Tuesday, December 31, 2013

The bird snakes (Pseustes & Spilotes) rearranged

The genus Pseustes Fitzinger, 1843 is composed of three known species, Pseustes poecilonotus, P. shropshirei and P. sulphureus. Pseuestes sulphureus may be the largest sized colubrid snake in the New World, although Drymarchon corias has a similar or possible greater size. But, both species may exceed 3 meters in total length.

Pseustes has been classified as belonging to numerous other genera, over the years, including: Ahaetulla, Chironius, Coluber, Dipsas, Herpetodryas, Natrix, Phrynonax, Spilotes, Synchalinus, Thamnobius and Tropidodipsas. Pyron et al. (2013) found support that Pseustes sulphureus is the sister taxon to Spilotes pullatus, both members of the Colubrinae. However, the estimated phylogenetic position of this species was only based on a single 12S gene fragment as part of a large study. The study, used genes fromk 4161 species of squamates.  

In a forthcoming paper, Jaden et al. used multiple individuals of Pseustes across Central and South America and they analyzed the genus to infer the phylogenetic position of Pseustes within the Colubrinae, assess the relationship between Spilotes and Pseustes, and determine whether species of the genus Pseustes form a monophyletic group, infer phylogenetic relationships within Pseustes, and species-level diversity to resolve historical taxonomic debates. 

The authors examined four species from multiple specimens across their distribution and analysed one nuclear and two mitochondrial genes to determine the phylogenetic placement of the genus and infer relationships among Pseustes lineages. They found strong support for the paraphyly of Pseustes with respect to the monotypic genus Spilotes, both of which are nested within a clade of at least 23 other New World Colubrinae genera. 

The results produced a new view of the genera Psuestes and Spillotes. The authors resurrected the taxon P. polylepis for populations of P. poecilonotus from South America and moved P. sulphureus to the genus Spilotes which renders both genera monophyletic. Psuestes sulphureus is the type species of the genus Pseustes, and moving it to the genus Spilotes requires the allocation of the senior synonym Phrynonax be considered for the remaining Pseustes taxa.

Jadin RC., Burbrink FT, Rivas GA, Vitt LJ, Barrio‐Amorós CL, & Guralnick RP. (2013). Finding arboreal snakes in an evolutionary tree: phylogenetic placement and systematic revision of the Neotropical birdsnakes. Journal of Zoological Systematics and Evolutionary Research. DOI: 10.1111/jzs.12055

Saturday, December 21, 2013

Four-lined Snake Phylogeography

Elaphe quaturolineata, Photo credit: Carlo Catoni
The four-lined snake, Elaphe quatuorlineata, has a fragmented distribution, restricted in continental regions of Europe and islands in the Italian and Balkan peninsulas.

Within E. quatuorlineata, several subspecies have been recognized (E. q. parensis from Paros Island, central Aegean; E. q. scyrensis from Skyros Island, northern Aegean; and E. q. muenteri from several central Aegean islands, this also includes the uniformly patterned Elaphe rechingeri from Amorgos Island. Elaphe  q. quatuorlineata is distributed in the remaining part of the species’ range.

The subspecies are differentiated on the based on differences in body size, mid-body scale rows, and color patterns in juvenile, subadult and adult animals. The insular subspecies (E. q. parensis, E. q. scyrensis and E. q. muenteri) are significantly smaller, while E. q. quatuorlineata (found on mainland but also on several islands) is one of the largest European snakes.

In an early on-line view of a new study in Zoologica Scripta, Panagiotis Kornilios and colleagues used mtDNA sequences to investigate the four-lined snake's evolutionary and biogeographical history. The authors report the phylogeography of Elaphe quatuorlineata is the result of both vicariant and dispersal events, some of them over water and others with the help of  human transport.

Four-lined snakes started to diversify approximately 3.5 Mya and it continued during the Pleistocene glacial periods, when the snake’s distribution was restricted in the Italian and Balkan peninsulas. Populations subsequently expanded from subrefugia, which acted as pockets of biodiversity.  The study supports the recognition of three genetic lineages that roughly correspond to the morphological subspecies, although the authors suggest morphological characters used for their discrimination should be re-evaluated because some subspecies correspond to ecomorphs associated with changes in body size due to the the island-dwarfism phenomenon.

The formation of clade A, occurred about 3.5 Mya and corresponds to a sea barrier between Evvoia and Andros Island. This land connection that was never re-established, despite sea level changes caused by the glacial cycles. The separation of clade B occured about 3 Mya when specimens colonization Skyros Island by over-watder dispersal. Clade C includes all the remaining continetal populations (Italian and Balkan peninsulas) as well as several islands of the Adriatic. Within clade C, four subclades with unresolved relationships were found. This radiation  is probably related to climatic fluctuations, occurred in the Pleistocene.

Two specimens in clade C from Italy are not associated with the Italian subclade, but instead belong to the Balkan clade One of these shares the same mtDNA haplotype with a specimen from southern Greece, differing only by a single substitution. The authors suggest this could have resulted from a very recent, possibly human-induced dispersal from Greece to Italy. They note an old and close relationship between humans and this particular snake species.

The four-lined snake was considered sacred by ancient Greeks and Romans, and it was used in religious rituals from Roman times until the present day in central-southern Italy. Elaphe quatuorlineata and other non-venomous serpents were used in shrines of the Greco-Roman god of medicine (Asklepios or Aesculapius), because they were believed to have the power of healing superficial lesions with their saliva. Italian researchers have suggested the healing power occurs of skin growth factors present in the saliva of the four-lined snake.

