Hispaniolan solenodon DNA sequenced

This video says about itself:

4 May 2016

Researchers from the University of Illinois and the University of Puerto Rico sequenced the DNA of Hispaniolan solenodons, revealing the mammal to be approximately 78 million years old.

From GigaScience:

Menomous [sic; Venomous] Solenodon, last survivor of a branch of mammals that appeared at the time of the dinosaurs, sequenced

March 16, 2018

Summary: An article presents a draft genome of a small shrew-like animal, the venomous Hispaniolan solenodon. This unusual animal is one of the only extant venomous mammals, and it is the sole remaining branch of mammals that split from other insectivores at the time of the dinosaurs. The solenodon genome sequence revealed the answer to several evolutionary questions, such as whether the solenodon species indeed survived the meteor impact that killed the dinosaurs.

Published today, in the open-access journal GigaScience, is an article that presents a draft genome of a small shrew-like animal, the venomous Hispaniolan solenodon (Solenodon paradoxus). This species is unusual not only because it is one of the very few venomous mammals, it is also the sole remaining branch of mammals that split from other insectivores at the time of the dinosaurs. The genome sequencing and analysis of this endangered animal was carried out by an international team lead by Dr. Taras K. Oleksyk from the University of Puerto Rico at Mayagüez. The availability of the solenodon genome sequence allowed the researchers to answer several evolutionary questions, particularly whether the solenodon species indeed survived the meteor impact that laid waste to the dinosaurs.

As one of the only extant mammals that are venomous, the Solenodon’s venomous saliva flows from modified salivary glands through grooves on their sharp incisors (“solenodon” derives from the Greek for “grooved tooth”). They also have several other primitive and very unusual characteristics for a mammal: very large claws, a flexible snout with a ball-and-socket joint, and oddly positioned teats, which are on their rear. While the mammalian tree of life has been heavily researched, this is the most distantly related branch to be added to the ‘genome club’. It has particular importance and implications for conservation because morphometric studies have suggested that southern and northern Hispaniolan solenodons may be subspecies rather than separate species.

Solenodon is not just genetically but also geographically isolated. Highly endangered, they remain only in a few remote corners of the Caribbean islands of Cuba and Hispaniola. Its nocturnal lifestyle makes it even more elusive and therefore less studied. Thus, it was crucial for the researchers to work with local experts at the Instituto Tecnológico de Santo Domingo and Universidad Autónoma de Santo Domingo and with local guides who helped them track and ambush passing solenodons at night.

One of the lead authors, Dr Juan Carlos Martinez-Cruzado, noted that “local resources are absolutely necessary for this kind of work; only they truly know their animal’s behavior.” He added, “this project may open doors to many others to come, and we always assumed this to be one of many projects that will help research, education and conservation efforts in the Dominican Republic.”

For this project, there was more than just the challenge of obtaining the organisms for blood samples, the solenodon genome proved particularly difficult to sequence. Carrying out genomics research in remote parts of the Caribbean provided a challenge, particularly in transporting high quality DNA to the lab. Due to the constraints of poor quality DNA as well as a limited budget, the commercial lab used to carry out the sequencing turned out a very low coverage per individual.

Having already ventured into the jungle, the researchers embraced this new challenge by coming up with novel approaches to assemble the genome. First, the researchers reasoned that because the species has existed for tens of millions of years in isolation, it was extremely inbred and had a very homozygous genome. This lead to a potential work-around, because the five collected sets of genomic data could be pooled to increase the coverage. Despite initial doubts, this worked better than expected especially when that strategy was combined with using a string graph approach rather than the more standard de Brujn graph assembly method. String graphs incorporate more of the sequencing data than de Brujn graphs. Based on the results here, this new technique provides a low budget alternative for genome assembly, particularly in the highly homozygous genomes of endangered species.

The first author of the paper, Kirill Grigorev elaborates: “For me, perhaps the most interesting part of this research was the challenge of delivering a de novo genome assembly that was suitable for comparative genomics, using an amount of sequencing data much smaller than in other similar projects.”

After carrying out their assembly, the researchers had data of sufficient quality for answering many scientific questions on solenodon evolution. With regard to conservation plans, the data supports that there was a subspecies split within the Hispaniolan solenodon at least 300,000 years ago, meaning the northern and southern populations should be treated as two separate conservation units and may therefore need independent breeding strategies.

These data also shed light on the initial speciation event for this branch, and showed that solenodons likely diverged from other extant mammals 73.6 million years ago. Dr. Oleksyk said: “We have confirmed the early speciation date for Solenodons, weighing on the ongoing debate on whether the solenodons have indeed survived the demise of dinosaurs after the asteroid impact in the Caribbean.”

