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.

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.

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.

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

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

Western Australia's New Gecko in the Genus Underwoodsaurus

More than 40 species of geckos in four families inhabit western Australia's Pilbara. Three species of carphodactylid geckos are known in the Pilbara by three species in two genera (Nephrurus and Underwoodsaurus).The Pilbara Nephrurus include two relatively common and widespread endemic subspecies; N. levis pilbarensis and N. wheeleri cinctus. Underwoodisaurus is much rarer, and known from relatively few specimens and scattered observational records An undescribed Underwoodisaurus was first collected in 1997, but lack of further specimens prevented a proper assessment of its taxonomic distinctiveness. Bought and Oliver (2011) now report on recent collections and photographic records which provided sufficient material for a comparison with U. milii, the other Pilbara Underwoodsaurus, and evidence to warrant its formal description as a new species. The describe Underwoodisaurus seorsus, a new species similar to U. milii, but differing in its plain dorsal and head patterns; sparsely scattered pale tubercles; more gracile build; longer snout, limbs and digits; smaller and more numerous fine scales on the dorsum, and the enlarged tubercles on the tail tending not to form transverse rows. Underwoodisaurus seorsus is known from few specimens and has only been encountered at mid elevations in the Hamersley Ranges, widely separated from the closest populations of U. milii in the northern Goldfields and Shark Bay in Western Australia. U. seorsus has only been collected from rocky areas, and U. milii are frequently associated with rocks. The distribution of U. seorsus and U. milii suggests that their common ancestor was once more widely distributed, but aridification and increasing temperatures eliminated populations in the Gascoyne region. The rocky gorges and moderately high elevations of the southern Pilbara ranges may have acted as a relatively moist and potentially cooler refugium, allowing an isolated population of Underwoodisaurus to persist at mid elevations. Given its rarity and small distribution it may be in need of protection.

Doughty P. and P. M. Oliver. 2011.A new species of Underwoodisaurus (Squamata: Gekkota: Carphodactylidae) from the Pilbara region of Western Australia. Zootaxa 3002: 20–30.

Retraction on Prebutton Stuff

Howdy Herpers,

Abraham Lincoln once said: "It is better to be silent and be thought a fool, than to open ones' mouth and remove all doubt."

On the other hand:

"What's the sense in being stoopid if you can't prove it?"

Mike Cardwell has convinced me that my little atrox did indeed shed their prebuttons.

Mike has given me permission to quote his words:

"Why do you think the tip of your neonatal sheds are wide open and oval in shape? Why isn't the end all shriveled like the rest of the exuvium - or like that of sheds from older snakes, for that matter? It's held open by the birth button inside! Turn one inside-out... or cut it open. I've attached a photo of two post-partum exuvia from C. mitchelli pyrrhus, with one turned inside-out. I know that scuts, cerastes, and helleri all shed the birth button and I'd bet a lot of money that all rattlesnakes do it the same way. (Be careful there, Mike. You're starting to sound like Roger Repp). I have other photos (somewhere) of back-lit birth buttons on neonates where you can see the first "permanent" button forming inside. The birth button comes off with the post-partum shed!"

Image 1: Mike's image of prebuttons of neonate speckled rattlesnake sheds:
Mike's effort inspired me to go back after my little atrox shed skins. Following his advice, I pulled the prebutton inside out, and took some photos. (The process of pulling the prebutton inside out could be likened to pulling the feces out of a fly's rectum. You sure know how to have fun Mike!)

Image 2 and 3: Ladies and gentlemen, I am proud to present the prebutton of Crotalus atrox.

Now that I understand what a prebutton is, I have a newfound lack of respect for it. Talk about much adieu over nothing? A mucous membrane dingleberry? Why..........there ain't enough there to make a jock strap for a flea............

Now, will somebody please go and wake up the clouds?

Best to all, "Wrong Again Roger"

Suizo Report -- Shattering the Pre-button Myth

Howdy Herpers,

In discussing the monsoons of 2011, when it comes to our beloved Suizo Study Plot, it could be worse. We could be in Texas! To my friends in Texas, let me say that on occasion, you guys are in my thoughts and prayers for rain. But it’s pretty hard to get past reserving my thoughts and prayers for our own area. It has not been all that great here, either. In fact, this just might be the worst monsoon we’ve ever seen. (And we’ve seen some bad ones……..)

