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Tuesday, May 28, 2013

Basics of Snake Taxonomy

A while back, medical-doctor-turned-snake-blog-post-translator-extraordinaire1 Alvaro Pemartin asked me to write an article covering basic snake taxonomy. Taxonomy is the branch of biology that deals with naming and classifying organisms. Biologists still use the Linnean hierarchical system for taxonomy, which is convenient for grouping organisms, but there is a move towards using phylogenetic systematics and the evolutionary species concept in taxonomy, particularly in the sense that recognizing and giving names to non-monophyletic groups is discouraged.2 We'll primarily stick with the Linnean system in this article, which uses particular suffixes to denote the taxonomic level (for example, all animal families end in '-idae' and all subfamilies end in '-inae'). However, I've also included some cladograms, which are the most useful figures for understanding evolutionary relationships. If you haven't read one before, you can read up on them here, here, or here, but just know that they essentially work just like a family tree.

Snake Diversity

My only criticism of this film:
not enough snakes
There are about 3,400 species of snakes in the world. All are placed in the suborder Serpentes (aka Ophidia) of the order Squamata, which also includes lizards, from which snakes evolved about 190 million years ago during the Jurassic Period. Extant (modern or living) snakes are divided into two major groups, the blindsnakes (aka threadsnakes or scolecophidians) and the advanced or true snakes (alethinophidians). Advanced snakes are also divided into two non-monophyletic groups, the "older snakes" (henophidians) and the "recent snakes" (caenophidians). The vast majority of all living snakes, about 77% or 2,650 species, are caenophidians, including most of the snakes you've probably heard of: rattlesnakes, cobras, kingsnakes, and many others. A few well-known snakes are henophidians, namely boas and pythons. Most scolecophidians are poorly known. Let's break down each of these groups in slightly more detail.


Ramphotyphlops braminus,
a parthenogenetic blindsnake
There are about 400 species of scolecophidians, divided into five families and found mostly in the tropics. They are commonly called blindsnakes, because many have vestigial eyes as a result of their fossorial lifestyle, or threadsnakes, because most are very thin. Most have unspecialized ventral scales, shed in thick rubbery rings, and have a spine at their tail tip. Many eat termites and ants. Most are probably oviparous, or egg-laying, but their reproductive biology is poorly known. Scolecophidians diverged from alethinophidians about 125 million years ago during the Cretaceous Period. You can read more about a fascinating mutualism between a blindsnake and an owl here, or about basic blindsnake biology here.

Phylogenetic tree showing currently accepted hypotheses of snake relationships. Figure from Lee et al 2007.
Thick lines are supported by both morphological and molecular studies, thin solid lines are supported
primarily by similarity of morphology, dotted lines are supported primarily by molecular analyses.


Anilius scytale
Red Pipesnake
"Henophidians" are a diverse, if species-poor, group of snakes. I mentioned earlier that they are non-monophyletic, meaning that some henophidians are more closely related to caenophidians than others, which is why the name of their group is in quotation marks. All henophidians shared a common ancestor about 98 million years ago, during the Cretaceous Period. There is some pretty major uncertainty about how henophidians are related to one another, but many taxonomies divide them into four superfamilies (which end in '-oidea' under the Linnean system). The most primitive, the Uropeltoidea, is comprised of five families (Aniliidae, Tropidophiidae, Anomochilidae, Cylindrophiidae, and Uropeltidae) that lack the ability to open their mouths very widely. These snakes have stout skulls with few lizard-like teeth, short tails, and poorly developed ventral scales. Most are viviparous, meaning that they give birth to live young, except the anomochilids, which are oviparous. There is better evidence linking the former two and latter three groups than there is for combining all five families together into a single superfamily. Also, two enigmatic species in the genus Xenophidion might belong somewhere in here.

Calabaria reinhardtii,
the Cameroon Burrowing Boa,
the only oviparous booid
The rest of the henophidians together with the caenophidians are often called the macrostomatans, because they have the ability to open their mouths (Greek: stomata) very wide and consume very large (Greek: macro) prey items. The most primitive of these are the oviparous Pythonoidea, a superfamily including true pythons (Pythonidae) as well as two small lesser-known groups respectively known as the Asian and Neotropical sunbeam snakes, the xenopeltids and the loxocemids. Pythonoids and a superficially similar but surprisingly unrelated group, the  viviparous booids (consisting of true boas and their less well-known relatives, the ungaliophine dwarf boas and the erycine sand boas),  diverged from other henophidians about 75 million years ago. Finally, the most advanced henophidians, the oviparous splitjaw snakes (aka Round Island "boas" or bolyeriids), diverged just slightly later than or around the same time as the true boas. Because the splitjaw snakes constitute only a single family and were historically considered boas, you don't usually hear them referred to as a fourth superfamily.


