Tuesday, April 30, 2013

A new squamate phylogeny

This new study finds rubber boas are not erycines but more closely related to Ungaliophis.
Lizards and snakes (living squamates) number about 9,400 known species. Despite Squamata being one of the most diverse and conspicuous radiations of terrestrial vertebrates, no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to address their classification. Alexander Pyron and colleagues (2013) present the first large-scale phylogenetic estimate for Squamata.

Their estimated phylogeny contains 4161 species, representing all currently recognized families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy.

This study provides a phylogenetic estimate for 4161 squamate species, based on a supermatrix approach. The results provide important confirmation for previous studies based on more limited taxon sampling, and reveal new relationships at the level of families, genera, and species. The authors also provide a phylogenetic framework for future comparative studies, with a large-scale tree including a common set of estimated branch lengths. Also provided is a revised classification for squamates based on this tree, including changes in the higher-level taxonomy of gymnophthalmid and scincid lizards and boid, colubrid, and lamprophiid

Some of the more interesting relationships suggested by this work include the following.

(1) The authors found strong support for the basal squamate relationships in the tree. The family Dibamidae is the sister group to all other squamates, and Gekkota is the sister group to all squamates excluding Dibamidae as in some previous studies. The results also corroborate that the New World genus Anelytropsis is nested within the Old World genus Dibamus, but the associated branches are weakly supported.

(2) Within Gekkota, they corroborate both earlier morphological and recent molecular estimates in supporting a clade containing the Australian radiation of "diplodactylid" geckos (Carphodactylidae + Diplodactylidae) and the snakelike pygopodids. As in previous studies, Carphodactylidae is the weakly supported sister group to Pygopodidae, and this strongly supported clade is the sister group to Diplodactylidae. They recover clades within the former Gekkonidae that correspond to the strongly supported families Eublepharidae, Sphaerodactylidae, Phyllodactylidae, and Gekkonidae as in previous studies.

(3) They found find strong support for monophyly of Toxicofera (Anguimorpha, Iguania, and Serpentes), and moderate support for a sister-group relationship between Iguania and Anguimorpha. Relationships among Anguimorpha, Iguania, and they also corroborate previous studies placing Anguimorpha with Iguania.

(4) The more advanced snakes (alethinophidians) showed a mixture of strongly and weakly supported nodes. The authors found strong support for a clade containing Anomochilidae + Cylindrophiidae + Uropeltidae. This clade of three families is strongly supported as the sister taxon to Xenopeltidae + (Loxocemidae + Pythonidae). Together, these six families form a strongly supported clade that is weakly supported as the sister group to the strongly supported clade of Boidae + Calabariidae.

(5) As for the Pythonidae, the genus Python is the sister group to all other genera. Some species traditionally referred to as Python (P. reticulatus and P. timoriensis) are instead sister to an Australasian clade consisting of Antaresia, Apodora, Aspidites, Bothrochilus, Leiopython, Liasis, and Morelia. These taxa (P. reticulatus and P. timoriensis) have been referred to as Broghammerus, a name originating from an act of "taxonomic vandalism" (i.e. an apparently intentional attempt to disrupt stable taxonomy) in a non-peer reviewed organ without data or analyses. The authors suggest this name should be ignored and replaced with a suitable substitute.

(6) Within Boidae this study and other recent studies have converged on estimated relationships that are generally similar to each other but which differ from traditional taxonomy. However, the classification has yet to be modified to reflect this, and we rectify this situation here. The authors found that Calabariidae is nested within Boidae, but this is poorly supported, and contrary to most previous studies. While Calabaria has been classified as an erycine boid in the past, this placement is strongly rejected by this work and other studies. If the current placement of Calabaria is supported in the future, it would require recognition as the subfamily Calabariinae. The Malagasy boine genera Acrantophis and Sanzinia are placed as the sister taxa to a weakly-supported clade containing Calabariidae and a strongly supported clade comprising the currently recognized subfamilies Erycinae, Ungaliophiinae, and other boines . Regardless of the position of Calabariidae, this placement of Malagasy boines renders Boinae paraphyletic. The authors therefore resurrect the subfamily Sanziniinae for Acrantophis and Sanzinia. This subfamily could be recognized as a distinct family if future studies also support placement of this clade as distinct from other Boidae + Calabariidae.

(7) The genera Lichanura and Charina are currently classified as erycines , but are strongly supported as the sister group to Ungaliophiinae, as in previous studies . The authors expand Ungaliophiinae to include these two genera, rather than erect a new subfamily for these taxa. The subfamily Ungaliophiinae is placed as the sister group to a well-supported clade containing the rest of the traditionally recognized Erycinae and Boinae. And, they restrict Erycinae to the Old World genus Eryx.

An early version of the entire article is available on-line.

Pyron, A. R., F. T. Burbrink, & J.J. Wiens, 2013. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evolutionary Biology 2013, 13:93 doi:10.1186/1471-2148-13-93.

