Tuesday, December 16, 2014

What's the big deal about these snake genomes anyway?

This post will soon become available in Spanish

King Cobra (Ophiophagus hannah; top) and
Burmese Python (Python bivittatus; bottom),
the two snake species whose genomes
were fully sequenced in 2013
One year ago today, the first snake genomes ever sequenced hit the newsstands. OK, so two papers in Proceedings of the National Academy of Sciences isn't exactly the cover of Time magazine to most people, but it was big enough news that it was covered by The Huffington Post and the two most prominent interdisciplinary scientific journals, Science and Nature, the former devoting a special section to the event. One year later, dear reader, welcome to the Life is Short, but Snakes are Long coverage of the snake genome project. So just what is the big deal about these snake genomes anyway, and what's changed in snake biology in the year that they've been available?

In one way, sequencing a snake genome means that snakes finally join the illustrious ranks of lab animals like the mouse, rat, guinea pig, fruit fly, and amoeba, all of whom have already had their genomes sequenced. By now the genomes of several hundred species have been sequenced, starting with a virus in the 1970s, and the first archaeon, bacterium, and eukaryote within one year of one another in 1995-96. The first animal genome sequenced was that of the model nematode Caenorhabditis elegans in 1998, and the first vertebrate was a pufferfish, so chosen because its genome is so small, in 2002 (although an incomplete first draft of the human genome preceded that by a year). As of 2014, we're now up to just over 100 vertebrate species, about 60 of which have been annotated and formally published, as well as numerous other animals, plants, fungi, protists, and prokaryotes. Last week, Science highlighted drafts of 38 new bird and 3 new crocodilian genomes, the largest single release of vertebrate genomes to date. But we are still a long way from sequencing the genomes of all known species. Why have we chosen the species we have? What does it mean to sequence a genome, exactly, and why do we do it?

Breakdown of what the human genome
consists of. Exons are coding DNA.
From Reece et al. (2013)
We use the word genome to refer to all the DNA within a single organism. Confusingly, this is not quite the same thing as saying all the genes in an organism, because we usually only call sections of DNA "genes" if we know what they do. You've probably heard that 98% of the human genome is "junk", or non-coding, DNA, which is just another way of saying that we haven't figured out what it does yet. Actually, we now know lots of things that non-coding DNA is good for, but we still usually don't call most of that DNA "genes" because we use that word specifically to mean sections of DNA that are read out via RNA and translated (usually) into proteins, which then have obvious effects on cells and the body. Non-coding DNA can also have effects on the body, often by regulating other genes, but it works in a more complicated way that we don't yet fully understand, so we tend make over-generalizations about it or dismiss it as unimportant.

Avian tree of life based on whole-genome
sequences. We're still several years away from
a tree like this for squamate reptiles.
From Jarvis et al. 2014
When we say we have sequenced the genome of an organism, we mean that we have read the sequences of all of its DNA, every one of its genes and all of its non-coding DNA, even if we don't know what it all does. The -ome suffix is added to the word 'gene' to signify "all". Yogis will be familiar with the Sanskrit word Om, which means "the whole thing", something that encompasses the entire universe in its unlimitnedness. Other fields in biology that consider all constituents of something collectively have picked up on this neologism, so we have proteomics (the study of all the proteins in a particular organism), transcriptomics (the study of all the RNA), and so on. Genomes are huge1, and we've strategically chosen species to sequence that are scattered across the diversity of life so that we can construct a skeletal tree of life based on genomic data. We have high confidence in such a tree2 because whole genomes contain so much data that trees built from them are more likely to reflect true evolutionary relationships than trees built from just one or a few genes. So we've selected exemplars from each major group of organisms to start out with (e.g., one sea urchin, one sea squirt, one lamprey), and eventually we'll go back and fill in the gaps. By sequencing the King Cobra (Ophiophagus hannah) and Burmese Python (Python bivittatus) genomes first, we're setting these species up to become model organisms, exemplars, and in some ways stand-ins for all of snake diversity in many future studies.

Understanding the genes controlling variation among individuals
of the same species, like the color morphs of these Groundsnakes
(Sonora semiannulata), must await population genomics
and a better understanding of gene expression regulation
When we sequence a genome we read all the DNA from a single individual3. This is different from knowing all the possible variants (often called alleles) of those genes. It's often said that a person has "the genes for" something, when in reality all people have the same genes, with different alleles. For example, if the person whose genome was sequenced in the Human Genome Project had brown eyes, we'll just have the gene sequences for brown eyes, not for blue or green. In order to get an idea of all the possible variants of all the genes in a species, we'll need to sequence the genomes of many individuals. Some genes, such as those involved in the immune system, have over 1,500 alleles (the "gene pool"), no more than two of which occur within the genome of a single individual (one from the mother and one from the father). So understanding the entire gene pool of a species is a very daunting task, given that we only have whole genomes for a few hundred species (one individual each), with multiple individuals of a few species, including humans.4 Population genomics is an emerging field, yet to be applied to snakes in any form, although apparently a few projects are in the works.

So what have we learned from these snake genomes? Here are the basics:
  • Snake genomes are about half the size of the human genome (although an organism's complexity is not directly proportional to its genome size; for example, some salamander genomes are more than 60 times larger than the human genome).
  • The proportion of repetitive elements ("junk DNA") in snake genomes is about the same as that in humans (~60%).
  • Snakes have a faster baseline rate of evolution than other reptiles, birds, or mammals, as
    Red represents fast rates of neutral substitution
    From supplement to Castoe et al. 2013
    evidenced by their larger accumulation of neutral substitutions. and colubroid snakes have rates even faster than that of snakes at large.
  • Adaptive evolution (as evidenced by functional, non-neutral, changes to genes) in snakes has happened to over 500 genes, especially those involved in the development of the limbs, spine, skull, and eye, and those regulating the function of the cardiovascular system, lipid and protein metabolism, and cell birth and death. We already knew that all of these systems in snakes were highly modified relative to other vertebrates, and now we know that the genes that underlie them are too.
  • Some groups of genes have grown or shrank in snakes - for example, snakes have a lot more genes coding for vomeronasal receptors, and a lot fewer genes coding for opsins, which are light-sensitive proteins in the eye. This makes sense given what we know about snake sensory systems.
  • Changes to gene expression that happen after a snake feeds involve thousands of genes that control rapid changes in organ size - but genes that control cell division change in the kidney, liver, and spleen, organs that grow by cell division, but not in the heart, which grows when individual existing cells get larger.
  • Snake genomes contain endogenous viral elements from three families of viruses that have recurrently infiltrated their DNA over the past 50 million years. This is actually not rare, although it is bizarre and awesome that the 'fossils' of these ancient viral genomes can be identified in their host genomes even after tens of millions of years, and it can help us better understand both the biology of viruses and that of their snake hosts, including how viruses have contributed functions to the genetic repertoires of their hosts.
From the cobra genome in particular, we've learned or confirmed a great deal about the evolution of snake venoms. In particular, we now know that, unlike the venom of the platypus, the only other venomous vertebrate with a sequenced genome, snake venom has evolved primarily through gene duplication and restriction. Many venom proteins probably evolved like this:
  1. A snake has a gene that makes a protein somewhere in its body, including possibly in its salivary or venom gland5
  2. The gene for that protein is duplicated by accident during routine DNA replication or repair, resulting in a new, spare copy of the gene
  3. The effects of selection are relaxed on the duplicate gene, which gives it opportunities to mutate
  4. Mutations to transcription-factor binding sites change the signal for where the duplicate gene should be expressed, causing the new protein to be made only in the venom gland
  5. If the new protein helps the snake catch more prey, it improves fitness and causes natural selection
  6. Because the old protein is still being made, the new gene and protein are free to evolve to become more toxic or to take on some new function
  7. The new copy of the gene may become duplicated again, and subsequent new copies may mutate further, leading to diversification within a gene/toxin family6
The King Cobra venom gland, with
expression profiles of the venom (left) and
accessory gland (right). From Vonk et al. 2013
It's not yet clear to what extent the evolution of these novel toxic venom proteins corresponded with a shift to higher levels of their expression in the venom gland and lower levels of expression elsewhere. Although it seems obvious that their expression in non-venom-gland tissues would be harmful, their non-toxic orthologs are expressed in tissues as diverse as the kidney and brain in pythons, and no one has yet measured their expression outside of the venom gland in venomous snakes. Alternatively, gene duplication might have taken place after the change in function, if the genes in question were alternatively spliced to produce both toxic and non-toxic proteins from the same gene. Evolution  of siRNA and other regulatory elements (which is hard to detect because there's still a lot we don't understand about how it works) could then restrict expression of a particular splice variant to the venom gland, which could explain why we're seeing evidence that the venom protein genes themselves are often still expressed in other tissues even though they are capable of coding for highly toxic proteins that must be maintained in the venom gland in a competent but inactive state.