Acrochordus granulatus
Little Filesnake
This huge group is divided into two superfamilies, called Acrochordoidea and Colubroidea. The first is small, containing only three species of Acrochordus, the filesnakes of southeast Asia and north Australia. These diverged from other caenophidians about 60 million years ago. The second is huge and there is some uncertainty about the relationships therein, although thanks to recent work by Alex Pyron and his colleagues, the picture is becoming more clear. Traditionally, colubroids have been divided into groups based on their tooth morphology: those with fixed fangs were placed into Elapidae, those with folding fangs into Viperidae, and those without fangs lumped into Colubridae. The first two of these groups have proven to be for the most part monophyletic, certain exceptions notwithstanding. However, a more nuanced and accurate view of colubroid snake taxonomy is emerging thanks to a combination of molecular tools and decades of careful work by snake morphologists. Ready for it? Here it is:

Figure from Pyron et al. 2011
These snakes are exciting! These snakes have venom, excellent color vision, and sophisticated chemosensory, prey acquisition, and antipredator abilities. Also they have spines on their hemipenes. Also they are awesome. Can you tell which group is my favorite?

Dendrelaphis punctulatus
Common Treesnake
The traditional three-family tooth-morphology arrangement of colubroids has been replaced by the seven family arrangement seen above.3 Three of those seven families include several subfamilies. The most primitive colubroids are the xenodermatids, or odd-scaled snakes, which diverged from the others about 47 mya. The snail-eating pareatids are next, a group you'll be familiar with if you've been following this blog since the beginning. Next diverged the viperids or vipers, about 35 million years ago. There are three subfamilies of vipers: the old world viperines, the widespread crotalines (or pit vipers), and the monotypic Azemiopsinae, or Fea's Viper. True colubrids are still a large group, even though many species have been removed to the "new" families. The subfamilies are large and diverse, although most lack dangerous venom (a few species notwithstanding). You can read the story of the evolution of some of the subfamilies here. There are many well-known colubrids, including ratsnakes, kingsnakes, racers, hog-nosed snakes, and many others. Homalopsids, including some that chew their food, are a small but interesting group of semi-aquatic snakes found in southeast Asia. The front-fanged elapids (including cobras and coral snakes) have retained their monophyly, and little support has been found for recognizing the sea snakes as a separate family. Finally, we have the Lamprophiidae, a new family erected to contain former colubrids that turned out to be closer relatives of elapids. Lamprophiids also represent several interesting subfamilies, including the side-stabbing atractaspines, scale-polishing psammophines, and Malagasy pseudoxyrhophiines. I think Darren Naish would agree that there's plenty of fodder for future articles in these groups.

One a closing note, some non-snakes that are commonly mistaken for snakes, primarily because they have no legs, include:
  • Legless lizards: There are several groups of legless lizards. The North American glass lizards are among the most familiar. All have external ear openings and most have eyelids. In one sense, snakes are but one very diverse group of legless lizards.
  • Amphisbaenians: These are also technically lizards, but under some older taxonomies they are referred to as a separate group of reptiles, because they have a vestigial right lung and have a unique skeletal structure.
  • Caecilians: These most primitive of amphibians have slimy skin and are found underground in the world's tropics. Many are common prey of coral snakes.
  • Eels: Elongate fishes that actually do have limbs in the form of fins. There are several groups of fishes that are all colloquially called eels, including spiny eels, fire eels, electric eels, and true eels (Anguilliformes). Some amphibians are also sometimes called eels, including amphiumas or conger eels, sirens or mud eels, and rubber eels, a kind of caecilian.
  • Worms: There are several different major groups of worms, including roundworms (nematodes), flatworms (platyhelminths), and segmented worms (annelids).
Snake taxonomy is a complicated field and there is still much disagreement among experts. I have made several oversimplifications above, so if this is your area of expertise feel free to chime in with a comment or two. I hope you're looking as forward to reading more about many of these groups as I am looking forward to writing about them.

