Thursday, November 6, 2014

External genitalia in amniote evolution

When it comes to genitalia, nature enjoys variety. Snakes and lizards have two. Birds and people have one. And while the former group's paired structures are located somewhat at the level of the limbs, ours, and the birds', appear a bit further down. In fact, snake and lizard genitalia are derived from tissue that gives rise to hind legs, while mammalian genitalia are derived from the tail bud. But despite such noteworthy contrasts, these structures are functionally analogous and express similar genes.

How do these equivalent structures arise from different starting tissues?

This is a python embryo at 11 days after 
oviposition (egglaying). The right hemipenis
(genitalia) bud and vestigial limb-bud can be 
seen near the tail end of the embryo, in the 
center of the tail 'spiral'. (two white 'blobs'). 
Photo Credit: Patrick Tschopp.
Reporting in Nature, researchers in Harvard Medical School's Department of Genetics, led by departmental chair Clifford Tabin, have found that the answer is not unlike the real estate axiom Location, location, location.

The embryonic cloaca -- which eventually develops into the urinary and gut tracts -- issues molecular signals that tell neighboring cells and tissues to form into external genitalia. The cloaca's location determines which tissues receive the signal first. In snakes and lizards, the cloaca is located closer to the lateral plate mesoderm, the same tissue that makes the paired limbs, receives the signal. In mammals, the cloaca is closer to the tail bud.

To further confirm this finding, the researchers grafted cloaca tissue next to the limb buds in one group of chicken embryos, and beside the tail buds in a second group. They found that in both cases, cells closer to the grafted cloaca responded to the signals and partially converted toward a genitalia fate.

This proves that different populations of cells with progenitor potential are able to respond to cloaca signaling and contribute to genitalia outgrowth.

"While mammal and reptile genitalia are not homologous in that they are derived from different tissue, they do share a 'deep homology' in that they are derived from the same genetic program and induced by the same ancestral set of molecular signals," said Tabin, who is also the George Jacob and Jacqueline Hazel Leder Professor of Genetics.

"Here we see that an evolutionary shift in the source of a signal can result in a situation where functionally analogous structures are carved out of nonhomologous substrate," said Patrick Tschopp, an HMS research fellow in genetics in Tabin's lab and first author on the paper. "Moreover, this might help to explain why limbs and genitalia use such similar gene regulatory programs during development."


Tschopp P, Sherratt E, Sanger TJ, Groner AC, Aspiras AC, Hu JK, Pourquié O, Gros J, Tabin CJ. A relative shift in cloacal location repositions external genitalia in amniote evolution. Nature, 2014; DOI: 10.1038/nature13819

An amphibious ichthyosaur

Fossil remains show the first amphibious ichthyosaur found in China by a team led by a UC 
Davis scientist. Its amphibious characteristics include large flippers and flexible wrists, essential 
for crawling on the ground. Photo Credit: Ryosuke Motani/UC Davis
The first fossil of an amphibious ichthyosaur has been discovered in China by a team led by researchers at the University of California, Davis. The discovery is the first to link the dolphin-like ichthyosaur to its terrestrial ancestors, filling a gap in the fossil record. The fossil is described in a paper published in advance online Nov. 5 in the journal Nature.

The fossil represents a missing stage in the evolution of ichthyosaurs, marine reptiles from the Age of Dinosaurs about 250 million years ago. Until now, there were no fossils marking their transition from land to sea.

"But now we have this fossil showing the transition," said lead author Ryosuke Motani, a professor in the UC Davis Department of Earth and Planetary Sciences. "There's nothing that prevents it from coming onto land."

Motani and his colleagues discovered the fossil in China's Anhui Province. About 248 million years old, it is from the Triassic period and measures roughly 1.5 feet long.

Unlike ichthyosaurs fully adapted to life at sea, this one had unusually large, flexible flippers that likely allowed for seal-like movement on land. It had flexible wrists, which are essential for crawling on the ground. Most ichthyosaurs have long, beak-like snouts, but the amphibious fossil shows a nose as short as that of land reptiles.

Its body also contains thicker bones than previously-described ichthyosaurs. This is in keeping with the idea that most marine reptiles who transitioned from land first became heavier, for example with thicker bones, in order to swim through rough coastal waves before entering the deep sea.

The study's implications go beyond evolutionary theory, Motani said. This animal lived about 4 million years after the worst mass extinction in Earth's history, 252 million years ago. Scientists have wondered how long it took for animals and plants to recover after such destruction, particularly since the extinction was associated with global warming.

"This was analogous to what might happen if the world gets warmer and warmer," Motani said. "How long did it take before the globe was good enough for predators like this to reappear? In that world, many things became extinct, but it started something new. These reptiles came out during this recovery."


Motani R., Jiang D-Y, Chen G-B, Tintori A, Rieppel O, Ji C, Huang J-D. 2014. A basal ichthyosauriform with a short snout from the Lower Triassic of China. Nature, 2014; DOI: 10.1038/nature13866