The cobra genome by itself does not answer these questions, even with help from that of the python. In order to fully understand the evolution of snake venoms (with major implications for public health, particularly in developing countries, not to mention the potential of venoms to be used as drugs), we'll need genomic, transcriptomic, and proteomic data from numerous snake species.

Characterization of genomic biodiversity has the potential to change our understanding of evolution in fundamental ways. From explaining how snakes are capable of physiological feats to helping us understand how new genes appearwhat "junk DNA" does, and what the tree of life looks like, genome sequencing is one of the most exciting current frontiers in biology. As in many things, snakes are (one of) the last groups of vertebrates to the party (although it's worth noting that there aren't any fully annotated salamander or caecilian genomes yet). A snake genome doesn't add a whole lot to the picture of the vertebrate tree of life, because the Green Anole genome, sequenced in 2011, represents squamates on the tree, and no one is arguing that snakes aren't squamates. But, within squamates there are a number of puzzling unresolved relationships, including such fundamental questions as the origin of snakes and the placement of iguanians. In the interest of helping to shed light on these, and on the aforementioned complexity of snake venom evolution, another 10 or so snake genomes are likely to come out within the next couple of years, including those of the:
  • Texas Blindsnake (Rena dulcis)
  • Reticulate Wormsnake (Amerotyphlops reticulatus)
  • Red Pipesnake (Anilius scytale)
  • Mexican Burrowing Python (Loxocemus bicolor)
  • Round Island Splitjaw Snake (or "boa"; Casarea dussumieri)
  • Boa Constrictor (Boa constrictor)
  • Western Diamond-backed Rattlesnake (Crotalus atrox)
  • Speckled Rattlesnake (Crotalus mitchelli)
  • Copperhead (Agkistrodon contortrix)
  • Eastern Coralsnake (Micrurus fulvius)
  • Cloudy Snail-eating Snake (Sibon nebulatus)
  • Common Gartersnake (Thamnophis sirtalis)
As you can probably see if you know your snake taxonomy, these species represent a scattering of well-known snakes from each of the major branches of the snake tree. They have been strategically chosen to enable snake biologists to use them to put together a well-supported skeleton of the snake tree of life. However, several branches (such as the dwarf pipesnakes, acrochordids, and lamprophiids) are still missing.7 In particular, an atractaspidid genome would be useful in building a better understanding of the role of convergence in snake venom evolution - resolving the debate between proponents of a single ancient origin for venom and those of several more recent, independent origins. Genomes of scolecophidian blindsnakes and toxicoferan lizards such as Gila monsters will also help resolve this question. Hopefully, these genomes and others will continue to illuminate evolutionary biology for us in ways Darwin could have scarcely imagined.



1 Because genome sequences contain so much data, they are stored electronically and require a large amount of computing power and storage capacity. The computing power is actually more limiting than the biochemistry right now. A human genome contains about 6 billion base pairs (one for each person on Earth in 1999), which take up a couple of gigabytes. If that doesn't sound that impressive, imagine all that information stored 
in every one of your cells, then compare the size of a cell with that of a microchip here.



2 This is not to say that (as has been presumed by many) molecular data are inherently superior to morphological data, especially in the case of extinct fossil taxa, from which we cannot garner much molecular information (although that generalization too has been challenged).



3 How are the individuals whose genomes are sequenced chosen? The unsatisfying answer is that the scientists involved typically use whatever individuals are convenient. Specifically, the cobra and python genomes seem to have been taken from animals from the pet trade. We may not know the true geographic origin of these individuals, or even whether they might be the offspring of animals from two or more different parts of the species' range. Why is this important? If we sequence the genome of a cobra from Indonesia, but cobras in India have evolved different venom genes because of different evolutionary pressures, then we won't know that until we get some cobras from India. Taxonomic conclusions drawn from 
Boa constrictor gene sequences on GenBank are dubious because of the ambiguous origins of many of these specimensThe primary reasons to sequence a whole genome are subtly different from the reasons to sequence individual genes, and scientists doing these tasks have different questions. But, we should be cautious about inferring too much from the genome sequence of a single individual of any species.



4 Right now if you're a human you can actually get your whole genome sequenced for less than $5000, even though the first human genome cost over $3 billion, because we've optimized the process.



5 It's unclear how many venom proteins were originally made in the venom gland before they became toxic, and how many were recruited to this tissue following duplication. The original cobra genome paper by Vonk et al. implies that the latter is most common, whereas subsequent work by Hargreaves et al. uses gene expression data from Leopard Gecko salivary glands
 to suggest the former. Reyes-Velasco et al. used the python genome and transcriptome to suggest that venom genes are recruited preferentially from genes that are expressed at low levels in most tissues but at more variable levels than average across tissues.



6 Of the approximately 24 gene families that code for snake venom proteins, those that produce toxins that are known to be important in prey capture (e.g., the three-finger neurotoxins) have undergone repeated duplication and selection, whereas venom components that perform ancillary functions, such as helping the snake to relocate its bitten prey, do not show high rates of duplication or selection. These rates are probably further influenced by the need to target diverse receptors in different types of prey (in snakes with broad diets), and by predator-prey co-evolutionary arms races (in snakes with narrow diets).



7 A recent effort by a different research group generated a tree for Caenophidia using 333 loci totaling 225,140 base pairs for each of 31 snake species, almost 80,000 of which were informative. This is a drastic improvement on the 10 loci and maximum of 5,814 base pairs of the most comprehensive previous studies, but it is still a long way from the entire genome. Incredibly, they were still unable to resolve certain difficult parts of the snake family tree.


ACKNOWLEDGMENTS

Thanks to JD Willson, Baloch Imrankhan, and Alison Davis Rabosky for the use of their photographs, and to Alison Davis Rabosky and Todd Castoe for providing me with information regarding genomics.

