Wednesday, August 10, 2016

Colubroid venom composition- an overview

The rear fang of the African Twig snake, Thelotornis capensis.
Snake venoms have been subjected to increasingly sensitive analyses for well over 100 years, but most research has been restricted to front-fanged snakes, which actually represent a relatively small proportion of extant species of advanced snakes. Because rear-fanged snakes are a diverse and distinct radiation of the advanced snakes, understanding venom composition among “colubrids” is critical to understanding the evolution of venom among snakes. In a new paper Junqueira-de-Azevedo and colleagues (2016) review the state of knowledge concerning rear-fanged snake venom composition, emphasizing toxins for which protein or transcript sequences are available. The authors have also added new transcriptome-based data on venoms of three species of rear-fanged snakes. Based on this compilation, it is apparent that several components, including cysteine-rich secretory proteins (CRiSPs), C-type lectins (CTLs), CTLs-like proteins and snake venom metalloproteinases (SVMPs), are broadly distributed among “colubrid” venoms, while others, notably three-finger toxins (3FTxs), appear nearly restricted to the Colubridae (sensu stricto). Some putative new toxins, such as snake venom matrix metalloproteinases, are in fact present in several colubrid venoms, while others are only transcribed, at lower levels. This work provides insights into the evolution of these toxin classes, but because only a small number of species have been explored, generalizations are still rather limited. It is likely that new venom protein families await discovery, particularly among those species with highly specialized diets. The authors conclude that it is now abundantly clear that the venoms produced among the colubrid rear-fanged snakes are homologous with the much better characterized venoms of the front-fanged snakes. As trophic adaptations that facilitate feeding, venoms vary in composition with several important factors, including phylogeny, and so it is to be expected that among the diverse colubrid lineages, novel compounds, and new functional variants of better-known venom proteins, will be encountered. Much progress toward understanding rear-fanged snake venom composition has been made in the last decade, but, as indicated above, we have barely begun to explore the diversity of advanced snakes that comprise the colubrids. Transcriptomic and genomic approaches will greatly facilitate this work, but it must be remembered that functional assays should also accompany analysis of any venom, because the common recurring motif in venom biochemistry is to make the most of a stable molecular scaffold, perhaps best exemplified by the varied pharmacologies of the three-finger toxin superfamily. These small, structurally conservative peptides have very similar crystal structures but affect systems as diverse as neurotransmission, the blood clot cascade, ion channel function, and salamander limb regeneration and courtship. As Dr. Jay Fox once said, in venoms “we find only what we are looking for”, and, to find truly novel toxins that will likely be present in some colubrid venoms, we will have to look beyond the “normal” families of venom proteins.

Junqueira-de-Azevedo, I. L., Campos, P. F., Ching, A. T., & Mackessy, S. P. (2016). Colubrid venom composition: an-omics perspective. Toxins, 8(8), 230.

Viper diversification examined

In a forthcoming paper in MPE Alencar et al (2016) look at the diversification of vipers. The cosmopolitan family contains about 329 venomous species showing a striking heterogeneity in species richness among lineages. While the subfamily Azemiopinae comprises only two species, 70% of all viper species are arranged in the subfamily Crotalinae or the “pit vipers”. The radiation of the pit vipers was marked by the evolution of the heat-sensing pits, which has been suggested to be a key innovation for the successful diversification of the group. Also, only crotalines were able to successfully colonize the New World. The authors present the most complete molecular phylogeny for the family to date that includes sequences from nuclear and mitochondrial genes representing 79% of all living vipers. They also investigated the time of divergence between lineages, using six fossils to calibrate the tree, and explore the hypotheses that suggest crotalines have undergone an explosive radiation. The phylogenetic analyses retrieved high support values for the monophyly of the family Viperidae, subfamilies Viperinae and Crotalinae, and 22 out of 27 genera, as well as well-supported intergeneric relationships throughout the family. The study found strongly supported sister clade to the New World pit vipers that comprises Gloydius, Ovophis, Protobothrops and Trimeresurus gracilis. Time of divergence estimates suggested that vipers started to radiate around the late Paleocene to middle Eocene with subfamilies most likely dating back to the Eocene. The invasion of the New World may have taken place sometime close to the Oligocene/Miocene boundary. Diversification analyses suggested a shift in speciation rates during the radiation of a sub-clade of pit vipers where speciation rates rapidly increased but slowed down toward the present. Thus, the evolution of the loreal pits alone does not seem to explain their explosive speciation rates. The auithor suggest that climatic and geological changes in Asia and the invasion of the New World may have also contributed to the speciation shift found in vipers.

