Virgin Birth, the Color of Fossil Snakes, and More Recent Updates

This post will soon be available in Spanish

As I did in March, I wanted to highlight some recent and exciting updates to some of my older articles.

Snakes That Give Virgin Birth

Phylogenetic pattern of parthenogenesis in snakes
Molecular tree on left, morphological tree on right
From Booth & Schuett 2016

When I wrote about asexual reproduction in snakes in February 2014, new records of this phenomenon were rapidly accumulating, from snakes as distantly related as cottonmouths and boa constrictors. In a new paper, Warren Booth and Gordon Schuett review the knowns and unknowns of "virgin birth" in snakes, a subject which has become their specialty (it even has its own Facebook group). Although obligate parthenogenesis is still known only from Brahminy Blindsnakes (Indotyphlops braminus), the new summary reports that facultative parthenogenesis has now been documented in 20 species of alethinophidian¹ snakes, and this list is anticipated to grow, although so far confirmed cases are limited to five lineages: boids, pythonids, Acrochordus, Crotalinae, and Natricinae. This new synthesis formalizes one of the trends that I wrote about in 2014, namely distinguishing between "Type A" facultative parthenogenesis, in which the offspring produced are large clutches of viable females that seem to have a strange "WW" sex chromosome arrangement (apparently typical of boas and pythons), and "Type B" facultative parthenogenesis, which is where all the offspring are male and few are born alive, many with extreme developmental abnormalities (apparently typical of colubroids).

Most intriguing is the hypothesis laid out for explaining this dichotomy: that boas and pythons (and possibly other basal alethinophidian snakes) might have an XY sex determination system rather than a ZW one like most snakes. Changes from ZW to XY or vice versa (and between genetic and temperature-dependent sex determination) have been documented in geckos and turtles, and could have been overlooked in boas and pythons due to their similar-looking sex chromosomes (tests are currently underway to falsify or verify this hypothesis). If true, this would explain the production of all-female offspring by facultative parthenogenesis; instead of WW, those females would be XX, just like humans!

Identifying Snake Sheds

True-color representation of the fossil snake
(MNCN 66503) in McNamara et al. 2016.
The dentition looks too solenoglyphous for a
colubrid, although the 10-million year old specimen,
which is missing its head, has not and
probably can not be identified to species.

Ever since the first reports of color from the skin and feathers of dinosaur fossils were published in Science in 2010, I've been fascinated by the ability of paleontologists to see in color when they look into the past. A new paper in the journal Current Biology reveals the color of a fossil snake, determined from using scanning electron microscopy (SEM) to examine microfossils of certain types of skin cells, called chromatophores. So far, only melanin-based chromatophores (melanosomes, which are responsible for brown and black color) have been detected in fossilized skin and feathers, probably because they are the most resistant to the decomposition process. But, this study was also able to detect and measure other types of chromatophores from fossilized skin, including xanthophores (responsible for yellow, orange, or red color, derived from carotenoids or pteridines) and iridophores (responsible for iridescence). By comparing the fossil's chromatophore abundance and position to that of living reptiles, they were able to reconstruct the original color and pattern of the fossil snake's skin. For example, in the skin of living snakes, xanthophores with many more pteridine granules than carotenoid granules produce a red hue, whereas xanthophores with equal amounts of carotenoid granules and pteridine granules—as in the fossil—produce yellowish hues. Skin regions with abundant iridophores and xanthophores, but relatively few melanophores, are associated with green hues in some living skinks, whereas skin regions with many melanophores, a few xanthophores, and no iridophores suggest correspond to dark brown or black tones. As you can see in the depiction, this snake seems to have had a pale, creamy venter and a green back and sides, with areas of brown/black and yellow/green, perhaps not unlike modern Green Watersnakes (Nerodia floridana) or Boomslangs (Dispholidus typus).

