Wednesday, October 31, 2012

[Ornithology • 2012] The Global Diversity of Birds in Space and Time | First Ever Family Tree for All Living Birds Reveals Evolution and Diversification

Analysis of the family tree shows when and where birds diversified — and that birds’ diversification rate has increased over the last 50 million years, challenging the conventional wisdom of biodiversity experts. (Credit: Image courtesy of Yale University)

Here we present, analyse and map the first complete dated phylogeny of all 9,993 extant species of birds, a widely studied group showing many unique adaptations. We find that birds have undergone a strong increase in diversification rate from about 50 million years ago to the near present. This acceleration is due to a number of significant rate increases, both within songbirds and within other young and mostly temperate radiations including the waterfowl, gulls and woodpeckers. Importantly, species characterized with very high past diversification rates are interspersed throughout the avian tree and across geographic space. Geographically, the major differences in diversification rates are hemispheric rather than latitudinal, with bird assemblages in Asia, North America and southern South America containing a disproportionate number of species from recent rapid radiations. The contribution of rapidly radiating lineages to both temporal diversification dynamics and spatial distributions of species diversity illustrates the benefits of an inclusive geographical and taxonomical perspective

Figure 2: Diversification across the avian tree.
Experts used the family tree to map out where the almost 10,000 species of birds live to show where the most diversification has taken place in the world.

First ever family tree for all living birds reveals evolution and diversification

The world’s first family tree linking all living birds and revealing when and where they evolved and diversified since dinosaurs walked the earth.

Experts used the family tree to map out where the almost 10,000 species of birds live to show where the most diversification has taken place in the world.

Researchers, from the University of Sheffield, Yale University, University of Tasmania and Simon Fraser University, say the creation of new species has speeded-up over the last 50 million years. Surprisingly, species formation is not faster in the species rich tropics, but was found to be faster in the Western Hemisphere compared to the Eastern Hemisphere as well as on islands.

As well as being the first time scientists have created a family tree for birds, it is hoped the research could help prioritise conservation efforts in a bid to save the most diverse species from extinction.

Dr Gavin Thomas, of the University of Sheffield’s Department of Animal and Plant Sciences, said: "We have built the first ever family tree showing the evolutionary relationship among the species of birds. We used fossils and genetic data to estimate the ages of all the different branches of the bird tree so that we could assess how diversity has accumulated through time. Our work is indebted to researchers from museums and universities who have collected astounding amounts of genetic data from birds around the world."

Despite major steps forward in modern super computers it has still taken the researchers almost five years to analyse the millions of year’s worth of fossil data, DNA, maths and maps, to create this never-before-snapshot of how the thousands of birds alive made it to where they are today.

To even enable the scientists to calculate which species were more or less diverse they had to create a new 'species rate' measure.

Dr Thomas added: "Diversification is the net outcome of new species arising, called speciation, and existing species going extinct. We combined this data with existing data on the geographic ranges of all living bird species so that we could map diversification across the world.

"This 'phylogeny' is important because it is the first that includes all living birds. It means we can ask questions about biodiversity and evolution on a global scale and gain new insight into how diversity has changed over millions of years as well as understand those changes. More widely, one way in which the phylogeny can be used, and which may not be obvious, is in helping to prioritise conservation efforts.

"We can identify where species at greatest risk of extinction are on the tree and ask how much distinct evolutionary history they represent. Some species have many close relatives and represent a small amount of distinct evolutionary history whereas others have few close relatives and their loss would represent the disappearance of vast amounts of evolutionary history that could never be recovered. Environmental change has very likely affected diversification over time. Climate change could be a part of that through its effects on the extent of different types of habitat."

Figure 3: Geographic variation in species-level lineage diversification rate and the richness of high-diversification rate species.

W. Jetz, G. H. Thomas, J. B. Joy, K. Hartmann & A. O. Mooers. 2012. The global diversity of birds in space and time. Nature. doi:10.1038/nature11631,  

First ever family tree for all living birds reveals evolution and diversification
The world’s first family tree linking all living birds and revealing when and where they evolved and diversified since dinosaurs walked the earth has been created by scientists from the University of Sheffield.  via @sheffielduni

First Ever Family Tree for All Living Birds Reveals Evolution and Diversification
Exhaustive Family Tree for Birds Shows Recent, Rapid Diversification

[Ornithology • 2012] The Genomic Landscape of Species Divergence in Ficedula flycatchers | Flycatchers' genomes explain how one species became two

Collared flycatcher. (Credit: Johan Träff)

Unravelling the genomic landscape of divergence between lineages is key to understanding speciation. The naturally hybridizing collared flycatcher and pied flycatcher are important avian speciation models that show pre- as well as postzygotic isolation. We sequenced and assembled the 1.1-Gb flycatcher genome, physically mapped the assembly to chromosomes using a low-density linkage map and re-sequenced population samples of each species. Here we show that the genomic landscape of species differentiation is highly heterogeneous with approximately 50 ‘divergence islands’ showing up to 50-fold higher sequence divergence than the genomic background. These non-randomly distributed islands, with between one and three regions of elevated divergence per chromosome irrespective of chromosome size, are characterized by reduced levels of nucleotide diversity, skewed allele-frequency spectra, elevated levels of linkage disequilibrium and reduced proportions of shared polymorphisms in both species, indicative of parallel episodes of selection. Proximity of divergence peaks to genomic regions resistant to sequence assembly, potentially including centromeres and telomeres, indicate that complex repeat structures may drive species divergence. A much higher background level of species divergence of the Z chromosome, and a lower proportion of shared polymorphisms, indicate that sex chromosomes and autosomes are at different stages of speciation. This study provides a roadmap to the emerging field of speciation genomics.

2012. The genomic landscape of species divergence in Ficedula flycatchers. Nature. DOI:

Flycatchers' genomes explain how one species became two

Just how new species are established is still one of the most central questions in biology. In an article in the leading scientific journal Nature, researchers at Uppsala University in Sweden describe how they mapped the genomes of the European pied flycatcher and the collared flycatcher and found that it is disparate chromosome structures rather than separate adaptations in individual genes that underlies the separation of the species.

