Genomics and Venomics of the sexually dimorphic Temple Pitviper

We invited Dr Ryan McCleary, Postdoctoral Researcher at Utah State University, to contribute a guest writeup about the effort to sequence the genome of the Temple Pitviper.

The Temple (or Wagler’s) Pitviper, Tropidolaemus wagleri, is a venomous snake found in tropical Asia, from southern Thailand; through peninsular Malaysia and Singapore; and into Indonesia (Sumatra and nearby islands). It belongs to the family Viperidae and subfamily Crotalinae (the pit vipers), which have the common characteristics of enlarged, front-rotating fangs and heat-sensing facial pits. The Temple Pitviper itself is extremely unique.

©Herpetological Society of Singapore
A male Wagler’s Pitviper from one of the HSS Herp Walks

Although most snakes have very minor differences between the sexes (what we call “sexual dimorphism”), the Temple Pitviper’s differences are extreme. The females get fairly large-bodied and have colorful spots over their surface, with white, yellow, green, and blue speckling over a black background with yellow bands. The males, on the other hand, are much smaller and narrower in girth, with a fairly uniform light green color and white and/or maroon spots or bars down the body. They are so different that it is really easy to mistake them as being different species. What is even more incredible is that both males and females start off looking the same…like little males! How the change occurs over time is really not known, nor is when exactly it happens.

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Female Wagler’s Pitviper, Photo by Serin Subaraj

Besides the sexual dimorphism, Temple Pitvipers also have a unique venom. Like many vipers, the venom is quite complex, with many different types of toxic proteins present. However, the Temple Pitviper is the only species known to contain a specific family of proteins, the waglerins, in its venom. These waglerins are relatively small (compared to many other toxin protein families) and function as extremely selective inhibitors of neuromuscular activity. It is because of this activity that their venom is currently being studied for potential use in human medicine.

Many Singaporeans may also be familiar with this snake because it is an abundant resident of the Temple of the Azure Cloud (Snake Temple) in Penang, Malaysia. In the Temple, the snakes go about their business unhindered by humans and vice versa. These snakes also rarely bite humans in nature.

We are interested in many aspects of this snake, starting with its natural history and going all the way through the evolution of its venom. We are interested in the genetic basis of the size and coloration differences between the sexes and how this relates to the habits of the species in nature. Do they consume different prey?

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Photo by Noel Thomas

Do they inhabit slightly different microhabitats? Is there a sex-based difference in venom composition? The genome will help us to understand the mechanisms by which these snakes produce their venom and exactly what compounds may be found in the venom, including some that may be used as leads for the development of human pharmaceuticals or research tools. Besides this, there are currently two other snake genomes that have been undertaken—the Burmese Python and the King Cobra. The addition of the Temple Pitviper will expand our understanding of snakes in general and venomous snakes in particular, both in terms of their evolution and their relationships with each other.

There is a lot to do before we can answer these questions, but we currently have a great opportunity. Although we have begun the sequencing of the genome, we have not yet utilized an extremely powerful tool known as PacBio sequencing, due to constraints on funding. This type of sequencing is very important to include for various reasons, but one way to think of it is that the normal sequencing is a bunch of puzzle pieces – with no direction and lots of time, you can still make the picture look right. However, PacBio sequencing is like having the photo on the puzzle box to help guide you and make things a lot easier. Pacific Biosciences (the creators of PacBio technology) have selected our project as one of five (out of 200+ applicants) to compete for complimentary PacBio sequencing, but we need your help!

If you would like to see our project—the only project from Singapore and the only one utilizing a herp species—succeed, you can help by voting for us. The winner of the competition will be selected by popular vote. Anybody can get on the website and vote once every day through the end of the competition (5 April 2017) using up to three different e-mail addresses per name.

Noel
Photo by Noel Thomas

 

The website for our project, which includes a video, can be found at:
http://www.pacb.com/smrt-science/smrt-grant/pag2017/temple-pitviper/
We have a Facebook page at:
https://www.facebook.com/TemplePitviperGenome/
And a Twitter feed at:
@TemplePitviper or #TemplePitviperGenome

The competition is stiff, and we need every vote we can get. Thanks for helping!

Ryan McCleary
Postdoctoral Researcher
Utah State University (previously with National University of Singapore)

2nd April 2017 (Sun): FREE Guided Herp Walk @ Sungei Buloh Wetland Reserve

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Did you know that these beautiful herptiles can be found in our local wetlands?

