Anaconda: The Educational Version

A friend sent this to me. It is just too good! Learn all about anacondas, the real ones. They are dope snakes, hon.





*contains some "language"

Snakes, An Origin Story

Quite honestly, I should have been reading a plant paper for my upcoming lab meeting. But then I stumbled across a really cool snake paper and, well, that won out. I regret nothing. As with most people, I will most likely read the plant paper right before the meeting anyway.

A paper published online today in Biology Letters takes a look at the phylogeny of squamate reptiles (lizards and snakes). This group of reptiles is one of the most diverse and well-known vertebrate groups including approximately 9000 species among 61 families. As with many groups, taxonomists and geneticists are trying to reconcile morphology and molecular analysis. This paper is taking the molecular approach, specifically looking at sister groups and interrelationships of major snake clades and iguanian families. Being a well-studied group, molecular analyses have been conducted in the past. These studies have suggested that squamate molecular phylogeny results differ quite a bit from morphological ones. This study takes one gigantic step forward, increasing the sampling of taxa dramatically and doubling the number of genes studied.

The researchers sampled 161 squamate species and 10 outgroup taxa, including mammals (Homo, Mus, Tachyglossus), crocodilians (Alligator, Crocodylus), birds (Dromaius, Gallus), turtles (Chelydra, Podocnemis) and a rhyncocephalian (Sphenodon). Then they sequenced portions of 44 nuclear genes, targeting single-copy genes evolving at appropriate rates. The nucleotide sequences were then translated into amino acids to aid alignment. This alignment consisted of 33,717 base pairs! I’m not going to go into all of the bootstrapping, likelihoods, and Bayesian analyses that were used (even the word Bayesian makes my brain shut down in protest). But suffice it to say that the different analysis techniques that were used yielded similar phylogenies, providing strong support for the relationships found.

The results of this molecular analysis were found to be consistent with other, recent, similar studies. However, there were some interesting relationships discovered. The first of these was that dibamid (legless lizards found in tropical forests) and gekkotans (geckos and the limbless Pygopodidae) are together the sister group to all other squamates. They also found strong support for paraphyly of scolecophidian snakes (blind snakes). Scolecophidians have reduced eyes and are specialized burrowers. Considering these traits, the paraphyly of this group suggests that it is the ancestral form, that other snakes may have been burrowers ancestrally. This makes sense if you compare the morphology of snakes to other burrowing species such as limb-reduced lizards. They both have short tails and elongate trunks. Very good for tunneling their way through the earth.

Overall, a really interesting study that was huge in its scope. I look forward to more of these kinds of studies in the future.


John J. Wiens, Carl R. Hutter, Daniel G. Mulcahy, Brice P. Noonan, Ted M. Townsend, Jack W. Sites Jr., & Tod W. Reeder (2012). Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species Biology Letters, 4 (11) DOI: 10.1098/rsbl.2012.0703

If you are a non-scientist and I used too many biology-jargony words for you or you just need a refresher on phylogeny, then I recommend looking through these sites:
Fullerton’s Biology 261 course page on Interpreting Cladograms
Berkeley’s Understanding Evolution page on reading phylogenetic trees

Here is some more information on blind snakes:
ScienceBlogs article Scolecophidians: seriously strange serpents

Also:
ScienceShot article: Snakes' Slitherin' Subterranean Kin


(images from  Encyclopedia of Life and Neoseeker, respectively)

Falling with Style

Its been a little while since I've posted anything. I suppose that's what the "semi-frequent" part of my blog description really means. So for the next couple of posts not only am I going to post them in rapid succession but they will also be slightly older stories. But, I figure, cool science is always cool science and so will allow myself to get away with it.

This story caught my eye because (1) I attended a talk by this researcher when I was in grad school and (2) it is about flying snakes.

You didn't know there were flying snakes? Well, then you are in for a treat, my friend, a real treat. Flying snakes or flying tree snakes belong to the genus Chrysopelea (family Colubridae) which can be found in Southeast Asia, India and southern China. Despite its name the snake doesn't actually fly. When they launch themselves off a tree they flatten their bodies and undulate to glide to their destination. Basically its body becomes like a big wing ideal for gliding.

The Paradise Tree Snake (Chrysopelea paradisi) is the most commonly studied of this genus. This snake is brightly colored, with a black body covered from head to tail with a yellow spotting pattern that at times can look stripped and has 5 yellow (sometimes orange) bars that span its width. It is native to the tropical forests of southern Thailand, Peninsular Malaysia, the Philippines, Singapore, and Indonesia. The vegetation in these forests can be quite diverse, including tropical broadleafed species and evergreens with little to no understory. Its diet consists of arboreal reptiles and amphibians (lizards, frogs, etc.) as well as small birds and even bats. Add together habitat and hunting and you can probably start see why this snake needs to fly.