REFERENCES

Alföldi et al. 2011. The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature 477:587-591 <link>

Armengaud, J., J. Trapp, O. Pible, O. Geffard, A. Chaumot, and E. M. Hartmann. 2014. Non-model organisms, a species endangered by proteogenomics. Journal of Proteomics 105:5-18 <link>

Castoe et al. 2013. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proceedings of the National Academy of Sciences 110:20645–20650 <link>

Cox, C. L. and A. R. D. Rabosky. 2013. Spatial and Temporal Drivers of Phenotypic Diversity in Polymorphic Snakes. The American Naturalist DOI: 10.1086/670988 <link>

Gauthier, J. A., M. Kearney, J. A. Maisano, O. Rieppel, and A. D. B. Behlke. 2012. Assembling the squamate Tree of Life: perspectives from the phenotype and the fossil record. Bulletin of the Peabody Museum of Natural History 53:3-308 <link>

Hargreaves, A. D., M. T. Swain, M. J. Hegarty, D. W. Logan, and J. F. Mulley. 2014. Restriction and recruitment-gene duplication and the origin and evolution of snake venom toxins. Genome Biology & Evolution 6:2088-2095 <link>

Hargreaves, A. D., M. T. Swain, D. W. Logan, and J. F. Mulley. 2014. Testing the Toxicofera: Comparative transcriptomics casts doubt on the single, early evolution of the reptile venom system. Toxicon. DOI:10.1016/j.toxicon.2014.10.004 <link>

Jarvis et al. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346:1320-1331 <link>

Losos, J., D. M. Hillis, and H. W. Greene. 2012. Who speaks with a forked tongue? Science 338:1428-1429 <link>

Mackessy, S. P. and L. M. Baxter. 2006. Bioweapons synthesis and storage: The venom gland of front-fanged snakes. Zoologischer Anzeiger 245:147-159 <link>

Pyron, R. A., C. R. Hendry, V. M. Chou, E. M. Lemmon, A. R. Lemmon, and F. T. Burbrink. 2014. Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia). Mol. Phylogenet. Evol. 81:221-231 <link>

Reyes-Velasco, J., D. C. Card, A. Andrew, K. J. Shaney, R. H. Adams, D. R. Schield, N. R. Casewell, S. P. Mackessy, and T. A. Castoe. 2014. Expression of venom gene homologs in diverse python tissues suggests a new model for the evolution of snake venom. Molecular Biology and Evolution <link>

Schweitzer, M. H. 2011. Soft tissue preservation in terrestrial Mesozoic vertebrates. Annual Review of Earth and Planetary Sciences 39:187-216 <link>

Vonk et al. 2013. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Proceedings of the National Academy of Sciences 110:20651–20656 <link>

Yadav, S. P. 2007. The wholeness in suffix -omics, -omes, and the Word Om. Journal of Biomolecular Techniques 18:277 <link>

Zelanis, A. and A. Keiji Tashima. 2014. Unraveling snake venom complexity with ‘omics’ approaches: challenges and perspectives. Toxicon <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.

Tuesday, November 25, 2014

The 9,999th Reptile

This post will soon become available in Spanish

Number of new snake species by decade, with highlights
Data from The Reptile Database
Linnaeus's 1758 Systema Naturae, the starting point of zoological nomenclature, described 118 species of reptiles, including 74 snakes (not counting the limbless lizards and amphibians he included in the same group). It took over 100 years for the number of described species of snakes to reach 1000, an event that probably passed without much notice amid the American Civil War. Since that time, new snake species descriptions have been added at the rate of about 15 a year, although molecular taxonomy has increased this pace over the last few decades. The trends for snakes and for reptiles as a whole have been similar, and on July 9th, 2014, a team of American, German, Lao, and Vietnamese scientists described a new species of gecko from Laos, which the journal Herpetological Review reported as the 10,000th reptile species. Needless to say, I was excited, but I was also extremely disappointed because I had been so hoping that it would be a snake! Rather than admit defeat and scrap this planned post, I emailed Peter Uetz at The Reptile Database, an incredible resource that I've praised before, to confirm that this gecko was indeed #10,000. As usual for taxonomy and as I should have suspected, the reality was a bit more complicated.

Although Cyrtodactylus vilaphongi was the 10,000th reptile species for a while, the order and position of entries in The Reptile Database is constantly changing. Although new species get added to the end of the list, it's common for two or more existing species to get synonymized or merged, which moves the position of all subsequent species up. Furthermore, sometimes species that were described long ago and subsequently synonymized are revalidated, leading to 'new' species that aren't really new in the sense that they have existed before. Finally, often existing species get split up, leading to additions that aren't as dramatic as legitimate new discoveries. This last complication is on the rise now that molecular systematics has enabled us to describe the cryptic diversity of some lineages, which are not all that morphologically distinct but may contain considerable genetic diversity.

At the time of my email to Peter last month, C. vilaphongi was the 9988th species, and (happily), a new snake, Siphlophis ayauma, was #10,000. Although this has probably changed again by now, I'm going to operate under the assumption that, since we can't really say with certainty that any particular species was #10,000, if it was a snake, it was probably one of the 11 brand new snake species that have been described so far this year. You can read about many of these on the blog 'Species New to Science', but I'm going to highlight them in a little more detail here.

Rhabdophis guangdongensis
From Zhu et al. 2014
The first new snake described this year, Rhabdophis guangdongensis, was collected by a team of Chinese herpetologists in Guangdong Province in 2008. The reason it wasn't described until the February 20th issue of the journal Zootaxa is because, as is often the case, it takes a couple of years to compare both the anatomy and the DNA of a suspected new species to reference specimens of known similar species and establish that the species really is new. In the past, particularly prior to the internet, the difficulty of doing this was a huge problem, resulting in close to half of all 'new' species later being invalidated as duplicates. The genus Rhabdophis  is distributed in southern and eastern Asia, and this is the 21st species. It's an extremely interesting genus from a chemical ecology perspective, because at least one species sequesters defensive chemicals from its prey and provisions them to its young (which I wrote about for Scientific American shortly after I started this blog). A recent paper by Yosuke Kojima and Akira Mori on the Japanese species R. tigrinus showed that females periodically leave wetlands for forest streams where they forage on toads, likely to obtain the necessary toxins for provisioning their offspring. The new species also has specialized structures, known as nuchal glands, on the back of its neck, so presumably it stores bufotoxins there as well, although this has yet to be verified.

Opisthotropis durandi
From Teynié et al. 2014
On March 3rd, a team of French, German, and Vietnamese scientists published a description of Opisthotropis durandi, a highly aquatic snake collected from the base of a waterfall in northern Laos. This is the seventh species of Opisthotropis described in the past 20 years, and the first from Laos (although other species are likely to occur there based on their occurrence in surrounding countries). Like the new Rhabdophis, it is also the 21st species in its genus. It is important to realize that, like most species new to science, this snake was already known by local people. It is called Ngou Koung or Ngou Kung, meaning “shrimp snake”, suggesting that it may eat shrimp. The pools at the base of the waterfall where the first specimen was found contained many small shrimp.

Eutrachelophis bassleri and its weird penis
From Myers & McDowell 2014
Harvey Bassler, a petroleum geologist, explored many of the Amazon's upper tributaries for his work during the 1920s and 30s, during which time he collected over 4,200 snakes on the side. Bassler deposited his magnificent collection in the American Museum of Natural History in 1934, and on March 6th this year Charles Myers and Samuel McDowell published a monograph in the Bulletin of the American Museum of Natural History describing a species of snake collected by Bassler in 1927, for which they erected a new genus, Eutrachelophis (‘beautiful-necked snakes’’). They also placed in this genus a species originally described by Boulenger in 1905, Rhadinaea steinbachi, which they renamed Eutrachelophis steinbachi. Although the two species (and a third, yet undescribed) have very similar skeletons, muscles, glands, viscera, and markings, they probably would have been placed in separate genera had they been described in the 19th or early 20th century because their hemipenes are so different. E. steinbachi has long but relatively normal-looking hemipenes, whereas E. bassleri  has extremely unusual heimpenes tipped with a dome-like structure so strange (at least within the world of snake hemipenes) that the authors wrote "we have seen nothing quite like [it]." Hemipenes were traditionally considered one of the most taxonomically-important structures in snakes1 because they were considered to be evolutionarily neutral (that is, unlikely to change in response to selection), but a growing awareness that evolution by both natural and especially sexual selection can influence the morphology of male genitalia led these authors to recognize that these two snakes were in fact close relatives. Although we await molecular confirmation, the authors propose a mechanism by which differential expression of Hox genes2 could cause such a rapid divergence in hemipenal morphology between two sister species.