In an effort to promote an awareness of Singapore’s natural and historical heritage and to promote conversations amongst Singaporeans, the HSS has begun the Herp Walk! We want to raise awareness, in particular, about Herps (reptiles and amphibians)! These misunderstood creatures are often thought of as scary or unnecessary. But we want to show Singaporeans that Herps are important and integral to the Singaporean ecosystem!

This walk, which marks our 2nd Year Anniversary will take place on Sunday, 2 April 2017, 8.00AM-11.00AM

Here’s your chance to explore the trails of Sungei Buloh Wetland Reserve with experienced nature guides and learn shareable facts about our local wildlife as we go. With enough luck, we may even chance upon the critically endangered Saltwater Crocodile. Register at this link! See you there!

FREE Guided Herp Walk @ Bukit Timah

©Herpetological Society of Singapore
Beautiful Wagler’s Pit Vipers are often encountered in BTNR!

In an effort to promote an awareness of Singapore’s natural and historical heritage, and to promote conversations amongst Singaporeans, the HSS has begun the Herp Walk! We want to raise awareness, in particular, about Herps! These misunderstood creatures are often thought of as scary or unnecessary. But we want to show Singaporeans that Herps are important and integral to the Singaporean ecosystem!

This walk will take place on Sunday, 12 February 2017, 8.00AM-11.00AM

Come down for a brisk walk up Bukit Timah Nature Reserve, which has recently re-opened! Learn about the Primary Rainforest and see the animals that live within! Hopefully, we’ll be able to see some reptiles and amphibians on the way up and down. Register at this link!

Herping Ubin

Today was the HSS’ first Herp Walk held on Pulau Ubin! Previously, night walks had been held in collaboration with the Vertebrate Study Group (VSG) branch of the Nature Society as part of Pesta Ubin 2016, and HSS members also helped survey for herptiles during BioBlitz Ubin in December last year. Given the rich herpetofauna that we observed during those events, it was a no-brainer to have our first Herp Walk of 2017 at everyone’s favourite kampong getaway. However, we were also heartbroken to learn that the recent oil spill had now affected the mangroves of Ubin; more about this towards the end of the post.

As we started off on the walk, we were greeted by two of Ubin’s iconic Oriental Pied Hornbills (Anthracoceros albirostris) just next to the jetty! These charismatic birds were once extinct from Singapore, before making a return through natural dispersal from Johor; Ubin was their first foothold. It was good to see them still doing well.

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Oriental Pied Hornbill (Anthracoceros albirostris)

Our first herp of the day proved to be a male Sumatran Flying Dragon (Draco sumatranus)! This amazing gliding lizard was high up a coconut tree, flashing its yellow dewlap to ward off rival males. As we scanned the trunks of the neighbouring trees, we spotted a Green Crested Lizard (Bronchocela cristatella) and two more Flying Dragons, basking in the bright sunshine. The Green Crested Lizard, like its introduced competitor the Changeable Lizard, is able to change colour; depending on its mood or need for camouflage, it can switch between black and green.

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Green Crested Lizard (Bronchocela cristatella
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Sumatran Flying Dragon (Draco sumatranus)

It wasn’t long before one of our participants spotted the first snake of the day: an adult Oriental Whip Snake (Ahaetulla prasina), probably the most commonly sighted snake in Singapore. A minute later, a juvenile Oriental Whip was discovered in a bush just next to the adult! Instead of being neon green, young Oriental Whips are a dull brown, perhaps so that their very slender bodies can better resemble small twigs.

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Adult Oriental Whip Snake (Ahaetulla prasina)
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Juvenile Oriental Whip Snake (Ahaetulla prasina)

As we moved on to the mangroves, the fiddler crabs (Uca sp.) were out in force, with dozens of males flashing their bright orange claws to defend their territories and attract females. Mangroves are important habitat for lots of animals including reptiles, such as monitor lizards, snakes, and crocodiles. The Restore Ubin Mangroves project, which aims to promote natural regrowth of the mangrove forests by making the hydrography more favourable for new seedlings to grow, will thus hopefully also create more habitat for these herps to flourish!

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Male Fiddler Crabs (Uca sp.)

Many birds made an appearance throughout the walk, including these two bright balls of energy: an Orange-bellied Flowerpecker (Dicaeum trigonostigma), and a Crimson Sunbird (Aethopyga siparaja)! The former was feeding on the berries of the Singapore Rhododendron (Melastoma malabathricum), also known as Sendudok, while the latter flitted about looking for flowers to suck nectar from. These birds are important to forest ecosystems as they disperse the seeds of plants and help pollinate their flowers.