Wednesday, November 5, 2014

Snakebite in rural Nepal, diagnosis of species responsible

Photo credit; DA Warrell
Starting with a simple DNA swab taken from fang marks on people bitten by snakes, an international research team correctly identified the species of the biting snake 100 percent of the time in a first-of-its-kind clinical study, according to data presented today at the American Society of Tropical Medicine and Hygiene's (ASTMH) Annual Meeting.
The study, conducted at three medical facilities in Nepal, found that if snake DNA could be isolated from the bite wound, the test identified the species of snake responsible every time.
"These findings represent a significant step toward improving care for patients in areas of the world where snakebites constitute a massive but neglected health risk," said François Chappuis, MD, PhD, chief of the division of tropical and humanitarian medicine at Geneva University Hospitals, Switzerland, who directed the study and presented the results. "This DNA test may hasten more effective bedside diagnostics for snakebite victims, giving them a better chance of surviving and making a full recovery."
Bites from venomous snakes are common in many parts of the world and an especially serious unresolved health problem to millions of people living in South and Southeast Asia, as well as Africa and Latin America. Although there are no reliable numbers at the global scale, a study published in 2008 estimated at least 421,000 cases of envenomation and up to 94,000 deaths occur worldwide from snakebite each year. However, experts warn that these figures may underestimate the real problem, which is believed to affect several million people bitten by venomous snakes annually and hundreds of thousands who die or survive disabled, suffering from amputation or deformed limbs as a result of unavailable or delayed treatment.
In some villages of the study area of southeast Nepal reported today, a community-based survey in 2002 revealed an estimated 1,162 snakebites and 162 snakebite deaths per 100,000 people per year, one of the highest rates ever reported. Likewise, a recent survey of more than one million deaths in India, published in the journal PLoS Neglected Tropical Diseases in 2011, found that 46,000 people die every year in India from snakebites. This figure is about 20 times the official death toll recorded in Indian hospitals, most likely because less than one in four fatal snakebite cases had received any hospital treatment, the study revealed.
"People bitten by snakes in South Asia often do not seek treatment at a medical facility, and if they do, the vast majority don't take the snake to clinics, although it is often killed, and can't identify the species that bit them," Chappuis said. "Yet knowing the species of snake is critical to determining the best course of treatment."
In Nepal, for example, cobras and kraits are among the most common venomous snakes. Their venoms attack the nervous system and can be fatal. Patients bitten by either snake have similar symptoms, such as nausea, headache, drowsiness and limb as well as respiratory paralysis. However, the toxins of these snakes and their mechanisms of action differ, and so does the response to antivenom and other drugs. For example, the locally available antivenom has limited or no efficacy against krait envenomation, which often leads to useless repeated doses resulting in increased cost and--possibly--adverse side effects, explained Chappuis. Also, bites by cobras and kraits lead to different complications that the attending physicians need to prevent or be prepared for. Therefore, positive identification of the biting species becomes important to effective treatment.
Preliminary results presented today show that among 194 bite-site DNA samples collected in Nepal during the study, 87 were from a venomous species. The spectacled cobra accounted for 42 bites and the common krait for 22. In 21 cases, the patients brought the dead snake with them, and in those cases expert examination of the snake and the DNA test, performed by different investigators, independently provided the correct identification. Snake DNA could be obtained from about one in four bite wounds. According to the researchers, one factor that excluded samples was if the patient attempted folk or home remedies tampering with the bite site prior to arriving at the medical clinic.
The research team also correlated clinical symptoms with the species biting patients. They found that krait bites happened more often at night, indoors, or while people were sleeping, while cobra or pitviper bites were more likely to cause swelling at the bite site. The technique also identified several species of non-venomous snake involved in bites.
"The proportion of non-venomous snakes that bite people is actually rather high," said Ulrich Kuch, PhD, of the department of tropical medicine and public health in the Institute of Occupational, Social and Environmental Medicine of Goethe University (Frankfurt, Germany), and developer of the snake DNA identification test. "Snakebite patients are kept in the hospital for 24-hour observation, which strains healthcare resources in many countries. By identifying species of nonvenomous snake, it is also possible to assist the local people and avoid hospital stays for those not at risk of envenomation."
The research team is currently developing a rapid diagnostic "dip-stick" test similar to a pregnancy test that could be used to rule out certain common venomous snakes and help physicians more quickly decide the best course of treatment. Conversely, if for example, krait venom is detected, doctors could quickly give antivenom instead of waiting for clinical signs of envenomation, as is current practice. They would also accelerate the transfer of patients to referral hospitals with intensive care units able to ensure adequate respiratory support. Such a test would be easy to administer in rural healthcare settings with limited resources, said Chappuis.
"That's where the recently developed DNA test could be most valuable," he added. While the DNA test is labor intensive and time consuming, making it impractical for day-to-day clinical use, its high accuracy could allow it to become a "gold standard" in clinical studies of rapid diagnostic tests under development. In addition, the DNA test could become a powerful epidemiological tool to determine which species of snake bite people in various tropical regions.
"Knowing the distribution of snakes and the number of snakebites within a region could help improve allocation of scarce antivenoms to areas where they are most needed" said Chappuis.
The researchers have completed small clinical studies in Nepal and Bangladesh and are preparing a larger multi-center clinical study using the DNA test in Myanmar and Nepal, countries with among the highest rates of snakebite deaths. The current study is funded by the UBS Optimus Foundation and the Swiss National Fund.
"We need new tools in order to save more lives," said Sanjib K. Sharma, MD, professor of medicine at the B.P. Koirala Institute of Health Sciences in Nepal, and the principal investigator of the study. "There is gross disparity in the management and outcome of snakebites since most occur in rural, agricultural areas while the great majority of healthcare workers are in urban locations."
"Most people are unaware that snakebite is a very real and serious threat both to the health and economic vitality of rural communities throughout much of the developing world," said Alan J. Magill, MD, FASTMH, president of the American Society of Tropical Medicine and Hygiene. "This innovative research may be enabling for the development of a point of care test to positively identify biting snakes. Accurate diagnosis would go a long way toward documenting the impact of snakebite and improving medical care for this often neglected yet pervasive problem."

Sharma SK, Kuch U, Höde P, Bruhse L. Pandey D, Chappuis F, Alirol E. 2014. Use of clinical predictors and molecular diagnosis to identify the species responsible for snakebite in rural Nepal. AmericanSociety of Tropical Medicine and Hygiene (Burness Communications). Abstract. ASTMH 63rd Annual Meeting Nov. 2-6. New Orleans.

Sunday, November 2, 2014

Frogs make their offspring grow at a faster rate

Breeding male of Rana arvalis from the study area. 
Photo Credit: Germán Orizaola.
Gobal warming is altering the reproduction of plants and animals, notably accelerating the date when reproduction and other life processes occur. A study by the University of Uppsala (Sweden), including the participation of Spanish researcher Germán Orizaola, has discovered that some amphibians are capable of making their offspring grow at a faster rate if they have been born later due to the climate.

