Raffles) and Trimeresurus gunaleni sp. nov. They selected a neotype for Trimeresurus sumatranus and restricted its type locality to the vicinity of Bengkulu, Bengkulu Province, Sumatra. The second taxon Trimeresurus gunaleni represents a distinct, previously unnamed species. The holotype of Trimeresurus gunaleni is from Mt. Sibayak, ca. 1,500–2,200 m ASL, west of Brastagi (Berastagi), Karo Regency (Kabupaten Karo), Sumatera Utara Province, Sumatra, Indonesia. The new species differs from Trimeresurus sumatranus by a lower number of ventrals in males (162–179 against 178–185) and females (164–171 vs. 175–191); a distinctly longer tail in males; the also differ in the color of the tail, the color of the eyes: (green in the new species, vs. dark grey in T. sumatranus), the color of the ventrals, which are green with a pale posterior suture in the new species and pale with dark posterior suture in T. sumatranus. The new species Trimeresurus gunaleni lives at higher elevations than T. sumatranus and seems to be endemic to the higher mountain ranges of western Sumatra and inhabits regions typically covered with tropical moist montane forests, from 1,500 m to as high as at least 2,000 m, perhaps as much as 2,200 m, where it has been observed by local insect collectors. There is no record of popu­lations lower than 1,500 m. On Mount Sibayak, Trimeresurus hageni occurs at elevation of 500 m, and Tropidolaemus wagleri at 200 m. Trimeresurus gunaleni is clearly isolated as a high mon­tane dweller. The female holotype of T. gunaleni was collected during the daytime in dense humid montane for­est scattered with tiny springs. The snake was resting on the ground under tree roots. In another instance, a male was seen perched at night on a tree branch about two meters above the ground. None of the specimens were found.


Vogle G, David P, Sidik I. (2014) On Trimeresurus sumatranus (Raffles, 1822), with the designation of a neotype and the description of a new species of pitviper from Sumatra (Squamata: Viperidae: Crotalinae). Amphibian & Reptile Conservation 8(2): 1–29.

Saturday, September 27, 2014

Gene duplication and the evolution of snake venom toxins

Gene duplication is a rare event in eukaryotic genomes and has been suggested as the major source of novel genetic material. Estimates of the rate of gene duplication in vertebrates vary from 1 gene per 100 to 1 gene per 1000 per million years and the most common fate for a duplicate gene is the loss of its function. However, in some cases a duplicate gene is retained in the population and undergoes either subfunctionalisation (where the two duplicates divide the sum of the ancestral role(s) between them) or neofunctionalisation (where one of the duplicates assumes a new role, independent of the ancestral function). This latter process of evolving an entirely new function is known to be incredibly rare and there are few conclusive examples of it in the literature.

The venom of advanced snakes has been hypothesized to have originated and diversified via gene duplication. Specifically, it has been suggested that both the origin of venom and the later evolution of novelty in venom has occurred as a result of the duplication of a gene encoding a non-venom physiological or “body” protein that is subsequently recruited, via gene regulatory changes, into the venom gland, where natural selection can act on randomly occurring mutations to develop and/or increase toxicity. In short, it has been proposed that snake venom diversifies via repeated gene duplication and neofunctionalisation, a somewhat surprising finding given the apparent rarity of both of these events.

Therefore, the hypothesis concerning the evolution of snake venom is very unlikely and should be regarded with caution, it is nonetheless often assumed to be established fact, hindering research into the true origins of snake venom toxins. To critically evaluate this hypothesis Hargreaves et al. (2014) generated transcriptomic data for body tissues and salivary and venom glands from five species of venomous and non-venomous reptiles. The comparative transcriptomic analysis of these data reveals that snake venom does not evolve via the hypothesized process of duplication and recruitment of genes encoding body proteins. Instead the results show that many proposed venom toxins are in fact expressed in a wide variety of body tissues, including the salivary gland of non-venomous reptiles and that these genes have therefore been restricted to the venom gland following duplication, not recruited. Thus snake, venom evolves via the duplication and subfunctionalisation of genes encoding existing salivary proteins. These results highlight the danger of the elegant and intuitive “just-so story” in evolutionary biology

Hargreaves AD, Swain MT, Hegarty MJ, Logan DW,  Mulley JF. 2014.  Restriction and recruitment – gene duplication and the origin and evolution of snake venom toxins. Genome Biology and Evolution Advance Access10.1093/gbe/evu166.