Kornilios P., Thanou E., Lymberakis P., Sindaco R., Liuzzi C. & Giokas S. (2013). Mitochondrial phylogeography, intraspecific diversity and phenotypic convergence in the four-lined snake (Reptilia, Squamata). —Zoologica Scripta

Concern and a Search for the African Python In Florida

The African Python, Python sebae

NaplesNews.com is reporting that Wildlife officials conducted a survey Friday just west of Miami in an area where 30 of the African pythons (Python sebae) have been captured over the past few years. The area is close to shopping centers, a major Indian gambling casino and residential neighborhoods, and not far from where a rock python killed a Siberian husky in the dog's backyard in September.

Four teams of biologists searched the tall, sharp-edged saw grass in search of the snakes but found none.

The state of Florida would like to prevent these pythons from joining the Burmese Python as an established, breeding species with no natural predators in Florida, said Jenny Ketterlin Eckles, a wildlife biologist with the Florida Fish and Wildlife Commission.

"We think, and we hope, that they haven't adapted to the Everglades yet," she said.

The rock python is the largest snake in Africa, routinely growing longer than seven feet and weighing 200 or more pounds. Eckles said there have been reports of rock python attacks on humans in Africa, and one was responsible for the deaths of two young boys in New Brunswick, Canada, in August.

The boys, brothers ages 4 and 6, were asphyxiated by the 14-foot snake as they slept in an apartment after the snake escaped from its glass enclosure. They were sleeping in the apartment of a pet store owner, a family friend.

In the U.S., it is illegal to own an African rock python as a pet or any other personal use or to sell one. Permits must be obtained to import one for a zoo or for research. Still, many of the snakes are smuggled illegally into the U.S. each year and find their way into people's homes, often later to be dumped outside because they are expensive to feed and don't have the friendliest disposition.

That's what officials think happened to establish the Miami-area colony of rock pythons. Eckles said it appears a significant number, perhaps a dozen or more, were dumped in the marsh area at one time, allowing the snakes to begin breeding and forming a colony. Officials have been trying to capture as many as possible to prevent them from spreading.

"We want these snakes away from the ecosystem. They don't belong here in Florida," said wildlife commission spokesman Jorge Pino. "We're trying to get ahead of the problem."

No one wants a repeat of the Burmese python invasion of the Everglades, which prompted Florida earlier this year to stage a "Python Challenge" that attracted 1,600 hunters and netted some 68 snakes. Pino said there's little hope of eradicating the Burmese pythons, which have become firmly established in South Florida and prey on native wildlife at an alarming rate. And the females can lay up 100 eggs at a time.

Florida announced in November the hunt won't be repeated next year. Instead, the state is beefing up established programs that train licensed hunters and people who regularly work in areas known to contain pythons to kill or report exotic snakes. They're also handing out flyers in nearby neighborhoods in English and Spanish that describe the snakes, including pictures, and give people numbers to call if they spot one.

People who own a python can surrender it or any other exotic animal with no questions asked as part of the state's pet amnesty program. Since 2006, 70 pythons have been handed over, wildlife officials say.

It should be noted that Python sebae has been known to be present in Florida since 2005, and all of the specimens collected have come from Miami-Dade County, with one from Sarasota County.

An increase in the number of species of African crocodiles

A slender-snouted crocodile in Gabon. Photo Credit: Matt Shirley, UF/IFAS)

Dec. 18, 2013 — African crocodiles, long thought of as just three known species, are among the most iconic creatures on that continent. But recent University of Florida research now finds that there are at least seven distinct African crocodile species.

The UF team's latest discovery, led by then-doctoral candidate Matthew H. Shirley, is that what had been believed to be a single species of slender-snouted crocodile, is actually two.

The findings, which have major implications for policy-makers and conservationists, are outlined in a paper published online last week by Proceedings of the Royal Society B.

The results emphasize how little is known about crocodile biogeography, or how species are distributed geographically over time, in Western and Central Africa, said Jim Austin, a co-author on the paper and Shirley's doctoral adviser at UF.

In the paper, Shirley and his team describe that West African populations of the slender-snouted crocodile do not share the same genetic or specific physical features as those populations in Central Africa -- and they estimate the two populations have been separated from each other geographically for at least 7 million years.

Biologists and conservation agencies need to know the precise taxonomy of animals and plants to avoid allocating precious conservation funding and effort working to protect species that may be more plentiful than believed, or -- as in this case -- ensuring that those resources can be directed toward species whose numbers are lower than believed.

Now that researchers know the West African slender-snouted crocodile is not the same species as its Central African cousin, Shirley said, that changes its standing.

"The West African slender-snouted crocodile is actually among the three or four most endangered crocodiles in the world," Shirley wrote in an email last week. "By finally recognizing that it is a unique species, we are in a much better position to advance its conservation and ensure its future."

Shirley likened the plight of the West African slender-snouted croc to the American alligator, which was on the cusp of extinction in the 1960s, but because it was protected, can now be easily observed in nature, be legally harvested at times, and helps drive Florida's tourism economy.

In Africa, crocodiles are traded and consumed as bush meat, making them a significant protein source for residents. They also play a major role at the top of the food pyramid, with significant influence on fish and crustraceans, much as lions control antelope populations.

"If we remove them from the ecosystem, then there may be profound effects on fisheries resources in the future," he wrote.

Crocodile species are often difficult to identify by physical characteristics alone. Most non-scientists can barely tell the difference between an alligator and a crocodile, in fact. So to bolster their genetic sleuthing, the UF team also looked at skull characteristics of slender-snouted crocodiles from museum collections and were able to find consistent differences between the species, Austin said.