Snakes Flying Without Planes

Photo and diagram of courtship behavior of Chrysopelea paradisi
Taken at the Sepilok Jungle Resort in Sabah, Malaysia
Female shown in gray, males in blue, green, and orange
From Kaiser et al. 2016

A new report on the mating behavior of Paradise Flying Snakes (Chrysopelea paradisi) showed that their courtship can involve multiple males. Although several experiments have been performed on the gliding behavior of these snakes, almost nothing is known about their natural history in the wild. Males of many species of snakes court females en masse by rubbing their chins along their bodies, a behavior which allows them to sense her sex pheromones and jockey for position. The role played by the female in choosing a male is unclear in most snake species; although conventional biological wisdom suggests that females should be the choosy sex, male-male competition seems to dominate courtship behavior in several species of snakes. Multi-male courtship behavior precedes mating in some well-studied temperate snakes (e.g., gartersnakes emerging from hibernation), as well as in some tropical species (e.g., anacondas, some other southeast Asian colubrids, such as Boiga irregularis and Dryophiops rubescens). Of course, it seems that most female snakes can store sperm for long periods of time, and they may have some control over which male's sperm to use to fertilize their eggs, so the genetic contribution of a female snake's male partners may not follow from their courtship or mating success. Unlike the terrestrial or aquatic mating balls documented for other snakes, the flyingsnakes in this observation were able to move as a unit for almost 50 feet through complex habitat—under a porch, up a tree—an adaptation that seems to fit their active, arboreal lifestyle and might help reduce the likelihood of a predatory attack during what must otherwise be a vulnerable time.

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1 In a few places, the authors use "alethinophidian" to refer to boas, pythons, and their relatives but not caenophidians, when instead they should have either used "henophidian" or "basal alethinophidian" (they mostly use the latter term throughout). Many people don't like the term "henophidian" because it is a paraphyletic group, but it is a convenient way to refer to non-scolecophidian, non-caenophidian snakes. In my mind it's essentially synonymous with "basal/stem alethinophidian". Alethinophidians are all snakes except for blindsnakes (scolecophidians), and Caenophidia is a subset of Alethinophidia. There are also at least three references to "Caenophidia + Colubroidea", which is confusing because Colubroidea is a subgroup of Caenophidia, and Caenophidia = Colubroidea + Acrochordus, which is perhaps what they meant.^↩

ACKNOWLEDGMENTS

Thanks to Gordon Schuett for clearing up some of the details of his recent paper.

REFERENCES

Booth W, Schuett GW (2016) The emerging phylogenetic pattern of parthenogenesis in snakes. Biological Journal of the Linnaean Society 118:172-186 <link>

Gamble, T., J. Coryell, T. Ezaz, J. Lynch, D. Scantlebury, and D. Zarkower. 2015. Restriction site-associated DNA sequencing (RAD-seq) reveals an extraordinary number of transitions among gecko sex-determining systems. Molecular Biology and Evolution 32:1296-1309 <link>

Kaiser H, Lim J, Worth H, O’Shea M (2016) Tangled skeins: a first report of non-captive mating behavior in the Southeast Asian Paradise Flying Snake (Reptilia: Squamata: Colubridae: Chrysopelea paradisi). Journal of Threatened Taxa 8:8488–8494 <link>

Kuriyama, T., K. Miyaji, M. Sugimoto, and M. Hasegawa. 2006. Ultrastructure of the Dermal Chromatophores in a Lizard (Scincidae: Plestiodon latiscutatus) with Conspicuous Body and Tail Coloration. Zoological Science 23:793-799 <link>

Li, Q., K. Q. Gao, J. Vinther, M. D. Shawkey, J. A. Clarke, L. D’Alba, Q. Meng, D. E. G. Briggs, and R. O. Prum. 2010. Plumage color patterns of an extinct dinosaur. Science 327:1369 <link>

McNamara, Maria E., Patrick J. Orr, Stuart L. Kearns, L. Alcalá, P. Anadón, and E. Peñalver. 2016. Reconstructing Carotenoid-Based and Structural Coloration in Fossil Skin. Current Biology <link>

McNamara, M. E., D. E. G. Briggs, P. J. Orr, D. J. Field, and Z. Wang. 2013. Experimental maturation of feathers: implications for reconstructions of fossil feather colour. Biology Letters 9 <link>

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

Dragonsnakes and Filesnakes Revisited

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I've written about both filesnakes (family Acrochordidae) and dragonsnakes (part of the family Xenodermidae¹) before. Traditional snake taxonomy suggests that, although they branch off from the main stem of the snake family tree at about the same time, they're not very closely related. But, new evidence emphasizes the uniqueness of dragonsnakes and thickens the plot in the unfolding story of the evolution of snakes.