Siphlophis ayauma
From Sheehy et al. 2014
On January 12th, 2008, a group of American and Ecuadorian herpetologists stopped for lunch at a grilled-chicken restaurant in Paute, Azuay province, Ecuador. They noticed a peculiar sun-faded snake on display in a jar of alcohol that they couldn't quite put a name to. Following negotiation with the restaurant owner, the specimen was acquired and determined to belong to the genus Siphlophis, but could not be identified to any known species. A few months later, another specimen was found alive about 100 miles to the north, and two more were discovered in 2011 about the same distance to the south. A fifth individual is now recognized to have been hiding out unnoticed in the collection of the Museo de Zoología, Pontificia Universidad Católica del Ecuador. Because of its red-banded head and its occurrence in the mountains near cold (achachay) streams, the new species was named Siphlophis ayauma after the Kichwa spirit Aya Uma, a good spirit devil who derives strength from nature, particularly from cold mountain pacchas (cascades) and is represented in Kichwa folklore as having a colorful red-banded head. This is the seventh species in the genus, the third species known from Ecuador, and the first new species of Siphlophis since 1940. The results are published in the April 1st issue of the South American Journal of Herpetology.

Philodryas amaru
From Zaher et al. 2014
In a montane grassland high in the Andes Mountains of southern Ecuador, another genus gained its 21st species this year: Philodryas amaru. Known to the Ecuadorian and Brazilian authors since 2005, a small population of these striped racers was formally described in Zootaxa on April 4th this year. The new species resembles Philodryas simonsii in color pattern, but differs noticeably in its hemipenis morphology. "Amaru" means "snake" in Kichwa, and is also the name of a snake deity who influences water and the economy. This diurnal snake lays clutches of 9-13 eggs underground in galleries and under decaying logs, and probably eats frogs and lizards. It is a close relative of the Galapagos racers that I've written about before.

Causus rasmusseni
From Broadley 2014; photo by Paul L. Lloyd
Night adders (genus Causus) are a small and unusual group of vipers found in sub-Saharan Africa. They were once thought to be the most primitive vipers and were placed in their own subfamily, but they are now grouped with the viperines even though they have a plethora of unusual features: platelike head scales, round pupils, a different hinge mechanism for their erectile fangs, incomplete fang canal closure, and elongate venom glands in most species. On April 25th of this year, Don Broadley3 described the first new species of Causus since 1905. He named it Causus rasmusseni after the late Jens Rasmussen, a Dutch expert on African snakes who died in 2005. This species is found only in the watershed between the Congo and Zambezi basins, where it co-occurs with three other species of Causus. Broadley first became aware that there might be a new species of night adder in this region in 1991, when he noticed pale gray C. rhombetaus from northwestern Zambia with black markings and low ventral scale counts. In 2013, someone sent him a picture of one eating a toad (another unusual adaptation that night adders share with several other snakes), which prompted him to look again at the unusual specimens and describe them as a new species. Few molecular data are available for Causus, so this diagnosis is based on morphology alone.

Micrurus potyguaraFrom Pires et al. 2014
Brazil is graced with nearly 400 species of snakes, including 30 of the world's ~80 species of coralsnakes. The morphology of coralsnakes is highly variable, and there are many misidentified specimens in museum collections, so it is often difficult to recognize new species. A group of Brazilian herpetologists working on the tri-colored coralsnakes from the endangered northeastern coastal forests discovered a new species, which they described in the June 5th issue of Zootaxa (if any of these dates are your birthday, then you share a birthday with that of a new species of snake!).

Top: Jaw of Lycodon aulicus
From Jackson & Fritts 2004
Middle: Lycodon zoosvictoriae
From Neang et al. 2014
Bottom: Lycodon cavernicolus
From Grismer et al. 2014
Wolfsnakes (genus Lycodon) are named for their fearsome-looking fang-like anterior maxillary teeth. Unlike the true fangs of vipers, elapids, and atractaspidids, wolfsnake teeth are not grooved or hollow and they have no venom. Instead, their strongly arched upper jaw helps them feed on skinks, whose hard, cylindrical bodies fit snugly into their diastema, or the gap between their anterior and posterior teeth. The wolf-like anterior teeth keep the skink from being squeezed out of the mouth, while the posterior teeth slice through the skink's cycloid scales. At least 16 of the nearly 60 species of Lycodon have been described since the 1990s, including two this June: Lycodon zoosvictoriae from the Cardamom Mountains of southwestern Cambodia, and L. cavernicolus from a limestone cave in peninsular Malaysia. The latter is a cave-adapted species, both specimens of which were found climbing several feet above the cave floor, in total darkness. It's likely that they eat a cave-adapted gecko. Many of the caves in this region are in immediate danger of being quarried for cement before their endemic fauna and flora can be fully documented. Both of these species were also described in Zootaxa, which is a relatively new journal dedicated almost exclusively to rapid publication of new species descriptions, with the stated goal of aiding conservation efforts by circumventing the lengthy delays normally associated with publication of new science. Since its inception in 2001, Zootaxa has become a daily journal that has published nearly one quarter of all new animal taxa and nomenclatural acts in the last five years, including over 400 new species of reptiles and the 7000th species of amphibian.

"Cloudogram" of Crotalus triseriatus species group
showing the new nine-species arrangement
From Bryson et al. 2014
Just three days before the new gecko, a team of scientists from Mexico, the USA, and Canada published a genetic analysis of the Crotalus triseriatus species group, which contains small montane rattlesnakes found in Mexico and the southwestern USA. Although five species were historically recognized within the group, an analysis of seven nuclear genes revealed that there are at least nine species, including two that were previously recognized as subspecies and two more that have not heretofore been formally recognized. The paper described the two new species: Crotalus tlaloci, named for Tláloc, the Aztec god of rain, and Crotalus campbelli, named for herpetologist Jonathan Campbell. The authors of this paper suggest that these rattlesnakes speciated rapidly from a single common ancestor during the uplifting of the Trans-Mexican Volcanic Belt near the end of the Neogene period 2.6 million years ago, which makes sense because they are not very mobile and populations of their common ancestor likely would have become isolated from one another  on various "Sky Islands" of suitable habitat during the genesis of this new mountain range. Many species are endemic to the high-altitude pine-oak forests and grasslands of this region, which has become famous as the overwintering grounds of the Monarch Butterfly.

Chironius diamantina
From Fernandes & Hamdan 2014
Surprise! Just when you thought we were through, at press time the description of four more new species of snake had just been published, all from relatively recent issues of Zootaxa. One is a Brazilian species of Chironius, one of my favorite genera. Chironius diamantina is the 16th species in the genus, which is unusual is having a very low, even number of dorsal scale rows (10 or 12), the central pair of which are strongly keeled, giving the snake a distinctly flat-backed appearance. This species is found in riparian forests along rocky streams in coastal Brazil, not too far south of the new coralsnake (above). Chironius are diurnal and generally eat birds and mammals. Another is a new Asian keelbackHerpetoreas burbrinki, from near the border of China, India, and Burma. which is relatively closely related to the Rhabdophis above. Finally, two new species from the large ground-dwelling Latin American genus Atractus, both small and described from single specimens collected decades ago in Colombia (perhaps they will one day be rediscovered). More new species from both of these groups will likely follow, given the taxonomic untidiness of their genera. [Update: shortly after publication David Salazar-Valenzuela alerted me to the fact that I had missed his description, with colleagues, of a third new Atractus from the cloud forests of northern Ecuador earlier this year, in the journal Herpetologica. They mention that some of the specimens were collected from under logs alongside an undescribed species of slender blindsnake of the genus Trilepida, so it seems we are at 3,500 this year without a doubt!] [[Update II: It seems I missed more than I thought - a new species of Trimeresurus from Sumatra was described in September from specimens collected in 1899, and a new Ninia from Trinidad was described in August from a 1988 specimen.]]

