Tuesday, March 31, 2015

A new squamate phylogeny that resolves from previous problems

Estimated phylogeny of squamate reptiles from 
likelihood analysis of combined morphological 
and molecular data, after removal of four “rogue” 
fossil taxa. Red dots indicate clades with 
bootstrap values from 90–100%, black dots 
indicate values from 70–89% (values <70 nbsp="" span="">
not shown; for bootstrap values for all branches 
see. Fossil taxa are indicated with “” and green 
branches. The four abbreviated fossil taxa in 
gray at the base of the phylogeny are the four rogue 
taxa (Eichstaetisaurus, Huehuecuetzpalli
SineoamphisbaeniaAMNH FR 21444), shown in 
their phylogenetic positions as inferred in the 
combined analysis including all taxa. Photos 
include representatives of Dibamidae (Anelytropsis), 
Gekkota Carphodactylidae:Underwoodisaurus), 
Scincoidea (Scincidae: Plestiodon), Amphisbaenia
(Bipedidae:Bipes), Mosasauria (Tylosaurus), 
Serpentes (Boidae: Exiliboa), Anguimorpha 
(Xenosauridae: Xenosaurus), Polyglyphanodontia 
(Polyglyphanodon), Acrodonta (Agamidae:
 Calotes), and Pleurodonta (Phrynosomatidae: 
Sceloporus). See Acknowledgments in 
original paper for photo credits (except for 
Anelytropsis from T. M. Townsend). 

In a new paper published in PLoS, Reeder et al. (2015) note that squamate reptiles (lizards and snakes) are an important and diverse group of terrestrial vertebrates, with more than 9,000 species and that studies of squamate biology are presently hampered by uncertainty over their phylogeny.
Higher-level squamate phylogeny is currently unresolved because of conflicts between hypotheses based on separate analyses of morphological and molecular datasets. 

Most attention has focused on the placement of iguanians (including iguanas, anoles, chameleons, dragons, and relatives), which are placed at the base of the squamate tree in morphological analyses, and in a clade (called Toxicofera) with snakes and anguimorphs (including monitor and alligator lizards, the Gila monster, and relatives) in molecular analyses. The largest morphological dataset (in characters) included 189 squamate taxa (140 living and 49 fossil; plus 3 outgroup taxa) and 610 characters (~33% missing data; Gauthier et al., GEA hereafter). 

The largest molecular dataset (in terms of characters) included 161 living taxa (plus 10 outgroup taxa) for up to 44 nuclear protein-coding loci (33,717 base pairs/characters; ~20% missing data); Wiens et al., (WEA hereafter). Given the unresolved conflict between these two large datasets over the placement of Iguania, some authors have considered higher-level squamate relationships to be unresolved. Some recent, prominent studies have considered the traditional, morphological tree only, ignoring the molecular hypothesis altogether.

In this study the authors perform an integrated analyses to resolve this conflict and further elucidate the relationships of both living and fossil squamates. First, they generated an expanded morphological dataset with taxon sampling largely matching that of GEA for extant taxa, adding new data from 81 additional characters (primarily from squamation) to the mostly osteological dataset of GEA. This is a 13% increase in characters (to 691), and the largest morphological dataset for squamates. Next, they expanded the molecular dataset of WEA by including published sequences from two additional loci (nuclear c-mos; mitochondrial ND2) for closely matched species yielding up to 46 protein-coding loci and 35,673 characters for each of 161 taxa. We then performed separate and combined analyses of each dataset using likelihood, Bayesian, and parsimony approaches, and evaluated the potential causes of conflict by examining trees from subsets of the molecular and morpohological data. Combined analyses included reweighting the molecular data such that genes were treated as equivalent to morphological characters.

The results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, the authors find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia), demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. These results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement.

The combined analyses strongly suggest that the phylogenetic hypothesis for living squamates based on the molecular data is correct. Specifically, the results support the hypothesis that Iguania is placed with snakes and anguimorphs, and not at the squamate root (as suggested by morphological data alone). The conclusions are based on several lines of evidence, including: (a) combined analyses of the relevant molecular and morphological data supports the molecular placement of Iguania, even when the molecular dataset is reduced to only 63 characters, less than one tenth the size of the morphological dataset, (b) mapping morphological characters on the combined-data tree shows that there is actually hidden support for the molecular hypothesis in the morphological data (similar to the number of characters supporting the morphological hypothesis), (c) the morphological dataset is dominated by misleading phylogenetic signal associated with convergent evolution of a burrowing lifestyle and associated traits, and a similar problem associated with feeding modes may explain the morphological placement of Iguania, and (d) the morphological hypothesis is unambiguously supported by only one of six subsets of the morphological data. Conversely, we find no evidence for hidden signal supporting the morphological hypothesis among the 46 genes in the molecular dataset; no genes support this hypothesis. Further, the failure of some genes to fully support the molecular placement of iguanians in Toxicofera seems to be associated with sampling error (i.e. shorter genes).


Reeder TW, Townsend TM, Mulcahy DG, Noonan BP, Wood PL Jr, et al. (2015) Integrated Analyses Resolve Conflicts over Squamate Reptile Phylogeny and Reveal Unexpected Placements for Fossil Taxa. PLoS ONE 10(3): e0118199. doi:10.1371/journal.pone.0118199.