Two hypotheses about the relationships of the major groups of snakes.
Left: tree based on nuclear genes, showing Acrochordidae and Xenodermidae
as successive outgroups to core Colubroidea
Right: tree based on mitochondrial genes, showing a sister relationship
between Acrochordidae and Xenodermidae
From Oguiura et al. 2009

Most phylogenetic analyses are pretty consistent in classifying both filesnakes and dragonsnakes as caenophidians, or "advanced" snakes. But, they differ in their placement of dragonsnakes and other xenodermids, including the truly strange and obscure odd-scaled snakes (Achalinus), bearded snakes (Fimbrios), stream, earth, or red snakes (Stoliczkia²), wood, mountain, or narrow-headed snakes (Xylophis), and a new genus, just described in 2015 and still without a common name, Parafimbrios. Most analyses group xenodermids with the colubroids (pareids¹, vipers, homalopsids, colubrids, lamprophiids, and elapids), albeit as the most basal branch. Many textbooks actually define Caenophidia as Colubroidea + Acrochordidae (aka Acrochordoidea), distinctly separating the colubroids from the filesnakes on the basis of shared, derived characteristics such as wide ventral scales, as well as features of the skull, hemipenes, and the muscles, cartilages, and arteries between the ribs. However, several recent trees based on DNA sequences suggest instead that filesnakes and dragonsnakes might be one another's closest living relatives.

Study	Acrochordid-Xenodermid Relationship	Support	How many species?	What data were used?
Boulenger 1893	X&A	-	-	Morphology
Kraus & Brown 1998	X+A	8%	37	ND4
Kelly et al. 2003	X+A	98%	98	4 mitochondrial genes
Vidal et al. 2007	A,X	not reported	25	7 nuclear genes
Wiens et al. 2008	A,X	>95%	50	20 nuclear genes
Wang et al. 2009	A,X*	100%	30	12 nuclear genes
Zaher et al. 2009	A,X	94%	131	2 mitochondrial genes + 1 nuclear gene
Pyron et al. 2011	A,X	97-100%	761	3 mitochondrial genes + 2 nuclear genes
Gauthier et al. 2012	X,A	95-100%	141 extant + 51 extinct	610 morphological characters
Wiens et al. 2012	A,X	100%	161	44 nuclear genes
Pyron et al. 2013	X+A	95%	4,161	5 mitochondrial genes + 7 nuclear genes
Pyron et al. 2014	A,X*	99%	32	333 nuclear loci with 100% coverage
Zheng & Wiens 2016	A,X	91%	4,162	5 mitochondrial genes + 47 nuclear genes

A selection of studies that have examined the relationship between acrochordids and xenodermids.

X+A means that the two are each other's closest relatives; A,X means that acrochordids are more distantly
related to colubroids than xenodermids; X,A means that xenodermids are more distant
*Relationships differed depending on which methods were used

Arafura Filesnake (Acrochordus arafurae)

For example, the first study to use DNA to examine the relationships of these two groups of snakes found some support for each hypothesis, concluding that the "potential sister-taxon relationship of acrochordids and xenodermines [is] a reasonable hypothesis requiring future testing." In 2003, data from three more mitochondrial genes resulted in the same relationship, causing the authors to suggest that xenodermids should be excluded from Colubroidea. However, since that time, numerous studies have not repeated this result. In 2009, one research group predicted that "these differences...are due to taxonomic sampling issues", predicting that as DNA was collected from more species of snakes, the basal position of Acrochordus would be confirmed.