Alencar, L. R., Quental, T. B., Grazziotin, F. G., Alfaro, M. L., Martins, M., Venzon, M., & Zaher, H. (2016). Diversification in vipers: Phylogenetic relationships, time of divergence and shifts in speciation rates. Molecular Phylogenetics and Evolution.

An endangered homalopsid snake, Enhydris jagorii

Jagor's Water Snake, Enhydris jagorii. Photo D. R. Karns

Jagor's water snake (Enhydris jagorii) is a freshwater snake endemic to the Chao Phraya-Ta Chin basin of Thailand. Habitat change and destruction are the main threats to this snake, where a large area of the wetland has been rapidly transformed into urban and agricultural areas. Moreover, uncontrolled fishing seriously threatens the what is most likely the last  remaining population of this snake. Pongcharoen et al. (2016) conducted a field study in the Bung Ka Loh wetland from October, 2010 to August, 2014 and collected 108 specimens of this species. Analysis of the stomach contents revealed that it is piscivorous, with cyprinids being the dominant prey. Prey items were usually less than 10% of the snake body mass and multiple prey items were occasionally found. No significant difference in diet was noted between the sexes. In addition, predation on this snake by Cylindrophis ruffus was first recorded in this study. The smallest gravid female collected had a snout-vent length of 34.0 cm. The clutch size and mass ranged from 1 to 28 embryos and 3.1–123.0 g, respectively, and both of these quantities increased significantly with increased female size. Reproduction was possibly seasonal and occurred in the rainy season. A preliminary study of other wetlands in the central plain of Thailand failed to detect the existence of this species. Accordingly, the conservation status of this species should be changed from Data Deficient to Critically Endangered.

Pongcharoen, C., Voris, H. K., Seelanan, T., Pradatsundarasar, A. O., & Thirakhupt, K. (2016). Diet, female reproduction and conservation of Jagor’s water snake, Enhydris jagorii in Bung Ka Loh wetland, Uttaradit province, Thailand. Agriculture and Natural Resources. Available online 25 June 2016

Friday, March 18, 2016

A giant viper from the Greek Pliocene

The type vertebra of Laophis crotaloides modified from
the original publication by Owen (1857). Image not to scale.
In 1857, British palaeontologist Richard Owen described Laophis crotaloides, a new species of viperid snake, on the basis of 13 large, fossilized vertebrae from Megalo Emvolon, near Thessaloniki, in northern Greece. According to Owen, the vertebrae belonged to a very large viperid with striking similarity to modern rattlesnakes of the genus Crotalus. Ever since, Laophis has been an enigma. Almost all subsequent authors neglected it or considering it problematic, possibly because it was estimated to reach three meters in length.

In a new paper Georgalis et al. (2016) report on a previously undescribed vertebra of a large snake from the area of the type locality of L. crotaloides in northern Greece. Although the vertebra is fragmentary, it shares with Laophis crotaloides an overall large size and clear viper features. The authors assigned the vertebrae to Laophis crotaloides. Unfortunately, the broken fossil precludes any precise conclusions about the taxonomic status of this fossil snake and the affinities of Laophis to the other members of the Viperidae. Nevertheless, this new material confirms the validity of the taxon and suggests certain vertebral characters featured in the original description by Owen (1857) were inaccurate. The maximum length of the condyle of the most recent specimen is 16.3 mm, the longest condyle reported for any European viperid. The vertebrae is from the Pliocene.

The mammal fauna of Megalo Emvolon is speciose and relatively well studied. It includes bovids, a suid, an equid, various rodents and lagomorphs, a canid, and a cercopithecid primate. A single species of bird is known from the site, a peafowl. Reptiles are represented by Laophis crotaloides (the only squamate) and numerous small and giant tortoises. The mammal fauna indicates the paleoenvironment of Laophis crotaloides was semi-arid.

Georgalis, G. L., Szyndlar, Z., Kear, B. P., & Delfino, M. (2016). New material of Laophis crotaloides, an enigmatic giant snake from Greece, with an overview of the largest fossil European vipers. Swiss Journal of Geosciences, 1-14.

A new colubrid genus and species from India

Wallaceophis gujarateneis sp. n 

A photograph of an uncollected snakes in 2007 paper depicted a small yellow snake with two dark stripes, the species discussed in the article lacked stripes, and a follow up investigation revealed a new species in a new genus with a very ancient history. Mirza et al. 2016 obtained a second specimen of the snake from Gujarta, India. Results from molecular data show that the snake belongs to a clade arid dwelling snakes with Platyceps, Eirenis, Spalerosophis, Macroprotodon and Lytorhynchus. The snake however greatly differs morphologically as well as genetically which warrants erection of a new genus to accommodate the new species from Gujarat.

