Thursday, December 25, 2014

Draco's bright coloration mimics falling leaves

Draco cornutus. Photo
credit Devi Stuart-Fox
By mimicking the red and green colors of falling leaves, Bornean lizards avoid falling prey to birds whilst gliding, new research has found. The work suggests that populations of the gliding lizard, Draco cornutus, have evolved extendable gliding membranes, like wings, which closely match the colors of falling leaves to disguise themselves as they glide between trees in the rainforest.

Found throughout South-East Asia, Draco is the only living genus of lizard with extendable gliding membranes -- call patagia -- which allow them to glide between trees in their territories.

Published Dec. 24 in the international journal Biology Letters, the study was conducted by PhD student Ms Danielle Klomp, based at both the University of Melbourne and the University of New South Wales with supervisors Dr Terry Ord and Dr Devi Stuart-Fox and collaborator Dr Indraneil Das from the University of Malaysia.

The team travelled to Borneo and observed two populations of a gliding lizard that have different colored gliding membranes and occupy very different habitats.

One population has red gliding membranes, which match the color of the red falling leaves of their coastal mangrove forest habitat. The other population has dark brown and green gliding membranes, which match the colors of falling leaves in their lowland rainforest habitat.

They determined how the colors would be perceived by a predatory bird and found that the gliding membrane color would be indistinguishable from a falling leaf in the same forest.

Birds can see ultraviolet light as well as the colors that humans see, so it is important to take into account how closely the colors would actually match to a bird, Ms Klomp said.

"It's a cool finding because these gliding lizards are matching the colors of falling leaves and not the leaves that are still attached to the tree. In the mangrove population the leaves on the trees are bright green, but turn red shortly before falling to the ground, and it is this red color that the lizards mimic in their gliding membranes. This allows them to mimic a moving part of the environment- falling leaves -- when they are gliding." Ms Klomp said.

Because some animals have developed color not only for camouflage, but also as a form of communication, we also wanted to watch the lizards interact in the wild and determine whether their gliding membranes were used for communication as well as gliding said Ms Klomp.
The team filmed hours of gliding lizard behavior to observe how often the colors were displayed to other lizards.

"We found that both the red and green/brown gliding membranes seem to have evolved to specifically resemble the falling leaves in each population's particular habitat, and are rarely used for communication," Ms Klomp said.

"Perhaps these populations may have originally had the same gliding membrane colors but as they have moved into different forest types their colors have adapted to closely resemble the colors of falling leaves in the different forests, known as divergent evolution."

Klomp DA, Stuart-Fox D, Das I, Ord TJ. 2014.  Marked colour divergence in the gliding membranes of a tropical lizard mirrors population differences in the colour of falling leaves. Biology Letters, 10 (12): 20140776 DOI:10.1098/rsbl.2014.0776

Thursday, December 11, 2014

Why does the pelagic sea snake dive?

Note: It is the end of the year and this blog is going to be in hibernation for a short time. So this post may be the last for several weeks. But it will be active again in the near future.

Species that forage exclusively at the sea’s surface but spend much of the rest of their time submerged could offer a rare opportunity to shed light on the evolution of diving behavior that is independent from foraging. The viviparous Yellow-bellied Sea Snake, Hydrophis (formerly Pelamis) platurus (Hydrophiinae), also known as the Pelagic Sea Snake, provides this opportunity.

In a recent paper in Animal Behaviour, Cook and Brischoux (2014) note the Pelagic Sea Snake drifts passively with surface and subsurface currents, spending its entire life cycle at sea. The result is a wide distribution covering the entire tropical Indo-Pacific basin, one of the largest distributions of any squamate reptile. Another remarkable feature of the Pelagic Sea Snake’s unusual life history, is it spends most of its day-to-day life floating in the water column 20 to 50 m deep. Submergence time is interrupted by surfacing, which can be brief to breathe or longer to forage. The foraging strategy of the Pelagic Sea Snake is remarkable for a marine tetrapod, it ambushes larval fish that are concentrated under debris on oceanic labile features such as slicks or drift lines, doing ‘float-and-wait’ foraging at the oceanic surface.  

Hydrophis platurus is the only marine tetrapod foraging specifically at the ocean surface, but spending a considerable proportion of its time budget submerged. An activity pattern offering a unique opportunity to study diving independently from foraging.

The authors found the Pelagic Sea Snake spends 95% of its time underwater, where it can dive to 50 m and stay for 3.5 hours without breathing. Dives are S-shaped, with a long phase of gradual ascent during which the snake is neutrally buoyant. Snake lungs deflate slowly during this phase at a rate that increases with water temperature, and thus metabolism. Dive duration is linked to inferred lung volume at the start of the dive, suggesting aerobic diving.

The pelagic sea snakes dive for multiple reasons, but the primary reason seems to be to avoid sea surface turbulence. Underwater, they can reduce metabolism by targeting cooler water layers. And by hovering in the water column, they reduce energy expenditure and escape both surface and bottom predators. At the same time they can more easily locating their own prey from underneath.

A detailed analysis of the diving behavior of H. platurus shows how this exclusively marine species of tetrapod manages its dive cycle and the influence environmental parameters have upon its diving and surfacing behaviors. This has opened the door to a better understanding of the adaptations developed by this species.

Interestingly, there is an important parallel in behavior between H. platurus and several species of marine turtles. Adaptations in both these lineages of reptiles reflect a response to pressures of the marine environment experienced during the evolutionary transition from terrestrial to oceanic life. Unfortunately, the behavior of sea snakes at sea is still inadequately known compared to that of marine turtles despite being a highly diversified group comprising four families and ca. 90 species.