Thursday, September 25, 2014

A new burrow-using, fanged frog from Sarawak

Limnonectes cintalubang, new species (KUHE 47859)
Borneo is famous for its diverse endemic amphibians and the diversity can be expected to increase with the discovery of cryptic taxa. Frogs of the Limmnoectes kuhlii complex have enlarged head with fang-like processes on lower jaw in males, thus they are commonly called fanged frogs. Usually they have a brown dorsum covered by tubercles in variying degrees, and inhabit mountain streams at various altitudes. Limnonectes kuhlii was once considered a wide-ranging species, but is now regarded as a complex of many distinct species that are phylogenetically remote from Javanese L. kuhlii (Tschudi, 1838). Several continental populations have been described as distinct species, studies of Bornean populations have been lacking. Matsui et al. (2014) report finding a new species of this clade during a  recent amphibian survey in Serian, southwestern Sarawak. The frog has a unique coloration, escape behavior, and an unusual natural history.

The new species, Limnonectes cintalubang is subterranean and all specimens were found at night near burrows on the forest floor. When disturbed they immediately disappeared down the burrow. However, they do not seem to dig the hole by themselves, instead they use burrows constructed by other animals. What species dig the burrows used by this frog is unknown.  The skin of the species is exceptionally fragile and tears easily when captured. The eggs of L. cintalubang are creamy white unlike other congeners. Among Bornean frogs creamy white eggs without dark animal hemisphere are known in several  genera and all of them breed in deep shaded microhabitats such as small underground streams, in mud, and under leaf litter on the bottom of deep pools. The authors hypothesize that, L. cintalubang lays its eggs shaded localities, possible in water in the burrows.

Limnonectes cintalubang was found in loose slopes of secondary forests with mixed bamboo and broad-leaf trees, always on the ground. The surface of the ground is flat and sparsely covered by dead leaves, but with plant roots and stones densely packing the shallow layers under the soil surface. Frogs were active after 1930 h and each stayed near a burrow up to ca. 5–10 cm in diameter with a long tunnel at a depth of 50–60 cm, it was impossible to dig out the frog. Although only one of about 20 burrows observed had underground water, there was no pool at the immediate vicinity of the holes. The nearest water body was a stream ca. 8–12 m apart from the area. Males did not call in March, July, or December at the type locality. However, females collected in early July possessed large ovarian eggs, the breeding season is thought to include summer seasons. Other species found in association with the present new species in the forest were: Leptolalax gracilis (Günther, 1872), Leptolalax sp., Meristogenys jerboa (Günther, 1872), Nyctixalus pictus (Peters, 1871), and Polypedates leucomystax (Gravenhorst, 1829).

Matsui, M., Nishikawa, K., & Eto, K. (2014). A new burrow-utilising fanged frog from Sarawak, East Malaysia (Anura: Dicroglossidae). RAFFLES BULLETIN OF ZOOLOGY, 62, 679-687.

A phylogeny of snake combat and mating behaviors

A small study suggests snakes may have developed courtship and male-to-male combat behavior, such as moving undulations, neck biting, and spur-poking, over time, according to a study published September 24, 2014 in the open-access journal PLOS ONE by Phil Senter from Fayetteville State University and colleagues.

Behaviors involved in courtship and male-to-male combat have been recorded in over 70 snake species from five families in the clade Boidae and Colubroidea, but before now, scientists had yet to look for evolutionary relationships between these behaviors.

The authors of this study analyzed 33 courtship and male-to-male combat behaviors in the scientific literature by plotting them to a phylogenetic tree to identify patterns. The authors identified the patterns in behaviors, which was not always possible, and then used the fossil record to match the behaviors to the snakes' evolution.

Researchers found that male-to-male combat of common ancestors of Boidae and Colubridae in the Late Cretaceous likely involved combatants raising the head and neck, attempting to topple each other. Poking with spurs may have been added in the Boidae clade. In the Lampropeltini clade, the toppling behavior was replaced by coiling without neck-raising, and body-bridging was added. Snake courtship likely involved rubbing with spurs in Boidae.

In Colubroidea, courtship ancestrally involved chin-rubbing and head- or body-jerking. Various colubroid clades subsequently added other behaviors, like moving undulations in Natricinae and Lampropeltini, coital neck biting in the Eurasian ratsnake clade, and tail quivering in Pantherophis. Although many gaps in the evolution of courtship and combat in snakes remain, this study provides a first step in reconstructing the evolution of these behaviors in snakes.