Wallaceophis gujarateneis sp. nov. measures SVL 250–930 mm and differs from most colubrid genera in lacking hypapophyses on posterior dorsal vertebrae  and in bearing nine maxillary teeth and the posterior-most teeth are subequal, nine palatine teeth. Dorsal scale reduction characterized by vertebral reductions, increase of scale rows posterior to neck, a single lateral reduction at midbody and regular vertebral reductions in posterior half of the body. Rostral not visible from above, a small presubocular present. Eight supralabials, fourth and fifth in contact with orbit, anal undivided, 215–216 ventrals, 51–54 subcaudals, hemipenis subcylindrical, spinose throughout and 3–4 dorsal scale row wide black longitudinal stripe running from the post nasal to the tail tip on each side on a wheat colored dorsum.

The type specimen was collected from a manmade water hole near an irrigation canal along with a few juveniles of Xenochropis piscator. The species appears to be diurnal as it was collected at ca. 11:15 hours. The type locality, Khengariya village, is situated in the dry plains of central-western region of Gujarat state. The type locality habitat is in an area of Desert thorn forest. The annual precipitation is 838mm. Majority of the precipitation occurs during the months of July and August. The temperature varies from as low as 12°C during winter and as high as 43°C during the hot summer days. The snake snakes behavior suggests it is aquatic and fossorial. An individual retained in captivity was readily ate a Hemidactylus gecko.

Mirza ZA, Vyas R, Patel H, Maheta J, Sanap RV (2016) A New Miocene-Divergent Lineage of Old World Racer Snake from India. PLoS ONE 11(3): e0148380. doi:10.1371/journal.pone.0148380

Irish Snakes?

If snakes were introduced to Ireland, surely they would hav to 
look like this.

The legend of St. Patrick banishing snakes from the emerald isle some 1,500 years ago is indelibly etched in folklore -- even if science suggests snakes were unlikely to have colonized the country following the last ice age.

But what would happen if St. Patrick's scaly foes were introduced now? Would Ireland's native wildlife sink or swim?

Experts from Trinity College Dublin believe snakes could certainly slither into Ireland's ecosystems if introduced but would likely cause trouble for native ecosystems. There are enough troublesome pests in Ireland today, such as the introduced New Zealand flatworm, which people would like to send on its merry way with some modern-day St. Patrick-style sorcery.

Associate researcher in Trinity's School of Natural Sciences, Collie Ennis, is a snake expert. He said: "If you look across the water, the UK has very similar environmental conditions to ours and snakes fit right in. Native animals that would not have evolved around snakes as predators would be lost if snakes were introduced here but snakes could probably persist."

Interestingly, a number of attempts have been made to introduce grass snakes, one of three species that are native to Britain, over the past 100 years. Until recently, grass snakes could even be bought in pet shops throughout the land.

Collie Ennis added: "There are anecdotal records of individuals releasing several grass snakes along the Royal Canal in Dublin but luckily the snakes failed to establish populations. This could simply be due to the small numbers of snakes introduced, the unappealing climate, or to a combination of these factors."

Worryingly, Professor of Zoology at Trinity, Yvonne Buckley, says there are lots of other invasive species that have established, and whose ecological influence is growing quickly. Some of these species present a real threat to Ireland's environment and economy.

Near the top of that list is the New Zealand flatworm, a relative newcomer to Ireland's shores, which feeds on native earthworms that provide important ecosystem services as well as currying favor with farmers for enhancing the fertility and drainage of agricultural soils.

Professor Buckley said: "New Zealand flatworms are not snakes but they are long and legless, and our ecosystems and farms would benefit from their removal. It certainly would be legendary if I could magically banish these legless interlopers! Unfortunately it costs a lot more to banish unwanted pests now than it did in St Patrick's day, so introduction of snakes would be a very expensive mistake."

Other invasive species that threaten Irish biodiversity and harm the economy include zebra mussels, muntjac deer, harlequin ladybirds, mink, mitten crabs, rhododendron and Japanese knotweed.

Trinity College Dublin. 

Wednesday, February 24, 2016

The first amphisbaenian from Texas

Amphisbaenians are a clade of fossorial squamates that are usually legless and have skull modified of burrowing. They appear to be the sister to the the Eastern Hemisphere lizards in the family Lacertidae. Five major clades  are recognized, but controversy exists as to which North American clade is the most basally diverging: the limbed Bipedidae according to morphological data or Rhineuridae as suggested by molecular evidence. Extinct North American amphisbaenians are represented by multiple skulls and postcranial remains from the Paleocene to the Recent.
This is the fossilized skull of Solastella 
cookei, a new genus and species of worm 
lizard. Photo Credit: Michelle Stocker 
and Chris Kirk

A new species of fossil amphisbaenian, Solastella cookei, was described in the Journal of Vertebrate Paleontology. Solastella is a Latinized form of lone star.