Monday, April 29, 2013

Correlations between habitat use and morphology in sea kraits

Laticauda colubrina. JCM

In a forthcoming article in the Journal of Zoology Wang et al. (2013) report on the variation of characters in three species of Laticauda at Orchid Island, Taiwan. Previous research revealed that the phylogenetic and taxonomic status of the laticaudine sea kraits had been widely discussed in the literature. They found all three species are amphibious, but they differ in their tendency to spend time in marine or terrestrial environments. These sympatric sea kraits are most conspicuous in coastal areas where they tend to be most active at night. Laticauda semifasciata tends to remain submerged in shallow coastal waters; L. laticaudata largely stay above water, but not far from the edge of the sea and L. colubrina exhibit a greater tendency to emerge from water and move farther away from it. Thus, the tendency toward more completely marine habits is highest in L. semifasciata, lowest in L. colubrina and intermediate in L. laticaudata. The authors test the hypothesis that such a species gradient in behavior should be correlated with parallel adjustments in morphological and physiological character states.

All three species move into coastal areas at night. Generally, Laticauda semifasciata remain submerged in sea water, L. laticaudata emerge onto land, but remain not far from the water’s edge, and L. colubrina tend to move farther inland away from the water. They measured parameters of the body shape, vascular lung, saccular lung and hematocrit of sea kraits to investigate possible morphological correlates of their physiology. The most aquatic species, L. semifasciata, had a significantly more laterally flattened body form, larger saccular lung volume and higher hematocrit than the other two species, whereas only few differences were found between the two less aquatic species. L. laticaudata had a significantly higher hematocrit than L. colubrina.

Wang, S., Lillywhite, H. B., Cheng, Y. C. and Tu, M. C. (2013), Variation of traits and habitat use in three species of sea kraits in Taiwan. Journal of Zoology, 290: 19–26. doi: 10.1111/jzo.12012

Saturday, April 27, 2013

Northern Broad-headed snake ecology

Hoplocephalus bungaroides. Photo from Wikipedia

Conservation of highly specialized animals require detailed information on habitat use, dispersal and movement patterns. This kind of data often is often difficult to gather, especially for endangered species because the animals are rare, and because research methods cannot further endanger the species. As a result,  knowledge of many endangered taxa is based on studies performed at only a single site where the species is abundant and easily observed. These kind of sites are atypical of conditions that pertain over most of the species’ range.

One such species is the broad-headed snake (Hoplocephalus bungaroides), an elapid that has drastically declined since European settlement of Australia. Broad-headed snakes rely on  habitat with specific features: they shelter beneath thin, sun-exposed exfoliated rocks on sandstone rock outcrops with western or north-western aspects. These retreat sites allow snakes to thermoregulate during winter and spring. Hoplocephalus bungaroides also exhibit life history traits that render them vulnerable to disturbance: they depend on high rates of adult survival;  breed only every 3 to 4 years; have low fecundity, 3 to 4 offspring per litter; they may take six years to mature; low rates of dispersal; and a small geographic range. All of these traits contribute to the endangered status of broad-headed snake. The habitat of H. bungaroides has become fragmented, and subject to vegetation overgrowth and removal of shelter-sites (exfoliated rock) for landscaping and gardening.

Genetic data show that the intensively-studied southern population belongs to a genetically distinct clade, with another isolated, evolutionarily significant unit identified in the north of the species range. Those two clades diverged approximately 800 000 years ago. Vegetation, temperatures and potential prey species differ between the northern and southern parts of the species’ range.

In a recently published paper, Croak et al. (2013) captured and radio-tracked 9 adult broad-headed snakes at sites in the northern part of the species’ distribution, to evaluate the generality of results from prior studies most of which had been conducted at a southern study site. The authors identify critical habitat components for this northern population. They found snakes spent most of winter beneath sun-warmed rocks then shifted to tree hollows in summer. Thermal regimes within retreat-sites support the hypothesis that this shift is thermally driven. Intervals between successive displacements were longer than in the southern snakes but dispersal distances per move and home ranges were similar. The northern snakes showed non-random preferences both in terms of macrohabitat by avoiding of some vegetation types and selecting microhabitats, that is th  hollow-bearing trees. Despite many consistencies, the ecology of this species differs enough between southern and northern extremes of its range that managers need to incorporate information on local features to most effectively conserve this threatened reptile.

Croak BM, Crowther MS, Webb JK, Shine R (2013) Movements and Habitat Use of an Endangered Snake, Hoplocephalus bungaroides (Elapidae): Implications for Conservation. PLoS ONE 8(4): e61711. doi:10.1371/journal.pone.0061711.

Friday, April 19, 2013

A new cat-eyed snake from India

The nocturnal, arboreal, rear-fanged colubrine snake genus Boiga (the cat-eyed snakes) is represented in Peninsular India by six species:  B. trigonataB. forsteniB. ceylonensisB. nuchalisB. dightoni and B. beddomei. Of these, the last four are characteristic of the wet hill-forest tracts of India’s Western Ghats, and, in the case of B. ceylonensis and B. beddomei, the wet-zone of central, hilly Sri Lanka as well.