The authors suggest the study of sea snakes can help interpret diving behavior in other lineages of marine reptiles.

Cook TR & Brischoux F (2014). Why does the only ‘planktonic tetrapod’dive? Determinants of diving behaviour in a marine ectotherm. Animal Behaviour, 98, 113-123.

Climate change & the ectotherm

Animals that regulate their body temperature through the external environment may be resilient to some climate change but not keep pace with rapid change, leading to potentially disastrous outcomes for biodiversity.

A study by the University of Sydney and University of Queensland showed many animals can modify the function of their cells and organs to compensate for changes in the climate and have done so in the past, but the researchers warn that the current rate of climate change will outpace animals' capacity for compensation (or acclimation).

The research has just been published in Nature Climate Change (Letters), written by Professor Frank Seebacher School of Biological Sciences and Professor Craig Franklin and Associate Professor Craig White from the University of Queensland.

Adapting to climate change will not just require animals to cope with higher temperatures. The predicted increase to fluctuations in temperature as well as to overall temperature would require animals to function across a broader range of conditions. This is particularly important for ectotherms, animals that rely on external sources of heat to control body temperature, and are therefore more influenced by environmental temperatures.

The research showed that many groups of ectotherms, which make up more than 90 percent of all animals, are able to change their physiological function to cope with an altered environment, but the rapid pace and fluctuations of human-induced climate change present serious challenges.

The researchers studied 40 years of published data to assess how biological functions change in response to a sudden fluctuations in environmental temperatures. They found that the physiological rates of ectothermic animals, such as heart rate, metabolism and locomotion, had already increased over the past 20 years with increasing average temperatures.

"It is important that animals maintain the right balance between the large number of physiological functions despite environmental fluctuations. An increase in temperature that leads to changed reaction rates can upset that balance and cause the decline of individuals and species," said Professor Seebacher. "For example, movement requires energy and oxygen to be delivered to muscles. However, if metabolism or the cardiovascular system can't cope with increased temperatures, animals can no longer move to forage, migrate or interact with each other.

"The overall trend in the last 20 years has been to increased physiological rates, and we predict that this would continue to increase with increasing temperature. "Even if animals are able to maintain the balance of their physiological functions in a warmer climate, increased metabolism leads to increases in the food resources needed and could upset the balance in ecosystems, particularly if predator and prey populations respond very differently to the environmental temperature change."


Seebacher F, White CR, Franklin CE. Physiological plasticity increases resilience of ectothermic animals to climate change. Nature Climate Change, 2014; DOI: 10.1038/nclimate2457

Tuesday, December 9, 2014

The Reptile Database updated

Some new lizard species described in 2014
The Reptile Database (RDB) is a very useful tool for herpetologists, and they released a new version a few days ago. The new version lists 10,119 species (including 139 described this year), up from 10,038 in August, 35,615 references (including 1,203 published this year), up from 34,104 in August, which resulted in almost 200 new and changed names.

The site also is importing references for all of the papers published in Herpetology Notes and BioGecko, and they have about a 1000 papers from Sauria now crossed reference and they can be individually ordered from the RBD.

The RDB Newsletter also noted some selected taxonomic news:

Homalopsidae: Murphy and Voris (2014) suggested a number of new genera and revalidated a few more, leading to 28 genera for just 53 species.

Boidae: Pyron et al. 2014 suggested to split the monophyletic boas into multiple families; we did not follow this suggestion following a discussion with the Scientific Advisory Board (see below). However, the new suggested families (such as “Sanziniidae) can be found in the database.

More species and genera split, including Lampropeltis, Blanus, Crotalus triseriatus, Hemidactylus fasciatus, and Pelomedusa subrufa. Guo et al. (2014) split the fairly large genus Amphiesma (43 species) into 3 genera. Only Amphiesma stolatum remains in the genus.

The RDB recently constituted a Scientific Advisory Board (SAB) to make general strategic decisions as well a decisions on controversial taxonomic issues. One of the first recommendations of the SAB was not to adopt the suggested Boid taxonomy suggested by Pyron et al. (2014, see above). We continue to consult individual experts in more special cases, e.g. on individual species or genera. There is a consensus that all published taxonomic changes should be in the Reptile Database but when it comes to valid names they can only show one “accepted” name for any given species even if several are in use. Instead of flip-flopping between names with each new publication, the result will be a bit more conservative but also more stable. The members of the SAB are listed on a new page at

Some new snake species described in 2014
In order to manage data curation and data import better, we have started to recruit editors for special tasks. 

Paul Freed and Sven Mecke are our first volunteer photo editors. They will receive the photos sent to the RDB, edit them, verify correct identifications with experts, find photos of species not pictured etc. This will also allow us to process photos faster. Thed RBD is looking for a photo editor taking care of turtles.

Similar to the photo editors, RBD is looking for volunteers willing to help with the curation of papers. Initially we will start with editors for turtles, crocodiles, and squamate families (or genera if they have a substantial number of species). The taxonomic editors will receive papers from which they are supposed to extract information that is relevant for the database such as taxonomic or nomenclatural changes, new distribution records, or databasable life history data.