Figure 3 from the paper with rattlesnake combat photos added. Scenario for the evolution of male-male combat behavior in snakes, based on data presented in Figure 1 in the paper. On the far right photos of Crotalus atrox in combat. Photo credit: Roger Repp.

Senter P, Harris SM, Danielle Kent DL. Phylogeny of Courtship and Male-Male Combat Behavior in Snakes. PLoS ONE, 2014; 9 (9): e107528 DOI: 10.1371/journal.pone.0107528

Wednesday, September 24, 2014

Cosumnes River Preserve restoration to protect Thamnophis gigas

The restored marsh and Thamnophis gigas. Photo credit CDFW
The California Department of Fish and Wildlife (CDFW) has completed an emergency restoration project at the Cosumnes River Preserve to help save a state and federal threatened species, the giant garter snake (Thamnophis gigas).

Snake Marsh at the Cosumnes River Preserve is home to a genetically unique population of giant garter snakes. With two consecutive years of drought, there was a significant chance of the marsh ponds drying up, potentially causing severe impacts to the snakes.

“The project consisted of well water being pumped into the marsh and the ponds where the snakes live. It was planned and carried-out on CDFW land that is part of the Preserve,” said CDFW Environmental Scientist Eric Kleinfelter. “We had very dedicated contractors and department staff who completed this project in just one month. The Nature Conservancy also played an important role by funding a hydrologic study that showed just how vulnerable to drought this aquatic system is. It was truly a collaborative effort.”

Endemic to California’s Central Valley, the non-venomous giant garter snake is olive to black in color with light yellowish stripes on each side and can grow from three to five feet long. Secretive and difficult to find, this aquatic snake will quickly drop into the water from its basking site before the observer can get close. When threatened, it will excrete a foul-smelling musk. It feeds primarily on fish, frogs and tadpoles and can live up to 12 years.

Located approximately 25 miles south of Sacramento near Galt, the Cosumnes River Preserve consists of approximately 48,000 acres of wildlife habitat and agricultural lands. The Preserve is buffered by a variety of agricultural operations and provides numerous social, economic and recreational benefits to local communities residing in the larger Sacramento and San Joaquin areas. The habitat supports many species of native wildlife, including greater and lesser Sandhill cranes, Swainson’s hawks and waterfowl that migrate throughout the Pacific Flyway.

Saturday, September 20, 2014

Side-blotch lizard thermoregulation & climate change

Top: A side-blotch lizard. Photo Credit M. Goller. Below 
Thermograms of temperature microhabitats in the overall 
landscape (A–B) and analysis of lizard and environmental
 temperature (C–D). Measurement of lizard average temperature
 (line) and perch temperature (outline) is seen in (C). (D) 
Determination of maximum lizard temperature (box) and 
environmental maximum and minimum from the entire visible 
substrate available to the lizard. Only the rock surface (arrows 
indicate rock outline) was included in environmental analyses.
Ectotherms are well known for using behavioral  thermoregulation  to optimize physiological processes. Thermoregulation is a complex problem because different physiological processes and behaviors achieve performance optima at different temperatures. Lizards usually  thermoregulate by choosing when to be active throughout the day and by shuttling between microhabitats of differing temperatures. Ectotherms usually follow a daily cycle of thermal microhabitat preference. Thus the potential for behavioral thermoregulation is limited by the available thermal niches, and the number of microhabitats available for regulating body temperatures.

In a recently published paper Goller et al. (2014) examined the impact of  habitat structural complexity on thermal microhabitats for thermoregulation using the side-blotch lizard, Uta stansburiana. Thermal microhabitat structure, lizard temperature, and substrate preference were simultaneously evaluated using thermal imaging.  Lizard thermal preference data were collected by measuring environmental and lizard temperatures simultaneously with an infrared camera.  The authors approached a lizard and either filmed at 10 frames/sec or photographed at 0.1 frames/sec for varying lengths of time (minimum of 10–25 min, up to several hours). The environment around the lizard was included in each frame, so that available thermal niches could be assessed.