Boiga flaviviridis from Kaigal, India. Photo Ashok Captain. 
In a recent paper Vogel and Ganesh (2013) describe a new species of cat snake, related to Boiga beddomei. The new species Boiga flaviviridis from the dry forests of eastern Peninsular India. It occupies a large geographic range from Berhampore, near the River Mahanadi in the northeast to Kaigal near the southern Eastern Ghats in the southwest. Boiga flaviviridis is diagnosed by having 19 dorsal scale rows at mid-body, a high number of ventral scales for the genus Boiga (248–259), a yellowish-green dorsal coloration with numerous faint black bands, an uniform, un-patterned yellow-colored venter and a relatively short tail (18-20% of the total length).

Vogel G. & S.R. Ganesh (2013) A new species of cat snake (Reptilia: Serpentes: Colubridae: Boiga) from dry forests of eastern Peninsular India. Zootaxa 3637:158-168.

Treeboa Ecomorphology

Neotropical treeboas (Corallus) form a monophyletic group of nine species distributed from south-eastern Guatemala to southeastern Brazil They occur on continental and oceanic islands and at elevations between sea level and about 1000 asl. All are moderately sized, with body lengths that are about 1.0–2.0 m, are relatively slender with laterally compressed bodies, thin necks, and large heads. They also have long, recurved teeth on the anterior portions of the maxilla and mandibles. As the common name suggests, they are arboreal and occur in forested habitats ranging from arid Acacia scrub
to primary rainforest, in mangrove swamps, fruit orchards, along gallery forests and riparian zones in Brazilian cerrado and caatinga, as well as urban and suburban situations where they will sometimes seek shelter in human dwellings. Prey is encountered during the night via active and ambush foraging, with some species employing both strategies.

Treeboa diets are largely comprised of lizards, birds, marsupials, rodents, and/or bats; prey is killed by constriction and, like all snakes, they are gape-limited. Several species undergo ontogenetic shifts in diet (e.g. lizards to rodents), some feed on birds and mammals, and others are stenophagic for mammals as adults.

In a forthcoming paper, Henderson et al. (2013) conducted the first study of morphology and diet that considers all nine treeboa species. Using adult specimens from museum collections, they examined several morphometric and meristic variables and their possible relationship to Corallus diets.

They found three basic morphologies within the genus: (1) a short, narrow head and a slender body (C. cookii, C. grenadensis, C. hortulanus, and C. ruschenbergerii), useful for exploiting a wide variety of prey (2) a relatively stout body with a long, wide head (C. batesii, C. caninus, and C. cropanii) associated with feeding on large mammals; and (3) an intermediate morphology, found in C. annulatus and C. blombergii, which may be indicative of endotherm generalists. These morphological and dietary patterns exhibit a strong degree of congruence with a recent molecular phylogeny of Corallus and highlight a heretofore unexamined ecological diversification within Corallus.

Henderson, R. W., M. J. Pauers, and T. J. Colston. 2013. On the congruence of morphology, trophic ecology, and phylogeny in Neotropical treeboas (Squamata: Boidae: Corallus). Biological Journal of the Linnean Society.

Monday, April 15, 2013

A new technology to deal with envenomation

Engineers at the University of California, San Diego have invented
a "nanosponge" capable of safely removing a broad class of 
dangerous toxins from the bloodstream, including toxins produced
 by MRSA, E. Coli, poisonous snakes and bees. The nanosponges 
are made of a biocompatible polymer core wrapped in a natural red
 blood cell membrane. Credit: Zhang Research Lab.
The only effective technology for dealing with envenomation from snakes has been the traditional use of antitoxins produced in a horse or a sheep. This technology was based upon observations made by Henry Sewall, at the University of Michigan in 1887. There now appears to be new technology on the horizon for removing toxins from the blood.

Engineers at the University of California, San Diego have invented a "nanosponge" capable of safely removing a broad class of dangerous toxins from the bloodstream – including toxins produced by MRSA, E. coli, poisonous snakes and bees. These nanosponges, which thus far have been studied in mice, can neutralize "pore-forming toxins," which destroy cells by poking holes in their cell membranes. Unlike other anti-toxin platforms that need to be custom synthesized for individual toxin type, the nanosponges can absorb different pore-forming toxins regardless of their molecular structures. In a study against alpha-haemolysin toxin from MRSA, pre-innoculation with nanosponges enabled 89 percent of mice to survive lethal doses. Administering nanosponges after the lethal dose led to 44 percent survival.

The team, led by nanoengineers at the UC San Diego Jacobs School of Engineering, published the findings in Nature Nanotechnology April 14.

"This is a new way to remove toxins from the bloodstream," said Liangfang Zhang, a nanoengineering professor at the UC San Diego Jacobs School of Engineering and the senior author on the study. "Instead of creating specific treatments for individual toxins, we are developing a platform that can neutralize toxins caused by a wide range of pathogens, including MRSA and other antibiotic resistant bacteria," said Zhang. The work could also lead to non-species-specific therapies for venomous snake bites and bee stings, which would make it more likely that health care providers or at-risk individuals will have life-saving treatments available when they need them most.