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Crimson Sunbird (Aethopyga siparaja)
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Orange-bellied Flowerpecker (Dicaeum trigonostigma)

We ended off the walk with a sighting of the introduced Changeable Lizard (Calotes versicolor), and another Green Crested Lizard (Bronchocela cristatella). Both these species have similar niches, though the more aggressive Changeable Lizard seems to have pushed the Green Crested out of parkland and urban areas. Ubin however seems to be one of the few places where both can be easily spotted, possibly due to the unique mix of secondary forest and kampong habitat found throughout the island.

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Bitter rivals: Changeable Lizard (Calotes versicolor) and Green Crested Lizard (Bronchocela cristatella)
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Guides and participants from today’s walk

After the walk ended, most of the guides headed over to Chek Jawa to take a look at the impact of the oil spill. Many of the mangrove roots were covered in sticky black oil, though most of the mudflat seemed clean. There were many workers deployed to clean up the oil that had evaded the absorbent booms just offshore, as well as some volunteers, all wearing protective body suits, boots and gloves. We also received word from our friends at NUS Toddycats that were helping with the cleanup, that a nationally Critically Endangered Keel-bellied Whip Snake (Dryophiops rubescens) had been found coated with oil. Gently retrieving the snake, we rushed it back to the NParks office on Ubin where it was slowly cleaned by staff and left to recover before release. Note: snakes should not be handled except by trained experts, and only where it is necessary and does not harm the snake’s welfare. Do not try this at home!

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Keel-bellied Whip Snake (Dryophiops rubescens). The grimy appearance of its scales is due to oil from the spill
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The snake being cleaned by NParks staff and HSS volunteer Noel Thomas
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Oil cleaned from the snake

 

 

 

 

 

 

 

 

 

 

As the example of the Keel-Bellied Whip Snake demonstrates, oil spills can affect a very wide variety of wildlife; even an arboreal snake like this one may accidentally stumble into oil that has been washed up onto mangrove trees. If we are to protect our biodiversity and herptiles from such threats, we need to be well-prepared to ensure that the oil never reaches the shore, or even better, doesn’t spill into the sea in the first place.  Given the large role that oil has in our economy, this will almost certainly not be the last such disaster. Hopefully going forward, this tragic incident will teach us the lessons needed to better handle future incidents and minimise the impact on our precious wildlife.

FREE Guided Walk @ Pulau Ubin

©Herpetological Society of Singapore
An Oriental Whip Snake (Ahaetulla prasina), one of the cool snakes you can expect to see on Ubin!

In an effort to promote an awareness of Singapore’s natural and historical heritage, and to promote conversations amongst Singaporeans, the HSS has begun the Herp Walk! We want to raise awareness, in particular, about Herps! These misunderstood creatures are often thought of as scary or unnecessary. But we want to show Singaporeans that Herps are important and integral to the Singaporean ecosystem! So join us for the first walk of the new year.

This walk will take place on Saturday, 7 Jan 2017, 9.00AM-1.00PM

Come down for a leisurely stroll at rustic Pulau Ubin. Learn about the biodiversity that still exists on this relatively isolated island. If we’re lucky, along the way, we can even spot some of our scaly friends!

Register at this link!

FREE Guided Walk @ Treetop Walk

In an effort to promote an awareness of Singapore’s natural and historical heritage, and to promote conversations amongst Singaporeans, the HSS has begun the Herp Walk! We want to raise awareness, in particular, about Herps! These misunderstood creatures are often thought of as scary or unnecessary. But we want to show Singaporeans that Herps are important and integral to the Singaporean ecosystem! So join us for this walk.

This walk will take place on Sunday, 18 December 2016, 8.00AM-12.00PM

Come down for a leisurely stroll along Treetop Walk. Let the guides regale you with tales about the natural history and transformation of the entire area. Learn about this green space in your very own backyard! If you’re lucky, you might get to see some of our scaly friends! So don’t wait! Register at this link

FREE Guided Herp Walk @ Bukit Timah!

DSC07270Wagler’s Pit Viper (Tropidolaemus wagleri) that we encountered in Bukit Timah Hill.

In an effort to promote an awareness of Singapore’s natural and historical heritage, and to promote conversations amongst Singaporeans, the HSS has begun the Herp Walk! We want to raise awareness, in particular, about Herps! These misunderstood creatures are often thought of as scary or unnecessary. But we want to show Singaporeans that Herps are important and integral to the Singaporean ecosystem!

This walk will take place on Sunday, 13 November 2016, 8.00AM-11.00AM

Come down for a brisk walk up Bukit Timah, which has only just re-opened! Learn about the Primary Rainforest and see the animals that live within! Hopefully, we’ll be able to see some reptiles and amphibians on the way up and down. Register at this link!