Friday, September 30, 2011

Which Species Will Survive Climate Change?

The speckled back salamander, one 
of the species studied could expand its current 
range (orange) into new territory (gray). 
Climate change, however will put new areas 
beyond the salamanders reach. Illustration 
Credit: Sax Lab, Brown University.

PROVIDENCE, R.I. [Brown University] — Species' ability to overcome adversity goes beyond Darwin's survival of the fittest. Climate change has made sure of that. In a new study based on simulations examining species and their projected range, researchers at Brown University argue that whether an animal can make it to a final, climate-friendly destination isn't a simple matter of being able to travel a long way. It's the extent to which the creatures can withstand rapid fluctuations in climate along the way that will determine whether they complete the journey.
   In a paper in Ecology Letters, Regan Early and Dov Sax examined the projected "climate paths" of 15 amphibians in the western United States to the year 2100. Using well-known climate forecasting models to extrapolate decades-long changes for specific locations, the researchers determined that more than half of the species would become extinct or endangered. The reason, they find, is that the climate undergoes swings in temperature that can trap species at different points in their travels. It's the severity or duration of those climate swings, coupled with the given creature's persistence, that determines their fate.
   "Our work shows that it's not just how fast you disperse, but also your ability to tolerate unfavorable climate for decadal periods that will limit the ability of many species to shift their ranges," said Sax, assistant professor of biology in the Department of Ecology and Evolutionary Biology. "As a consequence, many species that aren't currently of conservation concern are likely to become endangered by the end of the century."
   The researchers chose to study frogs, salamanders, and toads because their living areas are known and their susceptibility to temperature changes has been well studied. Based on that information, they modeled the migratory paths for each creature, estimating their travels to be about 15 miles per decade. The climate models showed fluctuations in temperatures in different decades severe enough that four creatures would become extinct, while four other species would become endangered at the least. The other seven would "fare OK," Early said, "but they all lose out a lot."
   The temperature swings can cause a species to be stopped in its tracks, which means that it has to do double time when the climate becomes more favorable. "Instead of getting warmer, it can get cooler," said Early, the paper's lead author, of the climate forecasts. "That means that species can take two steps forward, but may be forced to take one step backward, because the climate may become unsuitable for them. Unfortunately, if they take a step back, they have to make up all of that ground. That's what causes the gaps in the climate path."
   The study is unique also in that it considers at species' ability to weather adverse intervals. Early and Sax said unfavorable climate lasting a decade would put the species in a bind. If the interval lasted two decades or more, it was likely the species would become extinct. "We've identified one critical piece of information that no one's really thought about, and that is what's the ability of species to persist under non-optimal conditions," Sax said. "If you move to those conditions, can it hang on for a while? The answer will vary for different species."
   Rapid changes to climate already being witnessed underscores the study's value. A growing number of scientists believe climate change is intensifying so quickly that the planet is hurtling toward a sixth mass extinction in history — and the first widespread perishing of creatures since the dinosaurs' reign ended some 65 million years ago. For the first time, species are grappling not just with projected temperatures not seen for the last 2 million years but also with a human-shaped landscape that has compromised and fragmented animals' natural habitats.
   Confronted with these realities, Early and Sax say wildlife managers may need to entertain the idea of relocating species, an approach that is being hotly debated in conservation circles. "This study suggests that there are a lot of species that won't be able to take care of themselves," Sax said. "Ultimately, this work suggests that habitat corridors will be ineffective for many species and that we may instead need to consider using managed relocation more frequently than has been previously considered."

Citation
Early, R. and Sax, D. F. (2011), Analysis of climate paths reveals potential limitations on species range shifts. Ecology Letters. doi: 10.1111/j.1461-0248.2011.01681.x

New Frog Added to Trinidad's Herpetofauna

Scarthyla vigilans from southwest Trinidad. JCM
The tiny, grass-dwelling frog, Scarthyla vigilans (Hylidae) has been officially added to the herpetofauna of Trinidad. The frog avoided detection of previous researchers investigating the fauna of the continetal island until 2006 when J. Roger Downie and Joanna M. Smith collected striped tadpoles from an irrigation ditch in a coconut plantationin the southwest peninsula of the island. The tadpoles positioned themselves vertically in the water adjacent to submerged grass stems.The tadpoles did not match any of the known species from Trinidad.The tads weighed only 0.26 g and measured about 29 mm. Two adults were collected in 2007, and more were added in 2010. The frogs were discovered in Venezuela's Orinoco Delta in 2008, but the species was previously known from northeast Colombia and northwest Venezuela. The small size (14-19 mm) of adults, their very insect-like call, and their superficial similarity to the very common and widespread Scinax rubra has contributed to them going undiscovered. The full paper is available on-line.

Citation
Smith, J.M.; J.R. Downie; R.F. Dye; V. Ogilvy; D.G. Thornham; M.G. Rutherford; S.P. Charles; J.C. Murphy.2011. Amphibia, Anura, Hylidae, Scarthyla vigilans (Solano, 1971): Range extension and new country record for Trinidad, West Indies, with notes on tadpoles, habitat, behavior and biogeographical significance. Check List 7(5):574-577.

Thursday, September 29, 2011

Australian Tree Frogs Collect Condensation for Hydration

Research published in the October issue of The American Naturalist shows that Australian green tree frogs survive the dry season with the help of the same phenomenon that fogs up eyeglasses in the winter.

Christopher R. Tracy and colleagues found the Australian Green Treefrog, Litoria caerulea, remain active during the dry season with apparently no available water and at temperatures that approach their lower critical temperature. The authors hypothesized that when the frogs retreated to their refugia condensation forms on their cold skin — just like it does on a eye glasses or the widows of your car.  They used frogs retrieved from natural dens and artificial dens and found the frogs absorb the condensing moisture through their skin, to maintain hydration during periods of little or no rain.

Before this study, the frogs' dry-season excursions were a bit mysterious.

"Every once in a while, we would find frogs sitting on a stick under the open sky, on nights when it was so cold they could barely move," said Dr. Chris Tracy, who led the research. "It was a real puzzle."

Tracy and his colleagues thought this behavior might enable the frogs collect condensation, but the hypothesis had never been tested.

The researchers designed a series of experiments using real frog dens in eucalyptus trees and artificial ones made from PVC pipe. They wanted to see if the frogs could collect enough moisture through condensation to compensate for what they lost being in the cold. They found that a cold night out cost a frog as much as .07 grams of water. However, a frog could gain nearly .4 grams, or nearly 1 percent of its total body weight, in water upon returning to the warm den.

The researchers also tested how well a frog's skin could absorb water, and found that as much as 60 percent of each water drop could be absorbed.

The results show that frogs can use condensation to hydrate themselves. And in a place as arid as the Australian savannahs during the dry season, where there is essentially no rain from June through August, every little bit counts.

"When there's no water available, even a small amount can mean the difference between surviving the dry season or not," Tracy said.

Citation
Christopher R. Tracy, Nathalie Laurence, Keith A. Christian, 2011, Condensation onto the Skin as a Means for Water Gain by Tree Frogs in Tropical Australia." The American Naturalist 178:553-558.(October 2011)

Tuesday, September 27, 2011

MHC Genes Convey Resistance to Bd in Some Frogs

The BBC Science and Nature News is carrying this story by Richard Black. It comments on Bd research done at Cornell University by Anna E. Savage and Kelly R. Zamudio in an attempt to discover how amphibian populations might be best able to fight off the Bd fungus.

'Scientists have taken a big step toward understanding why some frogs survive the fungal disease chytridiomycosis while others quickly die.

A group from Cornell University, US, identified genetic factors that seem to make some individual frogs immune.

This could improve captive breeding schemes, the team writes in Proceedings of the National Academy of Sciences.

Chytridiomycosis is slowly spreading across the world, and has already sent a number of species extinct.