This research was the inaugural winner of the GigaScience prize at the International Conference on Genomics in Shenzhen on the 30st October 2017. Presenting in the prize track, the international panel of judges voted the paper the winner of the $1000 prize and trophy. The GigaScience prize track will run again at ICG-13, and the journal will begin taking papers for it next month. Follow GigaScience on social media for more information.


New Miocene fossil insectivore discovery

This 2012 video is called Miocene.

From the Asociación RUVID in Spain:

New 16 million-year-old insectivore species discovered

March 14, 2018

Palaeontologists Vicente D. Crespo, Francisco Javier Ruiz Sánchez and Plini Montoya, from the department of Botanics and Geology of the Universitat de València, and Marc Furió, from the Institut Català de Paleontologia, have discovered a new fossilised species of insectivore belonging to the unusual and extinct Plesiodimylus family. The identification of this group, related to the fauna that lived in Central Europe during the Miocene (16 million years ago), is based on the study of isolated teeth found in l’Alcora (Castellón), in the district of Araya.

This new species of insectivore, found in the palaeontological site Mas d’Antolino B, has been unveiled in the Historical Biology journal and has the scientific denomination Plesiodimylus ilercavonicus, in reference to the Iberian Ilercavones people, who inhabited part of what are the provinces of Castellón and Tarrragona today.

This family is defined by having teeth that protrude from the jaw, with thicker dental enamel than other mammals, as well as the presence of four molars (two in each jawbones, or one in each jawbone and then one more in each maxilla). These characteristics give them an unusual look — with overgrown teeth.

Furthermore, by studying the dentition of this species and specially with the type of wear suffered by the teeth’s enamel, one can surmise they would have fed mainly on gastropods, the most common group of mollusks, according to Crespo, Ruiz Sánchez and Montoya — also researchers for Valencia’s Natural History Museum -, and Marc Furió.

Until now, the finding of material from this animal group in Araya is the only one of its kind in the Iberian Peninsula, joining findings of other species from Central Europe such as some types of hamsters and other rodents, bats and insectivores, which reveal a phase of faunistic exchange between Iberia and Central Europe in the Lower Miocene.

In order to obtain the fossilised remains of these small mammals, a strenuous process to clean and sieve through tones of sediment was undertaken, as well as the examination of the residue obtained through this process. The studying of the specimens was performed with various techniques, including some derived from the use of electronic microscopy devices. The results of the study were unveiled at the 15th Annual Meeting of the European Association of Vertebrate Palaeontologists, held in Munich (Germany) during the summer of 2017.

In the Mas d’Antolino B palaeontological site, available since 2008, fossils of other species of shrews, squirrels, hamsters, dormice, bats or crocodiles have been unearthed, among others. These faunas, in a context of an environment similar to the current day rainforests, date back to the Aragonian age of mammals, also within the Miocene period. In this era there was a rainforest where Araya is currently located, with meadows, which would have been located near a great lake which reached most of today’s l’Alcora, Ribesalbes and Fanzara villages.

Mammal-like reptiles coexisted with dinosaurs, discovery

This 13 March 2018 video says about itself:

Mystery of the Phantom Fossil Footprints

A new study has re-discovered fossil collections from a 19th century hermit that validate ‘phantom’ fossil footprints collected in the 1950s showing dicynodonts coexisting with dinosaurs.

“The first skeletal evidence of a dicynodont from the lower Elliot Formation of South Africa” by Christian F. Kammerer, North Carolina Museum of Natural Sciences. Published: 3-14-2018, in Palaeontologia Africana.

Video by Adrian Smith

Narrated by Eban Crawford

Illustrations by Matt Celeskey & Dmitry Bogdanov

From the North Carolina Museum of Natural Sciences in the USA:

60-year-old paleontological mystery of a ‘phantom’ dicynodont

March 14, 2018

A new study has re-discovered fossil collections from a 19th century hermit that validate ‘phantom’ fossil footprints collected in the 1950s showing dicynodonts coexisting with dinosaurs.