Over recent decades many organisms, both plants and animals, have experienced a notable advance in the date when many of their life processes (like reproduction, migration or flowering) occur, attributed to the impact of climate change. An article published in the journal Ecology examines the effects that these changes in the reproduction date have on the life cycles of the amphibians.
"We specifically examined whether changes in the reproduction date of a common amphibian species in the north of Europe, Rana arvalis, can condition the growth and development of their offspring," the Spanish researcher Germán Orizaola, from the University of Uppsala (Sweden) and co-author of the study, said.

Results revealed that female frogs have the ability to influence both the growth rate and the development of their offspring, and they adjust it depending on the date of reproduction.
According to Orizaola, "the mechanism by which the female frogs can condition the growth of their larvae could be due to the genes associated with the maintenance of their biological clock being transferred to the embryos and becoming active even before fertilization. This would provide the larvae with the exact information regarding the progression of the growing season."

One of the characteristics associated with climate change is an increase in the inter-annual variability of climatic conditions, so organisms are also exposed to greater uncertainty when it comes to determining the right time to reproduce. This explains why the existence of mechanisms adjusting growth and development rates depending on the variation in the start of breeding is highly advantageous for many species.

In particular, as part of this study they observed that by delaying the date of reproduction (which simulated a time of environmental instability), the result was an equivalent reduction in the growth period for the larvae. "That means the later this species of frog breeds, the faster the larvae develop," explains the scientist.

An interesting aspect of the study is that the acceleration in growth is produced under constant lab conditions. "The larvae were not exposed to any outside sign that would indicate the progression of the growing season," adds Orizaola.

"This result is very novel and demonstrates that the acceleration in the development of the larvae is conditioned by the breeding females, which reveals the existence of a 'transgenerational effect' in which the breeding adults are capable of altering key aspects of the life cycle for the following generations, to better prepare them to survive the environmental conditions that they are going to experience," concludes the expert.

Richter-Boix A, Orizaola G, Laurila A. 2014 Transgenerational phenotypic plasticity links breeding phenology with offspring life-history. Ecology, 2014; 95 (10): 2715 DOI: 10.1890/13-1996.1

Thursday, October 30, 2014

The Asian keelback genus Amphiesma separated into three genera

Amphiesma stolatum from Thailand. JCM
Asia is the geographic center for the origin of most modern snake lineages. The Asian natricines known as keelbacks (Amphiesma) are widely distributed and inhabit a variety of niches and exhibit significant morphological variation. The genus keelbacks in the genus Amphiesma comprise at least 42 species of small to medium-sized (not exceeding one meter) of snakes. They are terrestrial to semiaquatic, oviparous, and generally considered harmless or mildly venomous. 

Species in this group range throughout southern, eastern, and southeastern Asia, from Pakistan and India to eastern China, north into southernmost Russia and Japan, and southwards to Sumatra. In the mid-20th century Edmund Malnate used morphological characters including hemipenial morphology, dentition, and external scalation to divided the genus Natrix sensu lato into several genera, revalidating the genus Amphiesma Duméril, Bibron, and Duméril with the type species Amphiesma stolatum. The diagnostic characters of Amphiesma are defined as: hemipenes and sulci spermaticus simple; maxillary teeth in continuous series, gradually becoming larger posteriorly in the series or the last two teeth abruptly enlarged; terrestrial; internasals broad anteriorly, nostrils lateral; apical pits present or absent. Recent molecular phylogenies suggest that this genus is not monophyletic, and that additional cryptic diversity is present. All analyses consistently show Amphiesma consists of three distinct, monophyletic lineages.

In a recently published paper Guo et al (2014) divide Amphiesma into three genera, Amphiesma, Hebius, and Herpetoreas. The genus Amphiesma is monotypic, Herpetoreas contains three species, and Hebius comprises the remaining 39 species. On the basis of a combination of molecular analyses and external morphological comparisons, they describe a new species in the Herpetoreas group from China as H. burbrinki sp. nov. Several other species are shown to be non-monophyletic or contain significant levels of intraspecific genetic diversity. They also found another Old World natricine genus, Xenochrophis non-monophyletic and suggest further taxonomic revisions are needed in the Natricinae, at multiple levels.


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

Giant tortoise reintroduction to Española Island, Galapagos

An endangered population of giant tortoises has recovered 
on the Galapagos island of Espanola. Photo Credit: 
James P. Gibbs, SUNY-ESF.
Some 40 years after the first captive-bred tortoises were reintroduced to the island by the Galapagos National Park Service, the endemic Española giant tortoises are reproducing and restoring some of the ecological damage caused by feral goats that were brought to the island in the late 19th century.

"The global population was down to just 15 tortoises by the 1960s. Now there are some 1,000 tortoises breeding on their own. The population is secure. It's a rare example of how biologists and managers can collaborate to recover a species from the brink of extinction, " said James P. Gibbs, a professor of vertebrate conservation biology at the SUNY College of Environmental Science and Forestry (ESF) and lead author of the paper published in the journal PLOS ONE.

Gibbs and his collaborators assessed the tortoise population using 40 years of data from tortoises marked and recaptured repeatedly for measurement and monitoring by members of the Galapagos National Park Service, Charles Darwin Foundation, and visiting scientists.

But there is another side to the success story: while the tortoise population is stable, it is not likely to increase until more of the landscape recovers from the damage inflicted by the now-eradicated goats.
"Population restoration is one thing but ecological restoration is going to take a lot longer," Gibbs said.