Dragonsnake (Xenodermus javanicus)

So, it was a real surprise when a 2013 analysis, the largest yet, including samples from 80% of all snake genera, placed Acrochordidae and Xenodermidae as sister groups. Neither a follow-up analysis combining that dataset with one containing data from many more genes nor an analysis using only the most complete data have settled the issue. The latter study compared several methods for generating phylogenetic trees and found that the relationship between acrochordids and xenodermids depended a lot on which methods were used. Part of the problem is that, even if they are each others' closest relatives, they still diverged between 70 and 80 million years ago, making them susceptible to a problem in phylogenetics known as long-branch attraction, which happens when the amount of evolutionary change within a lineage causes that lineage to appear similar (and thus closely related) to another long-branched lineage, solely because they have both undergone a lot of change, rather than because they are actually related.

Bearded Snake (Fimbrios klossi)

The truth is that both acrochordids and xenodermids are obscure snakes, and we don't have that much data on either one of them. They are both found in areas of the world that are hard to get to. Morphologically, they appear superficially similar, and an association between them was first hypothesized in 1893. But, even the most comprehensive morphological trait database for snakes is missing crucial data on their anatomy, such as whether or not their hemipenial spines are mineralized. This would be helpful to know because  the hemipenial spines of basal snakes such as boas and pythons are not mineralized, whereas those of definitive colubroids are heavily mineralized.

Parafimbrios lao
From Teynié et al. 2015

Within the past year, two new studies on the chromosomes of dragonsnakes (Xenodermus javanicus) have been published. In the first, the karyotype (the number of chromosomes and their shape) of dragonsnakes was reported for the first time. In humans, each cell normally contains 23 pairs of chromosomes, for a total of 46. In most snakes, each cell normally contains 18 pairs of chromosomes, for a total of 36. Usually, eight of these pairs are relatively large (called macrochromosomes), and the other ten are somewhat small (called microchromosomes). Dragonsnakes have 16 pairs of chromosomes, for a total of 32, of which seven are large and nine are small. The dragonsnake karyotype probably evolved by two fusion events, one of two macrochromosomes and the other between a macrochromosome with a microchromosome. There are some other exceptions to the 18-pair pattern; some snakes have as few as 12 or as many as 25 pairs, including the only other xenodermid to have been karyotyped, the Sichuan Odd-scaled Snake (Achalinus meiguensis), which has just 12 pairs of chromosomes.

Amami Odd-scaled Snake (Achalinus werneri)

From the 1960s to the 1980s, before DNA sequencing became cheap and easy, scientists invested heavily in collecting karyotypes from a diversity of species for comparative purposes, so we can say with pretty good certainty that the ancestral state for all snakes is 36 (18 pairs). That's the number in filesnakes, pareids, most vipers, homalopsids, and many colubrids, lamprophiids, and elapids, although there are lots of exceptions in the latter three groups.  The fusions in xenodermids emphasize their uniqueness, but unfortunately don't shed any new light on their phylogenetic placement.

Stoliczkia borneensis

The other study focused on the sex chromosomes. In humans, sex is determined by which combination of sex chromosomes a baby receives from its parents: two X chromosomes make a female, whereas an X and a Y chromosome make a male. It's pretty similar in snakes, with a twist: the sex chromosomes are called Z and W instead of X any Y, and females are the heterogametic sex (meaning that a Z and a W chromosome make a female, and two Z chromosomes make a male). Birds and many other reptiles also have ZW sex determination. In many colubroid snakes, the W chromosome is about twice the size of the Z,  and it is often unusual in other ways as well, such as having sections of highly condensed chromatin or a different centromere position. In contrast, filesnakes, boids, and other more basal snakes have morphologically indistinguishable Z and W chromosomes, although they still contain different genes and perform different functions.

Perrotet's Narrow-headed Snake (Xylophis perroteti)
Are members of this genus really xenodermids? Or, like the
former xenodermids Oxyrhabdium and Nothopsis, will they
prove to be more closely related to something else?