Just two years ago, researchers discovered how it kills - by damaging the skin so that key nutrients cannot pass through, resulting eventually in cardiac arrest.

Frogs and other amphibians that have no resistance succumb quickly, with some populations being extirpated in just a few weeks.

Yet some populations and some entire species survive intact, which has long perplexed researchers; and salamanders and caecilians (limbless amphibians bearing a superficial resemblance to earthworms or snakes) appear more resistant as groups than frogs - another mystery.


The Cornell group collected lowland leopard frogs (Lithobates yavapaiensis) from five places in Arizona.

"The study goes a long way toward understanding the genetic basis of resistance to the amphibian chytrid”

Reid Harris, James Madison University

In the lab, they infected the animals with the chytrid fungus (Batratochytrium dendrobatidis, or Bd).

All the frogs collected from three of the locations died; but from the other two locations, some survived, and fought off the infection completely within two weeks, remaining healthy.

The researchers traced the difference back to regions of DNA that form part of the immune system called the major histocompatibility complex (MHC).

Its role - in humans and other animals, just as in amphibians - is to "present" bits of invaders such as fungi or bacteria to other immune cells, identifying them as things that must be tackled.

"All amphibians (and for that matter, all vertebrate animals) have MHC genes that play the same 'gatekeeper' role in initiating immune responses," said lead researcher Anna Savage.

"So our finding that MHC genotypes contribute to chytridiomycosis outcomes has potential ramifications for all amphibian species currently threatened by Bd."

It appears likely that the two populations whose members survived infection in the lab are the ones that had been most strongly exposed to the fungus in the wild since it was detected in Arizona in the 1970s.

In this case, they probably carry the "resistant genes" because there has already been quite a lot of selection - only the strong have survived.

"It means frogs may have the evolutionary potential to adapt [to Bd]," Ms Savage told BBC News.

"Natural selection can only result in disease adaptation if genetic variation for that trait exists, and we have shown that it does."

The next step along this avenue of research is to find out whether the same thing provides immunity in other species - and whether it can explain why entire species such as the infamous cane toad survive Bd.

Then, conservationists will have to work out how the information can be used.

Ms Savage suggests a role in captive breeding programmes - the last resort for species that cannot remain in their native habitat because it is infested with chytrid.

Chytridiomycosis can kill amphibians in less than a week - depending on their genes
The idea would be to screen amphibians' MHC genes before breeding, to increase the odds of producing Bd-resistant tadpoles.

Prof Reid Harris, an amphibian specialist at James Madison University in Virginia who is trying to develop new treatments for chytrid, described the latest news as "very exciting".

"The study goes a long way toward understanding the genetic basis of resistance to the amphibian chytrid, and it opens up the possibility of selecting for resistance to the disease," he told BBC News.

"However, amphibian defences are multidimensional and include innate immune components and microbial defences.

"It is likely that a successful mitigation strategy will be multidimensional as well."

However, chytrid is only one of the many threats that amphibians face today.

The most profound is loss of habitat, as marshes are drained, forests cleared, and wild areas tamed for human use.

"Although our study provides a new hope that amphibians may bounce back from chytridiomycosis, it does not eliminate the need for human conservation efforts," Ms Savage stressed.

"Habitat loss, invasive species and habitat degradation are other major factors leading to amphibian declines; and if we can work to provide good habitats so that amphibian population sizes and genetic diversity can increase, they will be much more likely to have the genetic capacity to adapt to Bd."

Citation
Anna E. Savage and Kelly R. Zamudio 2011. MHC genotypes associate with resistance to a frog-killing fungus.PNAS Published online before print September 26, 2011, doi: 10.1073/pnas.1106893108

Ascension Island Sea Turtle Eggs Pre-Adapted For Warmer Temperatures

Photo Credit: Dr Sam Weber, University of Exeter
Ascension Island is one of those remarkable places on the Earth that serves as a reminder as to how the earth is constantly changing. The island sits on the mid-Atlantic Ridge. The place where the sea floor is being formed in the middle of the Atlantic and a point where Africa and South America were once joined to form the ancient continent of Gondwanaland. Today, the tiny island is used by diplomats, tourists, and most importantly sea turtles. The following is a press release about recent research on the island's sea turtles. The full article is available on-line.

Heat-proof' eggs help turtles cope with hot beaches 

Sea turtles face an uncertain future as a warming climate threatens to reduce their reproductive viability. However, new research led by the University of Exeter and published this week in Proceedings of the Royal Society B shows that some turtles are naturally heat-tolerant.

The study focused on green turtles nesting on Ascension Island, a UK overseas territory in the South Atlantic Ocean. Scientists from the Universities of Exeter and Groningen found that eggs laid by turtles nesting on a naturally hot beach withstand high temperatures better than eggs from turtles nesting on a cooler beach just a few kilometres away.
The warmer beach has dark sand, whereas the neighbouring beach is two to three degrees Celsius cooler because it has white sand. Green turtles travel from the coast of South America to the tiny island to nest. Most female turtles nest on the beaches where they themselves hatched, so populations can become adapted to specific nesting locations.

The researchers placed some of the eggs laid on each beach into incubators of either 32.5 degrees Celsius or 29 degrees Celsius and monitored their progress. They found that the eggs from the warmer beach were better able to thrive in the hot incubator than those from the cooler beach.

Dr Jonathan Blount, who led the research, said: "We believe this is the first time that adaptation to local environmental conditions has been demonstrated in sea turtles, which is all the more remarkable because the beaches in question are just six kilometres apart".

Heat-tolerant populations may be crucial in allowing species to adapt to a warming world, highlighting the need for conservation strategies which protect diversity in animal populations.

University of Exeter PhD student Dr Sam Weber, lead author of the study, said: "Such adaptations probably evolve over many generations, so whether turtle evolution can keep pace with the rapid climate change that scientists have predicted remains to be seen. However, occasional movements of heat-adapted turtles to other nesting sites could help to spread their favourable genes."

This research was funded by the Natural Environment Research Council, the Royal Society, the European Social Fund, Defra's Darwin Initiative and the Overseas Territories Environment Programme.

Citation

Sam B. Weber, Annette C. Broderick, Ton G. G. Groothuis, Jacqui Ellick, Brendan J. Godley, and Jonathan D. Blount 2011.Fine-scale thermal adaptation in a green turtle nesting population. Proc. R. Soc. B published online before print September 21, 2011, doi:10.1098/rspb.2011.1238

Sunday, September 25, 2011

Novel Squamates

In the 1970's I remember several conversations with zoo curators and reptile keepers who swore female snakes would give birth to offspring without ever being in the presence of a male or if they had been with a male it had been years before the offspring/eggs developed. The latter situation was often attributed to sperm storage. At the time, I was skeptical, but parthenogenesis was known in lizards since Ilya Darevsky discovered all female rock lizard, Lacerta saxicola, populations in 1958 in southern Russia. L. saxicola (Eversmann, 1834) has now been removed from Lacerta and placed in the genus Darevskia, with about 25 other species of rock lizards, the generic name derived from the name of the Russian herpetologist. But, four decades later parthenogenesis has been documented in many squamates, and it has apparently evolved at least 40 times independently. 
Squamate reptiles (lizards + snakes) are both numerous and diverse with 61 families and more than 9000 species. With the diversity come novel traits that have evolved multiple times - like parthenogenesis. In a forthcoming paper Sites et al. (2011) summarize many of these novel traits in squamates - traits like parthenogenetic, viviparity, limb-reduction and limb loss, herbivory, and venom. The authors note that squamates are the only vertebrate group with true parthenogenesis; the clade has more origins of viviparity than any other group of vertebrates; and squamates have undergone dramatic changes in body form (lizard-like to snake-like) dozens of times.