The RBD is asking instructors teaching herpetology or taxonomy to help improve data curation by using it in their classes. Students could curate papers, edit Wikipedia pages link to the Reptile Database, ID species, or find and analyze other information. There is always a large backlog of papers that need to be curated, including simple cases with new distribution data or more complicated ones. Please get in touch if you are interested. They have designed a few exercised and assignment for classroom use:
RDB has a large number of new photos (>1,500). However, these are added to the database independently of text, and thus have not been updated yet. This will probably take another few weeks or so, just in case you do not see the photos that you have submitted. In any case, more photos are always welcome! Please send photos (with location or coordinates) to

The RDB often use Google Maps to verify the localities reported in papers. However, Google Maps shows different maps in different countries. For instance, Google Maps in India shows Arunachal Pradesh as part of India. However, Google Maps in China shows Arunachal Pradesh as part of China. The RDB will replace current approximate maps with “real" distribution maps sooner or later, such details are important when you search the Reptile Database for geographic areas (or if you need a list of all Indian or Chinese reptiles). Right now, they treat Arunachal Pradesh as part of India. Finally, there are different names in different Google Maps versions. For instance, in the international version you can see the “Persian Gulf”. However, in Arabian countries it is called the “Arabian Gulf”. There are a number of other contentious borders or names, so please keep this in mind when you search the database.

In the course of history new countries form, such as the new countries that used to be Yugoslavia or North and South Sudan (which used to be Sudan). However, there are also new states, such as the new state of Telangana in India, and the Indian government apparently discusses the creation of another 21 new states (the current states are fairly new too, many formed in 1956). Obviously, this can cause headaches in trying to keep tabs on reptiles in those states, especially when they are species-rich such as those in India. Please let RDB know if you see discrepancies or errors.

A new web service and database, offers a scientific literature search engine that empowers you to find relevant research based on location and biophysical attributes combined with traditional keyword searches. Give it a try.

The RDB does not have funding. If you plan to submit a grant related to reptile taxonomy or with databasable information, they are asking members to consider including the Reptile Database as a subcontractor or collaborator. Or budget personnel to curate data for the RDB.

Since it is gifting season, the RDB is accepting donations now. Available money is used to buy literature, travel to libraries, or pay students to enter, scan, or process data. You can donate at this link:

Monday, December 8, 2014

A new model for the evolution of snake venom

Technology that can map out the genes at work in a snake or lizard's mouth has, in many cases, changed the way scientists define an animal as venomous. If oral glands show expression of some of the 20 gene families associated with "venom toxins," that species gets the venomous label.
But, a new study from The University of Texas at Arlington challenges that practice, while also developing a new model for how snake venoms came to be. The work, which is being published in the journal Molecular Biology and Evolution, is based on a painstaking analysis comparing groups of related genes or "gene families" in tissue from different parts of the Burmese python, or Python molurus bivittatus.
A team led by assistant professor of biology Todd Castoe and including researchers from Colorado and the United Kingdom found similar levels of these so-called toxic gene families in python oral glands and in tissue from the python brain, liver, stomach and several other organs. Scientists say those findings demonstrate much about the functions of venom genes before they evolved into venoms. It also shows that just the expression of genes related to venom toxins in oral glands of snakes and lizards isn't enough information to close the book on whether something is venomous.
"Research on venom is widespread because of its obvious importance to treating and understanding snakebite, as well as the potential of venoms to be used as drugs, but, up until now, everything was focused in the venom gland, where venom is produced before it is injected," Castoe said. "There was no examination of what's happening in other parts of the snake's body. This is the first study to have used the genome to look at the rest of that picture."
Learning more about venom evolution could help scientists develop better anti-venoms and contribute to knowledge about gene evolution in humans
Castoe said that with an uptick in genetic analysis capabilities, scientists are finding more evidence for a long-held theory. That theory says highly toxic venom proteins were evolutionarily "born" from non-toxic genes, which have other ordinary jobs around the body, such as regulation of cellular functions or digestion of food.
"These results demonstrate that genes or transcripts which were previously interpreted as 'toxin genes' are instead most likely housekeeping genes, involved in the more mundane maintenance of normal metabolism of many tissues," said Stephen Mackessy, a co-author on the study and biology professor at the University of Northern Colorado. "Our results also suggest that instead of a single ancient origin, venom and venom-delivery systems most likely evolved independently in several distinct lineages of reptiles."
Castoe was lead author on a 2013 study that mapped the genome of the Burmese python. Pythons are not considered venomous even though they have some of the same genes that have evolved into very toxic venoms in other species. The difference is, in highly venomous snakes, such as rattlesnakes or cobras, the venom gene families have expanded to make many copies of those shared genes, and some of these copies have evolved into genes that produce highly toxic venom proteins.
"The non-venomous python diverged from the snake evolutionary tree prior to this massive expansion and re-working of venom gene families. Therefore, the python represents a window into what a snake looked like before venom evolved," Castoe said. "Studying it helps to paint a picture of how these gene families present in many vertebrates, including humans, evolved into deadly toxin encoding genes."
Jacobo Reyes-Velasco, a graduate student from Castoe's lab, is lead author on the new paper. In addition to Castoe and Mackessy, other co-authors are: Daren Card, Audra Andrew, Kyle Shaney, Richard Adams and Drew Schield, all from the UT Arlington Department of Biology; and Nicholas Casewell, of the Liverpool School of Tropical Medicine.
The paper is titled "Expression of Venom Gene Homologs in Diverse Python Tissues Suggests a New Model for the Evolution of Snake Venom." The abstract is available online at:
The research team looked at 24 gene families that are shared by pythons, cobras, rattlesnakes and Gila monsters, and associated with venom. The traditional view of venom evolution has been that a core venom system developed at one point in the evolution of snakes and lizards, referred to as the Toxicofera, and that the evolution of highly venomous snakes, known as caenophidian snakes, came afterward. But little explanation has been given for why evolution picked just 24 genes to make into highly toxic venom-encoding genes, from the 25,000 or so possible.
"We believe that this work will provide an important baseline for future studies by venom researchers to better understand the processes that resulted in the mixture of toxic molecules that we observe in venom, and to define which molecules are of greatest importance for killing prey and causing pathology in human snakebite victims," Casewell said.
When they looked at the python, the team found several common characteristics among the venom-related gene families that differed from other genes. Compared with other python gene families, venom gene families are "expressed at lower levels overall, expressed at moderate-high levels in fewer tissues and show among the highest variation in expression level across tissues," Castoe said.
"Evolution seems to have chosen what genes to evolve into venoms based on where they were expressed (or turned on), and at what levels they were expressed," Castoe said.
Based on their data, the new paper presents a model with three steps for venom evolution. First, these potentially venomous genes end up in the oral gland by default, because they are expressed in low but consistent ways throughout the body. Then, because of natural selection on this expression in the oral gland being beneficial, tissues in the mouth begin expressing those genes in higher levels than in other parts of the body. Finally, as the venom evolves to become more toxic, the expression of those genes in other organs is decreased to limit potentially harmful effects of secreting such toxins in other body tissues.
The team calls its new model the Stepwise Intermediate Nearly Neutral Evolutionary Recruitment, or SINNER, model. They say differing venom levels in snakes and other animals could be traced to the variability of where different species, or different genes within a species, are along the continuum between the beginning and end of the SINNER model.
Castoe said the next step in the research would be to examine the genome of highly venomous snakes to see if the SINNER model bears out. For now, he and the rest of the team hope that their findings about the presence of venom-related genes in other parts of the python change some thinking on what species are labeled as venomous.
"What is a venom and what species are venomous will take a lot more evidence to convince people now," Castoe said. "It provides a brand new perspective on what we should think of when we look at those oral glands."