Austin is a faculty member in UF's Department of Wildlife Ecology and Conservation, part of the Institute of Food and Agricultural Sciences. The other team members were Kent Vliet, laboratories coordinator with UF's biology department, and Amanda Carr, an undergraduate in Wildlife Ecology and Conservation.

Austin said the team's work is leading to helpful information for American zoos and aquariums by decoding the correct identification and taxonomy of African crocodiles housed in these facilities. Without the correct species identification, zookeepers could interbreed these hard-to-distinguish species, rendering them ineffective as founder animals for conservation purposes. And captive breeding efforts may be wasted when individuals of different species simply won't breed.

"We're doing the work to see which species they actually have," Austin said.

M. H. Shirley, K. A. Vliet, A. N. Carr, J. D. Austin. Rigorous approaches to species delimitation have significant implications for African crocodilian systematics and conservation. Proceedings of the Royal Society B: Biological Sciences, 2013; 281 (1776): 20132483 DOI: 10.1098/rspb.2013.2483

Tuesday, December 17, 2013

Ancestral squamate viviparous?

The ancestor of snakes and lizards likely gave birth to live young, rather than laid eggs, and over time species have switched back and forth in their preferred reproductive mode, according to research published in print in Ecology Letters Dec. 17.

"This is a very unusual and controversial finding, and a major overturn of an accepted school of thought," said Alex Pyron, Robert F. Griggs Assistant Professor of Biology in the Columbian College of Arts and Sciences at the George Washington University. "Before, researchers long assumed that the ancestor of snakes and lizards laid eggs, and that if a species switched to live birth, it never reverted back. We found this wasn't the case."

The findings push researchers' understanding of the evolution of live birth a lot further back in time to 175 million years ago, showing that live birth has a much more ancient past as a strategy than previously believed. The findings are backed by several recent plesiosaur and mosasaur fossil discoveries and the fossil record of a few lizards from the Cretaceous Period, which had embryos in the mother and had live birth.

Dr. Pyron analyzed an evolutionary tree containing all groups of squamates -- the group that comprises lizards and snakes -- which he and a team of researchers published in the journal BMC Evolutionary Biology earlier this year. The tree, which uses DNA sequencing technology to group thousands of lizards and snakes, includes all families and subfamilies and most genus and species groups.

In total, about 115 groups of lizards and snakes, or about 2,000 species, have live birth. The other 8,000 species lay eggs -- at least right now.

Dr. Pyron is working next to analyze all tetrapods -- a group composed of animals with four legs, such as amphibians, reptiles, birds, mammals and turtles -- to see if there are any new surprises about the evolution of their reproductive modes. He also wants to test the genetics at work behind the evolutionary switching of reproductive mode.

R. Alexander Pyron, Frank T. Burbrink. Early origin of viviparity and multiple reversions to oviparity in squamate reptiles. Ecology Letters, 2013; DOI: 10.1111/ele.12168

Zoonotic pathogens in Crotalus viridis, is there potential for spillover?

Can handling rattlesnakes lead to a spillover of a zoonotic
 organisms to humans?

In his 2012 book Spillover, David Quammen examines zoonotic diseases, pathogens that jump from other animals to humans. The list of diseases that impact humans and have reservoirs in other species is lengthy and sobering. HIV, malaria, SARS, hantavirius, influenza, etc. Quammen does an excellent job tracing the origin of HIV in human populations to the early 20th century in West Africa and discussing the cut-hunter hypothesis. This idea suggests HIV moved from non-human primates (probably chimpanzees) to humans when hunters were butchering bushmeat (chimpanzzees). And, Quammen notes the evidence for at least 12 spillover events for HIV, that is humans were infected a minimum of 12 different times by HIV. While most of the zoonotic diseases that have impacted humans come from bats, rodents, or birds- reptiles seem to have been overlooked. But people certainly kill and butcher rattlesnakes in large numbers during rattlesnake round-ups, an excellent opportunity for a pathogen to jump from Crotalus to humans. A new article suggests the opportunity for a spillover event may be present during such events.

Rattlesnakes make ideal subjects for a variety of different scientific disciplines. The prairie rattlesnake (Crotalus viridis) in Colorado was selected for investigation of its relationship to colonies of black-tailed prairie dogs (Cynomys ludovicianus) to study spatial ecology. A total of 31 snakes were anesthetized and had radiotransmitters surgically implanted.

When captured the snakes underwent the following procedures: (1) they had bacterial culture taken from their mouths for potential isolation of pathogenic bacteria; (2) similarly, they had cloacal bacterial cultures taken to assess potentially harmful bacteria passed in the feces; and (3) they had blood samples drawn to investigate the presence of any zoonotic agents in the serum of the snakes.

The results of the bacterial studies and their implications are discussed in a new article by Kevin Fitzgerald and colleagues. A low incidence of bacterial wound infection has been reported following snakebite. Nevertheless, the oral cavity of snakes has long been known to house a diverse bacterial flora.Fitzgerald and colleagues study, 10 different bacterial species from the mouths of the rattlesnakes, six of which are capable of being zoonotic pathogens and inducing human disease. More studies are necessary to see why more rattlesnake bites do not become infected despite the presence of such pathogenic bacteria. The results of fecal bacteria isolated revealed 13 bacterial species, 12 of which can cause disease in humans. Of the snakes whose samples were cultured, 26% were positive for the presence of the pathogen Salmonella arizonae, one of the causative agents of reptile-related salmonellosis in humans.