They also note that new phylogenetic hypotheses are challenge our ideas about squamate biology and are emerging at all taxonomic levels. Phylogeny based research is revealing much about ecological aspects of of parthenogenesis as well as finer details about the origins of several forms of viviparity.

Citation
Sites, J. W., Jr, T. W. Reeder, J. J. Wiens. 2011. Phylogenetic Insights on Evolutionary Novelties in Lizards and Snakes: Sex, Birth, Bodies, Food, and Venom. Annual Review of Ecology, Evolution, and Systematics, DOI: 10.1146/annurev-ecolsys-102710-145051

Thursday, September 22, 2011

Diverse Ecosystems May Reduce Threat From Bd

The Western Toad, Anaxyrus boreas.

Photo Credit: Ivan Phillipsen, OSU

The following is a press release from Oregon State University.

CORVALLIS, Ore. – Researchers at Oregon State University have shown for the first time that loss of biodiversity may be contributing to a fungal infection that is killing amphibians around the world – a finding that provides more evidence for why biodiversity is important to many ecosystems.

The research, being published this week in Proceedings of the National Academy of Sciences, used laboratory studies of amphibians to show that increased species richness decreased both the prevalence and severity of infection caused by the deadly chytrid fungus, Batrachochytrium dendrobatidis.

“With greater diversity of species, you get a dilution effect that can reduce the severity of disease,” said Catherine Searle, an OSU zoologist and lead author on the study. “Some species are poor hosts, some may not get infected at all, and this tends to slow disease transmission.

“This has been shown in other systems like Lyme disease which infects humans, mice and deer,” she said. “No one has really considered the dilution effect much in amphibians, which are experiencing population declines throughout the world. It’s an underappreciated value of biodiversity.”

It’s generally accepted, the researchers said, that a high diversity of species can protect ecosystem function, help to recycle nutrients, filter air and water, and also protect the storehouse of plant or animal species that may form the basis of medicines, compounds or natural products of value to humans.

Protection against the spread of disease should more often be added to that list, they said.

“Emerging infectious diseases are on the rise in many ecosystems,” said Andrew Blaustein, a co-author on this study, professor of zoology at OSU and leading researcher on the causes of amphibian declines.

“Protection of biodiversity may help reduce diseases,” he said. “It’s another strong argument for why diverse ecosystems are so important in general. And it’s very clear that biodiversity is much easier to protect than it is to restore, once it’s lost.”

The fungus, B. dendrobatidis, can lead to death from cardiac arrest when it reaches high levels in its amphibian hosts. It is not always fatal at lower levels of infection, but is now causing problems around the world. One research team has called the impact of the chytrid fungus on amphibians “the most spectacular loss of vertebrate biodiversity due to disease in recorded history.”

Amphibians face threats from multiple causes, including habitat destruction, pollution, increases in ultraviolet light due to ozone depletion, invasive species, and infectious disease.

The dilution effect can occur in plants and animals, but also in human diseases. In a different report published last year in Nature, researchers noted an increased risk of West Nile encephalitis in the U.S. in areas with low bird diversity. And in more diverse communities, the infection of humans by schistosomiasis – which infects 200 million people worldwide – can be reduced by 25-99 percent.


Citation
Catherine L. Searle, Lindsay M. Biga, Joseph W. Spatafora, Andrew R. Blaustein. A dilution effect in the emerging amphibian pathogen Batrachochytrium dendrobatidis. Proceedings of the National Academy of Sciences, 2011; DOI: 10.1073/pnas.1108490108

Wednesday, September 21, 2011

Where's Waldo, Final Answers


How do you like that, I'm on a computer that allows me to put little colored circles on pictures. Will miracles never cease? (they will if I go back to my old work computer) Makes identifying the area a little easier even if you still can't see the animal.
Best,
Marty

Ok Herpers,

My mommy used to tell me that if I kept playing with myself, I'd go blind.
So, I just did it until I needed glasses. It might be time for some of you to
find another hobby as well.

Marty Feldner got the last two teasers, which are attached.

All the crying that spewed on me as a result of this particular series
has me ready to convert my office into a saltwater aquarium. Would
any of the crabs out there in Suizo-land care to move in?

Sorry guys, but Stevie Wonder could have found that mud turtle.

What I've learned here, besides proper floor-mopping techniques,
is to just send one image at a time. Make the file size larger, and make
sure that at least part of the animal is visible. That way, you guys can cheat easier,
and you don't have to blow up a low resolution image to kingdom come and back while
you cry "foul."

That is my promise to you all for any future Where's Waldo installments.

Meanwhile, good show, Marty! We could use a few more good men like you around here.
HE didn't do any sniveling about it all--he was too busy DOING IT.

Love to all, and really, all in good fun. We'll play nicer from now on.

roger
Ok Herpers,
We're going with attachments with this one, as inserting images makes it harder
for you all to cheat. We don't want to make this any harder than it already is!

Pics 1 and 2: (Original Image #1 and "new" image revealing what and where):
For crying out loud you guys! Look in the little puddle. It's a Sonoran Mud Turtle.
They sometimes choose some very bad places to hide. Congrats to Jeff and Marty
for finding. Circle by Mr. Moorbeck.





Pics 3 and 4: (Original image # 2 and "new" image revealing what and where):
Sonoran Desert Tortoise. Circle by Jeff, Marty was on it as well.





Pics 5 and 6: (Original image #3 w/Jeff Circle added, and a closer look at snake):
Our newest addition to the Suizo Mountain Study, a Mojave Rattlesnake. Note
the heft on this rascal. Despite their reputation of being a nasty snake, this male
is a sweetheart! Honorable mention to Marty as well.





Pics 7 through 9: (Original image 4, plus two more hints).
I'm still not telling you where it is, but the angle of Pic 8 should give
it away. Pic 9 shows how well he hides. What is it, where is it? I do believe
Marty got this one, but couldn't identify the animal.








Pics 10 through 12: (Original image 5, plus 2 hints):
Where and what is the snake in Pic 10? You can't see it in Pic 10,
but Pics 11 and 12 clearly drop a bomb of a hint as to where it is.

Still looking for answers on original image 4 and 5.

One-two-three---GO!







8-) roger

Suizo Report -- Where's Waldo?

Howdy Herpers,

I think it best to send these images out this way.

In order to make the game a little more fair to you all, I removed the original image #3, and replaced it with the original image #6.

There are now 5 images. If you guys don't get 1 through 3 now, it's not my fault.

Images 4 and 5 are just plain mean on my part. I only send these again to show the hot shots that I DO know the difference between hard and easy.
And the second I show a little flank in any images (WOOHOO!), the hot shots will find the animal.

The game for all 5 is still the same. Name it and find it.






Best to all, roger 

Monday, September 19, 2011

Copperhead Bites in Metro-Atlanta

Agkistrodon contortrix. JCM
WSBTX.com Atlanta is reporting an unusual number of bites from Copperheads (Agkistrodon controtrix) for this year.

ATLANTA -- Bill Murray was in the pool behind his Buckhead home when he encountered a copperhead snake, and he’s not alone this summer. Doctor’s at Atlanta’s Piedmont Hospital tell Channel 2’s Diana Davis they have seen an unusual amount of snake bites this year. The snakes are not aggressive, but experts say the shy snakes can bite when someone invades their turf. “I felt a sharp excruciating pain,” Murray told Davis. Brandon Berk lives about a mile from Murray. He was bit while cleaning out the gutters of his home. "I felt a sting on my finger and I looked up and saw two fang marks,” Berk said. “I’ve seen snakes but was not expecting that, especially not in Buckhead.” Herpetologists at Zoo Atlanta say copperhead snakes are common in metro Atlanta. More than 200 bites have been reported to the Georgia Poison Control so far this year.“There’s not as much water out there. They’re trying to find water. We’re watering our lawns and we have standing water around and they’re trying to find that,” Dr. Brad Lock of Zoo Atlanta told Davis. Lock said copperhead snakes often thrive in brushy areas and woodpiles. Piedmont Hospital has treated six patients for copperhead bites this year. Not all patients need anti-venom but everyone needs quick emergency care, doctors said. “The best thing to do is call 911. Don’t raise your leg. Don’t lower your leg. Keep it level with your body. Try to remain calm, that will prevent the blood from circulating too quickly,” Dr. Henry Siegelson said. The best prevention against snake bites can be clearing away brush in your yard and wearing gloves. Don’t stick your hand in a wood pile without checking it first with a rake or shovel. Copperhead bites are rarely deadly but the treatment can be lengthy and expensive. Berk said his treatment included six vials of anti-venom and two nights in the hospital.