The researchers are aiming to translate this work into approved therapies. "One of the first applications we are aiming for would be an anti-virulence treatment for MRSA. That's why we studied one of the most virulent toxins from MRSA in our experiments," said "Jack" Che-Ming Hu, the first author on the paper. Hu, now a post-doctoral researcher in Zhang's lab, earned his Ph.D. in bioengineering from UC San Diego in 2011.

Aspects of this work will be presented April 18 at Research Expo, the annual graduate student research and networking event of the UC San Diego Jacobs School of Engineering.

In order to evade the immune system and remain in circulation in the bloodstream, the nanosponges are wrapped in red blood cell membranes. This red blood cell cloaking technology was developed in Liangfang Zhang's lab at UC San Diego. The researchers previously demonstrated that nanoparticles disguised as red blood cells could be used to deliver cancer-fighting drugs directly to a tumor. Zhang also has a faculty appointment at the UC San Diego Moores Cancer Center.

Red blood cells are one of the primary targets of pore-forming toxins. When a group of toxins all puncture the same cell, forming a pore, uncontrolled ions rush in and the cell dies.

The nanosponges look like red blood cells, and therefore serve as red blood cell decoys that collect the toxins. The nanosponges absorb damaging toxins and divert them away from their cellular targets. The nanosponges had a half-life of 40 hours in the researchers' experiments in mice. Eventually the liver safely metabolized both the nanosponges and the sequestered toxins, with the liver incurring no discernible damage.
Each nanosponge has a diameter of approximately 85 nanometers and is made of a biocompatible polymer core wrapped in segments of red blood cells membranes.

Zhang's team separates the red blood cells from a small sample of blood using a centrifuge and then puts the cells into a solution that causes them to swell and burst, releasing hemoglobin and leaving RBC skins behind. The skins are then mixed with the ball-shaped nanoparticles until they are coated with a red blood cell membrane.

Just one red blood cell membrane can make thousands of nanosponges, which are 3,000 times smaller than a red blood cell. With a single dose, this army of nanosponges floods the blood stream, outnumbering red blood cells and intercepting toxins.

Based on test-tube experiments, the number of toxins each nanosponge could absorb depended on the toxin. For example, approximately 85 alpha-haemolysin toxin produced by MRSA, 30 stretpolysin-O toxins and 850 melittin monomoers, which are part of bee venom.

In mice, administering nanosponges and alpha-haemolysin toxin simultaneously at a toxin-to-nanosponge ratio of 70:1 neutralized the toxins and caused no discernible damage.

One next step, the researchers say, is to pursue clinical trials.

Che-Ming J. Hu, Ronnie H. Fang, Jonathan Copp, Brian T. Luk, Liangfang Zhang. A biomimetic nanosponge that absorbs pore-forming toxins. Nature Nanotechnology, 2013; DOI: 10.1038/nnano.2013.54

Sunday, April 14, 2013

Ripples in the ecosystem

Humans have been moving animals around the planet for thousands of years. Hunter and gathers took dogs with them as they migrated, and with the evolution of agriculture soon other domesticated animals were traded between populations. Like all animals, human alter the environments they live-in and so do their commensal species. But humans are special in that they can move quite large animals around unintentionally, bring together species that have not co-evolved and setting the stage for long term changes in ecosystems.

In 2012 Rogers et al. described the first landscape level natural experiment showing the impact of bird loss on the control of their prey, spiders, and the magnitude of effects generated from long-term, landscape-scale bird loss to the effects generated from bird exclusion experiments elsewhere.

They took advantage of the only place in the world where all avian insectivores have been extirpated from the landscape, the Western Pacific island of Guam. The brown tree snake, Boiga irregularis, was introduced to Guam in the mid-1940's. The snakes ate their way through the bird fauna, leading to the extirpation of all native insectivorous bird species from the majority of the island in the mid-1980's. There are only two insectivorous bird species remaining today, in extremely localized populations; the Micronesian Starling has a small population on Andersen Air Force Base at the northern tip of Guam and the Mariana Swiftlet inhabits three caves on the Naval Base in southern Guam. No non-native insectivorous bird species have colonized the forests of Guam, therefore, aside from these two locations on the military bases, the forests are devoid of insectivorous birds.

Rogers and colleagues focused on spiders because experimental studies showed a consistent top-down effect of birds on spiders. They conducted spider web surveys in native forest on Guam and three nearby islands with healthy bird populations. They found spider web densities on Guam were 40 times greater than densities on islands with birds during the wet season, and 2.3 times greater during the dry season.

The results confirm the general trend from manipulative experiments conducted in other systems however, the effect size was much greater in this natural experiment than in most manipulative experiments. In addition, bird loss appears to have removed the seasonality of spider webs and led to larger webs in at least one spider species in the forests of Guam than on nearby islands with birds.The results suggest that effect sizes from smaller-scale experimental studies may significantly underestimate the impact of bird loss on spider density as demonstrated by this large-scale natural experiment.