It has long been reported that captive reptiles have a much higher incidence than wild, free-ranging species. This study shows the incidence of Salmonella in a wild, free-ranging population of rattlesnakes. In addition, Stenotrophomonas maltophilia was isolated. This is a bacterium associated with wound and soft tissue infections that can lead to sepsis, endocarditis, meningitis, and peritonitis. In addition, this bacterium has been increasingly implicated as an opportunistic pathogen to humans during pregnancies, hospitalizations, malignancies and chemotherapy, chronic respiratory diseases, and presurgical endotracheal intubation. Furthermore, S. maltophilia has an intense resistance to broad-spectrum antibiotics, the results of this study showed the bacterium was resistant to multiple antibiotics.

The results of this work suggest anyone working with snake feces, dead skin, or their carcasses must follow reasonable hygiene protocols. Rattlesnakes tested for West Nile antibodies had positive results but these were invalidated owing to possible cross-reactivity with other unknown viruses, interference with snake serum proteins, and the fact that the test was not calibrated for rattlesnake serum. Still, the interesting implication remains, should we be regularly testing these animals as sentinels against potentially zoonotic diseases. The results of this study clearly show the value of veterinarians in a multidisciplinary study of this sort and the particular skill set they can offer. Veterinarians must get involved in conservation studies if the biodiversity of the planet is to be preserved.

Fitzgerald, Kevin T, Shipley, Bryon K., Newquist, Kristin L.,,Vera, Rebecca, Aryn A.2012. Additional Observations and Notes on the Natural History of the Prairie Rattlesnake (Crotalus viridis) in Colorado. Topics in Companion Animal Medicine. 28:167-176. http://dx.doi.org/10.1053/j.tcam.2013.09.008.

Quammen, D. 2012. Spillover, Animal Infections and the Next Human Pandemic. WW Norton & Co,

Xantusid phylogeny

Xantusia henshawi
The night lizards of the clade Xantusiidae are small-bodied, cryptic lizards endemic to the New World. The clade is characterized by several features that are of phylogenetic interest. (1) monophyletic status of extant taxa Cricosaura, Lepidophyma, and Xantusia; (2) a species endemic to Cuba (Cricosaura typica) of disputed age; (3) origins of the parthenogenetic species of Lepidophyma; (4) pronounced micro-habitat differences accompanied by distinct morphologies in both Xantusia and Lepidophyma; and (5) placement of Xantusia riversiana, the only vertebrate species endemic to the California Channel Islands, which is highly divergent from its mainland relatives.

Brian Noonan and colleagues examined data from multiple gene regions to investigate the phylogeny of Xantusiidae using the most comprehensive taxonomic sampling available to date. Parsimony and partitioned Bayesian analyses of more than 7 kb of mitochondrial and nuclear sequence data from 11 loci confirm that Xantusiidae is monophyletic, and comprises three well-supported clades: Cricosaura, Xantusia, and Lepidophyma. The Cuban endemic Cricosaura typica is well supported as the sister to all other xantusiids. Estimates of divergence time indicate that Cricosaura diverged from the (Lepidophyma + Xantusia) clade 81 million years ago (Ma), a time frame consistent with the separation of the Antilles from North America. Their results also confirm and extend an earlier study suggesting that parthenogenesis has arisen at least twice within Lepidophyma without hybridization, that rock-crevice ecomorphs evolved numerous times within Xantusia and Lepidophyma, and that the large-bodied Channel Island endemic X. riversiana is a distinct, early lineage that may form the sister group to the small-bodied congeners of the mainland.

Noonan, B. P., Pramuk, J. B., Bezy, R. L., Sinclair, E. A., de Queiroz, K., & Sites Jr, J. W. (2013). Phylogenetic relationships within the lizard clade Xantusiidae: Molecular Phylogenetics & Evolution 69:109-122.

Air flow in lizards and their relatives

The upper image is a colorized CT scan showing different airways in the lung of a monitor lizard. The bottom image shows how air flows in a mostly one-way loop through the lizard’s lung, as measured by sensors implanted as part of a University of Utah study. Note how the air flows through adjacent lateral airways (blue and purple) by moving through perforations in the airways’ walls. Photo credit: Emma Schachner, University of Utah.

Dec. 11, 2013 — Air flows mostly in a one-way loop through the lungs of monitor lizards -- a breathing method shared by birds, alligators and presumably dinosaurs, according to a new University of Utah study.
The findings -- published online Dec. 11 in the journal Nature -- raise the possibility this breathing pattern originated 270 million years ago, about 20 million years earlier than previously believed and 100 million years before the first birds. Why remains a mystery.

"It appears to be much more common and ancient than anyone thought," says C.G. Farmer, the study's senior author and an associate professor of biology at the University of Utah. "It has been thought to be important for enabling birds to support strenuous activity, such as flight. We now know it's not unique to birds. It shows our previous notions about the function of these one-way patterns of airflow are inadequate. They are found in animals besides those with fast metabolisms."

But Farmer cautions that because lizard lungs have a different structure than bird and alligator lungs, it is also possible that one-way airflow evolved independently about 30 million years ago in the ancestors of monitor lizards and about 250 million years ago in the archosaurs, the group that gave rise to alligators, dinosaurs and birds. More lizard species, such as geckos and iguanas, must be studied to learn the answer, she says.
Farmer conducted the study with two University of Utah biologists -- first author and postdoctoral fellow Emma Schachner and doctoral student Robert Cieri -- and with James Butler, a Harvard University physiologist.

The research was funded by the American Association of Anatomists, the American Philosophical Society, the National Science Foundation and private donor Sharon Meyer.