The Moluccan Short-tailed Snakes - The Most Basal Homalopsids

The Moluccan Short-tailed Snakes of the genus Brachyorrhos are poorly-known, terrestrial–fossorial snakes that eat worms and are endemic to eastern Indonesia. During the past 200 years the snakes in this genus have been assigned to at least six different families. In 1987 Samuel McDowell suggested that they may be homalopsids. This seemed unlikely- homalopsids are aquatic, they eat fish, crustaceans, and frogs; homalopsids also have enlarged grooved fangs on the rear of the maxillary bone, and none of the known species have a rostral scale that separates the nasal scales. However, in my 2007 book, Homalopsid Snakes, Evolution in the Mud, I listed the genus as being of uncertain status. In a recent paper, Murphy et al. (2011) recovered the first molecular sequences for Brachyorrhos and tested the position of the genus within snake phylogeny. Bayesian and Maximum Likelihood analyses of three mitochondrial and one nuclear gene strongly resolve Brachyorrhos within the rear-fanged semi-aquatic family Homalopsidae, as the sister to all other genera and sampled species. Thus, Brachyorrhos makes an excellent model for a possible ancestor of the homalopsids, an ancestor that was terrestrial-fossorial and fang-less and produced decedents that evolved aquatic lifestyles, rear-fangs, and fish-crustacean diets.

Murphy, J. C., Mumpuni, K. L. Sanders. 2011 (in press). First molecular evidence for the phylogenetic placement of the enigmatic snake genus Brachyorrhos (Serpentes: Caenophidia)  Molecular Phylogenetics and Evolution, doi:10.1016/j.ympev.2011.08.013.

Saturday, September 17, 2011

Good News For Sea Turtles

A Loggerhead Sea Turtle (Carretta caretta). 
Photo credit Brian Gratewicke
The following is a press release from Duke University.

DURHAM, NC - The number of sea turtles accidentally caught and killed in fishing gear in United States coastal waters has declined by an estimated 90 percent since 1990, according to a new study by researchers at Duke University Project GloBAL and Conservation International.

The report, published in the scientific journal Biological Conservation, credits the dramatic drop to measures that have been put into place over the last 20 years to reduce bycatch in many fisheries, as well as to overall declines in U.S. fishing activity.

The study's authors estimate that 4,600 sea turtles die each year in U.S. coastal waters.

Before measures to reduce bycatch were put in place, total sea turtle takes surpassed 300,000 annually. Of these, 70,000 turtles were killed.

The study used data collected from 1990 to 2007 by the National Marine Fisheries Service (NMFS) to determine bycatch rates across more than 20 fisheries operating in Atlantic waters from the Gulf of Mexico to the Canadian border, and in the Pacific Ocean, along the West coast and around Hawaii.

It found that overall turtle bycatch rates, including both fatal and nonfatal run-ins, have fallen about 60 percent since 1990.

Shrimp trawls in the Gulf of Mexico and southeastern U.S. accounted for up to 98 percent of all by-catch takes and deaths during the study period.

All six marine turtle species that occur in U.S. waters are categorized as threatened or endangered on the U.S. Endangered Species List. They are loggerheads, leatherbacks, hawksbills, olive ridleys, Kemp's ridleys and green sea turtles.

Bycatch is an acute threat to sea turtle populations worldwide. High bycatch rates can be indicative of unsustainable fishing practices that negatively impact the health of marine ecosystems.

"The reduction of bycatch and mortality shows important progress by NMFS, which serves as a model for reducing sea turtle bycatch in other parts of the world," says Elena Finkbeiner, a PhD student at Duke and lead author of the paper. "Our findings show that there are effective tools available for policymakers and fishing industries to reduce sea turtle bycatch, as long as they are implemented properly and consistently."
Among the mitigation strategies that have helped reduce bycatch are: the use of circle hooks and dehooking equipment in longline fisheries, to reduce the severity of turtle injuries; the use of turtle excluder devices (TEDs) in shrimp trawl nets to allow captured sea turtles to escape; and the implementation of time-area closures to restrict fishing activities at times and places turtles are most likely to be present in the highest numbers.

Piecemeal regulation remains a problem, the study notes. Sea turtles are currently managed on a fishery-by-fishery basis, which means that bycatch limits are set for each fishery without accounting for the overall population impacts of all the takes added together. This fragmented approach leads to total allowed takes that exceed what sea turtle populations can sustain.

"Bycatch limits must be set unilaterally across all U.S. fisheries with overall impacts to populations in mind, much as it's done for marine mammals," says co-author Bryan Wallace, director of science for Conservation International's Marine Flagship Species Program and adjunct faculty member at Duke's Nicholas School of the Environment.

The researchers note that actual bycatch rates are likely higher than what the study reports because in many fisheries, particularly the shrimp trawl fishery, the number of on-board observers who document bycatch on fishing vessels is low relative to the sheer volume of fishing that is occurring.

"This paper provides a baseline to examine what is working and what can be improved in preventing sea turtle bycatch," Finkbeiner says. "It (makes) a strong case for the need for increased observer coverage and bycatch reporting."


Citation
Elena M. Finkbeiner, Bryan P. Wallace, Jeffrey E. Moore, Rebecca L. Lewison, Larry B. Crowder, Andrew J. Read. Cumulative estimates of sea turtle bycatch and mortality in USA fisheries between 1990 and 2007. Biological Conservation, 2011; 144 (11): 2719 DOI: 10.1016/j.biocon.2011.07.033

Feathers from Canadian Dinosaurs

A feather trapped in Amber. University of Alberta 
The following is a press release from the University of Alberta.

(Edmonton) Secrets from the age of the dinosaurs are usually revealed by fossilized bones, but a University of Alberta research team has turned up a treasure trove of late Cretaceous feathers, which have been discovered trapped in tree resin.

The resin turned to resilient amber preserving some 80-million-year-old protofeathers, possibly from non-avian dinosaurs, as well as plumage that is very similar to modern birds, including those that can swim under water.

U of A paleontology graduate student Ryan McKellar discovered a wide range of feathers trapped in amber in collections at the Royal Tyrrell Museum and in the private collection of the Leuck family in Medicine Hat.

“Most of the feather specimens were probably blown into contact with the sticky surface of the resin and encapsulated by subsequent resin flows,” said McKellar.

The 11 feather specimens used by the U of A team were all found near the community of Grassy Lake in southern Alberta. The research specimens are described as the richest amber feather find from the late Cretaceous period.

“The amber preserves microscopic detail of the feathers and even their pigment or colour,” said McKellar. “I would describe the colours as typically ranging from brown to black.”

During the late Cretaceous, southern Alberta was a warm coastal region. “The trees that produced the resin were probably comparable to the redwood forests of the Pacific Northwest,” said McKellar.

No dinosaur or avian fossils were found in direct association with the amber feather specimens, but McKellar says comparison between the amber and fossilized feathers found in rock strongly suggest that some of the Grassy Lake specimens are from dinosaurs. The non-avian dinosaur evidence points to small theropods as the source of the feathers.