After the goats devoured all the grassy vegetation and were subsequently removed from the island, more shrubs and small trees have grown on Española. This hinders both the growth of cactus, which is a vital piece of a tortoise's diet, and the tortoises' movement. Chemical analysis of the soil, done by Dr. Mark Teece, an ESF chemistry professor, shows there has been a pronounced shift from grasses to woody plants on the island in the last 100 years.

The shrubs and trees also inhibit the movements of the endangered waved albatross that breeds on the island. Gibbs said the plants make it difficult for the ungainly sea birds to take flight.

"This is a miraculous conservation success accomplished by the Galapagos National Park Service," said Gibbs, " but there is yet more work to fully recover the ecosystem upon which the tortoises and other rare species depend."

Gibbs JP, Hunter EA, Shoemaker KT, Tapia WH, Cayot LJ. 2014. Demographic Outcomes and Ecosystem Implications of Giant Tortoise Reintroduction to Española Island, Galapagos. PLoS ONE, 2014; 9 (10): e110742 DOI: 10.1371/journal.pone.0110742

Wednesday, October 29, 2014

Rapid evolution of the hind feet of the green anole

The left hind foot of the green anole after evolution. 
Toe pad measurements were taken on the expanded 
scales at the end of the longest toe. Photo Credit: 
Yoel Stuart/U. of Texas at Austin

Scientists working on islands in Florida have documented the rapid evolution of a native lizard species -- in as little as 15 years -- as a result of pressure from an invading lizard species, introduced from Cuba.

After contact with the invasive species, the native lizards began perching higher in trees, and, generation after generation, their feet evolved to become better at gripping the thinner, smoother branches found higher up.

The change occurred at an astonishing pace: Within a few months, native lizards had begun shifting to higher perches, and over the course of 15 years and 20 generations, their toe pads had become larger, with more sticky scales on their feet.

"We did predict that we'd see a change, but the degree and quickness with which they evolved was surprising," said Yoel Stuart, a postdoctoral researcher in the Department of Integrative Biology at The University of Texas at Austin and lead author of the study appearing in the Oct. 24 edition of the journal Science.

"To put this shift in perspective, if human height were evolving as fast as these lizards' toes, the height of an average American man would increase from about 5 foot 9 inches today to about 6 foot 4 inches within 20 generations -- an increase that would make the average U.S. male the height of an NBA shooting guard," said Stuart. "Although humans live longer than lizards, this rate of change would still be rapid in evolutionary terms."

The native lizards studied, known as Carolina anoles or green anoles, are common in the southeastern U.S. The invasive species, Cuban anoles or brown anoles, are native to Cuba and the Bahamas. Brown anoles first appeared in South Florida in the 1950's, possibly as stowaways in agricultural shipments from Cuba, and have since spread across the southeastern U.S. and have even jumped to Hawaii.

This latest study is one of only a few well-documented examples of what evolutionary biologists call "character displacement," in which similar species competing with each other evolve differences to take advantage of different ecological niches. A classic example comes from the finches studied by Charles Darwin. Two species of finch in the Galápagos Islands diverged in beak shape as they adapted to different food sources.

The researchers speculate that the competition between brown and green anoles for the same food and space may be driving the adaptations of the green anoles. Stuart also noted that the adults of both species are known to eat the hatchlings of the other species.

"So it may be that if you're a hatchling, you need to move up into the trees quickly or you'll get eaten," said Stuart. "Maybe if you have bigger toe pads, you'll do that better than if you don't."

Stuart YE, Campbell TS, Hohenlohe PA, Reynolds RG, Revell LJ, Losos JB. 2014. Rapid evolution of a native species following invasion by a congenerScience,

A new leopard frog from the east coast

Rana (Lithobates) kauffeldi  discovered by Rutgers researchers and 
a team of others living along the I-95 corridor from Connecticut 
to North Carolina will be named after the ecologist who first 
noticed it more than a half century ago. 
Photo Credit: Rutgers University.
Note the authors described this frog as a member of the genus Rana, but it will likely be changed to the genus Lithobates in the near future. 

More than a half century after claims that a new frog species existed in New York and New Jersey were dismissed, a Rutgers researcher and team of scientists have proven that the frog is living in wetlands from Connecticut to North Carolina and are naming it after the ecologist who first noticed it.

"Even though he was clearly on to something, the claim Carl Kauffeld made in his 1937 paper fell short," said Rutgers doctoral candidate Jeremy Feinberg. "We had the benefits of genetic testing and bioacoustic analysis that simply weren't available to Kauffeld to prove that even though this frog might look like the two other leopard frogs in the area, it was actually a third and completely separate species."

In the paper, "Cryptic Diversity in Metropolis: Confirmation of a New Leopard Frog Species from New York City and Surrounding Atlantic Coast Regions," published in PLOS ONE, Feinberg and a team of seven other researchers revealed the scientific name for the new species: Rana kauffeldi. The leopard frog, first encountered by Feinberg on Staten Island six years ago not far from the Statue of Liberty, will be commonly referred to as the Atlantic Coast Leopard Frog.

During his career, Kauffeld, who died in 1974 at age 63, worked as the director of the Staten Island Zoo and at the American Museum of Natural History, wrote many books about amphibians and reptiles and is considered to have been an authority on the subject. Although Kauffeld's research was initially recognized by some of his colleagues, Feinberg said Kauffeld faced considerable scrutiny and failed to gain any lasting support for his proposal.

"After some discussion, we agreed that it just seemed right to name the species after Carl Kauffeld," said Feinberg. "We wanted to acknowledge his work and give credit where we believe it was due even though it was nearly 80 years after the fact."

Feinberg, the lead author, encountered the new species six years ago in one of the most developed, heavily populated areas in the world. Two years ago, he and scientists from Rutgers, UCLA, UC Davis, and The University of Alabama -- who had worked together to show that this frog was a brand new species -- made the initial announcement.