"Nothing has been called Solastella before, which is amazing to me because there are so many fossils from Texas. It's the one guy, and it's from the Lone Star State, so it just seemed to fit," said Michelle Stocker, a paleontologist who described the extinct reptile while earning her Ph.D. at the University of Texas at Austin's Jackson School of Geosciences. She is now a research scientist at Virginia Tech.

The second part of the scientific name honors botanist William Cook, a professor at Midwestern State University in Wichita Falls, which owns the property where the fossils were collected.

Worm lizard is the common name for a group of reptiles called amphisbaenians, whose long bodies and reduced or absent limbs give them an earthworm-like appearance. The group includes extinct species as well as ones still living today. Solastella belonged to a subgroup called Rhineuridae, a group with only one living member -- the Florida worm lizard.

Stocker identified Solastella as a new species by analyzing fossilized skulls that she unearthed in the Devil's Graveyard Formation in West Texas. She found that Solastella lived during the Late Middle Eocene, a geologic period about 40 million years ago, and that its eye socket was fully enclosed, a feature lacking in all living amphisbaenians but present in extinct relatives.

The discovery of an amphisbaenian in Texas helps bridge the gap between extinct species found in the western interior of the U.S. and the living worm lizard in Florida today. It also supports the theory that Texas served as a subtropical refuge for species that found it difficult to survive during the cooling climate of the Late Middle Eocene.

"What's special about reptiles is that they are ectothermic, or cold-blooded, so they need to maintain their body temperature to the external environment," Stocker said. "You can actually get a better sense at what the climate was like from reptiles than from mammals. We were very excited that we not only found Solastella at the site, but a whole bunch of other reptiles."

The presence of a variety of primate fossils in the same formation as Solastella also supports the idea that Texas was a refuge in a cooling climate, said Chris Kirk, a UT Austin anthropology professor who has conducted paleontological fieldwork in the Devil's Graveyard Formation since 2005.

"Primates are generally tropically adapted mammals that prefer warm climates," Kirk said. "The diverse primate community from the Devil's Graveyard Formation is another indicator that the Big Bend region of Texas was warm, equable and forested during the Late Middle Eocene."

Stocker said the discovery gives insight into how certain animal groups could respond to climate change in the future.

"With climate change, animals either adapt, or they move, or they go extinct. And so we can look at what's happened in the past and see that certain conditions caused certain things to happen in certain groups," Stocker said. "The great thing about the fossil record is that the experiment has already been done for us. We just have to collect the evidence."

Stocker MR & Kirk EC. (2016) The first amphisbaenians from Texas, with notes on other squamates from the middle Eocene Purple Bench Locality. Journal of Vertebrate Paleontology, e1094081.

Monday, February 8, 2016

First fossil chamaeleonid from Greece

Chameleo chameleo from Samos, Greece.. Benny Trapp
Chameleons  constitute a diverse clade of lizards with more than 200 species that are distributed in Africa, Madagascar and several Indian Ocean islands, southern Asia, Cyprus and southern parts of Mediterranean Europe. Cryptic diversity is common within the group. Several new species having been described in the current decade, mostly on the basis of molecular data. The size range of chamaeleonids is astonishing, with the larger members of the family surpassing 600 mm in total length, and the smallest species rank well among the tiniest known reptiles, the extant Brookesia micra, attaining only 29 mm and the extinct Jucaraseps grandipessimilar of similar size.

The Chamaeleonidae fossil record is very scarce and any new specimen is therefore considered important for our understanding of the evolutionary and biogeographic history of the group. In a new paper Georgalis et al. (2016) report on new specimens from the early Miocene of Aliveri (Evia Island) in Greece. These are the only fossils chamaeleons  from southeastern Europe. Although skull bones are tentatively attributed to the Czech species Chamaeleo cf. andrusovi, revealing a range extension for this taxon, the tooth-bearing bones are described as indeterminate chamaeleonids. The Aliveri fossils rank well among the oldest known reptiles from Greece, provide evidence for the dispersal routes of chameleons out of Africa towards the European continent and, additionally, imply strong affinities with coeval chamaeleonids from Central Europe.

Georgalis, G. L., Villa, A., & Delfino, M. (2016). First description of a fossil chamaeleonid from Greece and its relevance for the European biogeographic history of the group. The Science of Nature, 103(1-2), 1-12.