One reason the W chromosome looks so different from the Z in colubroids is that it contains repetitive elements called Bkm ('banded krait minorsatellite') repeats, which consist of the sequence "GATA" (sometimes "GACA") repeated thousands of times. Mammalian X chromosomes and avian W chromosomes also have these repeats. Cell biologists think that these repeats function to inactivate all the genes on the W chromosome except for those that determine sex³. Both mammalian X chromosomes and snake W chromosomes become very dense in body cells, so that none of the genes on them can be expressed. They only decondense and plays their brief, female-determining roles, in maturing eggs that are destined to become females. Unlike in mammals, the sex chromosomes of snakes span the gamut from completely identical to markedly differentiated, allowing biologists to study the evolution of chromosomal sex determination. The new study showed that female dragonsnakes have two different-looking sex chromosomes, with many Bkm repeats in the W, whereas the two Z sex chromosomes of male dragonsnakes look similar and lacked Bkm repeats, bolstering the relationship between xenodermids and other colubroids and diminishing the relationship between xenodermids and filesnakes.

The other major finding of the new study is the documentation that at least part of the sex chromosomes are homologous across all families of caenophidian snakes, suggesting that snake sex chromosomes emerged in the common ancestor of Caenophidia some 60-80 million years ago. One gene that is only on the Z chromosome in all caenophidians, including dragonsnakes, is also found on the W chromosome in filesnakes. The Z-chromosome-specific genes in caenophidians were on both the Z and W chromosomes in boas, pythons, and sunbeam snakes (Xenopeltidae), as well as in bearded dragons and anoles. Other toxicoferan lizards with ZW sex chromosomes, including chameleons and monitor lizards, seem to have evolved them independently.

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1 A recent article in the journal Herpetological Review pointed out that the grammatical rules for structuring family and subfamily names from genus names have recently been incorrectly applied in two cases involving snakes which concern this article: 1) Xenodermatidae/inae for the family/subfamily containing Xenodermus, the root of which is "dermus", a masculine noun with which the masculine specific epithet javanicus is correctly coupled (not the neuter javanicum; in contrast think of the neuter Heloderma horridum in family Helodermatidae). The correct family or subfamily name is thus Xenodermidae/inae. 2) Pareatidae or Pareatinae for the family containing Pareas, which is also masculine, making the correct family/subfamily name Pareidae/inae.^↩

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2 Don't confuse this snake genus (Stoliczkia) with a genus of extinct ammonite (Stoliczkaia), both named for Czech biologist Ferdinand Stoliczka. The extra "a" was added to the original spelling of the snake genus by Boulenger in 1899, probably by accident, and this genus is still widely misspelled today (e.g., on GenBank and on Wikipedia before I fixed it while writing this article).^↩

---

3 It's also thought that "GATA" is a particularly potent regulatory sequence, with the power to turn nearby genes on and off. In a way, the sex genes have essentially 'hijacked' the W chromosome, turning off all its other genes, and simultaneously creating a concentrated source of mutation-causing elements. Chromosomal sex determination may therefore constitute a unique and potentially very powerful genotypic mechanism for abruptly enhancing evolutionary rates, which might have contributed to the explosive radiations of species in clades with chromosomal sex determination, such as mammals, birds, squamates, and certain groups of insects.^↩

ACKNOWLEDGMENTS

Thanks to Thomas Calame, Sam Howard, Konrad Mebert, Zeeshan Mirza, Takehito Sato, and Stephen Zozaya for the use of their photos.

REFERENCES

Boulenger, G. A. 1893. Catalogue of the Snakes in the British Museum (Natural History). Volume I., containing the families Typhlopidae, Glauconiidae, Boidae, Ilysiidae, Uropeltidae, Xenopeltidae, and Colubridae Aglyphae, Part. Trustees of the British Museum, London. <link>

Boulenger, G. A. 1899. Description of three new reptiles and a new batrachian from Mt. Kina Balu, North Borneo. Annals and Magazine of Natural History 7:451-453 <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>

Jerdon, T. C. 1870. Notes on Indian Herpetology. Proceedings of the Asiatic Society of Bengal 1870:66-85 <link>

Jones, K., and L. Singh. 1985. Snakes and the evolution of sex chromosomes. Trends in Genetics 1:55-61 <link>