Today, the new research paper, which also includes Joanna Burger, professor in the Department of Cell Biology and Neuroscience in the School of Arts and Sciences, as well as scientists from Yale, Louisiana State University, SUNY College of Environmental Science and Forestry, and the New Jersey Division of Fish and Wildlife, completes that discovery. The paper has provided the critical evidence needed to formally describe and name the new frog and also presents information on the distribution, ecology, and conservation status of this species.

Historically, the new frog was confused with two closely related species -- including one to the north and one to the south -- because it looks so similar. As a result, it was not noticed as a distinct species. But after Feinberg's encounter in 2008, modern technology stepped in. Using molecular and bioacoustic techniques to examine the genetics and mating calls of leopard frogs from various parts of Northeast the scientists were able to positively determine that the frog found living in the marshes of Staten Island was, in fact, a new species that might also be hiding in ponds and wetlands beyond New York and New Jersey.

The news, Feinberg said, became a call to arms to biologists, hobbyists and frog enthusiasts from Massachusetts to Virginia to go out, look, and listen in order to determine if the new frog -- mint-gray to light olive green with medium to dark spots -- could be found beyond the New York metropolitan area.

Over the last two years, many frog lovers, including some involved with the North American Amphibian Monitoring Project -- a government project that observes frog habitats to determine if populations are declining -- have provided crucial information about where the frogs are living, what they look like and how they sound. One volunteer, in fact, noticed the new species' unusual and distinct 'chuck' call, and provided information that ultimately helped confirm populations of the new species in both Virginia and North Carolina.

"If there is a single lesson to take from this study, it's that those who love nature and want to conserve it need to shut down their computers, get outside and study the plants and animals in their own backyards," said co-author Brad Shaffer, professor in UCLA's Department of Ecology and Evolutionary Biology, who described the discovery as biological detective work. Although fun and satisfying work, the goal is to protect the biodiversity of the planet, he said.

Scientists say the fact that this new species -- which brings the total number of leopard frogs in the world to 19 -- remained under the radar in a highly populated area spanning eight east coast states and several major North American cities stretching 485 miles -- is remarkable.

"It is incredible and exciting that a new species of frog could be hiding in plain sight in New York City and existing from Connecticut to North Carolina," said Burger, Feinberg's advisor. "The process of recognizing, identifying and documenting a new species is long and arduous but it is important for our understanding of the wide ranging wildlife in urban as well as other environments."

Feinberg JA,  Newman CE, Watkins-Colwell GJ, Schlesinger MD, Zarate B, Curry BR, Shaffer HB Burger.J. 2014. Cryptic Diversity in Metropolis: Confirmation of a New Leopard Frog Species (Anura: Ranidae) from New York City and Surrounding Atlantic Coast Regions. PLoS ONE, 2014; 9 (10): e108213 DOI: 10.1371/journal.pone.0108213

Sunday, October 26, 2014

Molecular study reveals the small yellow treefrog Dendropsophus minutus to actually be 19-43 species