Friday, January 22, 2016

A new species of high elevation Liolaemus (Family Liolaemidae)

Liolaemus uniformis. Photo credit:  Jaime Troncoso-Palacios
During a field trip at 3000 metres above sea level, a group of scientists, led by Jaime Troncoso-Palacios, Universidad de Chile, discovered a new endemic lizard species, in the mountains of central Chile, scientists. Noticeably different in size and scalation, compared to the rest of the local lizards, what initially grabbed the biologists' attention was its colouration. Not only was it unlike the already described ones, but also appeared surprisingly consistent within the collected individuals, even regardless of their sex. Eventually, it was this peculiar uniformity that determined the lizard's name Liolaemus uniformis. The study is published in the open-access journal ZooKeys.

The researchers found the lizards quite abundant in the area, which facilitated their observations and estimations. Apart from a thorough description of the new iguana along with its comparisons to its related species, the present paper also provides an in-depth discussion about the placement of the new taxon, which had been confused with other species in the past.

While most of the other lizards from the area and its surroundings often vary greatly in colouration and pattern between populations and sexes, such thing is not present in the new species. Both males and females from the observed collection have their bodies' upper side in brown, varying from dark on the head, through coppery on the back and light brown on the tail. The down side of the body is mainly yellowish, while the belly -- whitish. The only variables the scientists have noticed in their specimens are slight differences in the shade with two females demonstrating unusual olive hues on their snouts. These differences in morphology were also strongly supported by the molecular phylogeny through the analysis of mitochondrial DNA, which was performed by Dr. Alvaro A. Elorza, from Universidad Andres Bello.

Accustomed to life in highland rocky habitats with scarce greenery, these lizards spend their active hours, estimated to take place between 09:00 h and 18:00 h hidden under stones. However, they might not be too hard to find due to their size of about 8.5 cm for the males and their abundance in the studied area. The females are more slender and measure 7 cm in length on average.

Having caught one of their specimens while holding a yellow flower in its mouth, the scientists conducted further examination of the stomach contents of the studied individuals and concluded that the species is omnivorous, feeding mainly on plants as well as insects and roundworms.

In conclusion, the researchers showed that there is still a huge gap in the knowledge of the close relatives of the newly described species and their "challenging taxonomy."

Jaime Troncoso-Palacios, Alvaro A. Elorza, German I. Puas, Edmundo Alfaro-Pardo. A new species of Liolaemus related to L. nigroviridis from the Andean highlands of Central Chile (Iguania, Liolaemidae). ZooKeys, 2016; 555: 91 DOI: 10.3897/zookeys.555.6011

Tuesday, January 19, 2016

Rapoport's rule & lizards

Left. Anna Pintor with a flap-footed lizards (Pygopodiae). Photo credit: Image 
courtesy of James Cook University.Right pygopodids are legless geckos. JCM

James Cook University scientists have found lizards exposed to rain, hail and shine may cope better with extreme weather events predicted as a result of climate change than their fair-weather cousins.

A new study by JCU PhD student Anna Pintor, published in the journal Ecological Monographs, is one of the first to test the Climatic Variability Hypothesis (CVH) -- which proposes that animals living in environmentally variable areas should be able to tolerate more environmental fluctuations as a result.

This idea is a key assumption of the controversial Rapoport's Rule -- which states that a species at higher latitudes with variable weather conditions leads to the evolution of wider environmental tolerances which leads to a requirement for a larger range size.

Ms Pintor, along with supervisors Professor Lin Schwarzkopf and Professor Andrew Krockenberger from the Centre for Tropical Biodiversity and Climate Change, used three groups of Australian skinks for their analysis.

Their results confirm, in all three groups, that species living in regions with greater temperature variability have both greater environmental tolerances and wider ranges -- both in terms of latitude and altitude.

Andrew Krockenberger explains the importance of this result to advancing scientific thought "The literature is full of examples of species that do and don't fit Rapoport's rule," he said. "We've shown what is important is the actual underlying mechanism -- that species that can deal with a high degree of variability at a single site also end up with more extensive geographic ranges.

"Arguing about whether or not Rapoport's rule is valid is irrelevant and misses the point -- let's start making sure we understand the underlying process instead."

Lead author Anna Pintor said if we want to understand impacts of climate change in the future, we need to know how species' current distributions come about it the first place.

"Understanding underlying mechanisms like the CVH is one way to do that, but we need to do a lot more before we can tell exactly how species will be impacted and how to best help them deal with climate change."