"We were surprised that such a large part of the genome was nearly identical in the two species," says Hans Ellegren, professor of evolutionary biology and director of the research team behind the new findings.
The big question in species-differentiation research today involves the genetic background of how two evolutionary lines gradually come to diverge from each other and ultimately cannot produce fertile young. Horses and donkeys, for instance, can crossbreed and produce mules and hinnies, but something in the genome of the latter makes them infertile. There must therefore be DNA sequences from diverging evolutionary lines that are not compatible.

Researchers at the Evolutionary Biology Centre, Uppsala University, are now presenting the genome sequence for the two flycatchers, which are the first organisms apart from so-called model organisms, to have their genome sequenced. They are also the first DNA sequences for a vertebrate to have been determined entirely by Swedish researchers and at a Swedish laboratory.

The Uppsala scientists have charted the genome of the flycatchers and then sequenced the entire genome of some ten individuals of European pied flycatcher and the collared flycatcher respectively. The two species occur together on the Baltic islands of Öland and Gotland, where they sometimes hybridize, that is, mate with each other.

The scientists have now managed to identify the regions in the respective flycatchers' genomes that are most clearly different. It turns out that it is a matter of one or a few regions per chromosome, and these regions coincide with the chromosome parts that are involved in meiosis and the production of gender cells (centromeres). This indicates that what underlies the separation of the species it is the disparate chromosome structures rather than different adaptations in individual genes.

"There is good reason to believe that this observation is highly generalizable and that it explains species differentiation across organism groups," says Hans Ellegren.

The European pied flycatcher, and later its close relative the collared flycatcher, have long been an important research organism for scientists at many universities. Their nesting (and thereby reproductive success) is rather easy to observe, as they readily inhabit deployed birdhouses. Over the years Uppsala research has laid a foundation for understanding many general aspects of ecology and evolution, with multiple doctoral dissertations and acclaimed research reports.

Flycatchers' genomes explain how one species became two: 

[PaleoIchthyology • 2013] Potanichthys xingyiensis • A new stem-neopterygian fish from the Middle Triassic of China shows the earliest over-water gliding strategy of the vertebrates

Potanichthys xingyiensis gen. et sp. nov. 
Reconstruction & Holotype (a) 

Flying fishes are extraordinary aquatic vertebrates capable of gliding great distances over water by exploiting their enlarged pectoral fins and asymmetrical caudal fin. Some 50 species of extant flying fishes are classified in the Exocoetidae (Neopterygii: Teleostei), which have a fossil record no older than the Eocene. The Thoracopteridae is the only pre-Cenozoic group of non-teleosts that shows an array of features associated with the capability of over-water gliding. Until recently, however, the fossil record of the Thoracopteridae has been limited to the Upper Triassic of Austria and Italy. Here, we report the discovery of exceptionally well-preserved fossils of a new thoracopterid flying fish from the Middle Triassic of China, which represents the earliest evidence of an over-water gliding strategy in vertebrates. The results of a phylogenetic analysis resolve the Thoracopteridae as a stem-group of the Neopterygii that is more crown-ward than the Peltopleuriformes, yet more basal than the Luganoiiformes. As the first record of the Thoracopteride in Asia, this new discovery extends the geographical distribution of this group from the western to eastern rim of the Palaeotethys Ocean, providing new evidence to support the Triassic biological exchanges between Europe and southern China. Additionally, the Middle Triassic date of the new thoracopterid supports the hypothesis that the re-establishment of marine ecosystems after end-Permian mass extinction is more rapid than previously thought.

Keywords: Thoracopteridae, Exocoetidae, flying fish, predator-driven evolution, Triassic

Reconstruction of the phenotype of Potanichthys xingyiensis gen. et sp. nov.

 Xu G-H, Zhao L-J, Gao K-Q, Wu F-X. 2013. A new stem-neopterygian fish from the Middle Triassic of China shows the earliest over-water gliding strategy of the vertebrates. Proc R Soc B. 20122261.

[Herpetology • 2012] Kihansi Spray Toad | Nectophrynoides asperginis • Reintroduction in Udzungwa Mountains, south-central Tanzania

‘Extinct’ Toad Returns Home

Kihansi Spray Toad, Nectophrynoides asperginis, is a dwarf toad, which rarely grows to be more than 2cm long.

The Kihansi Spray Toad, Nectophrynoides asperginis, was restricted to the smallest known range for any vertebrate species, with an estimated historic wild population of 17,000 toads found within 2 hectares of waterfall spray zone in the Kihansi Gorge of the Udzungwa Mountains in south-central Tanzania. Only discovered by scientists in 1996, the thumbnail-sized golden colored toad was believed to be extirpated from its small patch of habitat in 2004, and was officially declared Extinct in the Wild by the International Union for Conservation of Nature (IUCN) in October 2009.

In reference to the specialized biology of the Kihansi Spray Toad, University of Dar es Salaam professors, Dr. Charles Msuya and Dr. Kim Howell, one of the scientists to discover the toad in 1996, jointly wrote, “The Kihansi Spray Toad is unique because of its specialized habitat. It was endemic to Tanzania, in the ‘spray meadows’ at the base of the Kihansi Falls that received more than 70 mm of ‘rain’ per day in the form of spray from the falls prior to the construction of the Lower Kihansi Hydropower Project dam. Very few species of amphibians can survive in this habitat. The KST is also unusual because its life cycle does not have a free swimming tadpole stage, but rather, females give birth to tiny froglets.”

The species’ rapid decline followed hydroelectric dam construction upstream from its habitat that resulted in a nearly complete loss of the “spray meadow” habitat that the species depended on, and coincided with the emergence of the amphibian chytrid fungus, a disease that has been implicated in amphibian extinctions in several parts of the world. In November 2000, at the invitation of the Tanzanian Government, 499 toads were collected and transferred to the Wildlife Conservation Society’s Bronx Zoo, and later the Toledo Zoo, to initiate a captive breeding program which is now represented by over 6,000 toads. In 2010, a captive colony was established in Tanzania by University of Dar Salaam and National Environmental Management Council researchers who had facilities constructed specifically for the conservation of the small toad in Dar es Salaam and at the base of the Kihansi Gorge.