Sunday, March 29, 2015

The Python & the Marsh Rabbit in the Florida Everglades

The invasive Burmese python (Python molurus bivittatus or Python bivittatus) has been suspected in the drastic decline of mammal populations in Everglades National Park (ENP) over the last several decades, The park is globally recognized for its unique biotic communities, sits at the southern end of the Greater Everglades Ecosystem (GEE), a vast freshwater wetland (≈10 000 km2) encompassing most of the southern Florida peninsula. The ecological processes, functionality and restoration efforts within this distinct ecosystem are probably being substantially impaired by the disappearance of once common mammalian predators and herbivores. Declines in mammal populations in ENP appear to coincide temporally and spatially with the arrival and spread of invasive Burmese pythons, a large-bodied snake native to Southeast Asia that preys on vertebrates. Pythons were probably introduced into ENP several decades ago via releases or escapes from private ownership. Sightings and removals of pythons in ENP were sporadic in the 1980s and 1990s, and increased sharply in the early 2000s. During this time, gut content analysis of invasive pythons in ENP indicated that mammals accounted for about 75% of their diet.
Previous evidence linking pythons to mammal declines has been indirect, and there are reasons to question whether pythons or any predator could have caused the precipitous declines seen across a range of mammalian functional groups. Introduced predators, including snakes, have reduced or eliminated fauna on islands, yet there are no accounts of a lone introduced apex predator (apart from humans) removing a functionally diverse, continental mammal community. Additionally, ecological theory provides little support for the hypothesis that an apex predator could extirpate small, broadly dispersed, fecund, generalist herbivores.
In a new article in the Proceedings of the Royal Society of London B: Biological Sciences McCleery et al. (2015) test the hypothesis that pythons are driving the decline of mammal populations, and they experimentally manipulated the marsh rabbit (Sylvilagus palustris) populations in ENP.
Marsh rabbits are small (≈1 kg) lagomorphs found near fresh and brackish water throughout the southeastern USA. They are sexually active throughout the year and can produce up to six litters of three to five young annually. Through the 1980s, this species was one of the most commonly seen mammals in ENP. Despite having a wide variety of natural predators, marsh rabbits are still common in areas of the GEE outside of ENP. For these reasons, and because rabbit populations are generally resilient and capable of persisting under considerable predation pressure the authors  chose marsh rabbits as a model to understand the impacts of pythons on mammals in ENP. If pythons caused the declines of marsh rabbits in ENP, they predicted that (i) pythons would be the dominant cause of marsh rabbit mortality in ENP, (ii) mammals would cause more marsh rabbit mortalities in areas of the GEE where pythons were rare or absent, (iii) marsh rabbit populations introduced in ENP would not persist, and (iv) unlike endothermic predators (i.e. mammals), the timing of python-caused mortality would vary with seasonal climate conditions.
The authors experimentally manipulated the marsh rabbit populations to determine the role of pythons in driving mammal declines within ENP. They compared the risk of mortality from different causative agents in areas with established Burmese python populations to similar areas where pythons were rare or absent. The also evaluated the influence of environmental factors on temporal variation in mortality rates from the dominant predators of marsh rabbits (e.g. pythons and mammals) in the GEE.
They captured marsh rabbits from donor populations and randomly assigned them to one of three sites: two sites in ENP and a procedural control site in the GEE, where pythons had not been observed. The purpose of the procedural control was to account for the influence of translocation on mortality events. The also established a control site where pythons were rare or absent to compare causes of mortality in ENP with an established population of marsh rabbits that was not manipulated. At the control site, they captured and released rabbits without trans-locating them.
They captured, released and radiotracked 95 adult marsh rabbits from 14 September 2012 to 19 August 2013 (coastal ENP = 15, freshwater ENP = 16, procedural control = 15, control = 49). Eighty rabbits survived the 10-day adjustment period needed to reduce exploratory movements and acclimate to the sites. Additionally, 10 rabbits were censored after the 10-day adjustment period (e.g. lost signal from predation or equipment failure), and two rabbits were alive at the end of the study, so the study documented 68 rabbit mortalities. Classification of the cause of mortality for 55 rabbits was possible and the remaining 13 rabbit mortalities were listed as being from an unknown endothermic predator. Marsh rabbits in ENP faced the greatest risk of predation from pythons, which accounted for 77% of all mortalities. And, the authors attributed only one rabbit mortality in ENP to mammal predation. This was in stark contrast to results from control sites, where no rabbits were killed by pythons and they attributed 71% of classified mortalities to mammals. Only three rabbits (8%) at the control site were eaten by snakes, all native eastern diamondback rattlesnakes (Crotalus adamanteus).
The loss of marsh rabbits and other mammals from ENP  is probably causing a massive rearrangement of the ENP food web, losses in ecosystem function, and complex and unpredictable cascading effects. As prey and predators at multiple trophic levels, nutrient cyclers and engineers of vegetation, mammals are an indispensable component of the GEE. This research clearly establishes pythons as a causal agent of marsh rabbit declines, a species selected because of its theoretical resilience to predation pressure. Accordingly, pythons are a logical and likely explanation for the observed declines in less fecund mammalian prey found in ENP (raccoon, round-tailed muskrat, bobcat).
Only with the recovery of the parks mammal populations will it be possible to restore the health and functionality of this World Heritage Site. However, it seems unlikely that marsh rabbits and other mammal populations will rebound without action to manage pythons. Because pythons are capable of persisting in the environment by switching to different prey and going long periods without food controlling them is a difficult challenge. Without effective tools and a strategy for reducing the prevalence of these invasive snakes, the dire state of mammals in the Everglades will probably remain unchanged, and spread if python populations expand northward or become established elsewhere in the USA.


McCleery RA., Sovie A, Reed RN, Cunningham MW, Hunter ME, & Hart KM. (2015). Marsh rabbit mortalities tie pythons to the precipitous decline of mammals in the Everglades. Proceedings of the Royal Society of London B: Biological Sciences, 282(1805), 20150120.

Saturday, March 28, 2015

A giant temnospondylid amphibian from Portugal's Triassic

A previously undiscovered species of crocodile-like amphibian that lived during the rise of dinosaurs was among Earth's top predators more than 200 million years ago.

Paleontologists identified the prehistoric species -- which looked like giant salamanders -- after excavating bones buried on the site of an ancient lake in southern Portugal. The species was part of a wider group of primitive amphibians that were widespread at low latitudes 220-230 million years ago, the team says.

The creatures grew up to 2m in length and lived in lakes and rivers during the Late Triassic Period, living much like crocodiles do today and feeding mainly on fish, researchers say.

The species -- Metoposaurus algarvensis -- lived at the same time as the first dinosaurs began their dominance, which lasted for over 150 million years, the team says. These primitive amphibians formed part of the ancestral stock from which modern amphibians -- such as frogs and newts -- evolved, researchers say.