Somewhere within the bowels of my computer, I’ve buried 10,000 lamentations about what an absolute wretched spring and summer 2011 has been. A depressing report of death, blight, dementia, jock itch and the reality of global warming was one shaky trigger-finger away from being shipped to the lot of you.

When presented with the opportunity to snuff Gollum in J.R.R. Tolkien’s “The Hobbit,” Bilbo Baggins decided to play nice. “Pity stayed his hand.” (It’s a pity he didn’t throttle the miserable little SOB when he had the chance. That would have saved us a lot of useless-­if not enjoyable reading, and several epic movies in the process.)

Yup! “Pity” stayed my hand from having the moxie to snivel to you all about how downright disappointing it is to hope for the best--and get the worst, of what the true herp geeks in Arizona want to experience. We wait all damn year in anticipation to see towering thunderheads bearing down on us in early July. We wish, hope and pray for the first inklings of cold air to shove massive sandstorms of cold, dry air into every bodily orifice­-exposed or otherwise. The frigid rush of air and bead-blasting effect of harsh desert turf rapidly on-the-move has to be experienced to be believed. In a good monsoon, the relief that comes from this blast is followed by bone-chilling and torrential downpours that make even crossing the street an adventure. And in a good monsoon, this all happens every day!

But, no! None of that this summer. The few chances of the entire scenario happening ended with the sandstorms. The rain that was supposed to follow didn’t occur. Time-after-time, it was just a dry-assed blow that was followed by flat, featureless, lethargic and apathetic clouds. An absolute dud! And now all we can do is wait and hope for the summer 2012………….

How can anything in nature survive such a summer? Well….some didn’t survive. Their sad story may be told someday. But the fact remains that some of the herps under our watch not only survived-­they thrived!

This is our text.

Image 1: Meet one of our two new female Crotalus atrox, CA133. She was found by John Slone on the evening of 6 August 2011. She was exactly what we were looking for in terms of receiving a transmitter. But the complication to that decision was that she was pregnant, which makes for a difficult surgery. We decided to keep her until she gave birth.
Image 2: And on 17 August, she gave us 6 beautiful babies, 4 males, and 2 females:
Image 3: Now we’re going to take the opportunity to zero in on the rattles (pre-buttons) of two of these snakes. Keep in mind that it will be six more days before these snakes shed their skins as you look at these pre-buttons. (Don’t be distracted by anything else on the image guys! Stay focused on the pre-buttons­I’m trying to teach you something here!)
Image 4: And now, let’s take a look at the full button on one of the neonates that has shed:

Take a moment to absorb what you’ve just seen, and we’ll move on.

Got it? Image 3 depicts the pre-button as just a nub, and although poorly photographed, image 4 shows that after the snake has shed, a “flange” of sorts emerges to join the nub. And now, are you ready for this?

The pre-button does not come off when the snake sheds its skin! It grows to become a full button.

Image 5: Let’s take a look inside the tail/rattle portion of one of the neonate atrox shed skins. Do you see any pre-button inside of it? Nope! That’s because the pre-button is still on the snake, in the form of the top nub on the full button.
Image 6: A side look at the tail/rattle portion of a neonate shed skin. 

I tell you these things because there is a lot of misinformation out there about what happens to the button before and after a neonate rattler sheds its skin the first time. While there may be species of rattlesnakes that do something different, Crotalus atrox does not shed off its pre-button! End of lesson, but not this report.

Image 7: As I’m sure none of you remember, mention was made of two new females entering our study. Well, the second female is not actually new. She is an old friend. Thanks to the miracle of PIT tags, we were able to identify the atrox below as female CA87. She was first captured in April of 2005 and, at the time, deemed much too small to receive a transmitter. She was at that point in time only 2.5 years old-­a little 250 gram sweetie of a snake. And though we’ve been all over her turf in the six plus years that followed, we did not see her again until 7 August 2011. My how she has grown! Her mass was 739 grams at capture­she has tripled her size! Once again, this snake was deemed pregnant, and we decided to play it safe, let her have her kids, and then do the surgery.
Image 8: On 15 August, our old friend dropped 12 beautiful children for us. The sex ratio was 5 males, 7 females. Yay for the girls! The N of 12 is 3 more than we have ever seen come from the atrox on our plot. We have twice had females give birth to 9. Most events have had less than six. Say hi to the babies everybody!
Image 9: By 24 August, the little ones had all shed. Now it was time to get those shed skins.