In addition to these 15 species, there are a couple of species of snake which were described long ago but that were revalidated recently, including several scolecophidians (Typhlops silus, first described in 1959; Afrotyphlops angeli, first described in 1952; and Letheobia acutirostrata, first described in 1916) and a rattlesnake (Crotalus armstrongi, originally described as a subspecies in 1979 and elevated by the same group that described C. tlaloci and C. campbelli). These are typically announced with less fanfare than the truly new descriptions that I've highlighted above.

Although it's actually been the slowest year for new snakes since 19974, we have 15 new snakes this year, bringing snakes to a total of 3,499 (and 2014 isn't over yet!). We could make it to 3,500 snakes in the same year that we hit 10,000 reptiles. I think these milestones in taxonomy emphasize the importance of reptiles and how much we have left to learn about them. I doubt that the pace of new species descriptions will slow down anytime soon, as experts estimate that less than 15% of the species on Earth have yet been described. Increasingly, reptiles, and snakes in particular, are becoming poster-children for biodiversity and conservation, a welcome change from their history of being overlooked and maligned. Soon, we will have high-quality global range maps for all species of reptiles, an achievement reached some time ago by amphibians, mammals, and birds, which will enable their incorporation into global assessments of vertebrate diversity and conservation planning. It's an exciting time.

ACKNOWLEDGMENTS

Thanks to Peter Uetz at The Reptile Database for sharing with me some inside information, and to the authors of these papers for their photos.

REFERENCES

Newspaper clipping from 10 January 1960
showing Broadley with his amputated finger.
You can see more at the finger's Facebook page
or listen to Broadley describe the experience here.
Angarita-Sierra, T. 2014. Hemipenial Morphology in the Semifossorial Snakes of the Genus Ninia and a New Species from Trinidad, West Indies (Serpentes: Dipsadidae). South American Journal of Herpetology 9:114-130 <link>

Broadley, D. G. 2014. A new species of Causus Lichtenstein from the Congo/Zambezi watershed in north-western Zambia (Reptilia: Squamata: Viperidae). Arnoldia Zimbabwe 10:341-350 <link>

Bryson, R. J., C. W. Linkem, M. E. Dorcas, A. Lathrop, J. M. Jones, J. Alvarado-Diaz, C. I. Grunwald, and R. W. Murphy. 2014. Multilocus species delimitation in the Crotalus triseriatus species group (Serpentes: Viperidae: Crotalinae), with the description of two new species. Zootaxa 3826:475-496 <link>

Cope, E. D. 1895. The classification of the Ophidia. Transactions of the American Philosophical Society 18:186-219 <link>

Dowling, H. G. 1967. Hemipenes and other characters in colubrid classification. Herpetologica 23:138–142 <link>

Grismer, L. L., E. S. H. Quah, S. Anuar, M. A. Muin, P. L. Wood Jr, and S. A. M. Nor. 2014. A diminutive new species of cave-dwelling Wolf Snake (Colubridae: Lycodon Boie, 1826) from Peninsular Malaysia. Zootaxa 3815:51-67 <link>

Guo, P., Q. Liu, L. Zhang, J. X. Li, Y. Huang, and R. A. Pyron. 2014. A taxonomic revision of the Asian keelback snakes, genus Amphiesma (Serpentes: Colubridae: Natricinae), with description of a new species. Zootaxa 3873:425-440 <link>

Fernandes, D. and B. Hamdan. 2014. A new species of Chironius Fitzinger, 1826 from the state of Bahia, Northeastern Brazil (Serpentes: Colubridae). Zootaxa 3881:563-575 <link>
Trimeresurus gunaleni
From Vogel et al 2014

Jackson, K. and T. H. Fritts. 2004. Dentitional specialisations for durophagy in the Common Wolf snake, Lycodon aulicus capucinus. Amphibia-Reptilia 25:247-254 <link>

Köhler, G. and M. Kieckbusch. 2014. Two new species of Atractus from Colombia (Reptilia, Squamata, Dipsadidae). Zootaxa 3872:291-300 <link>

Linnaeus, C. 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata. [10th ed.]. Laurentii Salvii, Holmiae, Stockholm, Sweden <link>

Myers, C. W. and S. B. McDowell. 2014. New Taxa and Cryptic Species of Neotropical Snakes (Xenodontinae), with Commentary on Hemipenes as Generic and Specific Characters. Bulletin of the American Museum of Natural History 385:1-112 <link>

Neang, T., T. Hartmann, S. Hun, N. J. Souter, and N. M. Furey. 2014. A new species of wolf snake (Colubridae: Lycodon Fitzinger, 1826) from Phnom Samkos Wildlife Sanctuary, Cardamom Mountains, southwest Cambodia. Zootaxa 3814:68-80 <link>

Pires, M. G., N. J. da Silva Jr., D. T. Feitosa, A. L. d. C. Prudente, G. A. P. Filho, and H. Zaher. 2014. A new species of triadal coral snake of the genus Micrurus Wagler, 1824 (Serpentes: Elapidae) from northeastern Brazil. Zootaxa 3811:569-585 <link>


Atractus savagei
From Salazar-Valenzuela et al. 2014
Salazar-Valenzuela, D., O. Torres-Carvajal, and P. Passos. 2014. A New Species of Atractus (Serpentes: Dipsadidae) from the Andes of Ecuador. Herpetologica 70:350-363 <link>

Schneider, N., T. Q. Nguyen, M. D. Le, L. Nophaseud, M. Bonkowski, and T. Ziegler. 2014. A new species of Cyrtodactylus (Squamata: Gekkonidae) from the karst forest of northern Laos. Zootaxa 3835:80-97 <link>

Sheehy, C. M., M. H. Yánez-Muñoz, J. H. Valencia, and E. N. Smith. 2014. A new species of Siphlophis (Serpentes: Dipsadidae: Xenodontinae) from the eastern Andean slopes of Ecuador. South American Journal of Herpetology 9:30-45 <link>

Teynié, A., A. Lottier, P. David, T. Q. Nguyen, and G. Vogel. 2014. A new species of the genus Opisthotropis Günther, 1872 from northern Laos (Squamata: Natricidae). Zootaxa 3774:165-183 <link>

Uetz, P. 2010. The original descriptions of reptiles. Zootaxa 2334:59-68 <link>

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

Zaher, H., J. C. Arredondo, J. H. Valencia, E. Arbeláez, M. T. Rodrigues, and M. Altamirano-Benavides. 2014. A new Andean species of Philodryas (Dipsadidae, Xenodontinae) from Ecuador. Zootaxa 3785:469–480 <link>

Zhu, G.-X., Y.-Y. Wang, H. Takeuchi, and E.-M. Zhao. 2014. A new species of the genus Rhabdophis Fitzinger, 1843 (Squamata: Colubridae) from Guangdong Province, southern China. Zootaxa 3765:469-481 <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.