McKellar says that some of the feather specimens can take on water, enabling the bird to dive more effectively and are very similar to those of modern birds like the Grebe, which are able to swim underwater.

“The preservation of microscopic detail and pigmentation has provided a unique snapshot of feathers and their uses in the late Cretaceous forests of Alberta,” said McKellar.

The U of A team’s research was published Sept. 15, in the journal Science.

Thursday, September 15, 2011

Acherontisuchus guajiraensis Hastings et al. 2011 - A New Fossil Crocodilian

Acherontisuchus may have looked like this in its natural setting. Titanoboa
is shown in the background. Artist credit: Florida Museum of Natural History,
 illustration by Danielle Byerley.
Fossils of dyrosaurid mesoeucrocodylians are known from Africa, Eurasia, North America and South America and distributed from the Late Cretaceous to the late Eocene, a time span of about 65 MYA, and evidence that the clade survived the K-T extinction. Only three South America dryosaurids are known but Hastings et al. (2011) have added another in the last few days - Acherontisuchus guajiraensis from the Cerrejon Formation of northwest Columbia. The new species is based on three partial mandibles, maxillary fragments, teeth, and some postcranial material. Acherontisuchus' morphology suggests it may have may have inhabited slow moving rivers. Most dyrosaurids have been thought to be shallow, near-shore marine inhabitants that use axial swimming that is typical of living crocodilians, but they may have differed from modern species with greater tail undulatory frequency and more powerful forward thrust provided by expanded tail muscles. The authors estimate it was between 4.66 and 6.46 m in adult body length, while Cerrejonisuchus improcerus another dryosaurid that lived at the same locality, at the same time, was only about 2.2 m in length. Cerrejonisuchus had a more generalized bodied and may have preyed upon small vertebrates, while Acherontisuchus was more specialized and the authors suggest it preyed upon dipnoan and elopomorph fishes have been have also been found at the Cerrejon location. Also of interest, these dryosaurids lived at a time and place that was shared with the largest known snake, Titanoboa, a possible predator for both of these dryosaurids. The entire article is available on-line.

Hastings, A.K., Bloch, J. I., & Jaramillo, C.A. (2011). A new longirostrine dyrosaurid (Crocodylomorpha, Mesoeucrocodylia) from the Paleocene of north-eastern Colombia: biogeographic and behavioural implications for New-World Dyrosauridae Palaeontology, 54, 1095-1116.doi10.1111/j.1475-4983.2011.01092.

Global Snake Diversity

Pit vipers, represented by this Ridge-nose Rattlesnake were once thought to 
have evolved quite recently. Now, based on the DNA clock they are estimated 
to have first evolved about 35.6 million years ago. Today there are about 200 
species of pit vipers. But the colubrines evolved about the same time and have 
more than 600 species. In a forthcoming paper Pyron and Burbrink investigate 
why some clades of snakes are species rich, and others are species poor. JCM
Examine the numbers of amphibians and reptiles in various clades and a great disparity is readily apparent. The Lepidosauria (tuataras + (snakes+lizard)) is an excellent example, there are two species of living tuataras, but their sister group the Squamata (lizards+snakes) contains about 9000 species. This is not only true for snakes, salamander species number about 600, while frog species number more than 6000. Ideas to explain these kinds patterns have not been lacking. Species richness has usually been attributed to either the age of the clade (older clades have fewer species due to extinctions) or the rate of diversification (evolution rate of a particular clade) has been constrained by ecological factors, like the number of niches available.

In a forthcoming paper R. Alexander Pyron and Frank Burbrink examine global snake diversity and find it varies by two orders of magnitude in living lineages. Many older lineages contain only one or two species while a few younger clades may contain more than 700 species. They suggest that the patterns cannot be explained by background rates of speciation and extinction. Instead most of the diversity appears to derive from a radiation within the superfamily Colubroidea. After the colubroids evolved they invaded new geography and they evolution advanced venom-delivery systems. Pyron and Burbrink also found negative relationships between clade age, clade size, and the diversification rate suggesting the potential for possible bias in estimated diversification rates. This has been interpreted by some authors as support for ecologically mediated limits on diversity. However, evidence from the fossil record suggests that numerous clades were much more diverse in the past, and that extinction has been an important factor on the diversity patterns of living snakes. Thus, failure to adequately account for extinction appears to prevent both rate- and diversity-limited models from fully characterizing richness dynamics in snakes. The authors suggest that clade-level extinction may provide a key mechanism for explaining negative or hump-shaped relationships between clade age and diversity, and the prevalence of ancient, species-poor lineages in numerous groups.

Citation
Pyron, R. A. and Burbrink, F. T. (2011), Extinction, Ecological Opportunity, and the Orgins of Global Snake Diversity. Evolution doi: 10.1111/j.1558-5646.2011.01437.x

Wednesday, September 14, 2011

Buffer Zones For Snakes in Agricultural Landscapes

The Eastern Garter Snake, Thamnophis sirtalis. JCM
Roadside shoulders covered with vegetation, and gallery vegetation growing along streams that run through agricultural fields can act as buffers and corridors for wildlife. These linear strips of habitat are all that remains for hundreds of thousands of square miles that have been turned into the breadbasket for America. Land management agencies in the United States promote conservation buffer strips as beneficial to wildlife populations but little is known about how snake use these habitats, Knoot and Best (2011) evaluated the influence of buffer design, management, and surrounding landscape characteristics on snake occurrence in gallery grasslands along waterways in southeastern Iowa. They documented snakes in about 80% of the areas and captured 119 individuals representing five species (Storeria dekayi, Thamnophis sirtalis, Thamnophis radix, Liochlorophis (=Opheodrys) vernalis, Elaphe (=Pantherophis) vulpina). The Smooth Green Snake (Liochlorophis vernalis), is listed as a species of concern in Iowa. The width of the waterway was the best predictor of snake presence for three of the five species. The Plains Garter Snake was most often in grass-lined waterways farther from wooded habitat; a finding that is consistent with the observation that Plains Garter Snakes are more often found in open habitats; while the Smooth Green Snake was more often associated with waterways with greater plant litter cover but the reverse was the habitat most often assocaited with the Eastern Garter Snake. Most research on buffers in agricultural has focused habitat for birds and butterflies, but this project suggests that snakes can also be managed in these narrow buffer zones of habitat. This paper is available on-line.

Citation
Knoot, T. G. and L. B. Best. 2011. A multiscale approach to understanding snake use of conservation buffer strips in an agricultural landscape. Herpetological Conservation and Biology 6:191-201.

Suizo Report -- Where's Waldo?

Ok………… ok, Prima Donnas, 14 Sept 2011

Whatever we’re talking about with this missive will have nothing to do with U-no-what: (prebuttons).

You guys are good-­better than most even. I’ll admit, I underestimated some of you with my little “Where’s Waldo?” games of late. Now we are taking off the kid’s gloves for sure!

I’m going to share six images with the lot of you. Image 1 is easy (if we made it all too hard, none of you crybabies would play any more), image 2 is a little tougher. Image 3 is nearly impossible, images 4 and 5 are, in my estimation, definitely impossible. Image 6 is a hint for the image 3, but a true herper would only look to the hint in image 6 as a last resort.

The beauty of this particular installment of the game is that you all have one week to send me your answers. No need to rush things here. It’s not a matter of being first. It’s a matter of being right. Take your time………..

Come next Wednesday, 21 September 2011, I will tell you all how you did. And I will send you further hints for the ones that didn’t get found (if that happens.)

Are you ready? (That doesn’t matter­EYE am!)

One, two, three……….GO!

Image 1: Find the herp, and tell me what it is. (In the words of my favorite Canadian “Easy Peasy”):

How did you all do with that one? It stands out like goat turds in the milking pail me.