This Trinidad and Tobago frog, formerly regarded as 
Dedropsophis minutus is now Dendopsophus 
goughi (Boulenger). JCM
Cryptic genetic diversity is now so commonly reported in molecular studies of amphibian species that the existence of nominally widespread tropical species has been called into question. However, supposedly widespread species occurring across multiple biomes and countries are rarely comprehensively sampled across their complete geographic range in screenings of genetic diversity or phylogeographic studies. Sampling of species from across vast continental areas and across political borders is often handicapped by financial, logistic and political factors.
In the Neotropics, nominal taxa such as the toad Rhinella margaritifera (Bufonidae), the thin-toed frog Leptodactylus fuscus (Leptodactylidae), and the tree frog Scinax ruber (Hylidae) are prominent examples of anuran species once considered to occur across nearly the entire tropical lowlands of South America. Evidence has accumulated that many such putatively widespread species could in fact be complexes of cryptic taxa. However, given limited genetic sampling and the difficulty in reviewing material from all countries hosting populations, their relationships and systematics remain in many cases as unclear as they were decades ago.
Dendropsophus minutus (Peters, 1872) is a small hylid frog, 21–28 mm snout-vent length, distributed in Cis-Andean South America, including the Andean slopes, the Amazon Basin, the Guiana Shield, down to the Atlantic Forests of southeastern Brazil, with an elevational record from near sea level up to 2,000 m. Variation in coloration, osteology, advertisement calls and larval morphology, along with molecular data from limited parts of the species' distribution suggest that the nominal D. minutus might represent a species complex. However, the sheer size of its supposed geographical range along with nomenclatural and taxonomic complexity (six junior synonyms) and unresolved relationships in the D. minutus species group have so far made these frogs inaccessible to revision.
In a new study in PLoS ONE Gehara and colleagues (2014) use D. minutus to understand to what degree a tropical, small-sized anuran has the potential to be continentally widespread with limited genetic structure within its range, as expected for a single species. In addition to conservation concerns, this question has important implications for South American biogeography in general and amphibian systematics and evolution in particular. Evidence is accumulating that body size in amphibians has a positive correlation with range size, but contrary to this trend many Holarctic amphibians occur with little genetic substructure across the vast ranges they colonized after the last glaciation, despite sometimes moderate to small body sizes. Whether such patterns also exist across vast ranges in tropical regions, with their distinct historical climatic dynamics, is an open question. Deciphering possible cryptic diversity within the nominal D. minutus would also help inform conservation assessments which typically use species' geographic distributions as criteria for conservation status.
The 16S tree containing all Dendropsophus for which sequences were available recovered the monophyly of the D. minutus species group. Within the group, the clade containing samples representing lineages 19–43 received a maximal posterior probability (1.0) and is defined here as the D. minutus complex, given that lineage 25 contains samples from the type locality of D. minutus.
Most of the mitochondrial lineages containing more than one sample received strong nodal support. The lineages splitting off from basal nodes of the tree (lineages 1–18) are distributed in the Guiana Shield, and in the Andean region of Peru, Ecuador and Colombia, with an eastern extralimital clade assembling disjunct localities in Mato Grosso and Pará.
The remaining lineages are in general more widely distributed in central and eastern South America Lineages are largely allopatric but several cases of sympatry were observed. The uncorrected pairwise distances between lineages for the 16S gene ranged from 0.7 to 13%, while within-lineage p-distances ranged from 0.0 to 1.8%.
Most of the lineages (45%) were found in only one or two localities. Fifty per cent of the lineages were only found in areas smaller than 10 km2, and more than 70% have known ranges smaller than 10,000 km2. Eight out of the 43 lineages have a distribution larger than 100,000 km2. Largest range sizes were found in northeastern Brazil (Caatinga domain; 997,262 km2, lineage 36), eastern Bolivia and western Brazil (Cerrado, Chaco and Dry Forest domains; 293,321 km2, lineage 33) and the Guiana Shield (269,741 km2, lineage 2).
Among the D. minutus species group members external to the D. minutus complex, lineages 1–6 are Guianan, while 7–18 are primarily distributed along the Andean foothills, and all show well-pronounced molecular differentiation and divergence. Among lineages 1–6, there is moderate genetic differentiation. Considering mitochondrial reciprocal monophyly and GMYC results as criteria, and being taxonomically conservative, one available name, Hyla goughi Boulenger, 1911 (type locality: Trinidad), should likely be removed from the synonymy of D. minutus and allocated to populations comprised by all or some of lineages 1–6. As a conservative estimate, the authors hypothesize that lineages 7–18 comprise seven distinct species, i.e., five named taxa and two undescribed species (lineages 9+10 and 11+12).
Data presented herein provide conclusive evidence for a strong genetic subdivision of the nominal species Dendropsophus minutus as currently understood. Current taxonomy conservatively assumes a putatively widespread species encompassing a vast area of South America (from approximately latitude 11.0°N to 35.0°S), distributed across several biomes. Our results, however, reveal high genetic diversity within D. minutus that would suggest the existence of numerous distinct species, leading to an important increase in number of species. If this hypothesis is confirmed through further studies, the existence of an increased number of species with decreased range sizes would have important consequences for the definition of centers of endemism and for assessing conservation status.
Despite revealing a substantial amount of cryptic genetic diversity within D. minutus sensu lato, our results also confirm the existence of widespread Neotropical species of anurans. While the authors cannot yet confirm which of the mitochondrial lineages within the D. minutus complex will merit a status as separate species, the authors suggest they can inversely conclude that in most cases, all samples assigned to one mtDNA lineage should be conspecific. Although cases of distinct amphibian species with low mtDNA differentiation exist and phenomena of mtDNA introgression can potentially blur species identities, such cases remain exceptional. Therefore, these factors are unlikely to substantially affect the calculation of range sizes according to which a total of eight mtDNA lineages have ranges >100,000 km2 (lineages 2, 19, 33, 34, 36, 39 41, 42). In the most inflationist taxonomic scenario, with each of these lineages representing separate species, the dataset still provides evidence for a species of lowland Neotropical amphibian (lineage 36) occupying an area of almost one million km2, encompassing multiple biomes across a distance of about 1,600 km between its two most distant populations.
The most widespread lineages within D. minutus sensu lato have distributions restricted to or centered in Brazil and occur within rather open habitats, while lineage 2 of the D. minutus group (with a range of almost 270,000 km2) occurs in rainforest. Several of the lineages known from only few or single sites (e.g., lineages 8, 11, 12, 13, 14, 15, 16) occur in the Andean foothills or on mountain slopes. Nevertheless, in the Andean area, a higher sampling density is needed before it can be concluded with certainty that those lineages are restricted to small ranges. Hence, the distribution of mitochondrial lineages in the D. minutus group indicate that in open lowland areas of South America, small-sized species of anurans can be widespread.
Gehara M, Crawford AJ, Orrico VGD, Rodríguez A, Lötters S, et al. (2014) High Levels of Diversity Uncovered in a Widespread Nominal Taxon: Continental Phylogeography of the Neotropical Tree Frog Dendropsophus minutus. PLoS ONE 9(9): e103958. doi:10.1371/

Monday, October 13, 2014

Biodiversity hotspots produced multiple events

Over 90 percent of the more than 700 species of reptiles and amphibians that
live in Madagascar, like the jeweled chameleon (Furcifer campani) shown
here, occur nowhere else on Earth. A study of how Madagascar's unique
biodiversity responded to environmental fluctuations in the past suggests that
the climate change and deforestation that the island is experiencing today
will have varying effects on different species. Photo credit: Jason L. Brown.
No single "one-size-fits-all" model can explain how biodiversity hotspots come to be, finds a study of more than 700 species of reptiles and amphibians on the African island of Madagascar.

By analyzing the geographic distribution of Madagascar's lizards, snakes, frogs and tortoises, an international team of researchers has found that each group responded differently to environmental fluctuations on the island over time.

The results are important because they suggest that climate change and land use in Madagascar will have varying effects on different species, said Jason Brown of the City College of New York.
"It means that there won't be a uniform decline of species -- some species will do better, and others will do worse," said Brown, a co-author on the study appearing online in the journal Nature Communications.

The study is part of a larger body of research aimed at identifying the climate, geology and other features of the environment that help bring new species of plants and animals into being in an area, and then sustain once they're there.

Located 300 miles off the southeast coast of Africa, the island of Madagascar is a treasure trove of unusual animals, about 90 percent of which are found nowhere else on Earth. Cut off from the African and Indian mainlands for more than 80 million years, the animals of Madagascar have evolved into a unique menagerie of creatures, including more than 700 species of reptiles and amphibians -- snakes, geckos, iguanas, chameleons, skinks, frogs, turtles and tortoises.