However, changes in spider populations are not the only impact of bird loss on Guam. Spider-eating birds were decimated by the brown tree snake, but so were fruit eating birds that disperse seeds. McConkey and colleagues (2012) note that seed dispersal interacts decisively with the major drivers of biodiversity change: habitat fragmentation, over-harvesting, biological invasions, and climate change.

So, Guam’s forests are not only exceptionally quiet due to the loss of birds, but they are also thinning out. A four year study planned for this summer will examine the island for 16 tree species, looking at how the loss of seed dispersing birds, is affecting tree distribution.

While the brown tree snakes have been in Guam for almost 75 years, the presence of invasive constrictors in the Florida Everglades is more recent, probably less than 30 years. So, the Everglades, like Guam, will likely become a laboratory for studying the impact of invasive snakes on the ecosystem.

Martin, C. 2013. Where have the trees of Guam gone? Simthsonian.com

McConkey, K.R., S. Prasad, R. T. Corlett, A. Campos-Arceiz, J. F. Brodie, H. Rogers, & L. Santamaria, 2012. Seed dispersal in changing landscapes, Biological Conservation, 146, 1-13

Rogers H, J. Hille Ris Lambers, R. Miller, & J.J. Tewksbury (2012) ‘Natural experiment’ Demonstrates Top-Down Control of Spiders by Birds on a Landscape Level. PLoS ONE 7(9): e43446. doi:10.1371/journal.pone.0043446

Wednesday, April 10, 2013

Suzio Report Winter-Spring 2013

Howdy Herpers,                             13 April 2013

It is hoped that your inboxes have not been overtly cluttered with Suizo Reports of late?

Truth be told, a few months ago, I got in a bit of hot water at work when a hacker got into my company computer, and merrily bounced about 250,000 messages into cyberspace over the course of 24 hours. This did nothing to endear me to those who mind our server, not to mention those who sign my paycheck. There was no small measure of irritability directed at my person. My patented method of hang dog looks and blatant apologies did little to assuage their verbal onslaughts. And my highly effective foot-kissing technique was thwarted by feet that were doing the river dance. I’m not limber or fast enough to keep up with uncooperative foot apparel.

The whole incident caused a not entirely irrational fear of mass email missives to well up inside of typing boy here. That fear still manifests itself in every fiber of my being. Every time that I pull the trigger, I hear footsteps. They are Gestapo-like footsteps clomping down the hallway to get me.

But dammit, herp studies come, and herp studies go­and there will never be one like that in the Suizos. Who will ever do such a thing again? Twelve continuous years of radio telemetry on multiple species of venomous reptiles on one patch of ground?  Are you kidding me? No way! It has never happened before, and it will never happen again.

And now that spring is upon us, it’s showtime! For the herps, and for those of us who love them. Let’s rock!

The best place to start anew with these reports is January of this year. Normally, when discussing herp activity in January of any given year, there isn’t much to say. But there were two events that astonished even me.

The first event was one of our tiger rattlesnakes--a male, CT11, “Steven” to be specific. In late October of 2012, Steven moved into a north facing crevice and joined his lady tiger, one that he had dogged all summer long. His crack mate was CT12, “Ellie.” They both remained visible in the crevice throughout the fall of 2012 and early winter of 2013. He was always up front, but shifting around some, while she remained motionless about 300mm behind him­as if glued in place. On 19 January, Steven was viewed and photographed stretched out lengthwise in front of the crevice. Even though he was less than 300mm away from Ellie, his body temperature was 6 degrees C warmer than hers. That apparently was enough to set him motion, for he moved over 50 meters during the next week, implanting himself in the same major boulder stack where he had spent the winter of 2011-2012. We haven’t seen him since, and it may be another month before we do. A 50 meter move by a winter-dormant species like a tiger rattlesnake? Why did he leave his girlfriend behind? Was she a bitch, or what?

The second cool event to occur in January involved a black-tailed rattlesnake pairing­in the dead of winter. In this case, it was CM10, “Susan,” and our as yet un-named big guy, CM12. Susan moved into the same site that she had occupied during the winter of 2011-2012 in November of 2012. Fidelity to hibernacula is old news with Crotalids, so there was nothing new there. But she up and moved ~15 meters between 27 January and 2 February. She crawled under the same boulder that CM12 was occupying. In other words­she joined him! If we’ve learned anything with our study through the past 12 years, it is that it isn’t always the males that do the chasing.

While we’re on the subject of Susan joining our big guy, it should be reported that she has been dogging him this spring. Like our tiger Steven, he seems to be trying to get away from his girlfriend as well. And she keeps popping at sites that he has occupied the week before. What’s up with that? On top of all that, Susan went through a transmitter change recently. During the process, Dale DeNardo detected six follicles in her ovary. She is quite pregnant. She was visited by three different males that we know of last summer/fall, but CM12 was with her the longest. Is “papa” truly trying to get away from her, or leading her to food sources? We can only speculate.

We had a very peculiar winter weather-wise. In both January and February, we would set record lows one week, and record highs the next. Even during the warm weeks, the nights were cold. We have received an estimated 3.0 inches of rain thus far this year. There has been but a limited flower show out our way, for the rains came too late to set up anything spectacular. The strange weather has also set up a leisurely egress with our study animals.