The species were distant relatives of the salamanders of today, the team says. The discovery reveals that this group of amphibians was more geographically diverse than previously thought.

The species is the first member of the group to be discovered in the Iberian Peninsula, the team says.
Fossil remains of species belonging to the group have been found in parts of modern day Africa, Europe, India and North America. Differences in the skull and jaw structure of the fossils found in Portugal revealed they belong to a separate species.

The new species was discovered in a large bed of bones where up to several hundred of the creatures may have died when the lake they inhabited dried up, researchers say. Only a fraction of the site -- around 4 square meters -- has been excavated so far, and the team is continuing work there in the hope of unearthing new fossils.

Most members the group of giant salamander-like amphibians was wiped out during a mass extinction 201 million years ago, long before the death of the dinosaurs. This marked the end of the Triassic Period, when the supercontinent of Pangea -- which included all the world's present-day continents -- began to break apart. The extinction wiped out many groups of vertebrates, such as big amphibians, paving the way for dinosaurs to become dominant.

The study, published in the Journal of Vertebrate Paleontology, was funded by the German Research Foundation and the National Science Foundation, the Jurassic Foundation, CNRS, Columbia University Climate Center and the Chevron Student Initiative Fund. Additional support was provided by the Municipality of Loulé, Camara Municipal de Silves and Junta de Freguesia de Salir in Portugal.

Dr Steve Brusatte, of the University of Edinburgh's School of GeoSciences, who led the study, said: "This new amphibian looks like something out of a bad monster movie. It was as long as a small car and had hundreds of sharp teeth in its big flat head, which kind of looks like a toilet seat when the jaws snap shut. It was the type of fierce predator that the very first dinosaurs had to put up with if they strayed too close to the water, long before the glory days of T. rex and Brachiosaurus."

Dr Richard Butler, of the School of Geography, Earth and Environmental Sciences at the University of Birmingham, said: "Most modern amphibians are pretty tiny and harmless. But back in the Triassic these giant predators would have made lakes and rivers pretty scary places to be."

Dr Steve Brusatte will discuss his work on recently discovered species and other aspects of paleontology at a series of events at the Edinburgh International Science Festival, which runs from 4-19 April.

Brusatte SL, Butler RJ, Mateus Steyer JS. A new species of Metoposaurus from the Late Triassic of Portugal and comments on the systematics and biogeography of metoposaurid temnospondyls. Journal of Vertebrate Paleontology, 2015; e912988 DOI:10.1080/02724634.2014.912988

Monday, March 16, 2015

A new genus and species of xenodermatid snake from Laos

A) Fimbrios klossi, Paksong, Champasak Province. 
B) Parafimbrios lao, from the Muang Ngoi, Ngoi 
District, Louangphabang Province, Laos. 
Photo Credit: A. Teynié.
The Asian family Xenodermatidae includes five genera: Xenodermus Reinhardt, 1836 (1 species), Achalinus, Fimbrios, Stoliczkaia, and Xylophis, and hold a total of 17 species. The Philippine genus Oxyrhabdium has been removed from the family based on molecular evidence, nevertheless, its phylogenetic position should be further investigated as it is now classified as Elapoidea incertae sedis. This family has long been considered to be a subfamily of the Colubridae. Recent phylogenetic studies suggest this well-defined assemblage deserved family status. These genera include species with more or less highly modified cephalic (labials with raised and everted edges, presence of ridges of skin between rostral and internasals, and a large loreal) and dorsal scalation (usually small scales, subequal or intermixed with large scales). The Neotropical genus Nothopsis Cope, 1871, previously also referred to the family Xenodermatidae, but was transferred to the family Dipsadidae and the members of Xenodermatidae are currently known only from Asia, ranging from India eastward to Japan and Taiwan, and southward to Borneo and Java, possibly also the Philippines.

Malcom Smith erected the monotypic snake genus Fimbrios for Fimbrios klossi, and described it from Da Lat, Langbian Plateau in southern Vietnam in 1921. This species was subsequently recorded from the Elephant Mountains, in southwestern Cambodia, and from central and southern Vietnam. Although it has been recorded close to the Laotian border, it was not recorded from the Laos until 2008, when a specimen was collected in the Paksong District, Champasak Province, in Boloven Highlands. Two additional specimens, found in 2007 and 2008 in the same locality of the Boloven Highlands between 1,320 and 1,340 m asl. Fimbrios smithi was described in 2008 on the basis of a specimen obtained in the karst forest of Phong Nha—Ke Bang National Park, Quang Binh Province, in central Vietnam.

In a new paper Teynié et al. describe a new genus and species of xenodermatid snake from Laos based upon a specimen collected during a trip in the northern part of Louangphabang Province, which presented several diagnostic characters of the genus Fimbrios. The male snake and a second specimen observed in Houaphan Province, North Laos, share morphological characters with the Asian genus Fimbrios including erected edges on the first supra and infralabial scales, but differ in having fewer dorsal scale rows (25–27 vs. 30–33), fewer maxillary teeth (27 vs. 30–35), posterior teeth progressively slightly enlarged, and especially the correspondence of two dorsal scale rows per ventral plate throughout the body (i.e. the first dorsal scale row made of a small scale above the fore part of a ventral, followed by a much larger scale above its hind part), a condition known only in Xenodermus Reinhardt, 1836.

As the Laotian specimens differ in morphological and molecular characters from other xenodermatids, Teynié et al placed these specimens in a new genus, Parafimbrios and describe them as Parafimbrios lao. Besides the characters mentioned above, the new species is diagnosed by a combination of the following ones: small, strongly keeled dorsal scales; rostral and first four supra- and infralabials with raised, erected edges; horizontal tissue ridges above the rostral; loreal single, large, elongate; ventral scales 177–189; subcaudals 55–56, undivided; dorsal color purplish-grey, neck with a broad, very pale grey collar reaching downwards the pale grey color of the venter. Parafimbrios laos is the 111th snake species recorded from Laos.