1 His wife tells me that mediocre is actually more accurate

2 A monophyletic group is one that contains a common ancestor and all of its descendants. Examples include groups like animals, vertebrates, mammals, birds, amphibians, primates, and snakes. A non-monophyletic group is one that either omits some descendants (e.g., "reptiles", which does not include birds, or "fishes", which does not include tetrapods) or omits the common ancestor (e.g., warm-blooded vertebrates, which includes mammals and birds but not their cold-blooded common ancestor).


Thanks to ptrick127, Gary Nafis, Tein-Shin Tsai, and Stephen Zozaya for use of their photos.


Lee, M. S. Y., A. F. Hugall, R. Lawson, and J. D. Scanlon. 2007. Phylogeny of snakes (Serpentes): combining morphological and molecular data in likelihood, Bayesian and parsimony analyses. Systematics and Biodiversity 5:371-389 <link>

Pyron, R. A., F. Burbrink, and J. J. Wiens. 2013. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Biology 13. DOI: 10.1186/1471-2148-13-93 <link>

Pyron, R. A., F. T. Burbrink, G. R. Colli, A. N. M. de Oca, L. J. Vitt, C. A. Kuczynski, and J. J. Wiens. 2011. The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees. Molecular Phylogenetics and Evolution 58:329-342 <link>

Zaher, H., F. G. Grazziotin, J. E. Cadle, R. W. Murphy, J. C. Moura-Leite, and S. L. Bonatto. 2009. Molecular phylogeny of advanced snakes (Serpentes, Caenophidia) with an emphasis on South American Xenodontines: A revised classification and descriptions of new taxa. Papeis Avulsos de Zoologia (Sao Paulo) 49:115-153. <link>

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Life is Short, but Snakes are Long by Andrew M. Durso is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License.

Wednesday, May 15, 2013

Tibetan Hot-spring Snakes

Everyone likes a good soak in a hot spring now and again, but imagine spending your whole life in one! Now imagine being the size of a pencil and unable to regulate your own body temperature, and you're doing a pretty good approximation of a Tibetan Hot-spring Snake (Thermophis). These tiny snakes reach only 2.5 feet in length and are found at fewer than ten sites on the Tibetan plateau in the Himalayan Mountains of south-central China, all above 14,000 feet elevation. For comparison, that's at least as tall as Mt. Rainier in Washington, Pike's Peak in Colorado, or Mont Blanc in the Alps. To cope with the cold, hot-spring snakes inhabit marshes, rivers, and rocky areas around sulfur-free hot springs, where they eat amphibians and fishes, including the dicroglossid frog Nanorana parkeri, the minnow Schizothorax oconnori, and elongate stone loaches in the genus Triplophysa. As you can see from this video, these are highly charismatic snakes.

Frank Wall
Hot-spring Snakes were first described in 1907 by a physician and herpetologist living in India named Frank Wall. Wall received specimens of this snake sent  from Tibet by Lieutenant F. M. Bailey, who reported that local people familiar with the snake told him that it could be found within half a mile of certain hot springs at any time of the year (although he stated that they did not enter the spring water, which has since been shown to be false). Wall was impressed by the altitude at which the snakes were found, which to date is still higher than any other snake known! Wall named the snake Natrix baileyi after Bailey, and in 1953 herpetologist Edmond Malnate moved it into a newly erected genus, Thermophis, meaning "heat snake" in Greek, giving it the name is has today: Thermophis baileyi. In 2008 a second species of Thermophis was discovered which differs slightly in scale characters and body proportions. Peng Guo of Yibin University named it Thermophis zhaoermii for preeminent Chinese herpetologist Zhao Ermi.

Just how remarkable these snakes are was not fully realized until recently. In the past, analyses of evolutionary relationships were limited to comparisons of morphological characteristics (for snakes, early taxonomists primarily relied on features of the scales and of the male reproductive organs, called hemipenes, to inform their hypotheses on how snakes were related to one another). Modern advances in molecular biology have enabled taxonomists to compare genetic sequences of related organisms and discover the intricate branching pattern of the evolutionary tree of life, essentially the family tree of all life on Earth. Although molecular phylogenetics, as this branch of science is called, is not flawless, it can provide incredible insight into the ancestry of species that have no close living relatives and therefore are very unique morphologically, making them difficult to compare with other organisms. Hot-spring Snakes are in this very situation, and although to a non-specialist they look pretty much like any other snake, their evolutionary history remained a mystery until 2009, when a group of biologists led by Zhao Ermi published two papers on the evolutionary origins of Thermophis.