“The level of collaboration from the Tanzanian government and the participating zoos, to the Tanzanian field biologists and students who shared their knowledge with us, has been nothing short of inspiring. This is one of the great stories of amphibian conservation,” said R. Andrew Odum, curator of herpetology at the Toledo Zoo. “The Bronx Zoo has been working with our partners, including the Toledo Zoo, for more than a decade to save this species and reintroduce it back into the wild. This landmark occasion is reason to celebrate,” said Jim Breheny, Executive Vice President and General Director of WCS Zoos & Aquarium and Director of the Bronx Zoo.

In 2010, the Lower Kihansi Environmental Management Project (LKEMP) within Tanzania’s National Environmental Management Council (NEMC) and the University of Dar Salaam organized Tanzanian researchers and an international team of conservation biologists and pathologists from the Toledo Zoo, the Wildlife Conservation Society, the IUCN SSC Amphibian Specialist Group, the IUCN SSC Re-introduction Specialist Group, Global Wildlife Conservation, and other partners to develop a plan for reintroducing the Kihansi Spray Toad to its native habitat. The reintroduction plan set a timeframe to address causes of the KST decline as well as carry out a series of experiments to ensure the species’ survival in the wild. At this stage, preliminary ‘soft’ release studies involving toads within mesh cages situated in the native habitat have shown success.

Prior to its reintroduction, several initiatives were made to restore the Kihansi Gorge ecosystem. These included the installation of an expansive misting system designed to replicate the spray zone habitat that was lost after dam construction, and building of bridges and walkways to facilitate monitoring of the gorge. Funded by the World Bank and the Government of Norway, the misting system has been running since late 2000 in order to restore and maintain the native vegetation that the toads once lived amongst, and the invertebrates upon which they fed.

Today, October 30th, 2012, the missing amphibian that has been the focus of much attention in Tanzania and around the world was returned to its niche within this unique ecosystem. The initial release represents a total of 2,500 animals flown to Tanzania from the Toledo and Bronx Zoos in June and earlier this month. The animals made their international journey safely and were acclimatized before their release. Future releases are expected as researchers work towards reestablishing a viable population in the wild. The reintroduction of the Kihansi Spray Toad is being led by researchers from the University of Dar es Salaam, the National Environment Management Council of Tanzania, and Tanzania Wildlife Research Institute, in international collaboration with scientists from the University of Georgia’s Savannah River Ecology Laboratory, Toledo Zoo, Wildlife Conservation Society, IUCN SSC Amphibian Specialist Group, and Global Wildlife Conservation.

“Most reintroductions for amphibians and reptiles have been designed to establish or augment a population of a rare species, but it is extremely exciting to be involved in actually returning a species that was extinct in the wild back to its native habitat.” said Dr. Kurt Buhlmann and Dr. Tracey Tuberville, research scientists with the University of Georgia’s Savannah River Ecology Laboratory and Associate Conservation Scientists with Global Wildlife Conservation. Drs. Tuberville and Buhlmann went on to say, “This project is a shining example of international collaboration, linking tremendous effort by the Tanzanians to recreate the unique habitat, with successful captive breeding programs, and a scientific approach to implementing the reintroduction for a species that was nearly lost.”

A third of the world’s approximately 7,000 amphibian species are threatened with extinction. Hundreds of species are thought to have gone extinct within the past few decades due to habitat loss, disease, and other factors. The reintroduction of the Kihansi Spray Toad represents a tremendous success story in amphibian conservation thanks to swift action by the Tanzanian government and an international effort by collaborating organizations. It is one of only a handful of amphibian species, globally, to have been saved from extinction through an intensive captive breeding program. Now that it has returned to its restored habitat, the Kihansi Spray Toad represents the world’s first reintroduction of an ‘Extinct in the Wild’ amphibian.

“As a signatory to the Convention on Biological Diversity (CBD) and Convention on International Trade on Endangered Species (CITES), key decisions were taken followed by initiatives to restore the Kihansi Gorge ecosystem. Reintroduction of Kihansi Spray Toads and other ongoing efforts depict Tanzania’s commitment towards the conservation of biodiversity as well as balancing water needs among the different users.” said Mr. Sazi Salula, the Permanent Secretary of Tanzania at the Vice President’s Office.

Co-Chair of the IUCN SSC Amphibian Specialist Group, Dr. Claude Gascon, stated, “The success story of the small Kihansi Spray Toad can teach us big lessons for the future of biodiversity conservation. While amphibians and other species are incurring severe threats to their survival, it is never too late to use the best science and conservation action to save a species and its habitat. This success story has only been possible with the help and partnership of many organizations around the world and the leadership of the Government of Tanzania, and the belief that no species and no situation is too dire to try to save life on Earth. Extinction in the wild is not forever.”

Tuesday, October 30, 2012

[Herpetology • 2010] Born Knowing: Tentacled Snakes Erpeton tentaculatus Innately Predict Future Prey Behavior

Figure 1. The unusual anatomy of the tentacled snake's head under the scanning electron microscope. 
The scaled tentacles are sensitive mechanoreceptors that respond to water movements. These appendages likely aid snakes in locating fish at night, with the eyes the playing the dominant role under lighted conditions.

Aquatic tentacled snakes (Erpeton tentaculatus) can take advantage of their prey's escape response by startling fish with their body before striking. The feint usually startles fish toward the snake's approaching jaws. But when fish are oriented at a right angle to the jaws, the C-start escape response translates fish parallel to the snake's head. To exploit this latter response, snakes must predict the future location of the fish. Adult snakes can make this prediction. Is it learned, or are tentacled snakes born able to predict future fish behavior?