The holotype was discovered in a steep, rocky evergreen forest, with some trees of primary forest remaining, surrounding a rugged karst formation. The holotype was found lying motionless at night during the rainy season on a rocky outcrop among a large pile of rocks at the foot of a limestone cliff of the karst formation at an elevation of 360 m. The adjacent lowland is mainly covered with rice fields, patches of secondary forests and a few scrub and grasslands. The second specimen was observed near the city of Vieng Xai, where no large primary forest remain. This specimen was observed in the same general karstic environment as the holotype. Neither specimen displayed any reaction and remained perfectly motionless when they were photographed. When they were handled, they did not try to form a “ball”, a defensive posture frequent in Fimbrios klossi, nor did they display any other defensive action. Nothing else is known on the biology of Parafimbrios lao, stomachs of both specimens were empty.


Teynié, A., David, P., Lottier, A., Le, M. D., Vidal, N., & Nguyen, T. Q. (2015). A new genus and species of xenodermatid snake (Squamata: Caenophidia: Xenodermatidae) from northern Lao People’s Democratic Republic. Zootaxa, 3926(4), 523-540.

Thursday, March 12, 2015

Three-dimensional reconstruction of the Acanthostega gunnari, a tetrapod skull in transition between water and land

Here are the articulated cranium and lower jaws
shown in oblique right lateral view (A). Right facial
skeleton and skull roof shown in "exploded"
view to illustrate the nature of sutural contacts (B);
the left side of the cranium (braincase omitted) is
shown in internal view (C). The right lower jaw in
"exploded" view to illustrate sutural morphology.
Individual bones shown in various colors.
Artist Credit: Porro et al..

The first 3D reconstruction of the skull of a 360 million-year-old near-ancestor of land vertebrates has been created by scientists from the Universities of Bristol and Cambridge, UK. The 3D skull, which differs from earlier 2D reconstructions, suggests such creatures, which lived their lives primarily in shallow water environments, were more like modern crocodiles than previously thought.

The researchers applied high-resolution X-ray computed tomography (CT) scanning to several specimens of Acanthostega gunnari, one of the 'four-footed' vertebrates known as tetrapods which invaded the land during one of the great evolutionary transitions in Earth's history, 380-360 million years ago. Tetrapods evolved from lobe-finned fishes and display a number of adaptations to help them survive on land.

An iconic fossil species, Acanthostega gunnari is crucial for understanding the anatomy and ecology of the earliest tetrapods. However, after hundreds of millions of years in the ground fossils are often damaged and deformed. No single specimen of Acanthostega preserves a skull that is complete and three-dimensional which has limited scientists' understanding of how this key animal fed and breathed -- until now.

Using special software, the Bristol and Cambridge researchers 'digitally prepared' a number of Acanthostega specimens from East Greenland, stripping away layers of rock to reveal the underlying bones.

They uncovered a number of bones deep within the skull, including some that had never before been seen or described, resulting in a detailed anatomical description of the Acanthostega skull.
Once all of the bones and teeth were digitally separated from each other, cracks were repaired and missing elements duplicated. Bones could then be manipulated individually in 3D space. Using information from other specimens, the bones were fitted together like puzzle pieces to produce the first 3D reconstruction of the skull of Acanthostega, with surprising results.

Lead author, Dr Laura Porro, formerly of Bristol's School of Earth Sciences and now at the Royal Veterinary College, said: "Because early tetrapods skulls are often 'pancaked' during the fossilization process, these animals are usually reconstructed having very flat heads. Our new reconstruction suggests the skull of Acanthostega was taller and somewhat narrower than previously interpreted, more similar to the skull of a modern crocodile."

The researchers also found clues to how Acanthostega fed. The size and distribution of its teeth and the shape of contacts between individual bones of the skull (called sutures) suggest Acanthostega may have initially seized prey at the front of its jaws using its large front teeth and hook-shaped lower jaw.

Co-author, Professor Emily Rayfield, also from Bristol's School of Earth Sciences, said: "These new analyses provide fresh clues about the evolution of the jaws and feeding system as the earliest animals with limbs and digits began to conquer the land."

The researchers plan to apply these methods to other flattened fossils of the earliest tetrapods to better understand how these early animals modified their bones and teeth to meet the challenges of living on land.

Digital models of the original fossils and the 3D reconstruction are also useful in scientific research and education. They can be accessed by researchers around the world, without risking damage to fragile original fossils and without scientists having to travel thousands of miles to see original specimens. Furthermore, digital models and 3D printouts can be easily and safely handled by students taking courses and by the public during outreach events.

Porro LB, Rayfield EJ, Clack JC. 2015. Descriptive Anatomy and Three-Dimensional Reconstruction of the Skull of the Early Tetrapod Acanthostega gunnari Jarvik, 1952. PLOS ONE, 2015; 10 (3): e0118882 DOI:10.1371/journal.pone.0118882

Wednesday, March 11, 2015

Chameleons use nanocrystals to create color change

Many chameleons have the remarkable ability to make rapid and complex color changes in their social interactions. In a collaboration between biology sections researchers and physics at the Faculty of Science of the University of Geneva (UNIGE) results in the discovery of the mechanisms governing the phenomenon. In the study published by Nature Communications, the group co-led by Professors Michel Milinkovitch and Dirk van der Marel demonstrates that the changes occur through the active control of a nano-crystal mesh present in a surface layer of skin cells, the iridophores. The researchers also testify to the existence of a deeper layer of iridophores, whose crystals, bigger and less organized, reflect infrared light. Such a superposition of two different types of iridophores is new in evolutionary terms; it is what allows chameleons spend an effective camouflage a spectacular parade in record time; is that it also provides a passive thermal protection to the animal.

The colorful adornments that turn at the discretion of the popularity of behavior are male chameleon. While the mechanisms of change to a darker hue are known, those that govern the transition from a bright color to another flamboyant tone remained mysterious. Some species, such as the panther chameleon, for example, are able to make such a transition in one to two minutes, to woo a female or face another male.

The blue color of the chameleon structural
Besides brown pigments, red and yellow, chameleons and other reptiles have called structural colors. "These colors are actually created without pigments, via an optical interference phenomenon. They derive from interactions between certain wavelengths and nanoscopic structures such as tiny crystals in the skin of reptiles, "says Michel Milinkovitch, professor at the Department of Genetics and Evolution of the University of Geneva.These nanocrystals are arranged in alternate layers with the cytoplasm in iridophores named cells. Millefeuille formed selectively reflects certain wavelengths and this phenomenon contributes to the flamboyant colors many reptiles.