Visitors to the island may come across neon green geckos that can grow up to a foot in length, and tiny tree frogs that secrete toxic chemicals from their skin and come in combinations of black and iridescent blue, orange, yellow and green. They'll also find about half of the world's chameleons -- lizards famous for their bulging eyes, sticky high-speed tongues and ability to change color.

Researchers have long sought to understand how Madagascar -- a country that makes up less than 0.5 percent of the Earth's land surface area -- gave rise to so many unusual species.

Previous studies have linked the distribution of species to various factors, such as steep slopes that fuel diversity by creating a range of habitats in a small area. But few studies have integrated all of these variables into a single model to examine the relative influence of multiple factors at once, Brown said.

He and Duke University biologist Anne Yoder and colleagues developed a model that combines the modern distributions of 325 species of amphibians and 420 species of reptiles that live in Madagascar today with historical and present-day estimates of topography, rainfall and other variables across the island.

From steep tropical rainforests to flat, desert-like regions, the researchers analyzed three measures of biodiversity: the number of species, the proportion of unique species and the similarity of species composition from one site to another.

"Not surprisingly, we found that different groups of species have diversified for different reasons," Yoder said.

For example, changes in elevation -- due to the mountains, rivers and other features that shape the land -- best predicted which parts of the island had high proportions of unique tree frog species. But the biggest influence on why some areas had higher proportions of unique leaf chameleons was climate stability through time.

"What governs the distribution of, say, a particular group of frogs isn't the same as what governs the distribution of a particular group of snakes," Brown said. "A one-size-fits-all model doesn't exist."
Understanding how species distributions responded to environmental fluctuations in the past may help scientists predict which groups are most vulnerable to global warming and deforestation in the future, or which factors pose the biggest threat.

Other studies have found that some of Madagascar's reptiles and amphibians are already moving up to higher elevations due to climate change, and roughly 40 percent of the country's reptile species are threatened with extinction due to logging and farming in their forest habitats.

The difficulty of using this model to predict species' responses is that the environmental fluctuations the researchers examined occurred over tens of thousands of years, whereas the changes in climate and land use that Madagascar is currently experiencing are taking place over a matter of decades, said Brown, who was a postdoctoral research associate at Duke at the time of the research.

Making accurate predictions about the threat of future extinction requires determining the timescales at which current environmental changes pose a threat.

"One of the lessons learned is that when trying to assess the impacts of future climate change on species distribution and survival, we have to deal in specifics rather than generalities, since each group of animals experiences its environment in a way that is unique to its life history and other biological characteristics," Yoder said.

Brown JL, Cameron A, Yoder AD, Vences M. 2014. A necessarily complex model to explain the biogeography of the amphibians and reptiles of Madagascar. Nature Communications, 2014; 5: 5046 DOI: 10.1038/ncomms6046

Thursday, October 9, 2014

Rattlesnakes & Robotic Tech

Top. A sidewinder. Bottom A robot model.
The amazing ability of sidewinder snakes to quickly climb sandy slopes was once something biologists only vaguely understood and roboticists only dreamed of replicating. By studying the snakes in a unique bed of inclined sand and using a snake-like robot to test ideas spawned by observing the real animals, both biologists and roboticists have now gained long-sought insights.

In a study published in the October 10 issue of the journal Science, researchers from the Georgia Institute of Technology, Carnegie Mellon University, Oregon State University, and Zoo Atlanta report that sidewinders improve their ability to traverse sandy slopes by simply increasing the amount of their body area in contact with the granular surfaces they’re climbing.
As part of the study, the principles used by the sidewinders to gracefully climb sand dunes were tested using a modular snake robot developed at Carnegie Mellon. Before the study, the snake robot could use one component of sidewinding motion to move across level ground, but was unable to climb the inclined sand trackway the real snakes could readily ascend. In a real-world application – an archaeological mission in Red Sea caves – sandy inclines were especially challenging to the robot.
However, when the robot was programmed with the unique wave motion discovered in the sidewinders, it was able to climb slopes that had previously been unattainable. The research was funded by the National Science Foundation, the Army Research Office, and the Army Research Laboratory.
“Our initial idea was to use the robot as a physical model to learn what the snakes experienced,” said Daniel Goldman, an associate professor in Georgia Tech’s School of Physics. “By studying the animal and the physical model simultaneously, we learned important general principles that allowed us to not only understand the animal, but also to improve the robot.”
The detailed study showed that both horizontal and vertical motion had to be understood and then replicated on the snake-like robot for it to be useful on sloping sand.
“Think of the motion as an elliptical cylinder enveloped by a revolving tread, similar to that of a tank,” said Howie Choset, a Carnegie Mellon professor of robotics. “As the tread circulates around the cylinder, it is constantly placing itself down in front of the direction of motion and picking itself up in the back. The snake lifts some body segments while others remain on the ground, and as the slope increases, the cross section of the cylinder flattens.”
At Zoo Atlanta, the researchers observed several sidewinders as they moved in a large enclosure containing sand from the Arizona desert where the snakes live. The enclosure could be raised to create different angles in the sand, and air could be blown into the chamber from below, smoothing the sand after each snake was studied. Motion of the snakes was recorded using high-speed video cameras which helped the researchers understand how the animals were moving their bodies.
“We realized that the sidewinder snakes use a template for climbing on sand, two orthogonal waves that they can control independently,” said Hamid Marvi, a postdoctoral fellow at Carnegie Mellon who conducted the experiments while he was a graduate student in the laboratory of David Hu, an associate professor in Georgia Tech’s School of Mechanical Engineering. “We used the snake robot to systematically study the failure modes in sidewinding. We learned there are three different failure regimes, which we can avoid by carefully adjusting the aspect ratio of the two waves, thus controlling the area of the body in contact with the sand.”
Limbless animals like snakes can readily move through a broad range of surfaces, making them attractive to robot designers.
"The snake is one of the most versatile of all land animals, and we want to capture what they can do," said Ross Hatton, an assistant professor of mechanical engineering at Oregon State University who has studied the mathematical complexities of snake motion, and how they might be applied to robots. "The desert sidewinder is really extraordinary, with perhaps the fastest and most efficient natural motion we've ever observed for a snake."
Many people dislike snakes, but in this study, the venomous animals were easy study subjects who provided knowledge that may one day benefit humans, noted Joe Mendelson, director of research at Zoo Atlanta.
“If a robot gets stuck in the sand, that’s a problem, especially if that sand happens to be on another planet,” he said. “Sidewinders never get stuck in the sand, so they are helping us create robots that can avoid getting stuck in the sand. These venomous snakes are offering something to humanity.”
The modular snake robot used in this study was specifically designed to pass horizontal and vertical waves through its body to move in three-dimensional spaces.  The robot is two inches in diameter and 37 inches long; its body consists of 16 joints, each joint arranged perpendicular to the previous one.  That allows it to assume a number of configurations and to move using a variety of gaits – some similar to those of a biological snake.
“This type of robot often is described as biologically inspired, but too often the inspiration doesn’t extend beyond a casual observation of the biological system,” Choset said. “In this study, we got biology and robotics, mediated by physics, to work together in a way not previously seen.”
Choset’s robots appear well suited for urban search-and-rescue operations in which robots need to make their way through the rubble of collapsed structures, as well as archaeological explorations. Able to readily move through pipes, the robots also have been tested to evaluate their potential for inspecting nuclear power plants from the inside out.
For Goldman’s team, the work builds on earlier research studying how turtle hatchlings, crabs, sandfish lizards, and other animals move about on complex surfaces such as sand, leaves, and loose material. The team tests what it learns from the animals on robots, often gaining additional insights into how the animals move.
“We are interested in how animals move on different types of granular and complex surfaces,” Goldman said. “The idea of moving on flowing materials like sand can be useful in a broad sense. This is one of the nicest examples of collaboration between biology and robotics.”
Note you can see video of the snakes and robots inaction on several websites. Try this one.
Hamidreza Marvi, Chaohui Gong, Nick Gravish, Henry Astley, Matthew Travers, Ross L. Hatton,Joseph R. Mendelson III, Howie Choset, David L. Hu, and Daniel I. Goldman. 2014. Sidewinding with minimal slip: Snake and robot ascent of sandy slopes. Science  2014: 346 (6206), 224-229. [DOI:10.1126/science.1255718]