Anna F. V. Pintor, Lin Schwarzkopf, Andrew K. Krockenberger. Rapoport's Rule: Do climatic variability gradients shape range extent? Ecological Monographs, 2015; 85 (4): 643 DOI: 10.1890/14-1510.1

Sunday, January 10, 2016

Death by constriction, a fourth possible cause

A juvenile Burmese Python constricting a rat.
The evolution of constriction  was undoubtedly very important milestone in the evolution and radiation of snakes. Killing large prey quickly and reducing the chance of injury to a snake allowed snakes to subdue otherwise unobtainable, larger prey. Constricting snakes exert pressure by coiling around and squeezing their prey, usually killing it before swallowing. The process of constriction takes energy and time, and risks injury to the snake. A snake's ability to constrict and kill quickly is important because it impacts feeding success, and thus growth and fitness. Constriction pressures are generated by forces from the snake’s axial musculature applied to the prey. These forces are proportional to the cross-sectional area of active muscle, and therefore to the snake's diameter. In a new paper Penning et al. (2015) describe the ontogeny of constriction performance in Reticulated and Burmese Pythons. The authors also discuss the implications for the cause of prey death during constriction.

The study found both species constrict prey vigorously using coils of 1–4 loops. Reticulated Pythons exerted maximum pressures of 8.27–53.77 kPa, with larger individuals exerting significantly higher peak pressures than smaller individuals. Burmese Pythons constricted with maximum pressures of 18.0–42.93 kPa, with larger individuals also exerting significantly higher peak pressures than smaller individuals  The species or the number of loops in a coil did not significantly affect peak
pressure in either species.

Constriction pressures exerted by both pythons scale differently from those of other snakes, many of the highest pressures were probably enough to force blood into the brain at high pressure in mammalian prey. In addition to suffocation, circulatory arrest and spinal dislocation, the authors propose the ‘red-out effect’  as a fourth possible mechanism of prey death by constriction. The redout effect describes the effect of negative gravity on jet pilots during extreme flight manoeuvres, in which vision becomes reddened by uncontrollable blood flow to the brain and eyes. When fighter pilots experience negative gravitational accelerations (G-forces), they incur a rush of blood to the brain that causes rapid loss of consciousness. Constriction pressures above the venous blood pressure of the prey will impede blood flow and oxygen delivery to tissues.  Pressure from constriction  dramatically higher than the prey’s blood pressure could force blood away from the site of constriction and into the extremities, including the head and brain. Blood being pushed into the brain during peak constriction could cause the same red-out effect described above for pilots, and could cause extensive ruptures in cranial blood vessels.

Penning, D. A., Dartez, S. F., & Moon, B. R. (2015). The big squeeze: scaling of constriction pressure in two of the world's largest snakes, Python reticulatus and Python molurus bivittatus. Journal of Experimental Biology,218(21), 3364-3367.

Friday, January 1, 2016

Sex chromosomes in snakes

In two recently published articles Rovatsos et al. (2015 a, b) highly differentiated heteromorphic ZZ/ZW sex chromosomes with a heterochromatic W are  basic among the advanced snakes, Colubroidea, while other snake lineages generally lack them. The authors examined the dragonsnake, Xenodermus javanicus (family Xenodermatidae), which is phylogenetically nested between snake lineages with and without differentiated sex chromosomes. Although most snakes have a karyotype with a stable 2n chromosomal number of  36, the dragonsnake has an unusual, derived karyotype  2n = 32 chromosomes. The found that heteromorphic ZZ/ZW sex chromosomes with a heterochromatic W are present in the dragonsnake, which suggests that the emergence of a highly differentiated W sex chromosome within snakes predates the split of Xenodermatidae and the clade including families Pareatidae, Viperidae, Homalopsidae, Lamprophiidae, Elapidae, and Colubridae (the Colubroidae). Although accumulations of interstitial telomeric sequences have not been previously reported in snakes, by using FISH with a telomeric probe they discovered them in six pairs of autosomes as well as in the W sex chromosome of the dragonsnake. Similarly to advanced snakes, the sex chromosomes of the dragonsnake have a significant accumulation of repeats containing a (GATA)n sequence. The results facilitate the dating of the differentiation of sex chromosomes within snakes back to the split between Xenodermatidae and other advanced snakes, about 40-75 mya. In a second  article they document the stability of sex chromosomes in advanced snakes based on the testing of Z-specificity of genes using quantitative PCR (qPCR) across 37 snake species (their qPCR technique is suitable for molecular sexing all advanced snakes). They found that at least part of the sex chromosomes is homologous across all families of caenophidian snakes (Acrochordidae, Xenodermatidae, Pareatidae, Viperidae, Homalopsidae, Colubridae, Elapidae and Lamprophiidae). The emergence of differentiated sex chromosomes can be dated to about 60 Ma, a date that preceded the extensive diversification of advanced snakes, a group with more than 3000 species. The Z-specific genes of caenophidian snakes are (pseudo)autosomal in the snake families Pythonidae, Xenopeltidae, Boidae, Erycidae and Sanziniidae, as well as in outgroups with differentiated sex chromosomes such as monitor lizards, iguanas and chameleons. Along with iguanas, advanced snakes are therefore another example of ectothermic amniotes with a long-term stability of sex chromosomes comparable with endotherms.