Reyes-Velasco J, Card DC, Andrew AL, Shaney KJ, Adams, RH, Schield, DR, Casewell NR, Mackessy SP, Castoe, TA. (2014). Expression of venom gene homologs in diverse python tissues suggests a new model for the evolution of snake venom. Molecular biology and evolution, msu294.

Thursday, December 4, 2014

Humans consume an endangered iguana

The Valle de Aguán spiny-tailed iguana is a critically endangered species found in Honduras. A recent survey of people living in the region shows that, although residents are aware of the endangered status of the species, the iguana continues to be hunted for food. Of particular concern is the preference for the consumption of female iguanas that are gravid (carrying eggs in their body).

"In this study we worked to gain a better understanding of how humans are harvesting the species for food," said Stesha Pasachnik, Ph.D., a lead researcher on the study and a postdoctoral research associate for the San Diego Zoo Institute for Conservation Research. "The information we gained indicates a use that is not only not sustainable but is likely to accelerate this species' extinction due to the loss of gravid females."

Published in the December issue of Herpetological Conservation and Biology, the study gained firsthand information regarding the hunting, harvesting and consumption of the species. Although the study, supported by the Bay Islands Foundation and San Diego Zoo Global, highlights an area of serious concern, it also recommends work to educate residents about the species and ways that harvesting can be made more sustainable.

Bringing species back from the brink of extinction is the mission of San Diego Zoo Global. As a leader in conservation, the work of San Diego Zoo Global includes onsite wildlife conservation efforts (representing both plants and animals) at the San Diego Zoo, San Diego Zoo Safari Park, and San Diego Zoo Institute for Conservation Research, as well as international field programs on six continents. The important conservation and science work of these entities is made possible by the San Diego Zoo Wildlife Conservancy and is supported in part by the Foundation of the Zoological Society of San Diego.

Stesha A. Pasachnik, James A. Danoff-Burg, Edoardo E. Antúnez, and Jeffrey P. Corneil. Local Knowledge and Use of the Valle Deaguán Spiny-Tailed Iguana, Ctenosaura melanosterna, in Honduras. Herpetological Conservation and Biology, 2014

Thursday, November 27, 2014

Turtle relationships and their dispersal across the planet

The graphic abstract from Crawford et al. with photos added.
The question of what are turtles has been a source of a lively scientific debate over the past decades. Until recently, the phylogenetic placement of turtles within Amniota was uncertain and controversial. Molecular studies at the genome level confirm their sister relationship to archosaurs and rejected their relationship to lepidosaurs. However, relationships of lineages of turtles have not been studied using genomic techniques.

In a forthcoming paper in Molecular Phylogenetics and Evolution Crawford and colleagues (in press 2014) provide the first genome-scale analysis of turtle phylogeny. They sequenced 2381 ultraconserved element (UCE) loci representing a total of 1,718,154 bp of aligned sequence. The sampling includes 32 turtle taxa representing all 14 recognized turtle families and six additional outgroups.

This robust phylogeny shows that proposed phylogenetic names correspond to well-supported clades, and this topology is more consistent with the temporal appearance of clades and paleobiogeography.

The ultraconserved element (UCE) loci phylogeny supports the monophyly of Cryptodira, with Trionychia as the sister taxon to all other cryptodires. The clade including non-trionychian cryptodires was previously phylogenetically defined as ‘Durocryptodira’ by Danilov and Parham. The topology from ultraconserved elements and other molecular studies support the monophyly and the recognition of Durocryptodira, which is in contrast with the morphological hypothesis.