Monday, October 6, 2014

Australia sea snakes and the absence of Laticauda

Hydrophis czeblukovi a species found in Australian waters.
Globally there are about 70 species of sea snake (aquatic elapids, in the subfamilies Hydrophiinae and Laticaudinae), inhabiting tropical and subtropical waters of the Indian Ocean and the Pacific Ocean, from the east coast of Africa in the west to the Gulf of Panama in the east. Most species occur in the Indo-Malayan Archipelago, the China Sea, Indonesia, and the Australian region. The viviparous sea snakes (Hydrophiinae) originated in Australia, having descended from the country’s endemic front-fanged terrestrial hydrophiine snakes. The group has since radiated in shallow water marine habitats throughout the Indo-Pacific, with 62 recognized species in 7 genera. However, Australia supports the highest recorded diversity and endemism, with more than 35% of the described viviparous sea snake species recorded from its waters and five nationally endemic species: Aipysurus apraefrontalis, A. foliosquama, A. fuscus, Ephalophis greyae, and Hydrophis donaldi. Over the last 50 years 8 new species have been described from or adjacent to Australian waters, but large areas still remain much understudied. The addition of further species must be expected as the geographical ranges of existingspecies remain unknown and some of the published studies lack comprehensive review. The taxonomy of the  Australian sea snake species has been debated for the last 50 years without consensus being reached. However, a recent phylogenetic study using six molecular loci for 39 sea snake species in 15 genera recovered Hydrophis as broadly paraphyletic with respect to several other genera. Instead of erecting multiple new genera, the authors recommended dismantling the mostly monotypic genera Pelamis, Enhydrina, Astrotia, Thalassophina, Acalyptophis, Kerilia, Lapemis and Disteira, and recognizing a single genus, Hydrophis, for these taxa. This classification system avoids confusion and better reflects the history of the recent and very rapid diversification of these snakes.

In a recently published paper Rasmussen and colleagues present an updated reviewed checklist and a new complete identification key to sea snakes in Australian waters. The identification key includes 29 documented species and four species of questionable occurrence. The authors report no evidence for breeding populations of Laticauda in Australian waters, but include the genus on the list of possibly occurring taxa.

The countries around Australia have at least six Laticauda species. In the literature two species are reported from Australian waters: L. colubrina and L. laticaudata. At least 3 specimens of L. colubrina are deposited in the Australian Museum, Sydney. Three of the localities are in New South Wales and suggests the specimens are waifs, one is from inland western Victoria (the desert town Northern Hill) indicating an error. At least three Australian specimens of L. laticaudata are deposited in museum collections, one in BMNH: from Tasmania, one in ZMUC: 66265 from Sydney and one in Museum Victoria, Melbourne 60287 from Torres Strait also indicating waif specimens. The authors found no further specimens reported from Australia suggesting Laticauda is not breeding in Australian waters despite breeding populations in surrounding countries. A previous author suggested that competition from the Aipysurus species might, at least in part, be responsible for the rarity of Laticauda in Australian waters. And another author suggested that it may be due to the absence of coastal limestone rocks in northern Australia which is the preferred sheltering and egg-laying sites for these species. Further investigation in the northern part of coastal Australia is much needed before we can include Laticauda in the checklist; however, Laticauda sp. is included in the possible list.


Rasmussen RA., Sanders KL, Guinea ML, Amey AP. (2015). Sea snakes in Australian waters (Serpentes: subfamilies Hydrophiinae and Laticaudinae)—a review with an updated identification key. Zootaxa 3869 (4): 351–371.