Tuesday, October 28, 2014

How to teach yourself about an obscure snake

This article will soon become available in Spanish

The world is full of obscure snakes. According to Darren Naish at Tetrapod Zoology, the more you know about them, the better a person you are. Writing this blog, and in my research, I am often confronted with the challenging task of finding out something - anything at all - about a species of snake that I've never heard of before. This post is a walk-through of the process that I usually use to track down even the most basic information about obscure snakes, although it could be used as an example of how to find trustworthy information about any species of plant or animal. I'll use as an example the species Liophidium mayottensis (Peters's Bright Snake) - a lamprophiid colubroid found on the island of Mayotte. If you're like me then you're filled with questions right away: Who was Peters? What is so bright about this snake? Where's Mayotte?

Wikipedia page for Liophidium mayottensis
as of October 2014
I needed to know about this snake as part of a project I'm doing where we compare endangered species of reptiles with those that aren't to try and figure out if there are traits or features that the endangered species have in common (and the same for invasive species and other special groups). This kind of thing has been done for birds and fish, but not really for reptiles. It's a much larger effort than just me, and my part in it is small, usually tracking down basic information about the reptiles so that we can build a database of reptile life history traits. I'm talking about things like size, sexual dimorphism, whether they lay eggs or give birth to live young, how many eggs or young they have at a time and how often, where and in what kind of habitats they live, what they eat, that kind of thing. Sounds simple, right? We'll just go to Wikipedia...well, as of 2014 that wasn't very helpful.

When faced with a species about which I know almost nothing - in this case a species I had never even heard of before - there are a couple of resources that I generally go to first in order to figure out how I should proceed. The first is always The Reptile Database. This wealth of information is curated by Peter Uetz, Jakob Hallermann, and Jiri Hosek, three individuals to whom the whole of the herpetological world is indebted. Using the advanced search feature, you can look up any species of living reptile using its common or scientific name, including by an old scientific name (a "synonym") that is no longer used. This is important because scientific names change all the time, and sometimes the same species has gone by 10 or 20 different names over the course of its taxonomic lifetime. It is particularly important to know about these names because the species may have gone by them for a long time in older literature, which is sometimes the most important literature there is.

Liophidium mayottensis
Before searching TRD, I sometimes try to use the scientific name itself to figure out a little bit about what I'm looking for. It helps to know some Latin and Greek, and a handy reference that I use a lot is Borror's Dictionary of Word Roots and Combining Forms. In this case, the genus name Liophidium told me that this was a snake with smooth scales (the Greek prefix lio- meaning smooth + the Greek root ophid meaning snake + the Latin suffix -ium normally used to form abstract nouns). The specific epithet mayottensis means "from Mayotte" (the -ensis suffix is a common way to form an adjective indicating spatial or geographic origin in Latin, similar to the English suffix -ese, as in Maltese, Chinese, or Portuguese). Although the Latin and Greek origins of the scientific name can be helpful, they can also be misleading (for example, the North American Racer is called Coluber constrictor even though it is not a constrictor) or unhelpful (another familiar North American snake, Storeria dekayi, is named after two 19th century herpetologists, David H. Storer and James E. DeKay), so don't rely too much on these.

The Madagascan Biogeographic Realm
Mayotte is the southeasternmost island in the
Comoros chain, although politically it is part of France.
Many interesting snakes inhabit this realm, including bolyeriids
When searching TRD, I always put the full binomial I'm looking for into the 'Synonym' field of TRD's Advanced Search, because the 'Genus' and 'Species epithet' fields only search the current names, and who knows what name it goes by now. Barring any misspellings, at least one record usually turns up, sometimes more if the name I've used has been split into multiple species. In this case, it's just one, and it matches the name I used. From this record, I can find out the currently accepted higher taxonomy of my species. In addition to being a snake (which I already knew), I can see that it's in the recently-erected family Lamprophiidae, a group of snakes found mostly in Africa. Furthermore, I can see that Liophidium mayottensis is in the subfamily Pseudoxyrhophiinae, a group of snakes found almost exclusively in Madagascar. Because Mayotte is an island in the Comoro Island chain, lying just northwest of Madagascar, this subfamilial designation makes sense - we think that lamprophiids colonized Madagascar, Socotra, and the Comoros from Africa about 30 million years ago, one of several radiations of snakes onto these islands. However, in this case knowing the subfamily doesn't help us much in our search for natural history information. Unlike certain instantly-recognizable groups of snakes such as pareatids or xenodermatids, pseudoxyrhophiines are diverse, including almost 90 species with a wide variety of lifestyles. I've written about the genus Langaha, which belongs to this group, before.

The BHL is also a great source of artwork
in the form of old plates, like this mudsnake
from Duméril's Erpétologie Générale,
which adorns the logo of this blog
In order to go further we need look at the rest of the TRD record. Since we're looking for a description of the species, one of the most helpful pieces of information is the location of the original description in the scientific literature. You'll find the name of the person who originally described the species and the year they did it in the TRD record, right next to the scientific name. This is called the authority, and it's presented in parentheses if the name that person used has subsequently been changed. For instance, 11 of the 139 reptile species described by Linnaeus, the father of modern taxonomy, still retain the original names he gave them. You can tell because these are the ones without parentheses. If you look to the bottom of the record, you'll find a citation for the book or article in which that first description resides, along with other literature pertinent to the species. This literature is usually focused on taxonomic changes, although sometimes more general ecology or natural history literature is included as well. Following up on this literature is easier in some cases than others. One thing TRD has done to make it simple is provide links to the full-text if it's available for free online somewhere. A lot of older literature is becoming available through the Biodiversity Heritage Library, a partnership of libraries that have digitized what they call the "legacy literature" of biodiversity.

Wilhlem C.H. Peters
Our species was originally described in 1874 by Wilhelm Carl Hartwig Peters, a German naturalist and explorer, which explains the first part of the common name Peters's Bright Snake (which was probably not applied until much later, since it's considered presumptuous to name a species for oneself). Peters called it Ablabes (Enicognathusrhodogaster var. mayottensis, a confusing mess if there ever was one. His description was published in the journal Monatsberichte der Königlichen Preussische Akademie des Wissenschaften zu Berlin (which is obfuscatingly abbreviated Monatsber. Königl. Akad. Wiss. Berlin.), which roughly translates to 'Monthly Reports of the Royal Prussian Academy of Sciences in Berlin'. Not exactly the most widely read journal, even if it has existed in one form or another since 1700 and is still around today. Anyway, it's in German, so it'll prove difficult for us to read Peters's original description even if we can find it (which thanks to the BHL, we can). There's also the little problem of whether the issue it's in was published in 1873 or 1874, because the citation in TRD lists both, but fortunately we can check both quickly since the page numbers are also given (it's '73). The article starts on this page and the description is on this one. These days descriptions of new species usually get their own stand-alone articles, but back then it was common practice to shoehorn them into checklists, expedition reports, and other types of articles. There's a description of a new chameleon in the same article. In a way, it's one explanation for the prolific output of Peters, who described 122 new genera and 649 new species of amphibians and reptiles in his lifetime, 281 of which are still recognized today (only four people, all his contemporaries, have described more). The high attrition is partly because many species were inadvertently described more than once. The guys at TRD have done a fabulous job keeping track of all this confusing literature, and I cannot commend them highly enough for their efforts.