Methods and Findings
Laboratory-born, naïve snakes were investigated as they struck at fish. Trials were recorded at 250 or 500 frames per second. To prevent learning, snakes were placed in a water container with a clear transparency sheet or glass bottom. The chamber was placed over a channel in a separate aquarium with fish below. Thus snakes could see and strike at fish, without contact. The snake's body feint elicited C-starts in the fish below the transparency sheet, allowing strike accuracy to be quantified in relationship to the C-starts. When fish were oriented at a right angle to the jaws, naïve snakes biased their strikes to the future location of the escaping fish's head, such that the snake's jaws and the fish's translating head usually converged. Several different types of predictive strikes were observed.

The results show that some predators have adapted their nervous systems to directly compensate for the future behavior of prey in a sensory realm that usually requires learning. Instead of behavior selected during their lifetime, newborn tentacled snakes exhibit behavior that has been selected on a different scale—over many generations. Counter adaptations in fish are not expected, as tentacled snakes are rare predators exploiting fish responses that are usually adaptive.

Figure 2. Tentacled snake hunting posture and strategy.

 Catania KC (2010) Born Knowing: Tentacled Snakes Innately Predict Future Prey Behavior. PLoS ONE. 5(6): e10953. doi:10.1371/journal.pone.0010953

[Herpetology • 2010] Function of the appendages in tentacled snakes Erpeton tentaculatus

A tentacled snake (Erpeton tentaculatum) under the scanning electron microscope revealing the unusual pair of scaled appendages on the snout. Tentacled snakes are fully aquatic and prey almost exclusively on fish. In this issue Catania and colleagues investigate the function of the tentacles and find they are sensitive mechanoreceptors that respond to water movements. Responses from the tentacles project to the optic tectum, suggesting mechanosensory information about water movements is integrated with vision when the snakes hunt.

We investigated the function of the tentacles in aquatic, piscivorous tentacled snakes (Erpeton tentaculatus) by examining anatomy, peripheral innervation, and the response properties of primary afferents. We also investigated visual and somatosensory responses in the optic tectum and documented predatory strikes to visual stimuli and under infrared illumination. Our results show the tentacles are sensitive mechanoreceptors that respond to water movements. They are innervated by rami of the maxillary and ophthalmic branches of the trigeminal nerve and contain a dense array of fine terminal neurites that cross the interior of the tentacle orthogonal to its long axis. The optic tectum contained a retinotopic map of contralateral receptive fields with superior fields represented dorsally in the tectum, inferior fields represented laterally, nasal fields represented rostrally, and temporal fields represented caudally. Large somatosensory receptive fields were identified in deeper layers of the tectum and were in approximate register with overlying visual fields. Tentacled snakes struck accurately at a simulated digital fish, indicating that visual cues are sufficient to guide strikes, but they also captured fish under infrared illumination, suggesting water movements alone could be used to localize prey. We conclude the tentacles are mechanosensors that are used to detect fish position based on water movements and that visual and mechanosensory cues may be integrated in the tectum to enhance localization when visual cues are reduced.

Keywords: optic tectum, brain, mechanosensory, behavior, touch vision

Function of the appendages in tentacled snakes (Erpeton tentaculatus)

Monday, October 29, 2012

[PaleoIchthyology • 2014] อีสานอิกธิส เลิศบุศย์ศี | Isanichthys lertboosi • A new species of the ginglymodian fish Isanichthys (former Lepidotes) (Actinopterygii, Holostei) from the Late Jurassic Phu Kradung Formation, northeastern Thailand

อีสานอิกธิส เลิศบุศย์ศี | Isanichthys lertboosi 
Deesri, Lauprasert, Suteethorn, Wongko & Cavin 2012

A new ginglymodian fish, Isanichthys lertboosi, is described from the Phu Kradung Formation, north-eastern Thailand, a freshwater deposit of probable Late Jurassic age. The species is represented by four specimens, from the Phu Noi locality, associated with a rich fauna of sharks, turtles, crocodiles, and theropod and sauropod dinosaurs. One specimen is an isolated braincase, which provides characters rarely observed in extinct ginglymodians. The species is referred to the genus Isanichthys, a taxon originally described on the basis of a single specimen from the Phu Nam Jun locality, a slightly younger site approximately 75 km from Phu Noi. Isanichthys is mainly distinguished by frontals slightly narrower anteriorly than posteriorly, two anterior infraorbitals not in contact with the orbit, reduced preorbital region, and a small orbit and a cheek region completely covered by bones. The new species is characterized, among other characters, by a dermal component of the sphenotic visible on the cheek, one pair of extrascapulars plus a small median one, the presence of few suborbitals (circa 4 or 6) arranged in one row, and a median dorsal row of scales with spine. Comparisons with other ginglymodian taxa and a cladistic analysis indicates that Isanichthys (Lepidoteslatifrons from the Late Jurassic of England, as well as probably Isanichthys (Lepidotesluchowensis from the Early or Middle Jurassic of Sichuan, China, form a clade with both Thai  species of Isanichthys. The new species provides evidence of the high diversity of ginglymodian fishes in the Phu Kradung Formation and suggests a new hypothesis of phylogenetic relationships among extinct ginglymodians.

Key words: Holostei, osteology, braincase, phylogeny, Late Jurassic, south-east Asia.