Combining the UCE phylogeny with the known fossil record of turtles allows reconstruction of some global biogeographic patterns. Intercontinental dispersal of turtles is common, usually involving a limited number of species.

The earliest fossils of stem testudinoids, stem trionychians, and stem cryptodires are from Eurasia. Mapping this onto the UCE phylogeny suggests cryptodires originated in the Jurassic of Eurasian. The emergence of cryptodires in Eurasia is complemented by the concurrent origin of pan-pleurodires in the Southern Hemisphere (Gondwana). Given the distribution of the clades and the timing of their origin, the geography of the cryptodire-pleurodire split can be plausibly linked to the breakup of the supercontinent Pangaea; a pattern common to other terrestrial vertebrates (e.g., placental vs. marsupial mammals).

Despite the Jurrasic origin of cryptodiran turtles they did not dominate the fauna of northern continents for 100 million years (in the Cenozoic). Instead, stem turtles mostly the Paracryptodira) were diverse and abundant in North America during the Cretaceous and into the Cenozoic. In the late Cretaceous cryptodires started to appear in North America invading via high latitude dispersal routes. The UCE phylogeny confirms one of the North American durocryptodire lineages, the Americhelydia, underwent a modest radiation and accounts for 38 living species.

Warm periods in the Paleogene are responsible for the dispersal of many organinsism into North America through high latitude dispersal routes, including a wave of testudinoids. Two are modest radiations, four species of Gopherus (Testudinidae); nine species of Rhinoclemmys (Geoemydidae). Previous studies suggested that these genera are sister taxa to all of the Old World members of their respective clades. The authors sequenced GopherusRhinoclemmys, and representative divergent members of geoemydids and testudinids and confirm the basal position of these North American genera. This pattern links the overall diversification at the base of these clades with their intercontinental dispersal, which can logically be attributed to periods of warm climate.

Similar to the Americhelydia, short branches within the testudinoids also suggest a rapid adaptive radiation that coincides with high latitude intercontinental dispersal events. This pattern suggests that global climate change has a major impact on the diversity and distribution of turtles.

The end of the Paleogene (45–23 Ma) coincides with global environmental changes, with the climate becoming significantly cooler and drier, thus much less favorable to turtles. Many turtle lineages that inhabited the Western Interior, including the last stem cryptodires in North America, became extinct at this time. One testudinoid lineage took advantage of the subtropical southeastern portions of the continent and radiated into the diverse clade Emydidae (53 species).

The recent description of a fossil taxon on the stem of Platysternon megacephalum from the Eocene of North America raises possibility that the more inclusive Emysternia may also have an American origin. Depending on the resolution of that possibility, the UCE topology indicates that two dispersal events into North America led to the origin of 36–43% of the recognized families of turtles.

The entire article is available on-line.

Crawford NG, Parham JF, Sellas AB, Faircloth BC, Glenn TC, Papenfuss TJ, Henderson JB, Hansen MH, and Simison WB. 2014 (2015). A phylogenomic analysis of turtles. Molecular Phylogenetics and Evolution (2014).

Saturday, November 22, 2014

A large sea snake harvest that has gone unnoticed for a decade

Conservation of sea snakes is virtually nonexistent in Asia, and its role in human–snake interactions in terms of catch, trade, and snakebites as an occupational hazard is mostly unexplored. In a recent paper in Biological Conservation Nyguen et al (2014) report data on sea snake landings from the Gulf of Thailand, a hotspot for sea snake harvest by squid fishers operating out of the ports of Song Doc and Khanh Hoi, Ca Mau Province, Vietnam. The information was collected during documentation of the steps of the trading process and through interviewers with participants in the trade. Squid vessels return to their ports once per lunar synodic cycle and fishers sell snakes to merchants who sort, package, and ship the snakes to various destinations in Vietnam and China for human consumption. They are also used as a source of traditional remedies. Annually, 82 tons, roughly equal to 225,500 individual snakes, of live sea snakes are brought to ports. Knowledge of the harvest has been largely ignored and the rate of harvest constitutes one of the largest venomous snake and marine reptile harvest activities in the world today. In the harvest two species, Lapemis curtus and Hydrophis cyanocinctus, constituted about 85% of the snake biomass, and Acalyptophis peronii, Aipysurus eydouxii, Hydrophis atriceps, H. belcheri, H. lamberti, and H. ornatus made up the remainder. The results of this new paper establish a quantitative baseline for characteristics of catch, trade, and uses of sea snakes. Other key observations include the timing of the trade to the lunar cycle, a decline of sea snakes harvested over the study period (approximately 30% decline in mass over 4 years), and the treatment of sea snake bites with rhinoceros horn. Emerging markets in Southeast Asia drive the harvest of venomous sea snakes in the Gulf of Thailand and sea snake bites present a potentially lethal occupational hazard.