We began the year with 14 rattlesnakes with transmitters. We have one female western diamond-backed rattlesnake (Crotalus atrox), CA133.  We have six tiger rattlesnakes (Crotalus tigris), 3 males (CT10, CT11, and CT14), and 3 females (CT8, CT12, and CT13). And we have seven black-tailed rattlesnakes, 4 males (CM11, CM12, CM14 and CM16) and 3 females (CM10, CM15 and CM17).

We can easily start mowing down what the animals are doing by zeroing in on the tiger rattlesnakes first. Other than Steven’s escape from Ellie, they haven’t done much this year. As reported last fall, male CT14, AKA “Rhino K12,” jetted to the third highest peak of the Suizo Mountains proper, and has remained buried in a vertical cliff face ever since. We hope for movement, but I’ll bet he stays there until May. CT10, “Jeff,” has buried himself under a big gneiss boulder, not so much as a glimpse of him yet. Our longest running tiger, female CT8 “Zona” overwintered in the same rock shelf that she spent the winter of 2009-2010. She has just now begun to bask at the entrance. Ellie must have tired of her own bitching reverberating around her lonely crevice, and has made two minor moves. And female CT13, no name yet, has slipped from her caprock hibernaculum and dropped downslope about 5 meters. Tigers are very boring snakes in the winter, but we did have the benefit of seeing two of them all winter long.

Our lone atrox, CA133, affectionately dubbed “Slone’s bitch,” finally moved from her hibernaculum of a man-made boulder pile at the top of the front range of the Suizos proper. She was last tracked at the base of the same front range, and I expect she will be in Suizo Wash with the next tracking episode. She gave birth the previous two consecutive years­six young in 2011, and four in 2012. It is my extreme hope that she can skip a year, and regain some mass.

It was an off year for all nine of the atrox dens on our hill. We have been keeping our hands off these dens for two years now, in hopes that our lack of attention will benefit them. The short story is that only two atrox were viewed at AD1, four at AD7, and only one at AD8. This is the first year in the history of our study that dens AD4 and AD5 were unoccupied. The same story can be told for atrox dens on other hills under my watch. Thus far this year, I have racked up the pathetic total of 15 atrox. In years past, I’d routinely see twice that many--in one day! I’m not sure what to make of this­except to express the hopes that the downturn is temporary. It is worth mentioning that 2012 as a whole was a down year for this species of snake as well.

The black-tailed rattlesnakes have been nothing short of spectacular. This will be our first year ever of watching this species with any sort of N to back our observations. We are in awe of these impressive beasts, and hope to get some more into the study. The best way to tackle them on an individual basis is to lump them by the vast geographical differences of the terrain they have chosen to occupy. All seven were found near or on Iron Mine Hill, but only three of them remained there for the winter.

CM10, Susan, and her boyfriend CM12, the big guy, both remained on Iron Mine Hill. The only other molossus to remain on the hill this winter was CM16­a young male that “volunteered” for our study last fall. Since CM10 and CM12 each have a full year of observations on them, we know what to expect. But CM16 is new to us. The most remarkable feat he has done thus far is to find a hibernaculum that kept him consistently anywhere from 10 to 15 degrees C warmer than the all 13 snakes under watch. I wonder if there are any breaths of hot air under our little hill? (There are certainly plenty above it!) It is also possible that his transmitter is blipping off inaccurate readings.

Taking the remaining four molossus by number, we first discuss our male CM11, “Gus.” Gus does not let any grass grow under his belly. He is always on the move, and was viewed basking in direct sun several times this winter­the only snake to do this consistently this year. He over-wintered 2 kilometers away from some of his summer haunts, and is now bombing back toward Iron Mine Hill. The term “over wintered” was deliberately used here­as I don’t believe that he actually hibernated. Gus is a shaker!

Next is male CM14, “Marty the prick.” He earned his inappropriate moniker by first being named after his captor, and then constantly shifting from one side of Iron Mine Hill to the other during the summer. This can cause endless consternation and cussing when trying to set up tracking routes. And then he also took off for distant parts last fall. But unlike Gus, he did indeed hibernate­or at least stayed put for three months. He is now also on the move, and I almost dread where he will take us next.

Despite being a hard guy to stay on top of, in late August of 2012, Marty the prick led us to one of the delights of our plot­female CM15. With big, beautiful black doll eyes, and stunning greens and cream pattern, she is the prettiest molossus on our plot. Thus far under our watch, she hung around the eastern slopes of Iron Mine Hill, and then jetted over to the Suizo Mountains proper to hibernate. She emerged in mid-March, only to stake out under the escarpment of a small, flat rock for the next three weeks.  It is expected she will start slipping back toward Suizo Wash soon.