Image 2: Several of you have asked me of late “What does the “Suizo” in the “Suizo Report” mean?” Well, technically, Suizo is “Swiss” in Spanish. The 10+ year Schuett/Repp study occurs in a mountain range in Arizona that is formally named the Suizo Mountains. In this image we see roughly 50% of the Suizo (“Swiss”) Mountains, as viewed from our study hill (Iron Mine Hill). But all that is not the purpose of this image. Somewhere within the framework of this image is a cool herp. Name the species, and indicate the location.

Are you all still with me? Of course you are…….get a life!

Image 3: From me to you-­hot shots! As suggested earlier, this is a tough one, and your only hint in this installment of Where’s Waldo can be found in image 6. But there’s no need to cheat. A few of you are whales amongst minnows. Try to identify the herp in this image, and tell me where it is:

Image 4: One from the land of the impossible! Get this one right, and I’ll truly know it is time to take up stamp collecting. Identify the species, and tell me the location:
Awwwww! Was that too hard, herpers? Cry me a river………
Don’t worry, I’ll give you a hint in a week. Meanwhile, there’s this:

Image 5: Name the herp, and show me the location:
You’ll never get image 5. Don’t hurt yourself. Wait for the hint!

The weather report from the National Weather Service in Tucson reports that this past August was the second “warmest” on record, and the second “warmest” summer on record. When one includes “warmest” in a sentence describing Tucson, Arizona, that really means hotter than the hinges of hell. It has been rough on those of us who endure the rigors of field work­not to mention the herps that have to survive these conditions.

As for me, as a machine shop foreman, I earn my living surrounded by Republican values. When they tell me that this great country of ours was historically successful due to mining, agriculture, ranching, oil drilling and industry, I’m inclined to listen. But when they tell me that global warming has nothing to do with the aforementioned money-making, tax-paying, GNP-building schemes, that’s when I draw the line.

I’ve recently been digging into my own ancestral roots. Briefly, my descendants are Germans whose lineage goes all the way back to Adam and Eve. (Yes, as near as I can fathom, Adam and Eve were Germans). At one point, my ancestors decided they were tired of being Germans confined to Germany, and decided to settle along the Volga River in Russia. (The poor saps had no idea that there was such a place as Arizona.)

Well………….what does one do when one settles into a primitive area, and one has no idea what to do next? Chopping down trees for housing and fuel with reckless abandon occurred to them. Plowing fields, raising crops and running cattle happened next. This was all well and fine, until……..due to their efforts for sustenance, an all-out famine started kicking their Hiney backsides.

About 150 years after my favorite Germans altered the landscape around them, my distant cousin from 1924 , Adolf Grabowski, had this to say about the drought and ensuing famine that wiped out 70% of my ancestry:

“One could, of course, take measurements to neutralize the effects of climate change : through irrigation on a large scale, through comprehensive reforestation, through selection of seed grain”…..blah blah, insert the rhetoric of today’s sage ones.

It goes on and on. My cousin Adolf was on it like stink on a monkey. He had it all figured out in 1924. For heaven’s sake! How dare anybody say that we as humans can not be held accountable for the climatic events surrounding us today? Adolf would fit right in with today’s modern environmentalists. But if he were around today, I wonder if he too would be treated with the same disregard by the truly ignorant?

What does all that have to do with anything in this missive? Beats me! Perhaps Typing Boy here was just trying to fill some space before the hint for Image 3 appeared:

Image 6: Since none of you will likely identify and find the herp in image 3, I feel the urge to play nice. Identify the herp, and tell me the location.

In the likely event that none of you identify and find the herps in images 4 and 5, I’ll send some hints for those when I reveal the rest. One week. Meanwhile, try not to pop any veins out of your eyeballs just to wow me. It’s just not worth it!

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

Giant Snakes, Politics, and Science -A Hypocritical Mix

The Washington Wire is carrying astory this morning by Louise Radnofsky, Congressional Republicans Attack ‘Broken’ Rules System.

Radnofsky reports congressional Republicans are releasing a report critical of the Obama administration’s regulatory policy, a theme that will undoubtedly continue through the 2012 elections.

The bias oriented report suggests Federal agencies are ignoring the impact of their rules on small businesses and carrying out faulty analysis when weighing their costs and benefits, according to the report, which was written by Republicans on the House Oversight Committee, which is chaired by California Rep. Darrell Issa.

The Environmental Protection Agency comes under fire for ignoring the impact on small companies of a 2009 rule that toughened training requirements for home renovators working on dwellings with lead paint. Construction companies say the rule has increased their costs and they have lost work to contractors who don’t comply.

The report cites Small Business Administration criticism that the EPA failed to give serious consideration to less-burdensome alternatives.

The White House launched an initiative this year to root out regulations that could hinder job creation, and has recently announced plans to purge hundreds of regulations deemed unnecessary and outdated. It also surprised activists by scrapping other proposed rules, including one to toughen air-quality standards.

The report also criticizes Fish and Wildlife Service plans to define boa constrictors and some pythons and anaconda as “injurious” to humans and the environment, banning their transportation across state lines in most cases. The agency has been paying particular attention to a snake infestation in the Florida Everglades. The agency is accused of failing to consider scientific evidence that the snakes may not pose a risk in most of the country.

Amazing is it not - the Republicans want to include scientific evidence when it works in their favor! And of course ignore it when it is embarrassing - like stem cell research, climate change, and evolution. The link at the top of the page will take you to the full article. Be aware that the accompanying comments are racially and ethnically insensitive!

Monday, September 12, 2011

Reptiles Where They Don't Belong

The Northern Curly Tailed Lizard,  Leiocephalus carinatus armouri
is endemic to the the Little Bahama Bank. In the 1940's about 20 pairs
were intentionally introduced into Palm Beach. It now inhabits much of
Florida's Atlantic Coast.   Photo JCM
The most popular posting on Serpent ResearchAn Attempt to Reduce Invasive Predators in the Florida Keys, has had almost 2000 visitors, about 5% of the total traffic to this blog. Why this post should attract so much attention is somewhat of a mystery, the next most popular post is Amphibians Prey for Epomis Beetles  has received only 20% of the attention the Invasive Predator has seen. So here is another note on a similar topic.

By moving species around humans are homogenizing the flora and fauna. One place becomes more like every other place on the planet. Introduced species create a loss of local biodiversity and local natural history. Two recent articles in Current Zoology emphasize the problems invasive species create..

Witman and Fuller (2011) report 1,065 vertebrate species have been introduced into the United States and its territories (86 mammalian, 127 birds, 179 reptiles & amphibian, 673 fish species). They note that In the United States, there have been some successes in invasive species management and eradication both on the mainland and islands and note we are becoming more knowledgeable and pro-active in responding to invasive vertebrate species. But invasions continue.

Florida is overrun with introduced species and Engemen et al. (2011) consider Florida's reptile fauna to be dysfunctional. Florida's climate is favorable for many amphibians and reptiles species from around the world and exotic snakes, lizards, turtles, and crocodilians are all breeding in Florida. They write, "Waves of exotic lizards have swept across much of the state, only to be joined or supplanted by subsequent lizard species..." The largest snake in Florida is no longer the Eastern Diamondback Rattlesnake or the Eastern Indigo. The state is now inhabited by the world's largest constrictors. The general public is unaware of most of the invasive species; the large constrictors are the exception. Florida now has three times more non-native lizard species breeding in the state than the native species. Many of the invasive lizards feed on the native lizards and at the same time compete for food and space.

They discuss five examples in some detail: Argentine Black and White Tegus, Burmese Pythons, Green Iguanas, Spiny-tailed Iguanas, Nile Monitors, and Northern Curlytail Lizards.

Invasive exotic reptiles in Florida are severe problem for native species, and the authors suggest that diversity of invasives in the state merit eradication, or at least control; pointing out that prevention is the most efficient and economical means to deal with invasive species. But, it is too late for those already there. 