The authors suggest that the Gulf of Thailand/southern Vietnam is one of the largest harvests of venomous snake and marine reptiles in the world. Yet sea snakes are not even mentioned in studies concerning reptile exploitation in Asia or globally. This underreported status is particularly notable given that the Indonesian archipelago has the highest marine species diversity in general and specifically is among the areas ranked as having the greatest richness of sea snake species on Earth. Still, in this area an unexplained decline of sea snakes has been reported. The eight commercially traded sea snake species reported on represent a significant proportion of the 20 species known in the Gulf of Thailand and of the 25 species known from Vietnam, including the South China Sea.
Globally, 9% of sea snakes are threatened, 6% are near threatened, and 34% are data deficient, as defined by the International Union for the Conservation of Nature (IUCN). The species in this study, as well as all other species known from the Gulf of Thailand, are currently categorized as either least concern or data deficient. However, the results suggest that in the Gulf of Thailand a large subset of the sea snake species now considered as least concern or data deficient may, in fact, be in danger of having their populations damaged or destroyed through over harvesting. According to the results presented in this paper, the number of sea snakes harvested from the Gulf of Thailand by boats based at the study sites was 6.35 specimens per square kilometer per year. The authors could not exclude the possibility that sea snake species in addition to those observed were traded from other harvesting grounds (e.g., harvest landing in Vung Tau, Vietnam). The volume of harvested sea snakes documented is a conservative estimate of the total harvest from the Gulf of Thailand. It is very likely that more snakes were harvested by squid vessels and trawlers that originated from ports in Malaysia and Thailand. Sea snakes have been brought into the ports of Songkhla, Thailand, Kra Isthmus, Thailand, and Endau, Malaysia. Sea snake harvests similar to the one reported here could be occurring in (or spread to) other areas of the South China Sea and wider Southeast Asia. Ten years ago in Quảng Ng˜ai, the sea snake bycatch was discarded due to fear of bites and a lack of market; however, in 2011 their price was US$10–35/kg. Knowledge of the biology of sea snakes and their role in the ecosystem is limited. Thus, understanding of the effect that this harvest may have on populations or on the wider ecosystem is limited. The results supply evidence that the mass of snakes harvested from the Gulf of Thailand has been decreasing since 2009, and fishers interviewed consistently reported a decline since they first began capturing sea snakes as a commodity.

Snake bites during the trade process are occupational hazards that carry a high risk given the lethal venoms and lack of availability of antivenin therapy. The economic incentive of harvesting sea snakes, from the fishers’ and merchants’ perspectives, clearly outweighs the snake bite risk. With respect to fatalities the authors report, one affected family continued trading in sea snakes, while another family terminated participation in the snake trade.

The authenticity and effectiveness of rhinoceros horn and other locally used remedies for snake bites remains unproven. Yet, use of rhinoceros body parts in Vietnam has been directly linked to poaching of rhinoceros in South Africa. The observation suggests a link between rhinoceros poaching and sea snake harvest in the Gulf of Thailand. Both fishers and merchants take advantage of emerging market opportunities. According to the merchants, government, and nongovernmental officials interviewed, the large-scale harvest of sea snakes from the Gulf of Thailand is tied to economic prosperity and thus increase demand domestically in Vietnam and from China for snake products. The demand is due to the perceived health benefits of sea snakes and consumption of sea snakes as status
Items. This particular sea snake harvest has been going on essentially unnoticed by national and international conservation organizations for more than a decade, in part because it apparently does not overtly conflict with Vietnamese laws. Yet, given the volume of snakes and the wide spectrum of species extracted and that the environmental effects of the harvest are unknown, immediate attention by conservation organizations to sea snake harvesting appears warranted. Ironically, the enforcement of laws aimed at managing the trade in widely harvested terrestrial snakes, such as various cobra species (e.g., Naja spp., Ophiophagus hannah), may have the unintended consequence of increasing the market for sea snakes.


Nguyen C, Nguyen TT, Moore A, Montoya A, Rasmussen AR Broad K, Voris HK, Takacs Z. 2014. Sea Snake Harvest in the Gulf of Thailand. Conservation Biology 28: 1677-1687.

Monday, November 17, 2014

A new Chironius from Bahia, Brazil

Chironius diamantine. Photo credit: R. Santos
The Neotropical colubrid genus Chironius contains a monophyletic assemblage of snakes having very low (10 or 12) dorsal scale rows at midbody. Currently the genus includes 20 species of diurnal snakes distributed from Honduras south to Uruguay and northeastern Argentina. Recently, a lectotype was designated for Chironius flavolineatus, a widespread species in open formations of South America (particularly in the Cerrado and Caatinga), with records from Marajó island, northern Brazil. Chironius flavolineatus is distinguishable from other members of the genus by the presence of a conspicuous yellow vertebral stripe bordered anteriorly by black. In a new Zootaxa paper, Fernandes and Hamdan (2014) describe the 21st species of Chironius, C. diamantine which differs from other Chironius in the combination of its color pattern, 2-4 temporal scales, an entire anal plate, 6-10 rows of dorsal scales at midbody, and some other characters. The new species is known from municipalities of Morro do Chapéu, Rio de Contas, and Palmeiras in the Chapada Diamantina, Bahia, Brazil. All specimens were found between sea level 1000 m asl. One individual was observed foraging about 3:00 PM on the banks of a rocky river near a waterfall, a few minutes later plunged into the river and remained there for about two minutes.


Fernandes DS, & Hamdan B. 2014. A new species of Chironius Fitzinger, 1826 from the state of Bahia, Northeastern Brazil (Serpentes: Colubridae). Zootaxa, 3881(6), 563-575.