ตัวนักล่าสายพันธุ์ใหม่ “อีสานอิกธิส เลิศบุศย์ศีIsanichthys lertboosi” ปลานักล่าแห่งจูแรสสิก

Deesri, U., Lauprasert, K., Suteethorn, V., Wongko, K. and Cavin, L. 2014. A new species of the ginglymodian fish Isanichthys (Actinopterygii, Holostei) from the Late Jurassic Phu Kradung Formation, northeastern Thailand. Acta Palaeontologica Polonica. 59 (2): 313–331. doi:

 New species of Ginglymodian Fish from the Late Jurassic of northeast Thailand

[PaleoIchthyology • 2006] อีสานอิกธิส พาลัสทริส | Isanichthys palustris • A new Semionotiform (Actinopterygii, Neopterygii) from Upper Jurassic - Lower Cretaceous Deposits of northeastern Thailand, with Comments on the Relationships of Semionotiforms

อีสานอิกธิส พาลัสทริส 
Isanichthys palustris Cavin & Suteethorn 2006

  A new semionotiform fish, Isanichthys palustris gen. et sp. nov., is described from the Late Jurassic – Early Cretaceous Phu Kradung Formation, north-east Thailand. I. palustris is known from a single, nearly complete specimen found alongside abundant Lepidotes specimens at the Phu Nam Jun locality. I. palustris shows a mixture of semionotid-like characters, such as the pattern of cheek ossifications, and lepisosteid-like characters, such as the body shape and a dorsal fin opposed by an anal fin. I. palustris possesses only some of the characters currently used to define the Semionotidae. Cladistic analyses including various semionotid and gar taxa, together with Amia calva and Leptolepis coryphaenoides, suggest that the Semionotiformes (Lepisosteidae and ‘Semionotidae’) form a monophyletic clade, but the ‘Semionotidae’ taxa form an unresolved polytomy. The relationships between Semionotiformes, Halecomorphi and Teleostei are unresolved. When restricted to the best-known taxa, however, the analysis shows the monophyly of the Semionotidae sensu stricto (Semionotus + Lepidotes) and a sister-group relationship between halecomorphs and teleosts. These last two results are regarded as the preferred hypothesis for further studies. I. palustris is the only known example of a predaceous, probably piscivorous, ‘semionotid’. It illustrates the great diversity and ecological adaptation of the semionotiforms during the Late Jurassic – Early Cretaceous. We question the phylogenetic relationships of ‘ancient fishes’ founded on molecular-based trees because we suspect that the use of very few Recent taxa as representatives of previously diverse lineages is an inevitable, but important, bias in the construction of such trees.

Keywords: Actinopterygii; Semionotiformes; Lepisosteidae; new taxon; Thailand; Mesozoic; phylogeny

Cavin, L. & Suteethorn, V. 2006. A new Semionotiform (Actinopterygii, Neopterygii) from Upper Jurassic - Lower Cretaceous Deposits of North-East Thailand, with Comments on the Relationships of Semionotiforms. Palaeontology. 49, 339–353 :

[PaleoIchthyology • 2007] สยามเอเมีย นาคา | Siamamia naga • The first sinamiid fish (Holostei, Halecomorpha) from Southeast Asia (Early Cretaceous of Thailand)

ยามเอเมีย นาคา | Siamamia naga 
Cavin, Suteethorn, Buffetaut, Claude, Cuny, Le Loeuff & Tong 2007

 Siamamia naga, gen. et sp. nov, is described on the basis of three partly articulated skulls and a collection of isolated ossifications from a continental Early Cretaceous Formation of northeastern Thailand. The new taxon is a sinamiid halecomorph as demonstrated by the median parietal and other cranial characters. Sinamiidae is hitherto known by two genera occurring in Early Cretaceous freshwater deposits in China. Although a complete revision of all species within the family is necessary, the Thai material shows characters justifying a new genus. It is the first sinamiid found outside eastern Asia (South and North Chinese blocks, plus small Central Asian terranes), thus validating the close paleogeographical affinities between mainland Asia and SE Asia in the Early Cretaceous. A preliminary phylogenetic assessment of the new taxon with the data matrix of Grande and Bemis (1998) with the addition of data for Siamamia and Tomognathus provides a strict consensus tree similar to the phylogenetic hypothesis of Halecomorphi proposed by these authors, except the basal-most amiids which show a lower resolution in our hypothesis. The Sinamiidae appear as a monophyletic clade, but the four taxa included in the analysis form a polytomy

Etymology — Siam, geographic (former name of Thailand), referring to locality, + Amia (Greek); Naga, mythological creature living in the Kong River (Maekong).

Lionel Cavin, Varavudh Suteethorn, Eric Buffetaut, Julien Claude, Gilles Cuny, Jean Le Loeuff & Haiyan Tong. 2007. The first sinamiid fish (Holostei, Halecomorpha) from Southeast Asia (Early Cretaceous of Thailand). Journal of Vertebrate Paleontology. 27(4) 

[PaleoIchthyology • 2007] เฟอร์กาโนเซอราโตดัส มาร์ตินี | Ferganoceratodus martini • A new Thai Mesozoic lungfish (Sarcopterygii, Dipnoi) with an insight into post-Palaeozoic dipnoan evolution

We describe a new species of lungfish, Ferganoceratodus martini sp. nov., based on a single specimen discovered in the Late Jurassic – Early Cretaceous of the Phu Nam Jun locality, north-eastern Thailand. The material comprises an almost complete skull roof with associated upper and lower jaws, as well as some postcranial remains. F. martini shows characters unexpected and/or unknown in other Mesozoic lungfishes, such as pieces of a ‘hard snout’. The microstructure of the ‘hard snout’ provides support to the Bemis and Northcutt interpretation of the cosmine tissue of Palaeozoic lungfishes as homologous to the complex cutaneous vasculature of the living Neoceratodus. Because the homologies of the ossifications of the skull roof among lungfishes and among piscian sarcopterygians are unsatisfactorily understood, we use a topological nomenclature in the description of the specimen and in the discussion of post-Devonian dipnoan skull roof characters. We define a few characters for the cladistic analysis only, but these are regarded as less theory-laden. We propose a hypothesis of phylogenetic relationships for most of the post-Devonian forms known by skull remains. The main feature is the ancient dichotomy between the Neoceratodus lineage and most of the other Mesozoic forms, including the Lepidosirenids. The palaeobiogeographical pattern shows a series of vicariant events between Laurasia and Gondwana in the Late Triassic – Early Jurassic, followed by a vicariant event between Africa and South America.  

 Keywords: histology – new taxon – palaeoecology – palaeogeography – phylogeny – tooth plate.