Rovatsos, M., Johnson Pokorná, M., & Kratochvíl, L. (2015). Differentiation of Sex Chromosomes and Karyotype Characterisation in the Dragonsnake Xenodermus javanicus (Squamata: Xenodermatidae). Cytogenetic and genome research.

Rovatsos, M., Vukić, J., Lymberakis, P., & Kratochvíl, L. (2015). Evolutionary stability of sex chromosomes in snakes. In Proc. R. Soc. B (Vol. 282, No. 1821, p. 20151992). The Royal Society.

Tuesday, December 22, 2015

New range and habitat records for threatened Australian sea snakes

The rare short nosed sea snake discovered 
on Ningaloo reef, Western Australia. Photo 
Credit: Grant Griffin, W.A. Dept. Parks and 
Scientists from James Cook University have discovered two critically endangered species of sea snakes, previously thought to be extinct, off the coast of Western Australia.

It's the first time the snakes have been spotted alive and healthy since disappearing from their only known habitat on Ashmore Reef in the Timor Sea more than fifteen years ago.

"This discovery is really exciting, we get another chance to protect these two endemic Western Australian sea snake species," says study lead author Blanche D'Anastasi from the ARC Centre of Excellence for Coral Reef Studies at JCU.

"But in order to succeed in protecting them, we will need to monitor populations as well as undertake research into understanding their biology and the threats they face."

The discovery of the critically endangered short nose sea snake was confirmed after a Western Australia Parks and Wildlife Officer, Grant Griffin, sent a photo of a pair of snakes taken on Ningaloo Reef to Ms D'Anastasi for identification.

"We were blown away, these potentially extinct snakes were there in plain sight, living on one of Australia's natural icons, Ningaloo Reef," says Ms D'Anastasi.

"What is even more exciting is that they were courting, suggesting that they are members of a breeding population."

The researchers also made another unexpected discovery, uncovering a significant population of the rare leaf scaled sea snake in the lush seagrass beds of Shark Bay.

The discovery was made 1700 kilometres south of the snakes only known habitat on Ashmore Reef.

"We had thought that this species of sea snake was only found on tropical coral reefs. Finding them in seagrass beds at Shark Bay was a real surprise," says Ms D'Anastasi.

Both leaf scaled and short nosed sea snakes are listed as Critically Endangered under Australia's threatened species legislation, which means they have special protection.

Despite the good news of the find, sea snake numbers have been declining in several marine parks, and scientists are at a loss to explain why.

"Many of the snakes in this study were collected from prawn trawl by-catch surveys, indicating that these species are vulnerable to trawling," says Dr Vimoksalehi Lukoschek from the Centre of Excellence for Coral Reef Studies.

"But the disappearance of sea snakes from Ashmore Reef, could not be attributed to trawling and remains unexplained.

"Clearly we need to identify the key threats to their survival in order to implement effective conservation strategies if we are going to protect these newly discovered coastal populations," Dr Lukoschek says.

B.R. D'Anastasi, L. van Herwerden, J.A. Hobbs, C.A. Simpfendorfer, V. Lukoschek. New range and habitat records for threatened Australian sea snakes raise challenges for conservation. Biological Conservation, 2016; 194: 66 DOI: 10.1016/j.biocon.2015.11.032

Tuesday, December 8, 2015

Sea snake diversity in the Indo-Australian Archipelago

The Indo-Australian Archipelago is a marine biodiversity hotspot centred in Southeast Asia that contains many of the extant viviparous sea snakes. Points of origin of for snake radiations are of interest  in understanding the distribution of current diversity. In an early on-line view of a new paper in the Journal of Biogeography, Ukuwela and colleagues (2015) note that previouis studies found the ancestral area for viviparous sea snakes was Australasian about 6.9 million years ago. The Aipysurus group also originated and speciated in Australasia. However, of the Aipysurus group species, only the specialist fish egg-eaters (Emydocephalus ijimae, E. szczerbaki and A. eydouxii) have colonized Southeast Asia and none have expanded into the Indian Ocean beyond the coast of Western Australia. A Beast analyses recovered a Southeast Asian origin for the core Hydrophis group, and all three methods used indicated that subsequent diversification in this rapidly speciating clade occurred primarily in Southeast Asia, with subsequent dispersals into the Indian Ocean and re-colonization of Australasia.