Sunday, November 16, 2014

Relationships between some Old World Rat Snakes resolved

These snakes should all be placed in 
the genus Gonyosoma
The Old World Rat Snakes have been a source of confusion for many years, they have a diverse morphology and behaviors that have been a puzzle to herpetologists for some time - the kind of puzzle best solved with molecular techniques. The last decade has seen an incredible rise in the use of molecular phylogenies to examine relationships in snakes, assess biogeographic origins, understand processes of adaptive radiation and ultimately correct taxonomy with regard to paraphyletic and polyphyletic groups at multiple levels. The importance of using phylogenetic trees to uncover genealogical relationships and properly construct a taxonomy of organisms cannot be overstated. The development of DNA sequencing technology has increased the available genetic data for phylogenetic inference and the development of model-based statistical methods, such as maximum likelihood and Bayesian inference, which has enhanced the reliability of reconstructed phylogenies. Using molecular data to examine phylogenetic relationships provides evidence to clarify systematic ambiguities from morphological characters and helps avoid misleading relationships due to convergence of morphology. Therefore, an abundance of molecular data with information from independent loci is able to provide strong evidence to assess taxonomic composition and test monophyly.

Using one mitochondrial gene and five nuclear loci, Xin Chen and colleagues (2014) evaluated the taxonomic status of a rare Borneo endemic, the Rainbow Tree Snake Gonyophis margaritatus. The authors inferred a molecular phylogeny of 101 snake species. Both maximum likelihood and time- calibrated Bayesian inference phylogenies demonstrated that G. margaritatus is sister to the Green Trinket Snake, Rhadinophis prasinus of northern Thailand, previously considered to be part of a radiation of Old World ratsnakes. This group is in turn sister to a group containing Rhadinophis frenatus (India, southern China, Taiwan, and North Vietnam) and the Rhinoceros Ratsnake, Rhynchophis boulengeri with the entire clade originating in the mid-Miocene (~16 Ma) in Southeast Asia. This group is sister to the genus Gonyosoma and together originated in the early Miocene (~20 Ma). The authors discuss three potential solutions towards eliminating polyphyly of the genus Rhadinophis, but recommend using the genus name Gonyosoma for all species within this clade, which currently contains all of the species within the genera Gonyosoma, Gonyophis, Rhadinophis, and Rhynchophis.

Chen X, McKelvy AD, Grismer L, Matsui M, Nishikawa K, & Burbrink FT. 2014. The phylogenetic position and taxonomic status of the Rainbow Tree Snake Gonyophis margaritatus (Peters, 1871) (Squamata: Colubridae). Zootaxa, 3881, 532-548.

Friday, November 7, 2014

Origin of the ventilatory apparatus of turtles

A Computed Tomography rendering of a snapping turtle 
(Chelydra serpentina) showing the skeleton (white), lungs 
(blue), and abdominal muscles (red and pink) used to ventilate 
the lungs. Because turtles have locked their ribs up into the
 iconic turtle shell, they can no longer use their ribs to breathe as 
in most other animals and instead have developed a 
unique abdominal muscle based system. 
Photo credit: Emma R. Schachner.
Through the careful study of modern and early fossil tortoise, researchers now have a better understanding of how tortoises breathe and the evolutionary processes that helped shape their unique breathing apparatus and tortoise shell. The findings published in a paper, titled: Origin of the unique ventilatory apparatus of turtles, in the scientific journal, Nature Communications, on Friday, 7 November 2014, help determine when and how the unique breathing apparatus of tortoises evolved.

Lead author Dr Tyler Lyson of Wits University's Evolutionary Studies Institute, the Smithsonian Institution and the Denver Museum of Nature and Science said: "Tortoises have a bizarre body plan and one of the more puzzling aspects to this body plan is the fact that tortoises have locked their ribs up into the iconic tortoise shell. No other animal does this and the likely reason is that ribs play such an important role in breathing in most animals including mammals, birds, crocodilians, and lizards."

Instead tortoises have developed a unique abdominal muscular sling that wraps around their lungs and organs to help them breathe. When and how this mechanism evolved has been unknown.

"It seemed pretty clear that the tortoise shell and breathing mechanism evolved in tandem, but which happened first? It's a bit of the chicken or the egg causality dilemma," Lyson said. By studying the anatomy and thin sections (also known as histology), Lyson and his colleagues have shown that the modern tortoise breathing apparatus was already in place in the earliest fossil tortoise, an animal known as Eunotosaurus africanus.

This animal lived in South Africa 260 million years ago and shares many unique features with modern day tortoises, but lacked a shell. A recognizable tortoise shell does not appear for another 50 million years.

Lyson said Eunotosaurus bridges the morphological gap between the early reptile body plan and the highly modified body plan of living tortoises, making it the Archaeopteryx of turtles.
"Named in 1892, Eunotosaurus is one of the earliest tortoise ancestors and is known from early rocks near Beaufort West," said Professor Bruce Rubidge, Director of the Evolutionary Studies Institute at Wits University and co-author of the paper.

"There are some 50 specimen of Eunotosaurus. The rocks of the Karoo are remarkable in the diversity of fossils of early tortoises they have produced. The fact that we find Eunotosaurus at the base of the Karoo succession strongly suggest that there are more ancestral forms of tortoises still to be discovered in the Karoo," Rubidge added.

The study suggests that early in the evolution of the tortoise body plan a gradual increase in body wall rigidity produced a division of function between the ribs and abdominal respiratory muscles. As the ribs broadened and stiffened the torso, they became less effective for breathing which caused the abdominal muscles to become specialized for breathing, which in turn freed up the ribs to eventually -- approximately 50 million years later -- to become fully integrated into the characteristic tortoise shell.