Reconstitution of fossil lungfish Ferganoceratodus martini discovered in the Early Cretaceous (140 million years) in Thailand. © Lionel Cavin MHN / MHS

A, B: fossil lungfish Ferganoceratodus martini discovered in the Early Cretaceous (140 million years) in Thailand. C, D: Position of fossil inside the head of the animal. This fish has large enameled plates instead of teeth (visible between the eyes) he used to grind their food. E: reconstitution of lungfish. © Lionel Cavin MHN / MHS

Lionel Cavin, a paleontologist at the Natural History Museum of the City of Geneva (Switzerland) and Anne Kemp, a biologist at the Australian Rivers Institute, Brisbane (Australia), have recently shown that the lungfish, these curious primitive fish that have the both lungs and gills are much older and valuable than was previously thought.

Thailand discovering a fossil from the Lower Cretaceous (140 million years) belonging to this lineage of fish fossils and reviewing the Triassic (250 million years) from museum collections, the two researchers have shown that some lungfish belong to a branch very old, very special and long tree of evolution, as well as the famous coelacanth fish considered true living fossils.

Lungfish were widespread in the freshwaters of the world at the beginning of secondary. Helvetic-Australian study shows that it is in these times that distant line of lungfish is individualized and managed to survive until today in the form of a single species living in Australia.

This discovery provides novel arguments in favor of the protection of lungfish. According to Lionel Cavin and Anne Kemp, "we must now consider the fish as a living fossil part of our global heritage of biodiversity." It now appears particularly urgent to protect Neoceratodus forsteri, the endemic Australian species of about 120 cm long is weakened because it does (on) lives only in four small watersheds in the region of Brisbane (Queensland ). To preserve the unique Australian lungfish, it is essential to better manage the development and operation of waterways around Brisbane, a high growth area and among the most densely populated areas of Australia.

This study shows that paleontology, science based on the study of extinct for millions of years, can lead to very current issues related to the future of biodiversity.

The Australian lungfish Neoceratodus forsteri in the process of breathing air. Lungfish have both gills and lungs, which allows them to breathe in water as in the air. © Anne Kemp

2007. A new Thai Mesozoic lungfish (Sarcopterygii, Dipnoi) with an insight into post-Palaeozoic dipnoan evolution. Zoological Journal of the Linnean Society. 149: 141–177. [[Fulltext]]

Progress in Jurassic studies in Thailand in 2006 and early 2007

Sunday, October 28, 2012

[Invertebrate • 2012] Yoda purpurata'Yoda' Acorn Worm Named After Lovable Star Wars Character | Observations on torquaratorid acorn worms (Hemichordata, Enteropneusta) from the North Atlantic with descriptions of a new genus and three new species

Enteropneusts in the family Torquaratoridae were imaged using still and video cameras in the deep North Atlantic and then collected by remotely operated vehicles. From this material, we describe Yoda purpurata n. gen, n. sp., Tergivelum cinnabarinum n. sp., and Allapasus isidis n. sp. Individuals of the first two species were browsing completely exposed on the sea floor, whereas the specimen of the last species was encountered floating ~1 m above the sea floor. Living specimens of Y. purpurata were 12–19 cm long and had a dark reddish-purple proboscis, collar, and genital wings (folded dorsally over the anterior region of the trunk). Members of this species were hermaphrodites (the first ever discovered in the phylum Hemichordata), with numerous separate testes and ovaries in the genital wings. Living specimens of T. cinnabarinum were 12–26 cm long and had a cinnabar-colored proboscis, collar, and back veils (arising from the anterior region of the trunk); sexes were separate, and body shape and internal morphology closely resemble those of its brown congener, T. baldwinae, from the eastern Pacific. The only specimen of A. isidis collected was a male 13 cm long and pale yellow when alive. Its body shape was proportionally shorter and broader than that of its orange congener, A. aurantiacus, from the eastern Pacific, but the internal anatomy of the two species is virtually identical.  

Keywords: hermaphrodite; Torquaratoridae; benthopelagic lifestyle

Discovered a new type of acorn worm, scientists have. Named it after Yoda, they did.

The reddish-purple worm was found about 1.5 miles (2.5 kilometers) beneath the surface of the Atlantic Ocean, and has large lips on either side of its head region that reminded researchers of the floppy-eared Stars Wars character. Its full scientific name is Yoda purpurata, or "purple Yoda."

Researchers found the worm during the ECOMAR research program, which uses a remotely operated submersible to search for new animals along the seafloor at the Mid-Atlantic Ridge between Iceland and the Azores.

During the expedition, researchers from the University of Aberdeen in Scotland, also found two other new species of acorn worm. The animals are described in a study published in the September issue of the journal Invertebrate Biology.

Shallow water acorn worms live in burrows and are rarely seen, whereas deep sea species live on the seafloor, leaving spiral traces of poo that resemble crop circles. These traces have been seen in fossil form, but until recently, nobody knew what produced them.

Scientists are interested in these deep sea species, because they are close to the evolutionary link between vertebrates and invertebrates.

In other words, the force is strong with them.

But Yoda purpurata is hardly the only species to be named after a famous character, fictional or not. Recent examples include a horse fly named for Beyoncé, an isopod (this group includes pill bugs) near Zanzibar (an island of Tanzania in East Africa) named after Freddie Mercury ("arguably Zanzibar's most famous popular musician and singer") and slime mold beetles named after George Bush, Dick Cheney and Donald Rumsfeld.