Good old Gus led us to the last, and possibly most-likely-to-succeed molossus on our plot. Female CM17, “Ms. Gus,” was found in love’s embrace with Gus by Marty on 5 October 2012. Being the hopeless romantics that we are, we let them spend the night together, and captured Ms. Gus the next morning. She is one fat, healthy snake, and we expect that Gus is quite the potent dude. We expect Ms. Gus to drop some kids for us this year. We have not had the chance to gather much data on her yet, but I expect she will be another east side of Iron Mine Hill to Suizo Mountains proper kind of snake.

This spring has brought several other thrills our way. Our trips to the Suizo Mountains proper have thus far netted us two juvenile collared lizards. They are only rarely seen on Iron Mine Hill, but seem to have a good population in the Suizos proper. We hope to catch some adult action with them with our tracking duties ahead. We have also seen two young regal horned lizards, and six Gila Monsters. A highlight related to them occurred on 30 March. I looked into their communal denning hole, and came face-to-face with a ringtail. Thus far, our communal Gila Hole has been utilized by 12 Gila Monsters, 2 atrox, a tortoise, and now, the ringtail. I sure do wish that I had attempted a photo of that!

My apologies for the length of this report. I considered those readers who actually pay attention to these writings (both of you) in the preparation. Future reports will contain info on any or all of these rattlesnakes, and you may wish to keep this report to refer back to better understand who is who. From this point on, you will all just be getting numbers and names.

And, with future reports, I’m going to start making fun of people again. Ineptness on my part or that of others will be dealt with mercilessly.

It is now time to go to images. Refer to the text above if you want the long story.

Image01, Feldner: Male CT11 “Steven,” getting ready to leave CT12, Ellie, 19 January 2013

Image02, Feldner: Female CT8, “Zona” basking in front of her hibernaculum. 29 March 2013

Image03, Feldner: Female CM10, “Susan.” Our first good look at her this year. Note the heft toward the rear. 3 March 2013.

Image04, Feldner: Male CM12, Susan’s hibernating buddy. 11 March 2013.

Image05, Feldner: Male CM11 “Gus” basking in sun, 2 March 2013.

Image06, Feldner: Female CM15 emerging from her hibernaculum, 2 March 2013.

Image07, Feldner: Young male CM16, also just coming out of hibernation, 30 March 2013.

Image08, Feldner: Female CM17, “Ms. Gus.” Note the heft toward the rear. Two pregnant molossus? 29 March 2013.

Image09, Repp: Unknown atrox basking on the apron of AD1. 17 March 2013.

Image 10,Feldner: One of two young regal horned lizards seen thus far this year. 30 March 2013.

Image11, Repp: Female HS21, processed, pit tagged, and released 30 March 2013. She kind of stands out like goat turds in the milking pail, doesn’t she?

Image 12, Repp: Female HS21, close up. Fat, ain’t she? 30 March 2013.

Image 13, Feldner: Nice shot Marty! One of two collared lizards observed in the Suizo Mountains proper this year. 13 March 2013.

Image14, Feldner: We take what happens after the tracking much more serious than the tracking itself. This image will give you a small taste of what it is I’m talking about.

Many thanks to all of you who have made this all possible, both with your monetary contributions, and your sweat equity. We earnestly look forward to whatever comes next.

This here is Roger Repp, signing off from Southern Arizona, where the turtles are strong, the snakes are handsome, and the lizards are all above average.

Organic matter recovered from Early Jurassic dinosaur

Semitransparent flesh reconstruction of embryonic dinosaur
 inside egg, with skeleton (artwork by D. Mazierski).
A 190-million-year-old dinosaur bone bed near the city of Lufeng, in Yunnan, China has revealed for the first time how dinosaur embryos grew and developed in their eggs.

The great age of the embryos is unusual because almost all known dinosaur embryos are from the Cretaceous Period. The Cretaceous ended some 125 million years after the bones at the Lufeng site were buried and fossilized.

Led by University of Toronto Mississauga paleontologist Robert Reisz, an international team of scientists from Canada, Taiwan, the People’s Republic of China, Australia and Germany excavated and analyzed over 200 bones from individuals at different stages of embryonic development.

“We are opening a new window into the lives of dinosaurs,” says Reisz. “This is the first time we’ve been able to track the growth of embryonic dinosaurs as they developed. Our findings will have a major impact on our understanding of the biology of these animals.”

The bones represent about 20 embryonic individuals of the long-necked sauropodomorph Lufengosaurus, the most common dinosaur in the region during the Early Jurassic period. An adult Lufengosaurus was approximately eight metres long.

The disarticulated bones probably came from several nests containing dinosaurs at various embryonic stages, giving Reisz’s team the rare opportunity to study ongoing growth patterns. Dinosaur embryos are more commonly found in single nests or partial nests, which offer only a snapshot of one developmental stage.

To investigate the dinosaurs’ development, the team concentrated on the largest embryonic bone, the femur. This bone showed a consistently rapid growth rate, doubling in length from 12 to 24 mm as the dinosaurs grew inside their eggs. Reisz says this very fast growth may indicate that sauropodomorphs like Lufengosaurus had a short incubation period.