To determine how is the transition from a colorful adornment to another in the panther chameleon, researchers from two laboratories of the University of Geneva have worked hand in hand, combining the skills of experts in quantum physics and biology of evolution. "We found that the animal can change color by active adjustment of nanocrystals mesh. When the chameleon is calm, they are organized into dense network and reflect the lengths of blue waves. But the excitement causes release within iridophores of the animal and allows reflection of other colors, such as yellow or red "explain Jeremiah Teyssier physicist and biologist Suzanne Saenko, who are the co-first authors of the article. The set is a unique example of self-organized optical system controlled by the animal wearing it.

Crystals as heat shield
Scientists have also demonstrated the existence of a second layer of iridophores, deeper. "These cells, which contain larger crystals and less organized, reflect a significant proportion of infrared wavelengths," explains Michel Milinkovitch. This layer acts as a very effective protection against thermal effects due to exposure to the sun in low latitudes.

Furthermore, in terms of evolution, the organization of iridophores two layers is a novelty that allowed the passage chameleons in record time for an effective camouflage a spectacular parade, while providing thermal protection passive.

The researchers now intend to explore the cellular mechanisms that govern in the iridophores, change nanocrystals mesh, as well as the development of crystalline layers.


Teyssier JA, Saenko SV, van der Marel D, Milinkovitch MC 2015. Photonic crystals cause active colour change in chameleons. Nature Communication 6, http://dx.doi.org/10.1038/ncomms7368

Friday, February 27, 2015

Chytrid fungus detected in Madagascar frog species

Chytrid fungus was proved present on Platypelis pollicaris
from Ranomafana. Photo Credit: Miguel Vences / TU 
The chytrid fungus, which is fatal to amphibians, has been detected in Madagascar for the first time. This means that the chytridiomycosis pandemic, which has been largely responsible for the decimation of the salamander, frog and toad populations in the USA, Central America and Australia, has now reached a biodiversity hotspot. The island in the Indian Ocean is home to around 290 species of amphibians that are not found anywhere else in the world. Another 200 frog species that have not yet been classified are also thought to live on the island. Researchers from the Helmholtz Centre for Environmental Research (UFZ) and TU Braunschweig, together with international colleagues, are therefore proposing an emergency plan. This includes monitoring the spread of the pathogenic fungus, building amphibian breeding stations and developing probiotic treatments, say the scientists, writing in Scientific Reports, the acclaimed open-access journal from the publishers of Nature.

The entire amphibian class is currently afflicted by a global pandemic that is accelerating extinction at an alarming rate. Although habitat loss caused by human activity still constitutes the main threat to amphibian populations, habitat protection no longer provides any guarantee of amphibian survival. Infectious diseases are now threatening even seemingly secluded habitats. The most devastating of the known amphibian diseases is chytridiomycosis, which is caused by a deadly chytrid fungus (Batrachochytrium dendrobatidis, or Bd). The fungus attacks the skin, which is particularly important in amphibians because they breathe through it. A large number of species have already been lost in this way -- particularly in tropical Central America, where two-thirds of the colorful harlequin frog species have already been decimated across their entire area of distribution. Bd has now been identified in over 500 amphibian species, 200 of which have seen a significant decline in numbers. The pathogen is therefore classified worldwide as one of the greatest threats to biodiversity.

Until now, however, a few islands like Madagascar were thought not to have been affected. The last series of tests from 2005 to 2010 found no trace of the pathogenic fungus there. However, an analysis of the latest series of tests shows that the chytrid fungus also poses a threat to amphibians in Madagascar. "This is sad news for amphibian-lovers around the world," says Dr Dirk Schmeller of the UFZ, who was involved in analyzing the samples. "Firstly, it means that an island that is home to a particularly high number of amphibian species is now at risk. Several hundred species live only on this island. And, secondly, if the pathogen has managed to reach such a secluded island, it can and will occur everywhere."

For the study that has just been published, the research team analyzed samples from over 4000 amphibians from 50 locations in Madagascar taken since 2005. Samples from four species of Madagascan frog (Mantidactylus sp.) taken in 2010, and from one Mascarene frog (Ptychadena mascareniensis) taken in 2011 from the remote Makay massif tested positive for the fungus. In samples from 2013 and 2014 the pathogen was found in five different regions. Prof. Miguel Vences from TU Braunschweig says, "The chytrid fungus was found in all four families of the indigenous Madagascan frogs, which means it has the potential to infect diverse species. This is a shock!" The study also shows that the disease affects amphibians at medium to high altitudes, which ties in with observations from other parts of the world, where the effects of the amphibian epidemic have been felt primarily in the mountains.

The fact that the fungus has been identified in a very remote part of the island has puzzled the researchers. There is some hope that it may prove to be a previously undiscovered, native strain of the pathogen, which may have existed in the region for some time and have gone undetected because of a lack of samples. In this case, Madagascar's amphibians may have developed resistance to it. However, further research is needed to confirm this hypothesis before the all-clear can be given. It is also possible that the fungus was brought to the island in crustaceans or the Asian common toad (Duttaphrynus melanostictus), carried in by migratory birds or humans. "Luckily, there have not yet been any dramatic declines in amphibian populations in Madagascar," Dirk Schmeller reports. "However, the pathogen appears to be more widespread in some places than others. Madagascar may have several strains of the pathogen, maybe even the global, hypervirulent strain. This shows how important it is to be able to isolate the pathogen and analyze it genetically, which is something we haven't yet succeeded in doing." At the same time, the researchers recommend continuing with the monitoring program across the entire country to observe the spread of the disease. The scientists also suggest setting up extra breeding stations for key species, in addition to the two centers already being built, to act as arks, so that enough amphibians could be bred to recolonize the habitats in a crisis. "We are also hopeful that we may be able to suppress the growth of the Bd pathogen with the help of skin bacteria," says Miguel Vences. "It might then be possible to use these bacteria as a kind of probiotic skin ointment in the future." A high diversity of microbial communities in the water could also reduce the potential for infection, according to earlier investigations conducted by UFZ researchers and published in Current Biology.