Sunday, September 11, 2011

The African Snakebite Problem

© IRD / JF Trape
The following press eelease and some interesting photos can be found here.

A million and a half: the number of victims of poisoning after a snake bite each year in sub-Saharan Africa. An IRD researcher has analyzed hundreds of studies and medical reports published over the last forty years. So far, no large-scale review of the situation had been made and the health authorities underestimated the extent of the problem. Thus, today, only 10% of victims are treated because of lack of antivenoms and a non-medical staff awareness. However, clinical complications can be very serious or fatal. A bite of cobra or mamba can lead to death by asphyxiation - due to respiratory paralysis - in 6 hours following the accident. That of échide ocellated, a viper widespread in African savannahs, may in turn cause bleeding resulting in death within days. This new study provides the authorities with figures more accurate and reliable, allowing them to adjust their systems of care as close as needed

The best defense of snakes is a good offense. Some prove to be ruthless when they feel threatened. Each of his method. The Gabon viper, for example, injecting its venom deep into the muscles with its hooks than 5 cm long. The spitting cobra for his blind its victims of his venom. If only one bite of venomous snakes out of two, these reptiles are nonetheless a real danger to humans. The number of accidents is significant, particularly in sub-Saharan Africa where they constitute an important public health issue, neglected by health authorities.

Indeed, as recently shown in an IRD researcher, more than 300,000 people south of the Sahara are being treated each year as a result of a bite. But given the lack of access to health centers and the frequent use of traditional medicine, many cases go unreported. This figure does not reflect all of envenomation. Experts believe that it reflects that between one third and one fifth of reality. According to this new study, so there would be up to one and a half million victims a year. The death from a bite - probably also underestimated - reach for their number of 7000 and amputations in 6000 to over 14,000 per year.

While various specific studies have advanced estimates, no major review has been made so far. To fill this gap, the specialist conducted a meta-analysis, that is to say a critical review of existing scientific studies, taking into account the representation and heterogeneity of their results. To do this, he sifted through hundreds of scientific articles, conference proceedings, and clinical reports published from 1970 to 2010. This detailed study allows to announce much more reliable figures on the number of patients who had a snake.

This work has also helped point the finger at the conditions most conducive to accidents: 95% of bites occur in rural areas, especially in plantations. The people who run the greatest risk are farm workers. Yet in Africa, agriculture is the main economic activity.

Cities are not spared, even though the incidence of bites is about ten to twenty times lower than in rural areas. Thus, in some areas during the rainy season, the envenomation more than 10% of hospitalizations.

Among the most dangerous African species, two types of venom may be opposed, that of cobras and mambas, which is neurotoxic, and the snakes - which échide Frog Eye, the most common in savanna - which is bleeding and necrosis. In other words, the first cause respiratory paralysis, which can lead to death by asphyxiation between 1 and 6am. The second leads to edema and necrosis of the members and a hemorrhage can be fatal within days. The only effective treatment remains the injection of antivenin * intravenously as soon as possible after the bite to neutralize the toxic substance.

But the availability of these products is now small: only 10% of envenomations are treated. Given the lack of data so far, the problem remained underestimated by health authorities. Moreover, the high cost of these remedies and their short life span - 3-5 years - has discouraged supplies. Under these conditions, difficult to set budgets and allocate funds for the management of envenomation, the installation of equipment necessary for sensitization of medical personnel. In the absence of formation of the latter to the use of antivenoms, these treatments can produce disappointing results, discouraging reuse later. These chain reactions reduce claims. Manufacturers are reluctant to produce anti-venom so they are not safe to sell. Hence a reduction in terms of accessibility: the number of doses sold was divided by ten in Africa since the 1980s, from about 200,000 per year to less than 20,000 in the early 2000s.

This study suggests realistic figures needs antivenoms. Given the results, the specialist believes that 500 000 doses would be needed each year. The health authorities of these countries can now use these data to improve the quality of care for victims and deploy a system for identifying and monitoring.

Thursday, September 8, 2011

6.4 m Saltwater Crocodile Caught in Philippines

This photo and others available on the
Gardian's Website.
The following story has bee adapted from the BBC Science & Environment website. Visit the site to see the video.

A giant saltwater crocodile (Crocodylus porosus) weighing more than a ton and measuring 6.4 m (21 ft) and weighing 1,075 kg (2370 lbs) has been captured in the remote southern Philippine village of Bunawan . The hunt for the croc was initiated in mid-August following a series of attacks on humans and livestock.

Josefina de Leon, wildlife division chief of the environment ministry's protected areas and wildlife bureau, said it was likely to be the biggest crocodile ever captured. "Based on existing records, the largest that had been captured previously was 5.48m (18ft) long," she told AFP.

Crocodile hunter Rollie Sumiller led the hunt, and said this reptile may not be the killer they have been looking for after at least one attack on a human was reported in the area. "We're not really sure if this is the man-eater, because there have been other sightings of other crocodiles in the area," he told AFP.

The captured croc will now become the main attraction at a planned nature park in the area.

Remarkable Reproductive Behavior in Dwarf Hemiphractids.

Flectonotus fitzgeraldi. Female w/eggs. JCM
Five species of Dwarf Marsupial Frogs of the genus Flectonotus are found in Northern South America and Brazil. It now appears that they from two groups of species and each group forms a genus. These unique little frogs have females carry their eggs in dorsal pouches (hence the name marsupial) until the tadpoles hatch, at which time the female frogs deposit the tadpoles in leaf axial pools. Duellman et al. (2011) report observations on the reproductive behavior of Fritziana goeldii (Brazil) and Flectonotus pygmaeus (Venezuela) females that shows significant differences. A pair of goeldii goes into amplexus, the female replaces a mucus mass that is beat into foam by the male's hind feet, and while this is happening the skin on the female's back is stretched out by the male's front feet. As the eggs are laid, the male fertilizes them and moved them forward into the foam mass. Once the eggs are laid, the male abandons the female and she is left with a foam mass and the eggs on her back. Over the next 4 to 8 days the egg sac forms, apparently by her skin growing around the egg sac. The female did not start to forage for food until the sac was covered. At this time the eggs cannot be removed without injuring the female. The embryos develop during the next 17-23 days, at which time the female enters a water filled bromeliad tank and sloughs off the entire egg sac. Skin folds are visible for a few hours, but then disappear. The tadpoles escape the egg sac and feed on its remains as well as on other debris in the bromeliad tank, but tads that ate nothing metamorphosed in the same about of time. Metamorphosis is complete within the next 21 -25 days

Flectonotus pygmaeus, on the other hand actually has a fold of skin that forms a pouch and during amplexus, the female releases the mucus secretion, the male beats it into a foam, and as the eggs are laid, the male pushes the eggs into the skin folds - the pouch. The eggs are closely packed together but there is no egg matrix, and the eggs can be removed- they are not attached to each other. The female started to forage within 24 hours. After 23-26 days egg sac starts to split and the female transfers the tads to a leaf axial pool. She submerges a third of her body and the tadpoles swim out. The tadpoles do not feed, they continue to metamorphosis using stored yolk for another 11-17 days.

The authors remove the three species of Brazilian Flectonotus and reassign them to the genus Fritziana. The entire article can be found on-line.

Citation
Duellman, W.E., K.-H, Jungfer, and D. C. Blackburn 2011. The phylogenetic relationship of geographically separated “Flectonotus” (Anura: Hemiphractidae), as revealed by molecular, behavioral, and morphological data. Phyllomedusa, 9:15-29

Saturday, September 3, 2011

First Lizard Genome Sequenced - Anolis carolinensis


Photo by David E. Scott, Savannah River 
Ecology Laboratory, Aiken,SC, USA.
By Haley Bridger, Broad Communications, August 31st, 2011

The green anole lizard is an agile and active creature, and so are elements of its genome. This genomic agility and other new clues have emerged from the full sequencing of the lizard’s genome and may offer insights into how the genomes of humans, mammals, and their reptilian counterparts have evolved since mammals and reptiles parted ways 320 million years ago. The researchers who completed this sequencing project reported their findings August 31 online in the journal Nature.