Tidal Versus One-Way Airflow in the Lungs
Humans and most other animals have a "tidal" breathing pattern: Air flows into the lungs' branching, progressively smaller airways or bronchi until dead-ending at small chambers called alveoli, where oxygen enters the blood and carbon dioxide leaves the blood and enters the lungs. Then the air flows back out the same way.

Birds, on the other hand, have some tidal airflow into and out of air sacs, but their breathing is dominated by one-way airflow in the lung itself. The air flows through the lung in one direction, making a loop before exiting the lung.

In 2010, Farmer published a study showing that a mostly one-way or "unidirectional" airflow controlled by aerodynamic valves exists in alligators. That means the breathing pattern likely evolved before 250 million years ago, when crocodilians -- the ancestors of alligators and crocodiles -- split from the archosaur family tree that led to the evolution of flying pterosaurs, dinosaurs and eventually birds.

The new study found a mostly one-way, looping air flow in African savannah monitor lizards, Varanus exanthematicus -- one of roughly 73 species of monitor lizards -- although there was some tidal airflow in regions of the lungs. That means one-way airflow may have arisen not among the early archosaurs about 250 million years ago, but as early as 270 million years ago among cold-blooded diapsids, which were the common, cold-blooded ancestors of the archosaurs and Lepidosauromorpha, a group of reptiles that today includes lizards, snakes and lizard-like creatures known as tuataras.

One-way airflow may help birds to fly without passing out at high altitudes, where oxygen levels are low. Before the new study, Farmer and others had speculated that the one-way airflow may have helped dinosaurs' ancestors dominate the Earth when atmospheric oxygen levels were low after the Permian-Triassic mass extinction -- the worst in Earth's history -- 251 million years ago.

"But if it evolved in a common ancestor 20 million years earlier, this unidirectional flow would have evolved under very high oxygen levels," she says. "And so were are left with a deeper mystery on the evolutionary origin of one-way airflow."

How the Study was Performed
As in her earlier research on alligators, Farmer and colleagues demonstrated predominantly one-way airflow in the lungs of monitor lizards in several ways. They performed CT scans and made 3-D images of lizard lungs to visualize the anatomy of the lungs. They surgically implanted flow meters in the bronchi of five monitor lizards to measure airflow direction.

Using lungs removed from 10 deceased lizards, the researchers measured air flow as they pumped air into and out of the lungs. They also pumped water laden with sunflower pollen particles or plastic microspheres through lizard lungs, and the movement of the pollen and spheres also showed the unidirectional airflow.
Savannah monitor lizards were used in the research because they are relatively large and thus easier to study, weighing about a pound and measuring roughly 15 inches from head to tail tip. Monitor lizards also have some of the highest rates of oxygen consumption, partly because they breathe using not only their trunk muscles and ribs, but also using "gular pumping," which is when the lizards flare out their throat and pump air into their lungs.

Monitor lizards' lungs have more than a dozen chambers or bronchi in each lung. The primary airway runs the length of the lung, with lateral bronchi branching off of it.

The study showed that air enters the lizard's trachea or windpipe, then flows into the two primary airways, which enter the lung. But then, instead of flowing tidally back out the same way, the air instead loops back in a tail-to-head direction moving from one lateral airway to the next through small perforations between them.
The walls containing perforations that allow air to flow from one chamber to the next "are like lace curtains," Farmer says.

There appear to be no mechanical valves or sphincters, so the one-way airflow appears "to arise simply from jetting," or aerodynamic valves created when air flows around bends within the lung airways. That is supported by the fact that one-way airflow was observed even in lungs removed from dead lizards.

A 60-megabyte movie of CT scans of a lizard's airways may be downloaded here: http://www.hightail.com/download/OGhkQndONEg5eFZFQmNUQw

Emma R. Schachner, Robert L. Cieri, James P. Butler & C. G. Farmer. Unidirectional pulmonary airflow patterns in the savannah monitor lizard. Nature, 2013 DOI: 10.1038/nature12871

Wednesday, December 11, 2013

Lampropeltis triangulum now seven species

A new early on-line study examines reports unrecognized diversity in the milksnake (Lampropeltis triangulum) Coalescent species delimitation indicates that L. triangulum is not monophyletic and that there are multiple species of milksnake, which increases the known species diversity in the genus Lampropeltis by 40%. Both genealogical and temporal discordance occurs between gene trees and the species tree, with evidence that mtDNA introgression is a main factor. The highlights of the study include the following.

1) Lampropeltis triangulum: from Ontario, Canada along the Georgian Bay, throughout southern Quebec, and east of Lake Huron, extending throughout southern Maine, south through New England and New York to North Carolina and the extreme northern Alabama and Georgia and west to eastern Minnesota. Subspecies synonymized under L. triangulum would include L. t. syspila and any suspected “intergrades” that occur in Alabama, Indiana, Iowa, Illinois, Kentucky, Missouri, Mississippi, Tennessee, and possibly Arkansas north of the Arkansas River, and some milksnakes that have fallen under the subspecies L. t. amaura in northeastern Louisiana (specifically in La Salle Parish).

2) Lampropeltis gentilis: Found from the Panhandle of northern Texas, western Oklahoma, central and western Kansas, eastern Colorado, and south-central and southwestern Nebraska. The range of L. gentilis also includes the ranges of the following subspecies, which are synonymized with L. gentilis: L. t. amaura (part), found in eastern Texas, southeastern Oklahoma, Louisiana west of the Mississippi River, and southern Arkansas; L. t. celaenops in southeastern Arizona, New Mexico and adjacent eastern Texas; L. t. multistriata, found in northwestern Nebraska, the western half North Dakota, northern Wyoming, and southern Montana; and L. t. taylori found in Utah, northern Arizona, and western Colorado. In addition, L. gentilis includes L. t. annulata from at least central Texas and L. t. syspila from Nebraska, Kansas, and Oklahoma.