Reisz’s team found that the femurs were being reshaped even as they were in the egg. Examination of the bones’ anatomy and internal structure showed that as they contracted and pulled on the hard bone tissue, the dinosaurs’ muscles played an active role in changing the shape of the developing femur. “This suggests that dinosaurs, like modern birds, moved around inside their eggs,” says Reisz. “It represents the first evidence of such movement in a dinosaur.”

The Taiwanese members of the team also discovered organic material inside the embryonic bones. Using precisely targeted infrared spectroscopy, they conducted chemical analyses of the dinosaur bone and found evidence of what Reisz says may be collagen fibres. Collagen is a protein characteristically found in bone.

“The bones of ancient animals are transformed to rock during the fossilization process,” says Reisz. “To find remnants of proteins in the embryos is really remarkable, particularly since these specimens are over 100 million years older than other fossils containing similar organic material.”

Only about one square metre of the bone bed has been excavated to date, but this small area also yielded pieces of eggshell, the oldest known for any terrestrial vertebrate. Reisz says this is the first time that even fragments of such delicate dinosaur eggshells, less than 100 microns thick, have been found in good condition.

“A find such as the Lufeng bone bed is extraordinarily rare in the fossil record, and is valuable for both its great age and the opportunity it offers to study dinosaur embryology,” says Reisz. “It greatly enhances our knowledge of how these remarkable animals from the beginning of the Age of Dinosaurs grew.”

Reisz, R.T., T. D. Huang, E. M. Roberts, S.R.Peng, C. Sullivan, K. Stein, A. R. H. LeBlanc, D.B. Shieh, R.S. Chang, C.C. Chiang, C. Yang, S. Zhong. 2013. Embryology of Early Jurassic dinosaur from China with evidence of preserved organic remains. Nature, 496 (7444): 210 DOI: 10.1038/nature11978

Saturday, April 6, 2013

Venom evolution in lizards & snakes

Python bites can produce false positives when
using venom detection kits. JCM

In 2005 it became apparent that venom  first evolved in the ancestor of the the Iguiana Lizards, Anguingmoprh lizards and the snakes. These three clades form a larger clade now known as Toxicofera. In a forthcoming paper Fry et al. (2013)  examine the oral glands in both the upper and lower jaws of the toxicoferans and find they are all involved in making the various molecules found in venom. Even the poorly known rictal glands of snakes make a variety of molecules that are venom components.  Rictal glands were investigated in two studies about 100 years ago. The secretions were shown to be highly toxic to birds but  no  investigations followed up on these glands, until now. Fry and colleagues show the rictal glands are in fact derived from the well-studied venom glands.Suggesting that the secretion of venom by snakes is much more complex than previously thought.

Several other interesting pieces of evidence regarding the evolution of venom were found during this study. Pythons have a novel, low-molecular weight disulphide bridged peptide class. This is the first evidence that pythons are still carrying at least some of the genetic material to make venom, and transcribing those genes. Iguanian lizards maybe using their venom molecules to control microbes. And,  proteins with hemotoxic or neurotoxic activity at low levels occur in iguanian and anguimorph lizards and caenophidian snakes. Even the ‘basal’ snakes (like Cylindrophis) surprisingly were found to express the 3-finger toxin and lectin toxins as the dominant transcripts. Also, in the constricting pythonid and boid snakes, where the glands are predominantly mucous-secreting, low-levels of toxin transcripts can be detected. Venom  appears to play a minimal role in the feeding behavior of most iguanian lizards and constricting snakes, and the low levels of expression argue against a defensive role.

Doctors in Australia rely on the venom detection kit to aid in diagnosis of snake bite. False-positives could lead to patients getting very expensive antivenom they don’t need and  possibly triggering life-threatening allergies and reducing the supply for patients who actually need it. This paper shows a surprising potential source of false-positives: pythons. A previous study showed that pythons cross-react in the Snake Venom Detection Kit (sVDK) but this curious result was dismissed as an anomaly. Fry et al. show that even though python oral glands overwhelmingly secrete mucus to lubricate prey for swallowing, there is still a trace of venom in their oral secretions. The venom is not enough to harm a human or  kill  prey, but enough to confuse an extremely sensitive diagnostic tool like the sVDK. While this poses a problem for doctors and snakebite victims it also provides an opportunity. The low level of ancient venom still secreted in these glands contained novel compounds that were quite different than those from the  well-studied front-fanged snakes like rattlesnakes and  mambas. These novel molecules therefore represent an untapped resource for biodiscovery.

Bryan G. Fry, Eivind A.B. Undheim, Syed A. Ali1, Jordan Debono, Holger Scheib, Tim Ruder, Timothy N. W. Jackson, David Morgenstern, Luke Cadwallader, Darryl Whitehead, Rob Nabuurs, Louise van der Weerd, Nicolas Vidal, Kim Roelants, Iwan Hendrikx, Sandy Pineda Gonzalez, Alun Jones, Glenn F. King, Agostinho Antunes, Kartik Sunagar. 2013. Squeezers and leaf-cutters: differential diversification and degeneration of the venom system in toxicoferan reptiles. Molecular & Cellular Proteomics In press. M112.023143