Thermophis baileyi
As it turns out, Hot-spring Snakes are most closely related to South American snakes called xenodontines. Xenodontinae is one of the largest subfamilies of colubrid snakes, with about 90 genera and more than 500 species known. They are primarily tropical snakes previously thought to be restricted to the Americas, and they include several well-known (and many poorly-known) species, among them the South American Hog-nosed Snakes (genus Xenodon). Similarities of hemipenal morphology had hinted at a relationship between these taxa, but who would have guessed that the closest relatives of Hot-spring Snakes lived nearly 10,000 miles away on the tropical other side of the world? Not I, for one.

Thermophis baileyi
Hot-spring Snakes probably diverged from their "nearest" relatives about 28 million years ago. Despite the strengths of molecular phylogenetics, there is still some uncertainty about the position of Thermophis relative to other colubrid snakes because their branch of the tree arises near the base of a major clade (Xenodontinae), meaning that, as suspected, they have no close living relatives. In some phylogenies, Hot-spring Snakes are clustered with the "relict snakes of North America": CarphophisContia, Diadophis, Farancia, and Heterodon. Some of my favorite snakes, these are thought to have dispersed from Asia into North America during the Miocene, about 16 million years ago. (Diligent readers will recall that I've told this story before in my post on Rainbow Snakes, although I didn't know then about the involvement of Thermophis.)

Reproduced with permission from
Story in the Stone: The Formation of a Tropical Land Bridge
by Tom Gidwitz, illustration by David Stevenson & Greg Wenzel
Probably the common ancestor of all modern colubrids (Thermophis and NA relicts included) lived in Asia more than 30 million years ago. When the Bering Land Bridge connected North America and Asia, some of these snakes dispersed eastward across it, just like the ancestors of sabre-toothed tigers, woolly mammoths, and even Tyrannosaurus rex1. These evolved into a North American snake fauna, now largely extinct except for the few aforementioned relicts, and a hugely successful South American snake fauna, which was isolated from North America for a 5 million year period during the late Miocene-early Pliocene when the Isthmus of Panama was submerged by the ocean. One reason for this disparity is that two other groups of colubrid snakes, which are today the dominant colubrids of North America, the colubrines and the natricines, dispersed from Asia to North America around the same time as the xenodontines. Apparently ancestral colubrines and natricines dispersed more slowly than xenodontines, because they didn't reach South America before it separated. Instead, they only moved into South America following the most recent closing of the Isthmus of Panama in the late Pliocene, in an event known as the Great American Biotic Interchange. The GABI was responsible for allowing toads, treefrogs, opossums, armadillos, hummingbirds, and vampire bats to colonize North America, and salamanders, pit vipers, rabbits, squirrels, raccoons, deer, and jaguars (and colubrine and natricine snakes) to colonize South America. Assuming that Thermophis are all that's left of the original Asian proto-xenodontine snake stock, this pattern explains the evolutionary and biogeographic relationships of the Hot-spring Snakes and their relatives. However, given other recent discoveries in Asia, I wouldn't rule out the future discovery of another Asian proto-xenodontine more closely related to Thermophis than to any other known snake.

One reason we know only a little about Thermophis is its high mountain habitat. Most of the mountain ranges in China run east-west, but the Hengduan Mountains, where Hot-spring Snakes are found, stretch north-south (the name "Hengduan" means "to transect" and "cut downward" in Chinese). Parallel north-south sub-ranges of the Hengduans are separated by deep river valleys through which flow the famous Three Parallel Rivers: the Nujiang (Salween), Lantsang (Mekong), and Jinshajiang (Upper Changjiang or Yangtze). Thermophis baileyi is distributed west of the Salween, whereas T. zhaoermii is distributed east of the Changjiang. Geologic uplift of the intervening region of southern Tibet has lasted for about the last 20 million years, about the same age as the divergence between the two extant species of Thermophis. It is hypothesized that refuges in the Kyi Chu/Lhasa and Yarlung Zhangbo valleys during the last glacial maximum probably allowed T. baileyi to persist in the west, alongside such glacial relicts as neo-endemic ground beetles, juniper trees, and even humans. Following the end of the last Ice Age, they dispersed to other hot spring sites, and today connectivity among these sites is maintained when male snakes make rare movements among them, probably facilitated by the rivers and streams that connect the sites. Female snakes are less likely to disperse, because the plateau's short summers necessitate highly seasonal reproduction. Whether Thermophis are oviparous or viviparous is still unknown.