They found a broad range of microhabitat temperatures was available (mean range of 11°C within 1–2 square meters) while mean lizard temperature was between 36°C and 38°C. Lizards selected sites that differed significantly from the mean environmental temperature, indicating behavioral thermoregulation, and they maintained a temperature significantly above that of their perch (mean difference of 2.6°C). Uta's thermoregulatory potential within a complex thermal microhabitat structure suggests that a warming trend may prove advantageous, rather than detrimental for this population.

A result of climate change will be greater variation and an increase in temperature across the range of Uta stansburiana. Although an increase in several degrees will probably provide a more optimal thermal environment for temperate species, it will also increase the chance of overheating, and rising temperatures may render habitats with less thermal heterogeneity unsuitable for Uta. An increase in temperature may not be detrimental to the study population. Higher thermal microhabitat diversity is important as it may allow behavioral thermoregulation to a preferred temperature in varying temperature conditions. Ability to thermoregulate by moving into shaded microhabitats can be an important buffer of climate change and complex habitats provide shade more reliably.

Goller M, Goller F,  French SS. 2014. A heterogeneous thermal environment enables remarkable behavioral thermoregulation in Uta stansburiana.  Ecology and Evolution 2014; 4(17): 3319–3329.

Wednesday, September 10, 2014

Varanus olivaceus picks fruit from trees

Varanus olivaceus feeding in a Microcos tree – Polillo,
 May 2005. From video by Simon Normanton/ Steel Spyda.
Daniel Bennett (2014) used camera traps and direct observation to investigate the foraging behavior of the butaan, . This lizard is an obligatory frugivorous monitor lizard restricted to Luzon, Polillo and Catenduanes islands in the northern Philippines. Its diet consists almost entirely of fruit and snails. Auffenberg studied this species and stated it feeds exclusively on fallen fruit from the forest floor and rarely, if ever, took fruit from trees. However, a ten year study of the species on Polillo Island in Quezon Province found no evidence to support this assertion that the lizards typically forage on fallen fruit. Bennett gather evidence indicating that the butaan normally climbs fruiting trees of all species and picked the fruit directly from branches or syncarps. The study was carried in and around the Sibulan Watershed Reserve, Polillo Island Quezon Province in primary and secondary lowland dipterocarp forest.
Bennett found the lizards spend as little time on the ground as possible. However they never overnight in fruiting trees and suggests this is probably because the trees provide neither suitable hollows nor dense thickets in which to shelter. The lizards spent as little time as possible in fruiting trees before returning to larger trees that provide greater protection from predators, and that they appear to approach fruiting trees directly without searching for fallen fruit below the canopy makes it unlikely that they would preferentially take fruit from the ground. However, snails are probably found and consumed on the forest floor rather than in trees.


Bennett, D. (2014) The Arboreal Foraging Behavior of the Frugivorous Monitor Lizard Varanus olivaceus on Polillo Island. Biwak, 8(1), 15-18.

Nidovirus in Ball Pythons

Researchers have identified a novel virus that could be the source of a severe, sometimes fatal respiratory disease that has been observed in captive ball pythons since the 1990s. The work is published this week in mBio®, the online open-access journal of the American Society for Microbiology.

Investigators observed the virus, which they named ball python nidovirus, in eight snakes with pneumonia; virus levels were highest in the animals' lungs and other respiratory tract tissues. The team also sequenced the genome of the virus, finding it to be the largest of any RNA virus yet described.

Ball pythons have become one of the most popular types of reptiles sold and kept as pets, the authors said, because of their relatively modest size, docile behavior and ease of care. Respiratory disease has been noted in these animals since the 1990s but until now a potential cause has not been identified, said senior study author Joseph L. DeRisi, PhD, chair of the Department of Biochemistry and Biophysics at the University of California, San Francisco, in part because of the limitations of available technology.

"This is really exciting because up to this point there have been no known viruses of this type in reptiles," DeRisi said. "Some of the most feared diseases we know of, like Ebola virus, HIV, Middle East Respiratory Syndrome (MERS) and Severe Acute Respiratory Syndrome (SARS), did not arise from people but have been transferred originally from animals. Our work suggests there may be very large reservoirs of genetic diversity of viral families that can cause human disease in under studied organisms, like reptiles. We would do well to look broadly across all species."

DeRisi and colleagues at seven other institutions across the country studied tissue samples from ball pythons with symptoms of respiratory disease from seven collections in Florida, Oklahoma, Pennsylvania, Texas and Wisconsin. Autopsies on the animals found lesions in the animals' upper and lower respiratory tracts, and additional lesions in other areas of the body. Using an electron microscope, investigators observed virus-like particles in the cells lining the lungs of two snakes.