The outbreak of amphibian chytridiomycosis in Madagascar puts an additional seven per cent of the world's amphibian species at risk, according to figures from the Amphibian Survival Alliance (ASA). "The decline in Madagascan amphibians is not just a concern for herpetologists and frog researchers," says Dr Franco Andreone from the International Union for Conservation of Nature (IUCN), who is one of the study authors. "It would be a great loss for the entire world." In the coming months, the scientists therefore plan to work with the government to draw up an emergency plan to prevent this scenario.

Bletz MC, Rosa GM, Andreone F, Courtois EA, Schmeller DS, Rabibisoa NHC, Rabemananjara FCE, Raharivololoniaina L, Vences M, Weldon C, Edmonds D, Raxworthy CJ, Harris RN, Fisher MC, Crottini A. Widespread presence of the pathogenic fungus Batrachochytrium dendrobatidis in wild amphibian communities in Madagascar. Scientific Reports, 2015; 5: 8633 DOI:10.1038/srep08633

Thursday, February 26, 2015

A Miocene radiation of crocs in the Pebas Wetland

The massive wetlands once covered the Amazon River basin about
13 million years ago during the late middle Miocene. Three newly
discovered species of crocodylians, including Kuttanacaiman
iquitosensis (left), Caiman wannlangstoni (right) and Gnatusuchus
pebasensis (bottom), look for clams, which they could likely scoop up
with their mouths and crunch with their peglike teeth.
Artist Credit: Javier Herbozo

Thirteen million years ago, as many as seven different species of crocodiles hunted in the swampy waters of what is now northeastern Peru, new research shows. This hyperdiverse assemblage, revealed through more than a decade of work in Amazon bone beds, contains the largest number of crocodile species co-existing in one place at any time in Earth's history, likely due to an abundant food source that forms only a small part of modern crocodile diets: mollusks like clams and snails. The work, published today in the journal Proceedings of the Royal Society B, helps fill in gaps in understanding the history of the Amazon's remarkably rich biodiversity.

"The modern Amazon River basin contains the world's richest biota, but the origins of this extraordinary diversity are really poorly understood," said John Flynn, Frick Curator of Fossil Mammals at the American Museum of Natural History and an author on the paper. "Because it's a vast rain forest today, our exposure to rocks--and therefore, also to the fossils those rocks may preserve--is extremely limited. So anytime you get a special window like these fossilized "mega-wetland" deposits, with so many new and peculiar species, it can provide novel insights into ancient ecosystems. And what we've found isn't necessarily what you would expect."

Before the Amazon basin had its river, which formed about 10.5 million years ago, it contained a massive wetland system, filled with lakes, embayments, swamps, and rivers that drained northward toward the Caribbean, instead of today's pattern of eastward river flow to the Atlantic Ocean. Knowing the kind of life that existed at that time is crucial to understanding the history and origins of modern Amazonian biodiversity. But although invertebrates like mollusks and crustaceans are abundant in Amazonian fossil deposits, evidence of vertebrates other than fish have been very rare.

Since 2002, Flynn has been co-leading prospecting and excavating expeditions with colleagues at fossil outcrops of the Pebas Formation in northeastern Peru. These outcrops have preserved life from the Miocene, including the seven species of crocodiles discussed in Proceedings B. Three of the species are entirely new to science, the strangest of which is Gnatusuchus pebasensis, a short-faced caiman with globular teeth that is thought to have used its snout to "shovel" mud bottoms, digging for clams and other mollusks. The new work suggests that the rise of Gnatusuchus and other "durophagous," or shell-crunching, crocodiles is correlated with a peak in mollusk diversity and numbers, which disappeared when the mega-wetlands transformed into the modern Amazon River drainage system.

"When we analyzed Gnatusuchus bones and realized that it was probably a head-burrowing and shoveling caiman preying on mollusks living in muddy river and swamp bottoms, we knew it was a milestone for understanding proto-Amazonian wetland feeding dynamics," said Rodolfo Salas-Gismondi, lead author of the paper and a graduate student at the University of Montpellier, in France, as well as researcher and chief of the paleontology department at the National University of San Marcos' Museum of Natural History in Lima, Peru.

Besides the blunt-snouted crocodiles like Gnatusuchus, the researchers also recovered the first unambiguous fossil representative of the living smooth-fronted caiman Paleosuchus, which has a longer and higher snout shape suitable for catching a variety of prey, like fish and other active swimming vertebrates.

Besides the blunt-snouted caimanines with crushing dentition and stout jaws, and smooth-fronted caiman Paleosuchus, which possesses a relatively more generalist snout shape the authors report other caimanines with more specialized feeding habits. They included the following. The larger Purussaurus neivensis and Mourasuchus atopus (both previously known from other Miocene localities in the region). Purussaurus had a hulking skull and a mandible with large robust anterior teeth and smaller blunt posterior teeth. The ‘duck-faced’ taxon Mourasuchus had an exceptionally long, wide rostrum. Its feeding habits are controversial, although previous authors thought it ate small fishes by some kind of filtering strategy. A new, unnamed gavialoid is the only crocodylian with a longirostral morphotype in this community, a fact that contrasts with the high diversity of longirostrine crocodylians characteristic of Late Miocene Neotropical assemblages.

"We uncovered this special moment in time when the ancient mega-wetland ecosystem reached its peak in size and complexity, just before its demise and the start of the modern Amazon River system," Salas-Gismondi said. "At this moment, most known caiman groups co-existed: ancient lineages bearing unusual blunt snouts and globular teeth along with those more generalized feeders representing the beginning of what was to come."

The new research suggests that with the inception of the Amazon River System, mollusk populations declined and durophagous crocodile species went extinct as caimans with a broader palate diversified into the generalist feeders that dominate modern Amazonian ecosystems. Today, six species of caimans live in the whole Amazon basin, although only three ever co-exist in the same area and they rarely share the same habitats. This is in large contrast to their ancient relatives, the seven diverse species that lived together in the same place and time.