Sylvia Hofmann's photo of T. baileyi
made the cover of  the
Herpetological Bulletin
in 2007
Although the advantages of living around hot springs at high altitudes, where the temperature is relatively cold, are pretty obvious, recent surveys by Ding-qi Rao found that Hot-spring Snakes also live in fields and other areas far from hot springs, suggesting that the species' ecological niche may be wider than previously thought. This is fortunate, both because the growing exploitation of geothermal energy has led to destruction and degradation of hot spring habitats, and because global climate change will likely continue to cause mountaintop habitats around the world to shrink, necessitating a shift upward in elevation by high-altitude species in order to follow their habitat. This problem has been documented for pikas and for birds and will likely affect Hot-spring Snakes too. Because the ability of mountaintop species to disperse across intervening areas to higher mountain ranges is limited, many may go extinct. Will we one day see the top of Mount Everest as the last foothold for Hot-spring Snakes? Let's hope not.

1 Not all of these dispersal events happened at the same time. Evidence suggests that the Bering Land Bridge has connected North America with Asia several times over the last seventy million years: at least once during the time of the dinosaurs, again about 55 million years ago, another 20-16 mya, and more recently both 35,000 and 22-7,000 years ago. The ancestors of the New World xenodontines probably came across 20-16 million years ago.


Thanks to photographers Kai Wang, Daniel Winkler, Sylvia Hofmann, Brian McDiarmant, and Gavin Maxwell for use of their photographs, and to Tom Gidwitz, David Stevenson, and Greg Wenzel for allowing me to reproduce their artwork.

Guo, P, Liu S, Feng J, He M (2008) The description of a new species of Thermophis (Serpentes: Colubridae). Sichuan Journal of Zoology 27:321 <link>

Guo, P., S. Y. Liu, S. Huang, M. He, Z. Y. Sun, J. C. Feng, and E. M. Zhao. 2009. Morphological variation in Thermophis Malnate (Serpentes: Colubridae), with an expanded description of T. zhaoermii. Zootaxa 1973:51-60 <link>

He M, Feng J, Zhao E (2010) The complete mitochondrial genome of the Sichuan hot-spring keel-back (Thermophis zhaoermii; Serpentes: Colubridae) and a mitogenomic phylogeny of the snakes. Mitochondrial DNA 21:8-18 <link>

Hofmann S (2012) Population genetic structure and geographic differentiation in the hot spring snake Thermophis baileyi (Serpentes, Colubridae): indications for glacial refuges in southern-central Tibet. Molecular Phylogenetics and Evolution 63:396-406 <link>

Hofmann S, Fritzsche P, Solhøy T, Dorge T, Miehe G (2012) Evidence of sex-biased dispersal in Thermophis baileyi inferred from microsatellite markers. Herpetologica 68:514-522 <link>

Huang S, Liu S, Guo P, Zhang Y, Zhao E (2009) What are the closest relatives of the hot-spring snakes (Colubridae, Thermophis), the relict species endemic to the Tibetan Plateau? Molecular Phylogenetics and Evolution 51:438-446 <link>

Pinou, T., S. Vicario, M. Marschner, and A. Caccone. 2004. Relict snakes of North America and their relationships within Caenophidia, using likelihood-based Bayesian methods on mitochondrial sequences. Molecular Phylogenetics and Evolution 32:563-574 <link>

Sekercioglu, C. H., S. H. Schneider, J. P. Fay, and S. R. Loarie. 2008. Climate change, elevational range shifts, and bird extinctions. Conservation Biology 22:140-150 <link>

Wall, F. 1907. Some new Asian snakes. The Journal of the Bombay Natural History Society 17:612-618 <link>

Creative Commons License

Life is Short, but Snakes are Long by Andrew M. Durso is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License.