3) Lampropeltis elapsoides: southeastern US as far north as Virginia and Kentucky east of the Mississippi River and in eastern Louisiana. Suspected “intergrades” with L. triangulum from eastern Virginia to southern New Jersey are likely L. triangulum and not hybrids.

4) Lampropeltis annulata: Mexican states of Nuevo León, Querétaro, and Tamaulipas. It is likely that this species is also found in Coahuila, eastern San Luis Potosi, and Hidalgo. Subspecies synonymized with L. annulata include L. t. dixoni.

5) Lampropeltis polyzona: Mexican states of Colima, Guerrero, Hidalgo, Jalisco, Puebla, Michoacán, Oaxaca, Sinaloa, Sonora, and Veracruz. It is likely that this species is also found in Guanajuato, Morelos, and Nayarit, and western San Luis Potosí.

6) Lampropeltis abnorma: southern Veracruz and southeastern Guerrero ranging south through Nicaragua, Honduras, and western Costa Rica. This species is possibly in southern Oaxaca, and likely Campeche, Chiapas, Quintana Roo, Tabasco, and Yucatan as well as Belize and El Salvador. . Subspecies synonymized with L. abnorma include L. t. blanchardi, L. t. hondurensis, L. t. oligozona and L. t. stuarti.

7) Lampropeltis micropholis: eastern Costa Rica, throughout Panama, and south to Ecuador. It is likely found in Colombia and possibly Venezuela. Subspecies synonymized with L. micropholis include L. t. gaigeae and L. t. andesiana.

Sara Ruane, Robert W. Bryson, Jr., R. Alexander Pyron, and Frank T. Burbrink (2014) Coalescent Species Delimitation in Milksnakes (genus Lampropeltis) and Impacts on Phylogenetic Comparative Analyses. Systematic Biology early on-line December 10, 2013 doi:10.1093/sysbio/syt099

New molecular study provides insights into boa and python evolution

Henophidian snakes (boas, pythons, and their relatives) are one of the most spectacular groups of reptiles and constitute a vast diversity of morphologies, behaviors, body sizes and ecologies. This group include both the shortest (the black-bellied dwarf boa, Tropidophis nigriventris, about 250 mm in total length) and longest (reticulated python, about 10 m in total length henophidian snakes. These are constricting snakes, and include the 13 m Titanoboa cerrejonensis possibly the longest snake to ever exist. Henophidians are also represented by enigmatic and hyper-diverse families such as the Tropidophiidae (the dwarf boas) and Uropeltidae (the shield-tailed snakes); as well as by the nearly extinct insular Mascarene family Bolyeriidae. Boas (Boidae) and pythons (Pythonidae) represent highly diverse families with almost global tropical and subtropical distributions. Molecular phylogenetic and biogeographic studies of the boas and pythons have yielded important insights into evolutionary processes as well as an understanding of taxonomy, divergence, and diversification is becoming especially relevant given that many boa and python species are of significant conservation concern.

In an early online view of a new study Graham Reynolds and colleagues use both new and previously published sequence data, to produced a species-level phylogeny for 84.5% of boid species and 82.5% of pythonid species, set within a larger phylogeny of henophidian snakes. They obtained new sequence data for three boid, one pythonid, and two tropidophiid taxa which have never previously been included in a molecular study, in addition to generating novel sequences for seven genes across an additional 12 taxa. The authors compiled an 11-gene data set for 127 taxa, consisting of the mitochondrial genes CYTB, 12S, and 16S, and the nuclear genes bdnf, bmp2, c-mos, gpr35, rag1, ntf3, odc, and slc30a1, totaling up to 7561 base pairs per taxon.They analyzed this dataset using both maximum likelihood and Bayesian inference and recovered a well-supported phylogeny.

Significant evidence was found for the  discordance between taxonomy and evolutionary relationships in the genera Tropidophis, Morelia, Liasis, and Leiopython, and they found support for elevating two previously suggested boid species. they suggest a revised taxonomy for the boas (13 genera, 58 species) and pythons (8 genera, 40 species).

Some of the highlights of the study:

The authors continue to recognize Aniliidae for the Neotropical pipe snake. Tropidophiidae contains both Tropidophis (which is polyphyletic and Trachyboa). The Southeast Asian dwarf pipe snakes (Anomochilidae) are the sister to the Old World pipe snakes (Cylindrophiidae). Collectively the Eastern Hemisphere pipe snakes are the sister to the shield-tailed snakes (Uropeltidae). The sunbeam snakes form the family Xenopeltidae and the Mexican python is placed in the family Loxocemidae.Within the Pythonidae, Python is an Afro-Asian genus (regius, curtus, brogersmai, molurus, bivittaus, anchietae, and sebae). The new genus Malayopython  contains timorensis and reticulatus. Morelia  (carinata, bredi, spilota, viridis) is polyphyletic.

The new study recovered the monotypic Central American Loxocemidae (Loxocemus bicolor) as sister to the in-group pythons, while the East Asian Xenopeltidae (X. hainanensis and X. unicolor) form the sister to the clade (Pythonidae, Loxocemidae) in both analyses. Among the pythons, they found the African and southern Asian genus Python to be a monophyletic clade basal to the rest of the pythons. Within this genus there was support for a basal placement of the small-bodied West African P. regius and a derived clade of large bodied species (P. bivittatus and P. molurus) from southern Asia and a derived clade of the small-bodied Southeast Asian blood pythons (P. brongersmai and P. curtus). This suggests an evolution of gigantism separate from other giant members of the Australasian Pythonidae (Malayopython and Morelia). They also generated novel sequence data for the small-bodied Kalaharian P. anchietae. The subgeneric name Simalia Gray 1849 is used for the scrub python clade.