Another difference between the 1800s and now is that species descriptions today are generally much more complete. You might be surprised to learn that the International Commission on Zoological Nomenclature, which advises, arbitrates, and recommends rules for the zoological community on describing new species of animals, stipulates only that in order for a species description to count as official, it must include at a bare minimum just "a description or definition that states in words characters that are purported to differentiate the taxon", and even this 'strict' definition applies only to names published after 1930. Peters's description of Liophidium mayottensis (translated) reads:
17. Ablabes (Enicognathus) rhodogaster Schlegel var. mayottensis: 
Two young specimens from Mayotte seem to me to belong to the above species, although they do not have red coloration on the belly. Frontal a little longer than high; 8 supralabials, of which the 4th and 5th touch the eye; temporals 1+2+2; infralabials 9, the first pair of which is in contact behind the tapered mental; two pairs of chin shields. Body scales smooth, without apical pits, in 19 longitudinal rows. Ventrals 190, divided anal, subcaudals 99 pairs. Above olive-brown, a little darker along the middle and fourth-to-last row of scales. From the snout through the eye and the frenal region there is a black napkin which is indistinct on the side of the neck and disappears in the penultimate row of scales on the side of the body. Under this there is a bright yellow band, which goes to the mouth. There are three black spots on the rostral and upper lip. The chin and infralabials are spotted or marbled with black and yellow. On the neck are fine yellowish transverse lines. Ventral scales with 4-6 black dots; posterior ventral scales and subcaudals yellowish-white.
Liophidium rhodogaster
Gold-collared Snake
So we've got counts of the scales and descriptions of their position relative to one another, which is considerably more than it took back in the 1870s to name a new species. No drawings, no information on size, habitat, reproduction, nothing. It's forgivable when you know that Peters, by then a museum curator, was merely reporting on a collection of amphibians and reptiles he had been sent from Madagascar and nearby islands by two guys named Pollen and van Dam. Peters thought the snakes they had collected on Mayotte were a variant of a species that had already been described, the Gold-collared Snake of Madagascar, known then as Enicognathus rhodogaster and today as Liophidium rhodogaster (rhodogaster meaning 'red belly'). We learn from TRD that twenty years later Belgian-British zoologist George Boulenger (writing, mercifully, in English) elevated it to its own species and changed the genus so that it was known as Polyodontophis mayottensis. Boulenger is even lighter on details than Peters, saying only that it is very similar to rhodogaster but differs in that it has one more pair of dorsal scale rows, about 11 more ventrals, and about 15 more subcaudals, and that its neck pattern includes the same yellow lines mentioned by Peters. Since he's not trying to describe a new species, it's OK, but it's frustrating since we're looking for more detail about the animal's ecology and natural history.

It's likely that neither Peters nor Boulenger ever saw Liophidium mayottensis, or many of the other species they described, alive, so we can forgive them for not mentioning its habitat or patterns of activity (although they could have at least measured the specimen). Sometimes museum specimens yield information about diet (via stomach contents) or reproduction (via eggs or embryos in utero), but this does not seem to be the case for Peters's Bright Snake. To learn about these things, we'll have to sleuth out some other papers. The other two listed at TRD don't look too promising - one is a biography of Peters that's only available in print, and the other focuses on a different genus, Sibynophis, that's superficially similar to Liophidium but distantly related.

We can do a little better by checking some other common sources of information on the web. We already know that Wikipedia's useless (although the links at the bottom of some pages can be quite useful), but a general Google search for the scientific name typically turns up links to the pages for a species on several authoritative sites that aggregate biodiversity information online. In no particular order, I often check the University of Michigan Museum of Zoology's Animal Diversity Web. This is a great student-authored resource but it's still incomplete, and it doesn't even have a page for our genus yet (but check out their detailed pages on all three Acrochordus species). Other similar sites include the Encyclopedia of Life (species page incomplete for L. mayottensis, but check out Laticauda colubrina for a fairly good page), DiscoverLife (which is mostly links with little original content, and is unhelpful for our species, although they host a cool ID guide for North American snakes), and Map of Life (which has lots of cool mapping capabilities but not for our species). Citizen science projects can be a rich source of information on distribution, but such projects are in their infancy for herps. Two of the best are iNaturalist and HerpMapper, neither of which has any data on our species. Remember that none of these sources are peer-reviewed, so they may propagate misinformation (although I have found this to be rare).

One of Pagale Bacha's Flickr photos of L. mayottensis
ARKive is a film and image archive that generally has pictures of rare species when most other websites fail, and that is the case here, but as of 2014 it contained no additional information (contrast with their excellent accounts for snakes like Natrix natrix and Macroprotodon cucullatus). Flickr can be a good source of images too, in this case providing us with four additional images, all taken by the same person of the same individual snake. I have noticed that a culture of accurate species identification exists on Flickr that isn't found elsewhere on the Internet. For instance, don't ever trust Google Images when searching for rare species - in this case, only one of the hundreds of images returned is actually of our snake. Earlier I mentioned the Biodiversity Heritage Library, one of the most consistently useful resources on the web, and their search feature leads us to one new resource: a mention in a paper by John Cadle from 1999, focusing on morphological taxonomy of  Malagasy snakes (which states that Liophidium are diurnal and led me to a paper describing the smooth, hinged, spatula-shaped teeth of Liophidium and other snakes, an adaptation for grasping and swallowing hard-bodied prey, such as skinks their teeth fold backwards when forces are applied to their leading surface, but lock into an erect position if forces come from behind).

Some L. mayottensis DNA. It looks just like the DNA
of any other species, although there's a lot it can tell us.
Two other online databases are more authoritative than those previously mentioned, in that they are reviewed by experts. One is GenBank, the NIH genetic sequence database. A GenBank search reveals that five genes have been sequenced from L. mayottensis, which is more than for most reptilesThese include four mitochondrial genes (ND4CO1, and cyt-b, which are essential to the electron transport chain of cellular respiration, and 16S, part of the protein synthesis machinery of ribosomes) and one nuclear gene (c-mos, which plays a role in mitosis). These genes were chosen for their conserved functions and relatively slow rates of evolution, which makes them useful for phylogenetic purposes (except for CO1, which evolves at just the right rate for DNA barcoding, a technique which is used, among other things, to monitor trade of reptiles without specialized expert knowledge). A phylogenetic analysis was done to determine the relationship of Liophidium pattoni, a new species discovered in Madagascar in 2009, to the other species in the genus. The results placed L. pattoni as sister to L. rhodogaster, and L. mayottensis as sister to two other Malagasy species, L. torquatum and L. chabaudi. This may seem like a dry, mundane detail, but it actually tells us something very interesting about our species: it probably colonized Mayotte from Madagascar after the ancestors of Liophidium had already radiated there. It also says that Peters, who thought that L. mayottensis was a subspecies of L. rhodogaster, was way off - it's actually more closely related to almost any other member of the genus (although to be fair to Peters, none of those other members had been described yet when he named L. mayottensis — and morphology might lead you to believe that L. mayottensis was the most basal member of the group, since it has 19 dorsal scale rows whereas every other species has 17).

Liophidium pattoni and its relationship to some of its closest relatives, including L. mayottensis
From Vieites et al. 2010
IUCN categories
The other more authoritative online database is the IUCN Red List. The Red List assesses the conservation status of species and often includes a distribution map (although not in this case), some ecological information, and a short bibliography focused on ecology and conservation rather than on taxonomy. The IUCN page contains several useful nuggets, most of which come to us by way of expert knowledge and may or may not be published elsewhere. For instance, we learn that our species is classified as Endangered under the IUCN categories, which are based on quite rigorous and quantitative criteria. Peters's Bright Snake qualifies as Endangered despite very limited data because all known records are from a forested area of about 65 km2 in the center of Mayotte, which is subject to a continuing decline in quality (criterion B2b(iii)) and within which the actual occurrence records of the snake suggest that its populations are severely fragmented (criterion B2a). Even if the area of occupancy is underestimated, the entire terrestrial area of Mayotte is only 365 km2, which is still less than the minimum of 500 km2 that a species must exceed unless both it and its habitat are known to be contiguous and stable.