Lyson and his colleagues now plan to investigate reasons why the ribs of early tortoises starting to broaden in the first place. "Broadened ribs are the first step in the general increase in body wall rigidity of early basal tortoises, which ultimately leads to both the evolution of the tortoise shell and this unique way of breathing. We plan to study this key aspect to get a better understanding why the ribs started to broaden."


Lyson TR, Schachner  ER, Botha-Brink J, Scheyer TM, Lambertz M, Bever GS, Rubidge, BS de Queiroz K. Origin of the unique ventilatory apparatus of turtles. Nature Communications, 2014; 5: 5211 DOI: 10.1038/ncomms6211

Thursday, November 6, 2014

External genitalia in amniote evolution

When it comes to genitalia, nature enjoys variety. Snakes and lizards have two. Birds and people have one. And while the former group's paired structures are located somewhat at the level of the limbs, ours, and the birds', appear a bit further down. In fact, snake and lizard genitalia are derived from tissue that gives rise to hind legs, while mammalian genitalia are derived from the tail bud. But despite such noteworthy contrasts, these structures are functionally analogous and express similar genes.

How do these equivalent structures arise from different starting tissues?

This is a python embryo at 11 days after 
oviposition (egglaying). The right hemipenis
(genitalia) bud and vestigial limb-bud can be 
seen near the tail end of the embryo, in the 
center of the tail 'spiral'. (two white 'blobs'). 
Photo Credit: Patrick Tschopp.
Reporting in Nature, researchers in Harvard Medical School's Department of Genetics, led by departmental chair Clifford Tabin, have found that the answer is not unlike the real estate axiom Location, location, location.

The embryonic cloaca -- which eventually develops into the urinary and gut tracts -- issues molecular signals that tell neighboring cells and tissues to form into external genitalia. The cloaca's location determines which tissues receive the signal first. In snakes and lizards, the cloaca is located closer to the lateral plate mesoderm, the same tissue that makes the paired limbs, receives the signal. In mammals, the cloaca is closer to the tail bud.

To further confirm this finding, the researchers grafted cloaca tissue next to the limb buds in one group of chicken embryos, and beside the tail buds in a second group. They found that in both cases, cells closer to the grafted cloaca responded to the signals and partially converted toward a genitalia fate.

This proves that different populations of cells with progenitor potential are able to respond to cloaca signaling and contribute to genitalia outgrowth.

"While mammal and reptile genitalia are not homologous in that they are derived from different tissue, they do share a 'deep homology' in that they are derived from the same genetic program and induced by the same ancestral set of molecular signals," said Tabin, who is also the George Jacob and Jacqueline Hazel Leder Professor of Genetics.

"Here we see that an evolutionary shift in the source of a signal can result in a situation where functionally analogous structures are carved out of nonhomologous substrate," said Patrick Tschopp, an HMS research fellow in genetics in Tabin's lab and first author on the paper. "Moreover, this might help to explain why limbs and genitalia use such similar gene regulatory programs during development."


Tschopp P, Sherratt E, Sanger TJ, Groner AC, Aspiras AC, Hu JK, Pourquié O, Gros J, Tabin CJ. A relative shift in cloacal location repositions external genitalia in amniote evolution. Nature, 2014; DOI: 10.1038/nature13819

An amphibious ichthyosaur

Fossil remains show the first amphibious ichthyosaur found in China by a team led by a UC 
Davis scientist. Its amphibious characteristics include large flippers and flexible wrists, essential 
for crawling on the ground. Photo Credit: Ryosuke Motani/UC Davis
The first fossil of an amphibious ichthyosaur has been discovered in China by a team led by researchers at the University of California, Davis. The discovery is the first to link the dolphin-like ichthyosaur to its terrestrial ancestors, filling a gap in the fossil record. The fossil is described in a paper published in advance online Nov. 5 in the journal Nature.

The fossil represents a missing stage in the evolution of ichthyosaurs, marine reptiles from the Age of Dinosaurs about 250 million years ago. Until now, there were no fossils marking their transition from land to sea.

"But now we have this fossil showing the transition," said lead author Ryosuke Motani, a professor in the UC Davis Department of Earth and Planetary Sciences. "There's nothing that prevents it from coming onto land."

Motani and his colleagues discovered the fossil in China's Anhui Province. About 248 million years old, it is from the Triassic period and measures roughly 1.5 feet long.

Unlike ichthyosaurs fully adapted to life at sea, this one had unusually large, flexible flippers that likely allowed for seal-like movement on land. It had flexible wrists, which are essential for crawling on the ground. Most ichthyosaurs have long, beak-like snouts, but the amphibious fossil shows a nose as short as that of land reptiles.

Its body also contains thicker bones than previously-described ichthyosaurs. This is in keeping with the idea that most marine reptiles who transitioned from land first became heavier, for example with thicker bones, in order to swim through rough coastal waves before entering the deep sea.

The study's implications go beyond evolutionary theory, Motani said. This animal lived about 4 million years after the worst mass extinction in Earth's history, 252 million years ago. Scientists have wondered how long it took for animals and plants to recover after such destruction, particularly since the extinction was associated with global warming.

"This was analogous to what might happen if the world gets warmer and warmer," Motani said. "How long did it take before the globe was good enough for predators like this to reappear? In that world, many things became extinct, but it started something new. These reptiles came out during this recovery."


Motani R., Jiang D-Y, Chen G-B, Tintori A, Rieppel O, Ji C, Huang J-D. 2014. A basal ichthyosauriform with a short snout from the Lower Triassic of China. Nature, 2014; DOI: 10.1038/nature13866