As for the Boidae, the authors found weak support for a sister relationship of the non-boid Calabaria to the Madagascan boids. As this is not well supported and inconsistent with previous studies, which have all found Calabaria to be basal to the rest of the boid radiation they consider Calabaria as the closest extant relative to the Boidae. Among Malagasy species they found strong support for the distinction of Sanzinia and Acrantophis.

They recovered the Central American Ungaliophis and Exiliboa as sister taxa to the North American boids Charina and Lichanura, with support for the distinction of C. bottae and C. umbratica.

With the first published sequence data for the African species Eryx muelleri, they found strong support for the placement of this species as sister to the south Asian E. jayakari. And found evidence for interdigitation of Eryx species between Africa and south Asia suggesting repeated dispersal events. No evidence was found for the continued use of the generic name Gongylophis.

Among western hemisphere boids, support was found for the recognition of B. imperator and recommend the epithet B. imperator.

As in previous studies the South American Eunectes and Epicrates were recovered as sisters with support for the distinction of the five mainland species of Epicrates. And, they found support for the continued use of the genus Chilabothrus for the island boas formerly in the genus Epicrates.

Graham Reynolds, R., M. L. Niemiller, L. J. Revell. (2013) Toward a Tree-of-Life for the boas and pythons: Multilocus species-level phylogeny with unprecedented taxon sampling. Molecular Phylogenetics and  Evolution. http://dx.doi.org/10.1016/j.ympev.2013.11.011

Monday, December 9, 2013

Crocodilians Lure Prey

Dec. 4, 2013 — Turns out the crocodile can be a shrewd hunter himself. A University of Tennessee, Knoxville, researcher has found that some crocodiles use lures to hunt their prey.
A mugger crocodile balances twigs on its nose to tempt birds 
collecting small branches to build nests with, at Madras 
Crocodile Bank, Tamil Nadu in India. Photo Credit: Vladimir Dinets.
Vladimir Dinets, a research assistant professor in the Department of Psychology, is the first to observe two crocodilian species -- muggers and American alligators -- using twigs and sticks to lure birds, particularly during nest-building time.

The research is published in the current edition of Ethology, Ecology and Evolution. Dinets' research is the first report of tool use by any reptiles, and also the first known case of predators timing the use of lures to a seasonal behavior of the prey -- nest-building.
Dinets first observed the behavior in 2007 when he spotted crocodiles lying in shallow water along the edge of a pond in India with small sticks or twigs positioned across their snouts. The behavior potentially fooled nest-building birds wading in the water for sticks into thinking the sticks were floating on the water. The crocodiles remained still for hours and if a bird neared the stick, they would lunge.

To see if the stick-displaying was a form of clever predation, Dinets and his colleagues performed systematic observations of the reptiles for one year at four sites in Louisiana, including two rookery and two nonrookery sites. A rookery is a bird breeding ground. The researchers observed a significant increase in alligators displaying sticks on their snouts from March to May, the time birds were building nests. Specifically, the reptiles in rookeries had sticks on their snouts during and after the nest-building season. At non-rookery sites, the reptiles used lures during the nest-building season.

"This study changes the way crocodiles have historically been viewed," said Dinets. "They are typically seen as lethargic, stupid and boring but now they are known to exhibit flexible multimodal signaling, advanced parental care and highly coordinated group hunting tactics."
The observations could mean the behavior is more widespread within the reptilian group and could also shed light on how crocodiles' extinct relatives -- dinosaurs -- behaved.

"Our research provides a surprising insight into previously unrecognized complexity of extinct reptile behavior," said Dinets. "These discoveries are interesting not just because they show how easy it is to underestimate the intelligence of even relatively familiar animals, but also because crocodilians are a sister taxon of dinosaurs and flying reptiles."
Dinets collaborated with J.C and J.D. Brueggen from the St. Augustine Alligator Farm Zoological Park in St. Augustine, Fla. More of his crocodile research can be found in his book "Dragon Songs."

V. Dinets, J.C. Brueggen & J.D. Brueggen , Ethology Ecology & Evolution (2013): Crocodilians use tools for hunting, Ethology Ecology and Evolution,

Monday, December 2, 2013

Two snake genomes

The Burmese python's ability to ramp up its metabolism and enlarge its organs to swallow and digest prey whole can be traced to unusually rapid evolution and specialized adaptations of its genes and the way they work, an international team of biologists says in a new paper. Lead author Todd Castoe, an assistant professor of biology at The University of Texas at Arlington College of Science, and 38 co-authors from four countries sequenced and analyzed the genome of the Burmese python, or Python molurus bivittatus. Their work is scheduled for publication this week (Dec. 2) by the Proceedings of the National Academy of Sciences along with a companion paper on the sequencing and analysis of the king cobra (Ophiophagus hannah). The papers represent the first complete and annotated snake genomes.

Python bivittatus (top), Ophiophagus hannah (bottom)
Because snakes contain many of the same genes as other vertebrates, studying how these genes have evolved to produce such extreme and unique characteristics in snakes can eventually help explain how these genes function, including how they enable extreme feats of organ remodeling. Such knowledge may eventually be used to treat human diseases.

"One of the fundamental questions of evolutionary biology is how vertebrates with all the same genes display such vastly different characteristics. The Burmese python is a great way to study that because it is so extreme," Castoe, who began working on the python project as a postdoctoral fellow at the University of Colorado School of Medicine in the laboratory of associate professor and paper corresponding author David D. Pollock.