Hinged teeth of Liophidium rhodogaster
From Savitzky 1981
The IUCN record also lists several other pieces of information. It tells that the known records are all between 144 and 653 meters above sea level. It states that "this snake is diurnal, ground-dwelling and very secretive", "observed in natural forests and plantations", and is egg-laying. This last tidbit is pretty helpful, and it's no surprise that we haven't encountered it before - it's from a field guide written in French by Danny Meirte, covering the terrestrial fauna of the Comoros, published in 1999 and updated in 2004. As for conservation, it says that our species is not used by humans for any known purpose, but that an introduced civet may be a threat. All native reptile species on Mayotte are protected by law, and several nature reserves may benefit L. mayottensis, but no data is available on the snake's occurrence at these sites.

Finally, the IUCN record notes that "the extreme scarcity of observations may be attributed to the cryptic habits of this snake, but also suggests that L. mayottensis is not common". No shock there. The short bibliography includes both the old and new editions of the field guide and a paper by Oliver Hawlitschek in the journal ZooKeys that used field surveys and remotely sensed data to assess the conservation status of Comoran reptiles, upon which most of the conservation assessment is based. The profile also cites another work in preparation by Hawlitschek, who was also an expert reviewer for the species and took the Arkive photograph. I visited his website and was able to learn that he is a German PhD student studying herp conservation & phylogeography in the Comoros.

Phylogenetic tree of Malagasy reptiles based on CO1 DNA barcodes
Liophidium is near the top right
From Nagy et al. 2012
Now we're getting somewhere, although we're still looking for body size and clutch size, two of the most basic species attributes. Usually, after checking all off the above sources, I repeat the whole process on Google Scholar and track down any promising articles. Often , I'll add a search term for the particular attribute I'm looking for (e.g., "clutch size", "svl") to see if that helps. In this case, even Google Scholar didn't turn up much specific to our species. I was about to give up when I decided to contact Oliver Hawlitschek. When I went to look up his email address, I noticed that he recently published a paper in the journal PLoS ONE, which of all places is known for its free and open accessibility to all. The paper, titled "Island Evolution and Systematic Revision of Comoran Snakes: Why and When Subspecies Still Make Sense", includes supplementary material that finally gives us the answer to our seemingly simple question of "how long is Liophidium mayottensis"? The average adult total length is about 80 cm for both sexes, maximum 1 meter  (3 feet), with the tail making up about 30% of the body. When I contacted Oliver he confirmed this, and he also told me that as far as he knew no information on clutch size was available (although he expected it would be small, like that of most other island snakes). From reading his paper, I also learned that this is by far the largest species of Liophidium (the next is L. therezieni at 72.6 cm) and the only one with 19 dorsal scale rows instead of 17. Oliver's paper suggested that Comoran Liophidium (and the snake Lycodryas and lizard Oplurus) are larger than their Malagasy congeners because they are released from competition with larger species that do not occur in the Comoros.

Liophidium mayottensis skull (with tooth closeup, inset)
Image by Cynthia Wang
Oliver also put me in touch with Cynthia Wang, another graduate student who is using high-resolution X-ray computed tomography to make 3-D scans of the skulls of snakes. Turns out she recently scanned a L. mayottensis skull. You can see the spatula-shaped, hinged teeth characteristic of the genus, although the connective tissue is missing. He also told me that he will be returning to the Comoros this November, and that L. mayottensis will be his #1 target while he's there. All in all, a pretty satisfying conclusion.

This was a long article; congratulations if you made it to the end! I justified the length partly in celebration of my birthday this month and partly in celebration of this blog reaching 250,000 views! I hesitated writing this article because I base a lot of my articles around obscure snakes and I was afraid that writing a how-to would amount to writing myself out of a lot of subject matter. On the other hand, I suppose I enjoy the chase, and I think this overly-long article's length goes to show just how much actually is out there, even for really obscure species, if you're willing to look (and there are certainly resources I've missed! Let me know about them in the comments.). I also think that this process is easily generalizable to non-reptiles - there are some great resources out there for amphibians, birds, algae, echinoderms, insects, and much else. Whatever you're interested in, happy researching!

Update: In December 2014, Ludovic Montfort, Cynthia Wang, Oliver Hawlitschek, and Mark Scherz found a L. mayottensis atop Mt. Benara during their field work on Mayotte!


Cynthia Wang with L. mayottensis in December, 2014.
Photo by Matthias Deuss
ACKNOWLEDGMENTS

Thanks to Oliver Hawlitschek, Cynthia Wang, Matthias DeussHenry Cook, and Pagale Bacha for the use of their images.

REFERENCES

Bauer, A. M., R. Günther, and M. Klipfel. 1995. The Herpetological Contributions of Wilhem CH Peters (1815-1883). SSAR Facsimile Reprints in Herpetology:114.

Boulenger, G. A. 1893. Catalogue of the snakes in the British Museum (Natural History). Trustees of the British Museum, London <link>

Cadle, J. E. 1999. The Dentition, Systematics and Phylogeny of Pseudoxyrhopus and Related Genera from Madagascar (Serpentes: Colubridae) with Descriptions of a New Species and a New Genus. Bulletin of the Museum of Comparative Zoology at Harvard College 155:381-443 <link>

Hawlitschek, O., B. Brückmann, J. Berger, K. Green, and F. Glaw. 2011. Integrating field surveys and remote sensing data to study distribution, habitat use and conservation status of the herpetofauna of the Comoro Islands. ZooKeys 144:21–78 <link>

Hawlitschek, O., Nagy, Z., & Glaw, F. 2012. Island evolution and systematic revision of Comoran snakes: why and when subspecies still make sense. PLoS ONE 7:e42970 <link>

Hedges, S. B. 2013. Revision shock in taxonomy. Zootaxa 3681:297-298 <link>

Meirte, D. 2004. Reptiles. Pages 201-224 in M. Louette, D. Meirte, and R. Jocqué, editors. La faune terrestre de l'archipel des Comores. MRAC, Tervuren.

Nagy, Z. T., U. Joger, M. Wink, F. Glaw, and M. Vences. 2003. Multiple colonization of Madagascar and Socotra by colubrid snakes: evidence from nuclear and mitochondrial gene phylogenies. Proceedings of the Royal Society of London. Series B: Biological Sciences 270:2613-2621 <link>

Peters, W. C. H. 1873. Über eine von Hrn. F. Pollen und van Dam auf Madagascar und anderen ostafrikanischen Inseln gemachte Sammlung von Amphibien. Monatsberichte der Königlichen Preussische Akademie des Wissenschaften zu Berlin 1873:792-795 <link>

Savitzky, A. H. 1981. Hinged teeth in snakes: an adaptation for swallowing hard-bodied prey. Science 212:346-349 <link>

Uetz, P. 2010. The original descriptions of reptiles. Zootaxa 2334:59-68 <link>

Vieites, D. R., F. M. Ratsoavina, R.-D. Randrianiaina, Z. T. Nagy, F. Glaw, and M. Vences. 2010. A rhapsody of colours from Madagascar: discovery of a remarkable new snake of the genus Liophidium and its phylogenetic relationships. Salamandra 46:1-10 <link>

Zaher, H., F. G. Grazziotin, R. Graboski, R. G. Fuentes, P. Sánchez-Martinez, G. G. Montingelli, Y. P. Zhang, and R. W. Murphy. 2012. Phylogenetic relationships of the genus Sibynophis (Serpentes: Colubroidea). Papeis Avulsos de Zoologia (Sao Paulo) 52:141-149 <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.