Lawson, R., J. B. Slowinski, B. I. Crother, and F. T. Burbrink. 2005. Phylogeny of the Colubroidea (Serpentes): new evidence from mitochondrial and nuclear genes. Molecular Phylogenetics and Evolution 37:581-601 <link>

Kelly, C. M. R., N. P. Barker, and M. H. Villet. 2003. Phylogenetics of advanced snakes (Caenophidia) based on four mitochondrial genes. Systematic Biology 52:439-459 <link>

Kraus, F., and W. M. Brown. 1998. Phylogenetic relationships of colubroid snakes based on mitochondrial DNA sequences. Zoological Journal of the Linnean Society 122:455-487 <link>

Oguiura, N., H. Ferrarezzi, and R. Batistic. 2009. Cytogenetics and molecular data in snakes: a phylogenetic approach. Cytogenetic and Genome Research 127:128-142 <link>

O’Meally, D., H. R. Patel, R. Stiglec, S. D. Sarre, A. Georges, J. A. M. Graves, and T. Ezaz. 2010. Non-homologous sex chromosomes of birds and snakes share repetitive sequences. Chromosome Research 18:787-800 <link>

Pokorna, M., and L. Kratochvíl. 2009. Phylogeny of sex‐determining mechanisms in squamate reptiles: are sex chromosomes an evolutionary trap? Zoological Journal of the Linnean Society 156:168-183 <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>

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 13:53 <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). Molecular Phylogenetics and Evolution 81:221-231 <link>

Rovatsos, M., M. Johnson Pokorná, and L. Kratochvíl. 2015. Differentiation of sex chromosomes and karyotype characterisation in the Dragonsnake Xenodermus javanicus (Squamata: Xenodermatidae). Cytogenetic and Genome Research 147:48-54 <link>

Rovatsos, M., J. Vukić, P. Lymberakis, and L. Kratochvíl. 2015. Evolutionary stability of sex chromosomes in snakes. Proceedings of the Royal Society B: Biological Sciences 282:20151992 <link>

Savage, J. M. 2015. What are the correct family names for the taxa that include the snake genera Xenodermus, Pareas, and Calamaria? Herpetological Review 46:664-665 <link>

Sharma, G., and U. Nakhasi. 1980. Karyological studies on six species of Indian snakes (Colubridae: Reptilia). Cytobios 27:177-192 link>

Teynié, A., P. David, A. Lottier, M. D. Le, N. Visal, and T. Q. Nguyan. 2015. A new genus and species of xenodermatid snake (Squamata: Caenophidia: Xenodermatidae) from northern Lao People’s Democratic Republic. Zootaxa 3926:523-540 <link>

Vicoso, B., J. Emerson, Y. Zektser, S. Mahajan, and D. Bachtrog. 2013. Comparative sex chromosome genomics in snakes: differentiation, evolutionary strata, and lack of global dosage compensation. PLoS Biology 11:e1001643 <link>

Vidal, N., A. S. Delmas, P. David, C. Cruaud, A. Couloux, and S. B. Hedges. 2007. The phylogeny and classification of caenophidian snakes inferred from seven nuclear protein-coding genes. Comptes Rendus Biologies 330:182-187 <link>

Wang, G., S. He, S. Huang, M. He, and E. Zhao. 2009. The complete mitochondrial DNA sequence and the phylogenetic position of Achalinus meiguensis (Reptilia: Squamata). Chinese Science Bulletin 54:1713-1724 <link>

Wiens, J. J., C. A. Kuczynski, S. A. Smith, D. G. Mulcahy, J. W. Sites, T. M. Townsend, and T. W. Reeder. 2008. Branch lengths, support, and congruence: testing the phylogenomic approach with 20 nuclear loci in snakes. Systematic Biology 57:420-431 <link>

Wiens, J. J., C. R. Hutter, D. G. Mulcahy, B. P. Noonan, T. M. Townsend, J. W. Sites, and T. W. Reeder. 2012. Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species. Biology Letters 8:1043-1046 <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>

Zheng, Y., and J. J. Wiens. 2016. Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species. Molecular Phylogenetics and Evolution 94:537-547 <link>

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

Can snakes hear?