To identify a cause of disease, the scientists used a technique called shotgun metagenomics to sequence RNA of eight of the snakes, finding a novel nidovirus in all of them, but not in a search of tissues from 57 other snakes not affected by pneumonia, collected for other studies. Additional work found that the virus was most prevalent in the sick animals' respiratory tract tissue, and that the nidovirus is most similar to a subset of the nidoviruses called toroviruses, which infect mammals and ray-finned fish.

"The identification of a novel nidovirus in reptiles contributes to our understanding of the biology and evolution of related viruses, and its association with lung disease in pythons is a promising step toward elucidating an etiology for this long-standing veterinary disease," DeRisi said. "Our report will enable diagnostics that will assist in determining the role of this virus in the causation of disease, which would allow control of the disease in zoos and private collections."

Yet to be determined, said study coauthor Mark Stenglein, PhD, is how the virus is spread, whether ball pythons are the primary natural host for the virus, and how widespread the virus is in the wild. In a previous study published in mBio in August 2012, DeRisi, Stenglein and colleagues discovered the first reptile arenavirus. The team is continuing work identifying reptilian viruses. "I think it's the tip of the iceberg," DeRisi said. Indeed, within the same month, two additional groups reported identification of a nearly identical virus, in a total of five additional pythons, all with lung disease.


Mark D. Stenglein et al. Ball Python Nidovirus: a Candidate Etiologic Agent for Severe Respiratory Disease in Python regius. mBio, September 2014 DOI: 10.1128/mBio.01484-14

Wednesday, September 3, 2014

Could ecdysis in wild reptiles be influenced by environmental conditions?

Anecdotal reports that ecdysis in the Southeast Asian tropical viper Calloselasma rhodostoma occurs when humidity is high. Humidity may be important during ecdysis to prevent dehydration, a risk of the increased activity required for shedding and potentially increased rates of cutaneous water loss. However, little is known about the role of humidity in ecdysis cycles in natural populations of reptiles. We here report an aggregation of Eastern Ratsnakes (Pantherophis alleghaniensis, formerly Elaphe obsoleta) that exhibited synchronized ecdysis, apparently linked to humidity. The thermal ecology of P. alleghaniensis has been relatively well described, but there seems no existing information on the role of humidity in behavior, nor of synchronized ecdysis in wild populations. Bradley Carlson and colleagues made observations at Penn State University’s Russell E. Larson Agricultural Research Center at Rock Springs, Centre Co., Pennsylvania, suggesting humidity stimulates ecdysis in the Eastern Ratsnake. On May 13, the authors first noticed P. alleghaniensis in the rafters of an old barn located on the edge of the forest. Over the next 11 days, P. alleghaniensis were observed in the barn on most days, appearing to be absent only during particularly hot or cool weather. As many as six P. alleghaniensis were observed at one time. They were usually motionless, coiled up, or stretched along a beam. Many of the snakes, exhibited cloudy, bluish eyes and/or dull body coloration, indicative of the onset of ecdysis. On 29 May, shed skins (but no snakes) were found in the barn, and no recent skins had been found before this date. The authors collected the skins determined they were from at least four individuals based on the number of heads represented and the total length of the skins. No other snake species besides P. alleghaniensis occur at this location consistent with the size and scalation on the shed skins. An examination of weather records from the nearest weather station indicated that this large number of shed skins appeared after a day characterized by a high peak in humidity and a significant rain event during the observation period. This was preceded about one week earlier by elevated humidity and rainfall as well. This strengthens previous suggestions of synchronized shedding in wild snakes. Furthermore, it suggests that these ratsnakes took refuge at the same (and potentially environmentally favorable) site for ecdysis until some environmental factor may have triggered ecdysis. The most probable cause appears to be favorable levels of humidity coupled with rainfall, which may have been potentiated by an earlier period (19–23 May) of elevated humidity and rain. The authors could not rule out other environmental factors or that shedding occurred at certain period after the snakes emerged from a hibernacula or in preparation for egg laying.

Carlson, B. E., Williams, J., & Langshaw, J. 2014. Is synchronized ecdysis in wild ratsnakes (Pantherophis alleghaniensis) linked to humidity? Herpetology Notes, SEH 7: 471-473