Salas-Gismondi R, Flynn JJ, Baby P, Tejada-Lara JV, Wesselingh FP, Antoine P-O. 2015. A Miocene hyperdiverse crocodylian community reveals peculiar trophic dynamics in proto-Amazonian mega-wetlands. Proceedings of the Royal Society B  DOI: 10.1098/rspb.2014.2490

Wednesday, February 25, 2015

New drug potential from Heloderma

Heloderma suspectum

Lizards and other reptiles are not normally considered venomous, but a number of lizard species actually do produce and use venom. The most classic venomous lizard is no doubt the gila monster -- a heavy-bodied lizard. As the first in the world, a group of researchers has made a comprehensive description of the proteins in the venom which can prove to be relevant in connection with developing new types of drugs.

Gila and beaded lizards are the classic venomous lizards. However, it was recently shown that venom is also used by a number of other species, such as the awesome Komodo monitors -- the largest present-day lizards. Lizard venom has much in common with snake venom, and the current theory is that the venom production apparatus in lizards and snakes is related, but has developed in different directions. Gila and beaded lizards mainly use venom to defend themselves, while snakes use their venom to attack prey. However, the composition of venom proteins is similar in lizards and snakes.

Venom research is a large field, especially due to the pharmaceutical potential of the venom proteins. The idea here is that venom proteins are capable of affecting the body's cells. Excessive amounts can be harmful and even lethal in some circumstances, but if the right dose is used, the venom proteins can be used to treat certain diseases. Snake proteins that normally cause prey to bleed can be used in small doses to treat blood clots, for example. In the same way, work is currently being done to develop spider venom proteins to provide pain relief. The Aarhus researchers focused on Gila lizards, and these are currently being used in pharmaceutical contexts. Gila lizards produce exendin-4, a small venom protein used in the treatment of diabetes and obesity, which is a competitor to Victoza® -- produced by Novo Nordisk.

A method called proteomics was used in the Aarhus study to make the first overall description of venom proteins in Gila lizards. Individual proteins such as exendin-4 used to be purified from Gila lizard venom, and this resulted in a number of interesting results. However, an overall analysis of all the venom proteins has not been undertaken before, which therefore made it easy to overlook the potentially important components in the venom.

Making a comprehensive analysis of the venom protein composition was not an easy task. "The work was complicated by the fact that the Gila lizard genome hasn't been isolated, and genomes normally provide a map to navigate when you're using proteomics for protein identifications," says Associate Professor Kristian Wejse Sanggaard. "We therefore used a more manually based approach to identify the proteins in the Gila lizard venom. This succeeded, and we've identified nineteen proteins that no one previously knew existed in the venom," he concludes.

Based on these identifications, the researchers have gained new knowledge about the function of the venom proteins, and have also gained greater insight into the evolutionary contexts of venom proteins. In addition, there are now new proteins that can potentially be used to develop future drugs.

Sanggaard KW, Dyrlund TF, Thomsen LR, Nielsen TA, Brøndum L, Wang T, Thøgersen IB, Enghild JJ. Characterization of the gila monster (Heloderma suspectum suspectum) venom proteome. Journal of Proteomics, 2015; 117: 1 DOI: 10.1016/j.jprot.2015.01.004

Thursday, February 19, 2015

The Spider-tailed Viper in action

The following video was sent to me by Patrick Prévost (Amneville Zoo, France). Video of captives moving their tail on a sand substrate have been available on You-Tube. This video shows a snake catching a bird. Sorry about the ad!

La vipère araignée by Spi0n

A second chance for two Australian sea snakes (Aipysurus) presumed extinct

Photographs A,C: A. apraefrontalis (SAMA R68142)
from Ashmore Reef; and B, D:Aipysurus foliosquama
(WAM R150365) from Barrow Island.
One in five reptile species are estimated to be at risk of extinction and many are thought to have become extinct within the last 50 years. Threats to reptiles include habitat loss and degradation, climate warming, and overharvest for food, traditional medicines and leather. Rediscoveries of presumed extinct species inspire optimism, but many such rediscovered species remain at immediate risk of extinction and require urgent assessment of population status and threats in their remaining range to guide management actions.

In a new paper published in PLoS ONE, Sanders, Schroeder, Guinea and Rasmussen (2015) report on the critically endangered leaf-scaled (Aipysurus foliosquama) and short-nosed (A. apraefrontalis) sea snakes. Species currently recognized only from Ashmore and Hibernia reefs ~600km off the northwest Australian coast. Steep population declines in both species were documented over 15 years and neither has been sighted on dedicated surveys of Ashmore and Hibernia since 2001. The authors examine specimens of these species that were collected from coastal northwest Australian habitats up until 2010 (A. foliosquama) and 2012 (A. apraefrontalis) and were either overlooked or treated as vagrants in conservation assessments. Morphological variation and mitochondrial sequence data confirm the assignment of these coastal specimens to A. foliosquama (Barrow Island, and offshore from Port Hedland) and A.apraefrontalis (Exmouth Gulf, and offshore from Roebourne and Broome). Collection dates, and molecular and morphological variation between coastal and offshore specimens, suggest that the coastal specimens are not vagrants as previously suspected, but instead represent separate breeding populations. The newly recognized populations present another chance for leaf-scaled and short-nosed sea snakes, but the coastal habitats in northwest Australia are threatened by infrastructure developments and sea snakes are presently omitted from environmental impact assessments for industry. The authors note further studies are urgently needed to assess these species’ remaining distributions, population structure, and extent of occurrence in protected area.


Sanders KL, Schroeder T, Guinea ML, Rasmussen AR (2015) Molecules and Morphology Reveal Overlooked Populations of Two Presumed Extinct Australian Sea Snakes (Aipysurus: Hydrophiinae). PLoS ONE 10(2): e0115679. doi:10.1371/journal.pone.0115679.

Body size and extinction


A new University of Toronto study may force scientists to rethink what is behind the mass extinction of amphibians occurring worldwide in the face of climate change, disease and habitat loss.