Yikes! Open carefully!

Image 10: They may be cute, but each and every one of these were little demons from the depths of hell in temperament. Biting worms, all of them! They were striking at anything that came close. As I transferred each one from their “nest” to a clean box, I did so at eye level. As I did so, several launched strikes at my face. How can something so tiny have such a big, fearsome mouth? Yehaw!
A side observation is in order. Prior to shedding, the little guys did not climb to the top of their nest box. Once they shed, they did so earnestly. I have noticed that in the wild, the neonates tend to go vertical.

I counted each one as I transferred them to their new quarters. At one point in the count, I jostled their nest box, and it crashed to the floor. But I thought I was on it quick enough. I continued on with the transfer.

“One-two-three…CRASH! "CRAP!" Four-five…………ten-eleven!


I could visualize the topic of conversation that morning with my long-suffering wife Dianna. “Uh…….heh-heh, Sweetie? I think it might be a good practice to wear combat boots around the house for, oh, say….. the next year or so………..”

But I groped about on all fours, and found number 12 snuggled against the side of one of coolers on the floor. Whew! That was WAY close!

Image 11: This was the mess that stared me in the face when the shed-gathering was done:
Image 12: As each individual shed skin contains its own DNA, they have to be bagged separately. Thanks to the gentle, patient hands of Dianna Repp, the snarl depicted above eventually became:
And so now, they’re all bagged and tagged, and ready to hand off to the gel jockeys. Everybody is back out on the plot again. I had hoped to stage some photographs of the moms with their babies in the wild­-but that wasn’t going to happen. In their angst to gain their freedom, the babies morphed into whipsnakes, and scattered like dust in the wind. Trying to control that melee would have been several bites in the making.

With the next report, I will cover some of the birthing that occurred in the wild. But for now:

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

And may the sun someday be more than a few inches from the top of our heads!

Friday, September 2, 2011

Salamanders, Rattlesnakes, & Tortoises - Conservation News

The Center for Biological Diversity Announces news for endangered herps. Each announcment is linked to a longer press release.

47,000 Acres Protected for California Tiger Salamander
In response to a Center for Biological Diversity lawsuit, the U.S. Fish and Wildlife Service this week designated 47,383 acres of federally protected "critical habitat" for the California tiger salamander's Sonoma County population. The move reverses a 2005 Bush decision to set aside no critical habitat; it protects many "vernal pools" that host the salamander during winter rains as well as increasingly rare grasslands and oak woodlands.

The Center earned protection for the Sonoma County tiger salamander in 2003. This yellow-spotted, black amphibian is threatened by development, pesticides, hybridization with nonnative salamanders, disease and predation.

Declining Rattlesnakes
Just days after one snake species, the Lake Erie water snake, was declared recovered thanks to the Endangered Species Act, a snake researcher and the Center for Biological Diversity petitioned to save another snake under the successful law. The eastern diamondback rattlesnake -- the largest rattlesnake in the world -- is native to the Southeast but dwindling fast due to habitat loss and human exploitation, especially through "rattlesnake roundups" -- grisly festivals that encourage the collection and slaughter of these imperiled snakes.

"The Endangered Species Act just saved the Lake Erie water snake -- it's the surest tool we have to save the diamondback rattlesnake too," said Collette Adkins Giese, the Center's attorney devoted to saving reptiles and amphibians.

Recovery Plan Weakens Desert Tortoise Protection
Instead of upgrading protections for the Mojave's desert tortoise, the species' new federal recovery plan makes matters worse for the ancient, threatened reptile. Until the new plan was released last Friday, the tortoise's recovery plan -- a document laying out steps and criteria for removing the species from the endangered list -- hadn't been updated since 1994. And now, while tortoise populations continue to crash, the revised plan fails to address some of the direst threats to the species, including livestock grazing, off-road vehicles, nonnative plants, climate change and energy development.