Pride IG, Osborn KJ, Gebruk AV, Johnes D, Shale D, Rogacheva A, Holland ND (2012) Observations on torquaratorid acorn worms (Hemichordata, Enteropneusta) from the North Atlantic with descriptions of a new genus and three new species. Invertebrate Biology. DOI: 10.1111/j.1744-7410.2012.00266.x

Newly-Discovered 'Yoda' Acorn Worm Named After Lovable Star Wars Character
Deep-sea worm recalls Star Wars favourite  

[Herpetology • 2012] Lygosoma veunsaiensis • A new species of the genus Lygosoma Hardwicke & Gray, 1827 (Squamata: Scincidae) from northeastern Cambodia, with an updated identification key to the genus Lygosoma in mainland Southeast Asia

We describe a new species of the genus Lygosoma from northeastern Cambodia based on a single voucher specimen collected from Veun Sai Proposed Protected Forest, Veun Sai District, Ratanakiri Province. Lygosoma veunsaiensis sp. nov. is differentiated from all congeners occurring in mainland Southeast Asia by the combination of the following characters: outer ear opening absent; supranasals distinct and separated from each other by frontonasal; supranasals not fused with nasals; midbody scales in 22 rows; fontoparietals paired; five supralabials; a light stripe present on outer edge of the dorsum; and a dark dorsolateral stripe present, from behind the eye to the tail. A key to the Southeast Asian mainland species of Lygoma is provided.

Key words: taxonomy, L. veunsaiensis sp. nov., Veun Sai Proposed Protected Forest, Ratanakiri Province, Indochina

GEISSLER, PETER; TIMO HARTMANN & THY NEANG. 2012. A new species of the genus Lygosoma Hardwicke & Gray, 1827 (Squamata: Scincidae) from northeastern Cambodia, with an updated identification key to the genus Lygosoma in mainland Southeast Asia. Zootaxa. 3190: 56–68

[Invertebrate • 2012] Deuterostomic Development in the Protostome Priapulus caudatus | 'Penis worm' pokes holes in evolutionary dogma: Priapulid highlights the need to rename the largest animal group

The fate of the blastopore during development in the bilaterian ancestor is currently not well understood. In deuterostomes, the blastopore forms the anus, but its fate in protostome groups is variable. This variability, combined with an absence of information from key taxa, hampers the reconstruction of the ancestral developmental mode of the Protostomia and the Bilateria. The blastopore fate of the bilaterian ancestor plays a crucial role in understanding the transition from radial to bilateral symmetric organisms. Priapulids have a conservative morphology, an abundant Cambrian fossil record, and a phylogenetic position that make them a key group in understanding protostome evolution. Here, we characterize gastrulation and the embryonic expression of genes involved in bilaterian foregut and hindgut patterning in Priapulus caudatus. We show that the blastopore gives rise to the anus at the vegetal pole and that the hindgut markers brachyury and caudal are expressed in the blastopore and anus, whereas the foregut markers foxA and goosecoid are expressed in the mouth in the animal hemisphere. Thereby, gastrulation in the conservatively evolving protostome P. caudatus follows strictly a deuterostomic pattern. These results are more compatible with a deuterostomic rather than protostomic (blastopore forms the mouth) or amphistomic (mouth and anus are formed simultaneously) mode of development in the last common bilaterian ancestor.

A study on the development of priapulids or ‘penis’ worms throws doubt on a feature that has been thought for more than 100 years to define the largest branch of the animal tree of life. Members of this branch — the protostomes — have historically been defined by the order in which they develop a mouth and an anus as embryos. But gene-expression data suggest that this definition is incorrect, researchers report this week in Current Biology.

Evolutionary biologists will need to rename the protostomes. To do that, “we need to rethink how our earliest ancestors developed,” says Andreas Hejnol, an evolutionary developmental biologist at the University of Bergen in Norway and lead author on the report.


'Penis worm' pokes holes in evolutionary dogma: Priapulid highlights the need to rename the largest animal group

José M. Martín-Durán, Ralf Janssen, Sofia Wennberg, Graham E. Budd, Andreas Hejnol. 2012. Deuterostomic Development in the Protostome Priapulus caudatus. Current Biology. DOI:

Saturday, October 27, 2012

[Mammalogy • 2012] Dryadonycteris capixaba • New genus and species of nectar-feeding bat from the Atlantic Forest of southeastern Brazil (Chiroptera, Phyllostomidae, Glossophaginae)

Atlantic Forest Long-nosed Bat | Dryadonycteris capixaba 
Nogueira, Lima, Peracchi & Simmons 2012

The lowland Atlantic Forest of southeastern Brazil is well known for its biological diversity and numerous endemic taxa. Among bats collected recently at the Reserva Natural Vale and previously in the Floresta Nacional de Goytacazes, in the state of Espírito Santo, are specimens easily recognized as nectar-feeding glossophagines, but that exhibit a suite of morphological traits that preclude assignment to any of the 10 genera currently recognized in the subfamily Glossophaginae. Here we describe a new genus and species based on this material. This new taxon, named Dryadonycteris capixaba, is diagnosed based on both external and craniodental features, including traits not seen in other nectar-feeding phyllostomids, such as similar-sized calcar and foot and inflated maxillary bones. The combination of character states seen in Dryadonycteris suggests that it belongs in the Tribe Choeronycterini, subtribe Choeronycterina, but the mosaic nature of primitive and derived states seen in this taxon precludes easy assessment of its relationships to other choeronycterine genera. Future explicit phylogenetic analyses of morphological data and DNA sequencing studies will be necessary to resolve its phylogenetic position within Choeronycterini.

Keywords: Atlantic Forest, endemic, Glossophaginae, morphology, Espírito Santo.

Type Locality: Brazil, state of Espírito Santo, municipality of Linhares, Reserva Natural Vale, approximately 60 m elevation.

Etymology: In the first phytogeographic system proposed for Brazilian vegetation, the 19th-century German naturalist Karl Friedrich Philipp von Martius ascribed names of nymphs from Greek mythology to each of the major provinces he described (Martius, 1824). To the province we now recognize as Atlantic Forest, he gave the name “Dryades” (from the Greek Dryas, a wood nymph) for the immortal nymphs of the forest. The generic epithet proposed here means, therefore, “bat from Dryades,” hence “bat from the Atlantic Forest,” in reference to the endemic character of this taxon. The species name capixaba, a noun in apposition, is from the Tupi language and designates natives from the state of Espírito Santo.