A Virginia Tech researcher, John Socha, studies the kinematics of these snakes. He published a short article in Nature in 2002 (and a similar one in The Journal of Experimental Biology in 2005) where he looked at the full three-dimensional gliding trajectory of these snakes. First, in an open field, he built a 10 meter high tower/platform with a horizontal branch extending from the top. Then he carried his snakes to the top of the platform and videotaped and photographed them jumping off the branch and gliding to the ground. Besides the flying snake (which is obviously so very cool) my favorite part is the undergrad let's-call-them-lackeys running to get the escaping snake once it reaches the ground.

Anyway, he found that the snake prepares for take-off by hanging the front part of its body off the branch looped into a J-shape. When the snake jumps it accelerates up and way from the branch, straightening its body and flattening it by stretching out its ribs. The body width of the snake actually doubles and the stretching of the ribs curves the belly into a concave shape. Because the snake is falling it will gain speed and as it does that it will pitch its body downwards and curve into an S-shape. Then the snake starts undulating from side-to-side, starting at the front and moving down the body. This creates lift and allows it to go a further horizontal distance rather than falling straight down to the ground. C. paradisi is very adept at aerial manoeuvring, being able to turn without banking. It can even out-glide other gliders like flying squirrels (Petaurista petaurista) and flying frogs (Rhacophorus nigropalmatus).

Recently there have been some articles in various major news outlets about Socha's new research presented at the American Physical Society Division of Fluid Dynamics meeting in Long Beach, California and a paper accepted for publication in the journal Bioinspiration & Biomimetics. He explains in further detail the gliding motion of these snakes, having developed a mathematical model that explains how they travel such long distances. Basically it takes the gliding description above and explains it mathematically as well as explaining the gliding techniques of other species (mammals, frogs, lizards, etc.). The U.S. Pentagon and the Defense Advanced Research Projects Agency (DARPA) has had a big interest and funded a lot of this research, although they have yet to explain their big interest in the work.

Here is Socha's kinematics paper:
Socha, J.J. (2002) Kinematics: Gliding flight in the paradise tree snake. Nature: 418 (6898), 603–604. (DOI:10.1038/418603a)

This is Socha's flying snake page. It includes some great images and videos of his experiments as well as a fantastic links page to find out more about these snakes. I highly recommend checking it out!
http://flyingsnake.org/

News stories:
http://www.huffingtonpost.com/2010/11/23/flying-asian-snakes-being_n_787534.html
http://news.discovery.com/animals/snakes-flight-aerodynamics.html
http://www.popsci.com/technology/article/2010-11/serpent-science-darpa-wants-know-flying-snakes-secret

Warning Sounds

Researchers at Cornell University have published a paper in Conservation Biology that used modelling to investigate population-level responses of timber rattlesnakes to habitat fragmentation. In general, habitat fragmentation reduces the ranges of many species, limits resources, increases competition, alters community structure, decreases species diversity and abundance, increases edge effects, and has many other consequences. Anthropogenic habitat fragmentation can result from a variety of things such as roads, farming, buildings, cities, etc -- basically anything that prevents or severely hinders a species' ability to move across the landscape to favorable areas to live. The results of the model show that habitat fragmentation caused by roads have a significant effect on the genetic structure of these rattlesnakes, they are barriers to gene flow and decreasing genetic diversity. This decrease in diversity has its own set of problems, not the least of which is making the population more susceptible to illness and less adaptable to environmental changes.

Additionally, the researchers looked at these rattlesnakes in 19 different hibernacula (shared wintering quarters) at four regions of New York. Using microsatellite markers they tracked the dispersal patterns of these populations as they left their hibernacula, also tracking their reproductive patterns. They compared these data to the layout of roads and to natural barriers in the areas and found that the roads altered gene flow, effectively isolating these populations. These results were seen in each of the regions and were not affected by road type or age.

The article:

Clark, Rulon W., et al. (2010) Roads, Interrupted Dispersal, and Genetic Diversity in Timber Rattlesnakes. Conservation Biology: published online. (DOI: 10.1111/j.1523-1739.2009.01439.x)

and http://www.sciencedaily.com/releases/2010/04/100421102449.htm

p.s. Don't run over snakes with your car, its bad for the snakes and bad for the environment (not to mention its just plain mean).

Cobra Attack

The cobra's hood, very cool. But how does it work? A study in the Journal of Experimental Biology takes a look at just that.

Cobras belong to the Elapidae family of snakes. This is a family of venomous snakes which are found in tropical and subtropical regions around the world. Skeletally, the bones in the hood of the cobra evolved from ribs and the associated muscles evolved along with them. Scientists have taken a look at the cobra's defensive display, the "hood flare," and measured the electrical activity coming from the snakes' hood muscles to tease out which muscles are involved in the movement. This experiment found 8 muscles involved in the hood flare. Interestingly, these muscles are also present in non-hooding snakes. The muscles and the nervous system's control over them have evolved to spread the snake's hood. While this research was mostly identifying the muscles themselves, further research will delve into the evolution of these muscles in various snake species.

Here's the story: http://news.bbc.co.uk/2/hi/science/nature/8625553.stm