Castoe said: "We'd like to know how the snake uses genes we all have to do things that no other vertebrates can do."

The new python study calls into question previous theories that major obvious physical differences among species are caused primarily by changes in gene expression. Instead, it contends that protein adaptation, gene expression and changes in the structure of the organization of the genome itself are all at work together in determining the unusual characteristics that define snakes, and possibly other vertebrates.

Pollock said the python and king cobra studies represent a significant addition to the field of "comparative systems genomics -- the evolutionary analysis of multiple vertebrate genomes to understand how entire systems of interacting genes can evolve from the molecules on up."

He said: "I believe that such studies are going to be fundamental to our ability to understand what the genes in the human genome do, their functional mechanisms, and how and why they came to be structured the way they are."

The Burmese python's phenotype, or physical characteristics, represents one of the most extreme examples of evolutionary adaptation, the authors said. Like all snakes, its evolutionary origin included reduction in function of one lung and the elongation of its mid-section, skeleton and organs. It also has an extraordinary ability for what researchers call "physiological remodeling."

Physiological remodeling refers to the process by which pythons are able to digest meals much larger than their size, such as chickens or piglets, by ramping up their metabolism and increasing the mass of their heart, liver, small intestine and kidneys 35 percent to 150 percent in only 24 to 48 hours. As the digestion is completed, the organs return to their original size within a matter of days. The authors suggest that understanding how snakes accomplish these tremendous feats could hold vital clues for the development of treatments for many different types of human diseases.

"The Burmese python has an amazing physiology. With its genome in hand, we can now explore the many untapped molecular mechanisms it uses to dramatically increase metabolic rate, to shut down acid production, to improve intestinal function, and to rapidly increase the size of its heart, intestine, pancreas, liver, and kidneys," said Stephen Secor, associate professor of biological sciences at the University of Alabama and a co-author on the paper. 'The benefits of these discoveries transcends to the treatment of metabolic diseases, ulcers, intestinal malabsorption, Crohn's disease, cardiac hypertrophy and the loss of organ performance."

To complete their work, the research team aligned 7,442 genes from the python and cobra with genes sequences available in the Ensembl Genome Browser from other amphibians, reptile, bird and mammals. They used a statistical method called "branch site codon modeling" to look for genes that had been positively selected (or evolutionarily changed due to natural selection) in the python, the cobra, and early in snake evolution in the common ancestor of these two snakes. They found changes in hundreds of genes. They believe the results demonstrate that natural selection-driven changes in many genes that encode proteins contributed substantially to the unique characteristics of snakes.

Analyses showed a remarkable correspondence between the function of the selected genes, and the many functionally unique aspects of snake biology -- such as their unique metabolism, spine and skull shape and cell cycle regulation, Castoe said. Many of the altered genes the team observed also have prominent medical significance. For example, the python genome showed some changes to the gene GAB1, which other research suggests plays a role in breast cancer, melanomas and childhood leukemia.

In addition to changes to individual genes and their expression, researchers also found that the extreme characteristics in snakes could also be linked to duplications or losses in multigene families. Some of those include ancient loss and more recent re-evolution of high resolution vision, and their ability to detect chemical cues from the environment. Researchers also observed that, while most assume that reptile genes and genomes change at a very slow rate, snake genomes evolve at one of the fastest rates of any vertebrate.

Freek J. Vonk, Nicholas R. Casewell, Christiaan V. Henkel, Alysha M. Heimberg, Hans J. Jansen, Ryan J. R. McCleary, Harald M. E. Kerkkamp, Rutger A. Vos, Isabel Guerreiro, Juan J. Calvete, Wolfgang Wüster, Anthony E. Woods, Jessica M. Logan, Robert A. Harrison, Todd A. Castoe, A. P. Jason de Koning, David D. Pollock, Mark Yandell, Diego Calderon, Camila Renjifo, Rachel B. Currier, David Salgado, Davinia Pla, Libia Sanz, Asad S. Hyder, José M. C. Ribeiro, Jan W. Arntzen, Guido E. E. J. M. van den Thillart, Marten Boetzer, Walter Pirovano, Ron P. Dirks, Herman P. Spaink, Denis Duboule, Edwina McGlinn, R. Manjunatha Kini, and Michael K. Richardson. 2013. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. PNAS 2013 ; published ahead of print December 2, 2013, doi:10.1073/pnas.1314702110.

Todd A. Castoe, A. P. Jason de Koning, Kathryn T. Hall, Daren C. Card, Drew R. Schield, Matthew K. Fujita, Robert P. Ruggiero, Jack F. Degner, Juan M. Daza, Wanjun Gu, Jacobo Reyes-Velasco, Kyle J. Shaney, Jill M. Castoe, Samuel E. Fox, Alex W. Poole, Daniel Polanco, Jason Dobry, Michael W. Vandewege, Qing Li, Ryan K. Schott, Aurélie Kapusta, Patrick Minx, Cédric Feschotte, Peter Uetz, David A. Ray, Federico G. Hoffmann, Robert Bogden, Eric N. Smith, Belinda S. W. Chang, Freek J. Vonk, Nicholas R. Casewell, Christiaan V. Henkel, Michael K. Richardson, Stephen P. Mackessy, Anne M. Bronikowsi, Mark Yandell, Wesley C. Warren, Stephen M. Secor, and David D. Pollock. 2013. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. PNAS 2013 ; published ahead of print December 2, 2013, doi:10.1073/pnas.1314475110