Click here to read this post in Spanish.
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Last month I wrote about whether snakes sleep, a topic that is far more interesting than the minuscule amount of research devoted to it. Another common question is whether snakes can hear, since they don't have external ear openings. The short answer is yes, snakes can hear, but the long answer is (as usual) more complicated. Happily, there is a good deal of research on this question, including a recent review. In general, many popular sources and some scientific ones have incorrectly claimed snakes to be deaf, whereas a plethora of behavioral, neurological, and physiological experiments, particularly those performed by the eminent Princeton hearing researcher Ernest Glen Wever in the 1960s and 70s, by UC-San Diego neurologist Peter Hartline in the 1970s, and by herpetologist and anatomist Bruce Young from the 1990s to the present, have conclusively shown that snakes can detect and respond to sounds.

Anatomy of the human ear

Most tetrapods have a three-part ear (outer, middle, and inner) that is useful for detecting airborne sounds. The boundary between the outer and middle ear is called the tympanic membrane or "ear drum", and its function is to convert airborne sounds from the outer ear into fluid-borne ones in the inner ear¹, by way of one or more middle ear bones. Sounds are ultimately converted by auditory hair cells called stereocilia into nerve impulses, which travel to and are interpreted by the brain. At many stages along the way, the sounds are amplified by the vibrations they produce in the different parts of the ear, including the middle ear bones (more on these in a minute). It's been suggested that this three-part system evolved (possibly multiple times) around the beginning of the Triassic Period, in concert with the evolution of sound production in insects, the probable prey of many early amniotes. Many modern animals, such as songbirds, bats, dolphins, humans, frogs, and crocodilians, have very sensitive hearing that can detect extremely quiet airborne signals in spite of the presence of other competing noises.

Micro-CT scan of a ball python's skull and ear.
Red: mandible; dark blue: quadrate;
green: columella; purple/light blue: inner ear chambers
From Christensen et al. 2012
Click here for an interactive 3-D model.

You're probably familiar with the three bones of the middle ear in mammals, the malleus, incus, and stapes (also known as the hammer, anvil, and stirrup). Snakes and other reptiles have only a single middle ear bone, which is usually called the columella, although it is homologous with the mammalian stapes. The malleus and the incus evolved from the articular and quadrate bones in the lower jaw of early mammal-like reptiles, leaving modern mammals with a single lower jaw bone, the dentary. Modern reptiles still have three bones in their lower jaws, where they play a role in detecting vibrations, particularly those propagating through the ground. Most modern lizard ears are essentially like those of modern mammals, with a small external ear leading to a large ear drum close to the body's surface, which passes sound from the air (or the jawbones) to the columella and thence to the inner ear. In contrast, snakes lack all traces of an outer ear as well as an ear drum. Instead, a snake's columella is in direct contact with, and picks up vibrations from, its quadrate bone (the dark blue bone in the diagram above). You might suspect that this arrangement would only be useful for detecting ground-borne vibrations, and you'd be partially right: snakes are exquisitely sensitive to ground-borne vibrations. But, they can also detect airborne sounds.²

Diagram of the ear of a watersnake (Nerodia)
Modified from Wever 1978

Both older and several more recent experiments suggest that snakes can hear the vibrations produced by airborne sounds. Physiological data suggest that they are able to detect certain airborne frequencies directly using the inner ear, although the specific bioacoustic mechanisms remain poorly known. Instead, most airborne sounds are probably detected in using "somatic hearing". This happens when airborne sound waves strike a snake's body  and some of their energy is transferred to its bones, tissues, and organs, particularly the head and lung. The snake's vibration-sensitive hearing system can then pick up on and translate the vibrations from the rest of its body into fluid-borne vibrations and, ultimately, nerve impulses. So a snake probably can't hear, say, most music³ or human speech directly, but it can hear the sound of its own body vibrating in response to those sounds. So, instead of being deaf, snakes essentially have two auditory systems that are at least peripherally distinct. Whether signals from these two systems are integrated into a single neural pathway, as is the case for the eye and the pit organ, or whether they serve different functions, remains to be studied and determined.