The Center for Biological Diversity has been working to save the desert tortoise since the '90s, when we filed our first appeals to stop harmful livestock grazing in tortoise habitat. So Center biologist Ileene Anderson has good authority to compare the old and new plans: "The new recovery plan only exacerbates the ongoing problem of desert tortoise recovery, which has been the failure to implement most of the science-based recommendations in the old plan. This plan simply doesn't cut it."

The Evolution of Communication: Tungara Frogs & Trachops Bats

Tungara Frog, Engyostomops pustulosus. JCM
A research team that included Hamilton E. Farris, PhD, Research Assistant Professor of Neuroscience and Otorhinolaryngology at LSU Health Sciences Center New Orleans, reveals that two entirely different species show similar perception of auditory cues that drive basic biological functions; that these perceptions may be universally shared among animals; and that such perception may also limit the evolution of communication signals.

The work is published in the August 5, 2011 issue of Science.

Using the labs at the Smithsonian Tropical Research Institute in Panama, the team tested whether psychophysical laws explain how female túngara frogs and frog-eating bats compare male frog calls and whether the rules for perception constrain how communication signals evolve.

Animals, including humans, continuously make decisions based on comparing external stimuli from the environment. However, the decisions are not based on the actual, but rather the perceived physical magnitude of the stimuli. A perceptual rule called Weber's Law proposes that stimuli are compared based on ratios, not absolute differences. For example, distinguishing between a 1-lb. object and a 2- lb. object is easier than comparing a 50-lb. object vs a 51-lb. object. The comparison does not depend on the absolute difference (1 lb. in each case), but the relative difference (100% vs. 2%).

The researchers tested whether Weber's law or alternative hypotheses explain túngara frog mate choice. Male túngara frogs produce a vowel-like "whine," followed by 0-7 consonant-like "chucks." They placed wild-caught females in a sound chamber and alternately broadcast two call types with varying numbers of chucks from two speakers on opposite sides of the chamber. Choice was quantified as walking to within 10 cm of either speaker.

"By giving females a choice between calls with different numbers of chucks, we found that the female frogs prefer calls with the most chucks, but based on the ratio of the number of chucks.," notes LSUHSC's Dr. Farris. "This means that as males elaborate their signals by adding more chucks, their relative attractiveness decreases due to the perceptual constraint on the part of females."

To more fully understand how females' perception influences the evolution of the males' calls, the research team then tested fringe-lipped bats, a natural predator of túngara frogs who select their prey based on the calls of the male frogs. Using this rare case in which two very different species, amphibian and mammal, have evolved the same behavioral approach to the same communication signal, the research team asked whether hunting bats choose their prey based on chuck number ratio as well. Testing bats in a behavioral test similar to that used with female frogs, the team showed that bats compared calls using chuck number ratio as well.

"It is astounding that two disparate animals use the same perceptual scale, suggesting a generality in how animals compare stimuli," says Dr. Farris.

As males increase chucks, so do their neighbors. With a fixed difference of one chuck between neighbors, both the risks and benefits of adding chucks decrease with increasing elaboration. Adding one chuck to many chucks adds less risk than adding one chuck to few chucks. Adding multiple chucks to outcompete neighbors will not succeed because males maintain a fixed difference.

"Natural selection and bat predation are not limiting male call evolution, This supports our conclusion that it is the females' cognition that is limiting the evolution of chuck number," says Dr Farris. "The results are significant because we show that certain types of perception may be universal. Furthermore, with respect to the evolution of communication signals, we propose that by limiting signal elaboration, ratio-based coding could favor the evolution of signal innovation. That is, Weber's law would favor the evolution of a signal along a completely different perceptual axis."

The research team consisted of Dr. Karin Akre, Ms. Amanda Lea and Dr. Michael Ryan of the University of Texas-Austin, as well as Dr. Rachel Page of the Smithsonian Tropical Research Institute, Panama. The research is supported by grants from the National Institutes of Health, the National Science Foundation, and the American Association of University

Karin L. Akre, Hamilton E. Farris, Amanda M. Lea, Rachel A. Page, Michael J. Ryan. Signal Perception in Frogs and Bats and the Evolution of Mating Signals. Science, 2011; 333 (6043): 751-752 DOI: 10.1126/science.1205623