Marcelo R. Nogueira, Isaac P. Lima, Adriano L. Peracchi, and Nancy B. Simmons. 2012. New genus and species of nectar-feeding bat from the Atlantic Forest of southeastern Brazil (Chiroptera, Phyllostomidae, Glossophaginae). American Museum novitates. 3747

Nova espécie de morcego é descoberta em Linhares, no ES. | New bat species is discovered in Linhares, ES.

[Mammalogy • 2012] Transient yellow colouration of the bat Artibeus jamaicensis coincides with pollen consumption

Fig. 1. Images of Artibeus jamaicensis fur colouration types. (a) Normal grey-brownish colouration; (b) atypical yellow colouration observed during January in the Yucatan.

Atypical colouration of the fur is not commonly recorded in bats. Here we report a transient yellow colouration attributed to dietary components in Artibeus jamaicensis in 2004 and 2005 at two localities of Yucatan, Mexico. Change in colouration was recorded in January when 62% of A. jamaicensis captured (n = 50) appeared yellow. All faecal samples collected from atypically coloured individuals consisted mainly of Ceiba pentandra pollen, which was also recovered from the fur. Carotenoid pigments contained in pollen ingested during peak Ceiba flowering appear to be incorporated into the hairs of A. jamaicensis. Further investigations are required to understand how pigment is transferred between the pollen and the hairs of A. jamaicensis.

Keywords: Chiroptera; Diet; Moult; Neotropical bats; Pollen

Transient yellow colouration of the bat Artibeus jamaicensis coincides with pollen consumption

Friday, October 26, 2012

[Paleontology • 2012] Ornithomimus ‘Bird mimic’ dinosaur hints that wings evolved for show not flight | Feathered Non-Avian Dinosaurs from North America Provide Insight into Wing Origins

Artistic reconstruction of feathered ornithomimid dinosaurs found in Alberta.
Reconstruction by Julius Csotonyi |

Previously described feathered dinosaurs reveal a fascinating record of feather evolution, although substantial phylogenetic gaps remain. Here we report the occurrence of feathers in ornithomimosaurs, a clade of non-maniraptoran theropods for which fossilized feathers were previously unknown. The Ornithomimus specimens, recovered from Upper Cretaceous deposits of Alberta, Canada, provide new insights into dinosaur plumage and the origin of the avian wing. Individuals from different growth stages reveal the presence of a filamentous feather covering throughout life and winglike structures on the forelimbs of adults. The appearance of winglike structures in older animals indicates that they may have evolved in association with reproductive behaviors. These specimens show that primordial wings originated earlier than previously thought, among non-maniraptoran theropods.

Ornithomimus edmontonicus specimen with traces of wing feathers, Royal Tyrrell Museum

The ostrich-like dinosaurs in the original Jurassic Park movie were portrayed as a herd of scaly, fleet-footed animals being chased by a ferocious Tyrannosaurus rex. New research published in the prestigious journal Science reveals this depiction of these bird-mimic dinosaurs is not entirely accurate —ornithomimids, as they are scientifically known, should have had feathers and wings.

The new study, led by paleontologists Darla Zelenitsky from the University of Calgary and François Therrien from the Royal Tyrrell Museum of Palaeontology, describes the first ornithomimid specimens preserved with feathers, recovered from 75 million-year-old rocks in the badlands of southern Alberta, Canada. This discovery represents the first feathered dinosaur specimens found in the Western Hemisphere.

"Despite the many ornithomimid skeletons known, these specimens are the first to reveal that ornithomimids were covered in feathers, like several other groups of theropod dinosaurs," says Zelenitsky, assistant professor at the University of Calgary and lead author of the study. Until now, the absence of feathers in previously discovered ornithomimid specimens has been a mystery. It was not known if these animals were simply featherless in life or if feathers were just not preserved in these other specimens."

The researchers found evidence of feathers preserved with a juvenile and two adults skeletons of Ornithomimus, a dinosaur that belongs to the group known as ornithomimids. Like other groups of theropod dinosaurs, such as tyrannosaurs and raptors, ornithomimid dinosaurs would also have been covered in feathers.

Skeleton of juvenile ornithomimid dinosaur from Alberta preserving fossil feathers.
The specimens reveal an interesting pattern of change in feathery plumage during the life of Ornithomimus. "This dinosaur was covered in down-like feathers throughout life, but only older individuals developed larger feathers on the arms, forming wing-like structures," says Zelenitsky. "This pattern differs from that seen in birds, where the wings generally develop very young, soon after hatching."

This discovery of early wings in dinosaurs too big to fly indicates the initial use of these structures was not for flight. "The fact that wing-like forelimbs developed in more mature individuals suggests they were used only later in life, perhaps associated with reproductive behaviors like display or egg brooding," says Therrien, curator at the Royal Tyrrell Museum and co-author of the study. " Such a idea for the role of early wing feathers has been proposed previously, although fossil evidence was lacking until now."

Until now feathered dinosaur skeletons had been recovered almost exclusively from fine-grained rocks in China and Germany. "It was previously thought that feathered dinosaurs could only fossilize in muddy sediment deposited in quiet waters, such as the bottom of lakes and lagoons," says Therrien. "But the discovery of these ornithomimids in sandstone shows that feathered dinosaurs can also be preserved in rocks deposited by ancient flowing rivers."

Because sandstone is the type of rock that most commonly preserves dinosaur skeletons, the Canadian discoveries reveal great new potential for the recovery of feathered dinosaurs in North America and elsewhere.

Zelenitsky, Therrien, Erickson, DeBuhr, Kobayashi, Eberth & Hadfield. 2012. Feathered Non-Avian Dinosaurs from North America Provide Insight into Wing Origins. Science

Press Release: Canadian researchers discover fossils of first feathered dinosaurs from North America 
: Significant find provides clues on early wing uses

A new feathered dinosaur shows we still have lots to learn 

Images: top reconstruction by Julius Csotonyi; middle by Royal Tyrell Museum; 
phylogeny from paper; Zelenitsky by Riley Brandt
‘Bird mimic’ dinosaur hints that wings evolved for show not flight

Canadian researchers discover fossils of first feathered dinosaurs from North America | @UCalgary