The green anole lizard (Anolis carolinensis) – a native of the Southeastern United States – is the first non-bird species of reptile to have its genome sequenced and assembled. Broad researchers have assembled and analyzed more than 20 mammalian genomes – including those of some of our closest relatives – but the genetic landscape of reptiles remains relatively unexplored.

“Sometimes you need to be at a certain distance in order to learn about how the human genome evolved,” said Jessica Alföldi, co-first author of the paper and a research scientist in the vertebrate genome biology group at the Broad Institute. “You have to look out further than you were looking previously.”

Lizards are more closely related to birds – which are also reptiles – than to any of the other organisms whose genomes have been sequenced in full. Like mammals, birds and lizards are amniotes, meaning that they are not restricted to laying eggs in water. “People have been sequencing animals from different parts of the vertebrate tree, but lizards had not been previously sampled,” said Kerstin Lindblad-Toh, scientific director of vertebrate genome biology at the Broad and senior author of the Nature paper. “This was an important branch to look at.”

Four hundred species of anole lizards have fanned out across the islands of the Caribbean, North America, Central America, and South America, making them an appealing model for studying evolution. Although much is known about their biology and behavior, genomic information may be a critical missing piece for understanding how the lizards have become so diverse. “Anoles are rich in ecology and morphology and have just the right amount of diversity to make them interesting yet tractable to study,” said Jonathan Losos, an author of the paper, professor at Harvard University, and author of the book Lizards in an Evolutionary Tree: Ecology and Adaptive Radiation of Anoles. “But a big stumbling block in studying them has been that they have not been great organisms for classical genetic study. The genome is going to revolutionize our ability to study that aspect of their evolutionary diversification.”

One of the questions this newly sequenced genome may help resolve has to do with the origin of conserved, non-coding elements in the human genome. These regions do not contain protein-coding genes but are thought to have critical roles since they have remained unchanged for millennia. Scientists wondered where these mysterious elements came from and hypothesized that they may be the relics of transposons – jumping stretches of DNA that were at one time able to copy and paste themselves throughout the genome. In humans, many of these so called “jumping genes” have lost their jumping ability, but in anole lizards, they continue to hop.

“Anoles have a living library of transposable elements,” said Alföldi. The researchers aligned these mobile elements to the human genome, and found that close to 100 of the human genome’s non-coding elements are derived from these jumping genes. “In anoles, these transposons are still hopping around, but evolution has used them for its own purposes, turning them into something functional in humans.”

In addition to insights into human and mammalian genomes, the anole lizard’s genome also offers up clues about how lizard species evolved to populate islands in the Greater Antilles. Much like Darwin’s finches, anoles adapted to fill all of the ecological niches the islands have to offer. Some lizards have short legs and can walk along narrow twigs; others are green in color with big toe pads suited for living high up in trees; others are yellow and brown and live in the grass. But unlike the finches, lizards on different islands have independently evolved diverse communities of these twig, canopy, and grass dwelling species – almost identical lizard species have evolved in parallel on the islands of Hispaniola, Puerto Rico, Cuba, and Jamaica.

“These lizards have been compared to Darwin’s finches and in many respects they are similar,” said Losos. “They show the workings of natural selection as species adapted to different habitats. But the difference is in the case of the lizards, this evolution has happened four times, once on each of the different islands.”

By sampling the genomes of more than 90 species, the researchers were able to make a preliminary map of how these species evolved to colonize the islands.

“This is setting the stage for the research community to be able to look for signatures of adaptation in a very informative and well thought through way,” said Lindblad-Toh.

The researchers were also able to create a parts list of proteins found in green anole eggs, which they compared with those found in eggs from chickens and found that both bird and lizard egg genes are evolving rapidly. They also found many genes in the anoles genome associated with color vision, which anoles rely on to identify choice mates (males and females of some species display vividly colored flaps of skin beneath their necks called dewlaps).

“Anoles have extremely good color vision – some species can even see in the ultraviolet range,” said Losos. Other studies have shown that anoles can distinguish between similar colors and patterns. “It’s pretty clear that one function of the dewlap is to distinguish one species from others and that they use the dewlap to determine whether another individual is in another species or not.”

The researchers performed the first analysis of several other unusual features in the anole genome, including microchromosomes – tiny chromosomes sometimes found in reptiles, amphibians, and fish but never in mammals. They also found a complete lack of isochores, regions of the genome with high or low concentrations of the nucleotides “G” (guanine) and “C” (cytosine) which give human chromosomes a distinct banding pattern.

Additionally, the team found the sex chromosomes of the lizard – something that researchers had only been able to hypothesize about before. Like mammals, green anoles appear to have XX and XY chromosomes (unlike birds, in which males have two identical sex chromosomes called ZZ and females have two different ones known as ZW). The lizard’s X chromosome turned out to be one of its many microchromosomes.

Each of these insights is the fruit of collaborative efforts among scientists with expertise in the study of proteins, gene family evolution, green anole behavior and biology, computational analysis, and more. “This work represents a partnership between biologists and computational biologists,” said Federica Di Palma, a co-first author of the paper and assistant director of the Broad’s vertebrate genome biology group. “We were able to leverage all of these views to gain insight into genome evolution in general.”

Other researchers who contributed to this work include Manfred Grabherr, Christina Williams, Lesheng Kong, Evan Mauceli, Pamela Russell, Craig B. Lowe, Richard Glor, Jacob D. Jaffe, David A. Ray, Stephane Boissinot, Andrew M. Shedlock, Christopher Botka, Todd A. Castoe, John K. Colbourne, Matthew K. Fujita, Ricardo Godinez Moreno, Boudewijn F. ten Hallers, David Haussler, Andreas Heger, David Heiman, Daniel E. Janes, Jeremy Johnson, Pieter J. de Jong, Maxim Y. Koriabine, Peter Novick, Marcia Lara, Chris L. Organ, Sally E. Peach, Steven Poe, David D. Pollock Kevin de Queiroz, Thomas Sanger, Steve Searle, Jeremy D. Smith, Zachary Smith, Ross Swofford, Jason Turner-Maier, Juli Wade, Sarah Young, Amonida Zadissa, Scott V. Edwards, Travis C. Glenn, Christopher J. Schneider, Eric S. Lander, Matthew Breen, and Chris P. Ponting.

Funding for this work was provided by the National Human Genome Research Institute (NHGRI) with early support for anole genomics from the David and Lucile Packard Foundation. All sequence data was produced by the Genome Sequencing Platform of the Broad Institute.

About the Broad Institute of Harvard and MIT
The Eli and Edythe L. Broad Institute of Harvard and MIT was launched in 2004 to empower this generation of creative scientists to transform medicine. The Broad Institute seeks to describe all the molecular components of life and their connections; discover the molecular basis of major human diseases; develop effective new approaches to diagnostics and therapeutics; and disseminate discoveries, tools, methods and data openly to the entire scientific community.

Founded by MIT, Harvard and its affiliated hospitals, and the visionary Los Angeles philanthropists Eli and Edythe L. Broad, the Broad Institute includes faculty, professional staff and students from throughout the MIT and Harvard biomedical research communities and beyond, with collaborations spanning over a hundred private and public institutions in more than 40 countries worldwide. For further information about the Broad Institute, go to http://www.broadinstitute.org.

Citation
Alfoldi J et al. “The genome of the green anole lizard and a comparative analysis with birds and mammals.” Nature August 31, 2011 doi:10.1038/nature10390