Ukuwela et al. (2015) found evidence for 34 divergences between lineages older than 0.5 Ma (candidate speciation events); 22 of these have > 0.7 posterior probabilities of occurring in Southeast Asia, 10 in Australasia, and 2 in the Indian Ocean. This implies most sea snake diversity in South East Asia originated from a period of rapid in situ evolution. While viviparous sea snakes originated in Australasia, Southeast Asia and its Indo-Australian Archipelago appears to be their primary centre of speciation. This is contrary to predictions of the overlap or accumulation models. Taxa are not more likely to disperse into, rather than out of, Southeast Asia and the Indo-Australian Archipelago.

The majority of sea snake diversification, including the rapid core Hydrophis radiation, occurred during major climatic and geological events that drove vicariant population and species divergence in many of the region’s marine groups. Viviparous sea snakes might be particularly influenced by ‘soft’ biogeographical barriers (such as incomplete and thus permeable land bridges) because they give birth to live young and thus lack the dispersing planktonic larval stage that is expected to promote population connectivity in most other marine groups (many fish and invertebrates). Several sea snake species accordingly show strong intraspecific genetic structure corresponding to deep-water and historical land barriers. However, biogeographical patterns and the diversification dynamics of the entire sea snake radiation have not previously been quantitatively investigated.

Ukuwela, Kanishka DB, Michael SY Lee, Arne R. Rasmussen, Anslem Silva, Bryan G. Fry, Parviz Ghezellou, Mohsen Rezaie‐Atagholipour, and Kate L. Sanders. 2015. Evaluating the drivers of Indo‐Pacific biodiversity: speciation and dispersal of sea snakes (Elapidae: Hydrophiinae). Journal of Biogeography (2015).

Monday, November 30, 2015

Dinilysia's inner ear suggests it was a burrowing species, implications for the evolution of snakes

Modern snake skull, with inner ear shown in orange. 
Photo Credit: Hongyu Yi
Modern snakes probably originated as habitat specialists, but it is controversial unclear whether they were ancestrally terrestrial burrowers or marine swimmers. In a new paper Yi and Norell (2015)  use x-ray virtual models of the inner ear to predict the habit of Dinilysia patagonica, a stem snake closely related to the origin of modern snakes. Previous work has shown that modern snakes perceive substrate vibrations via their inner ear. The study's  data show that D. patagonica and modern burrowing squamates share a unique spherical vestibule in the inner ear, as compared with swimmers and habitat generalists. The authors built predictive models for snake habitats based on their vestibular shape, which estimated D. patagonica and the hypothetical ancestor of crown snakes as burrowers with high probabilities. This study provides an extensive comparative data set to test fossoriality quantitatively in stem snakes, and it shows that burrowing was predominant in the lineages leading to modern crown snakes.

Comparisons between CT scans of the fossil and modern reptiles indicate that snakes lost their legs when their ancestors evolved to live and hunt in burrows, which many snakes still do today.

The findings suggest snakes did not lose their limbs in order to live in the sea, as has been previously suggested.

Scientists used CT scans to examine the bony inner ear of Dinilysia patagonica, a 2-metre long reptile closely linked to modern snakes. These bony canals and cavities, like those in the ears of modern burrowing snakes, controlled its hearing and balance.

They built 3D virtual models to compare the inner ears of the fossils with those of modern lizards and snakes. Researchers found a distinctive structure within the inner ear of animals that actively burrow, which may help them detect prey and predators. This shape was not present in modern snakes that live in water or above ground.

The findings help scientists fill gaps in the story of snake evolution, and confirm Dinilysia patagonica as the largest burrowing snake ever known. They also offer clues about a hypothetical ancestral species from which all modern snakes descended, which was likely a burrower.

Dr Hongyu Yi, of the University of Edinburgh's School of GeoSciences, who led the research, said: "How snakes lost their legs has long been a mystery to scientists, but it seems that this happened when their ancestors became adept at burrowing. The inner ears of fossils can reveal a remarkable amount of information, and are very useful when the exterior of fossils are too damaged or fragile to examine."

Mark Norell, of the American Museum of Natural History, who took part in the study, said: "This discovery would not have been possible a decade ago -- CT scanning has revolutionised how we can study ancient animals. We hope similar studies can shed light on the evolution of more species, including lizards, crocodiles and turtles."


Yi, H. &  M.A. Norell. The burrowing origin of modern snakes. Science Advances, 2015; 1 (10): e1500743 DOI: 10.1126/sciadv.1500743