The length and arrangement of the auditory hairs in the inner ears of snakes appears to be fairly uniform across species, at least relative to the variation seen in lizards, which can have very different auditory hair anatomy among families and often even among closely-related species. Snakes mostly have simple, tuatara-like papillae, which suggests that they have secondarily lost a more complex type of auditory organ. This might be due to the aquatic or burrowing lifestyle of their ancestors and/or to specializations of their lower jaws in response to their unusual eating habits. There is some variation in inner ear anatomy (and presumably in hearing capacity) among snakes: burrowing snakes have the longest papillae, arboreal snakes the shortest, and terrestrial snakes have papillae of intermediate length. Many mammals have over 10,000 auditory hair cells, whereas most snakes have only about 250 (although acrochordids have nearly 1,500). Supporting cells of unclear function are relatively more numerous in snakes and these cells have ultrastructural features that suggest that they are more specialized than those of other reptiles.

Hearing range of various animals, not including snakes

The louder and lower frequency airborne sounds are, the more easily a snake can detect them. This isn't entirely unlike our own hearing—although we do hear high-pitched airborne sounds directly more easily than snakes do, we also rely on amplification provided by our ear drums, inner ear hairs, and other parts of our bodies. Studies have shown that snakes can hear sounds in the 80-600 Hz range optimally, with some species hearing sounds up to 1000 Hz (for comparison, the range of human hearing is from 20-20,000 Hz). This means that a snake could hear middle C on a piano, as well as about one octave above and two below, but neither the lowest key (which is 27.5 Hz) nor the highest (which is 4186 Hz). The average human voice is around 250 Hz, which means that snakes can hear us talking as well. Of course, there is likely a lot of variation among snake species, and the hearing of most species has not been examined, so these are generalizations.

Use the player above to hear how the airborne parts of Led Zeppelin's classic "Good Times, Bad Times" would sound to a snake. Parts of the song below 80 Hz (some bass & drums) or above 600 Hz (almost all guitar, vocals, and cymbals) have been muted. This doesn't include their sensitivity to the groundborne vibration parts of the song, which you could simulate by turning the bass on your speakers all the way up.

Audibility curves for living reptiles, including birds (left). The lower
the curve, the quieter a sound can be detected at a given frequency.
You can see that snakes cannot hear very quiet sounds, but
otherwise are not that much worse than other reptiles
(although their hearing sucks compared to, say, owls).
Note the different y-axes. From Dooling et al. 2000.

What do snakes do with their hearing? Unlike frogs, birds, and insects, snakes don't seem to use sound for communication with each other. Although many snakes hiss and some use tail rattling, growling, scale rubbing, or cloacal popping to send messages to their would-be predators, these sounds are mostly above 2,500 Hz, so the snakes themselves cannot hear them. Some species are capable of producing sounds whose frequency overlaps with their hearing range, such as the loud, robust hisses of pinesnakes and gophersnakes (Pituophis), the bizarre and intimidating growling sounds of king cobras (Ophiophagus), and the famous rattles of some large rattlesnakes (Crotalus). Some people have suggested that rattlesnakes find their hibernacula by following the rattling sounds of other rattlesnakes, but this idea has been disproven because the power output of rattling is insufficient to serve as a long-distance signal, and playback experiments have not yielded a behavioral response to rattling.

Snakes might eavesdrop on the alarm calls of other, more vocal animals, as some lizards do with bird alarm calls, but probably not since most of these calls are between 2,500 and 10,000 Hz, well above their optimal frequency range. Most likely, snakes use their hearing to monitor their environment for sounds produced by approaching predators or prey, many of which are ground-borne vibrations. Snakes can hear in stereo and can use their hearing to determine the directionality and thereby the sources of sounds. One genus of snakes that probably relies quite heavily on vibration to hunt are Saharan sand vipers (Cerastes). These snakes ambush lizards and rodents from a position partially or completely buried in sand. Experiments have shown that their reliance on chemosensing and thermal cues was minimal and that, although snakes with their eyes obscured had altered strike kinematics, they were still able to capture prey.