The old cliché "size matters" is in fact the gist of the findings by graduate student Stephen De Lisle and Professor Locke Rowe of U of T's Department of Ecology & Evolutionary Biology in a paper published today in Proceedings of the Royal Society B.

By examining research on global patterns of amphibian diversification over hundreds of millions of years, De Lisle and Rowe discovered that "sexually dimorphic" species -- those in which males and females differ in size, for example -- are at lower risk of extinction and better able to adapt to diverse environments.

Their work suggests the ability of males and females in sexually dimorphic amphibian species to independently evolve different traits -- such as size -- helps them survive extinction threats that kill off others, says De Lisle.

He says classic ecological theory would not have predicted that about amphibians, a class of vertebrates that includes frogs, toads, salamanders, newts and caecilians.

The conventional school of thought believes different-sized sexes of the same species take up more resources and are less able to adapt and diversify than species where ecologically relevant traits like size are basically the same between males and females.

"I think if our results bear on mass extinction at all, it suggests we maybe should start looking more closely at the traits of some of the species that are going extinct," says De Lisle.

"Scientists might start thinking in a new way about how other traits, like sex differences in habitat use or diet, might play a role."

While peacock feathers or deer antlers are understood to help males of those species successfully mate, less is understood about amphibians, which are being wiped out so fast many are going extinct before scientists can identify them.

Some estimate between 30 and 40 per cent of the world's approximately 7,000 species of amphibians are currently in danger of extinction -- more than any other animals on earth -- and their decline is a critical threat to global biodiversity.

Many scientists believe amphibians serve as "canaries in a coal mine," and declines in their populations indicate other groups of animals and plants will soon be at risk.

Amphibians are not only an important part of the food chain and biodiversity. Some have chemicals in their skins that can be developed into medicines to fight diseases such as cancer and perhaps even AIDS.

Because their skins are highly permeable and they have a two-staged life cycle that starts in water and then moves to land, amphibians may be more susceptible to temperature changes, water and air pollution than other animals.

The new study by De Lisle and Rowe adds another piece to the puzzle about why some species are doing well while others are in decline or disappearing.

For example, both the golden toad and the harlequin frog of Costa Rica's Monteverde Cloud Forest Preserve disappeared completely in the late 1980s despite living in what was considered a pristine habitat.

"Our work suggests we still maybe don't have the best understanding of what traits might be influencing these extinctions, although now we have the understanding that sexual dimorphism is an important trait," says De Lisle.

Stephen P. De Lisle, Locke Rowe. Independent evolution of the sexes promotes amphibian diversification. Proceedings of the Royal Society B, February 2015 DOI: 10.1098/rspb.2014.2213

Monday, February 9, 2015

Coral snake venom targets GABA(A) receptors

The rare coral snake Micrurus mipartitus (type locality, Caracas, 
Venezuela). Credit: Alejandro Solórzano
For more than a decade, a vial of rare snake venom refused to give up its secret formula for lethality; its toxins had no effect on the proteins that most venoms target. Finally, an international team of researchers figured out its recipe: a toxin that permanently activates a crucial type of nerve cell protein, preventing the cells from resetting and causing deadly seizures in prey. The details will be published online in the Proceedings of the National Academy of Sciences the week of Feb. 9.

"What we found are the first known animal toxins, and by far the most potent compounds, to target GABA(A) receptors," says Frank Bosmans, Ph.D., assistant professor of physiology and neuroscience at the Johns Hopkins University School of Medicine. "Once they bind to the receptors, they don't let go."

Biochemical studies revealed the identity of the venom's active ingredient: it's actually twin proteins, dubbed micrurotoxins (MmTX) after their serpentine source, the reclusive coral snake Micrurus mipartitus. Most toxins in snake venoms target specialized nicotinic acetylcholine receptors on the surface of nerve cells that make muscles contract, paralyzing the snakes' victims. But when the researchers tested MmTX on lab-grown cells saturated with nicotinic acetylcholine receptors, nothing happened. This was puzzling because, in mice, MmTX was known to cause a repeating pattern of relaxation and seizures, similar to what's seen in epilepsy.

By tagging the protein with a radioactive label, the team at Aix Marseille University was able to find out what protein it acted on. To the team's surprise, MmTX binds to GABA(A) receptors -- pores on nerve cells in the brain and spinal cord. GABA(A) receptors' job is to respond to the molecule GABA by opening to let negatively charged chloride ions flow into a nerve cell that has just fired. Doing so resets the cell's equilibrium so that it can fire another signal when needed.

Further testing showed that MmTX binds to GABA(A) receptors more tightly than any other compound known -- 100 times tighter than the plant-derived compound PTX, for example. MmTX also binds to a unique site on the GABA(A) receptor protein. Binding at that site changes the receptor's shape, making it far too sensitive to GABA molecules. When GABA binds, the receptor's pore opens permanently and the nerve cell is never able to reset, causing it to misfire, convulsing the animal and potentially causing death.

"Anti-anxiety medications like diazepam and alprazolam bind to GABA(A) receptors too, but they cause relaxation instead of seizures because they bind much more loosely," says Bosmans. His team plans to use MmTX as a tool for learning more about how GABA(A) receptors work. Since errors in the receptors can cause epilepsy, schizophrenia and chronic pain, the team hopes that their future work will be able to shed light on these and other disorders.

Other authors of the report include Jean-Pierre Rosso, Brigitte Ceard and Pierre Bougis of Aix Marseille University in France; Jurgen Schwarz and Matthias Kneussel of the University Medical Center Hamburg-Eppendorf in Germany; Marcelo Diaz-Bustamante of The Johns Hopkins University; Maria Gutierrex of the Universidad de Costa Rica; and Olaf Pongs of the Universitat des Saarlandes in Germany.

This work was supported by the Centre National de la Recherche Scientifique.


Rosso J-P, Schwarz JR, Diaz-Bustamante M, Céard B, Gutiérrez JM, Kneussel M, Pongs O, Bosmans F, and Bougis PE. MmTX1 and MmTX2 from coral snake venom potently modulate GABAA receptor activity. PNAS February 9, 2015 DOI: 10.1073/pnas.1415488112.