Before the dinosaurs, around 260 million years ago, a group of early mammal relatives called dicynodonts were the most abundant vertebrate land animals. These bizarre plant-eaters with tusks and turtle-like beaks were thought to have gone extinct by the Late Triassic Period, 210 million years ago, when dinosaurs first started to proliferate. However, in the 1950s, suspiciously dicynodont-like footprints were found alongside dinosaur prints in southern Africa, suggesting the presence of a late-surviving phantom dicynodont unknown in the skeletal record. These “phantom” prints were so out-of-place that they were disregarded as evidence for dicynodont survival by paleontologists. A new study has re-discovered fossil collections from a 19th century hermit that validate these “phantom” prints and show that dicynodonts coexisted with early plant-eating dinosaurs. While this research enhances our knowledge of ancient ecosystems, it also emphasizes the often-overlooked importance of trace fossils, like footprints, and the work of amateur scientists.

“Although we tend to think of paleontological discoveries coming from new field work, many of our most important conclusions come from specimens already in museums“, says Dr. Christian Kammerer, Research Curator of Paleontology at the North Carolina Museum of Natural Sciences and author of the new study.

The re-discovered fossils that solved this mystery were originally collected in South Africa in the 1870s by Alfred “Gogga” Brown. Brown was an amateur paleontologist and hermit who spent years trying, with little success, to interest European researchers in his discoveries. Brown had shipped these specimens to the Natural History Museum in Vienna in 1876, where they were deposited in the museum’s collection but never described.

“I knew the Brown collections in Vienna were largely unstudied, but there was general agreement that his Late Triassic collections were made up only of dinosaur fossils. To my great surprise, I immediately noticed clear dicynodont jaw and arm bones among these supposed ‘dinosaur’ fossils”, says Kammerer. “As I went through this collection I found more and more bones matching a dicynodont instead of a dinosaur, representing parts of the skull, limbs, and spinal column.” This was exciting — despite over a century of extensive collection, no skeletal evidence of a dicynodont had ever been recognized in the Late Triassic of South Africa.

Before this point, the only evidence of dicynodonts in the southern African Late Triassic was from questionable footprints: a short-toed, five-fingered track named Pentasauropus incredibilis (meaning the “incredible five-toed lizard foot”). In recognition of the importance of these tracks for suggesting the existence of Late Triassic dicynodonts and the contributions of “Gogga” Brown in collecting the actual fossil bones, the re-discovered and newly described dicynodont has been named Pentasaurus goggai (“Gogga’s five-[toed] lizard”).

“The case of Pentasaurus illustrates the importance of various underappreciated sources of data in understanding prehistory,” says Kammerer. “You have the contributions of amateur researchers like ‘Gogga’ Brown, who was largely ignored in his 19th century heyday, the evidence from footprints, which some paleontologists disbelieved because they conflicted with the skeletal evidence, and of course the importance of well-curated museum collections that provide scientists today an opportunity to study specimens collected 140 years ago.”


Archaeopteryx could fly indeed

This 2014 video says about itself:

Scanning the Teyler Archaeopteryx fossil at the ESRF Grenoble

2 November 2014

In order to study the Teyler Archaeopteryx fossil, it is being scanned in Grenoble using synchrotron X-ray microtomography. The end of the video shows the specimen fully wrapped and mounted on the object table in front of the beam that is coming out the square hole in the blue box.

From the European Synchrotron Radiation Facility:

The early bird got to fly: Archaeopteryx was an active flyer

March 13, 2018

The question of whether the Late Jurassic dino-bird Archaeopteryx was an elaborately feathered ground dweller, a glider, or an active flyer has fascinated palaeontologists for decades. Valuable new information obtained with state-of-the-art synchrotron microtomography at the ESRF, the European Synchrotron (Grenoble, France), allowed an international team of scientists to answer this question in Nature Communications. The wing bones of Archaeopteryx were shaped for incidental active flight, but not for the advanced style of flying mastered by today’s birds.

Was Archaeopteryx capable of flying, and if so, how? Although it is common knowledge that modern-day birds descended from extinct dinosaurs, many questions on their early evolution and the development of avian flight remain unanswered. Traditional research methods have thus far been unable to answer the question whether Archaeopteryx flew or not. Using synchrotron microtomography at the ESRF’s beamline ID19 to probe inside Archaeopteryx fossils, an international team of scientists from the ESRF, Palacký University, Czech Republic, CNRS and Sorbonne University, France, Uppsala University, Sweden, and Bürgermeister-Müller-Museum Solnhofen, Germany, shed new light on this earliest of birds.

Reconstructing extinct behaviour poses substantial challenges for palaeontologists, especially when it comes to enigmatic animals such as the famous Archaeopteryx from the Late Jurassic sediments of southeastern Germany that is considered the oldest potentially free-flying dinosaur. This well-preserved fossil taxon shows a mosaic anatomy that illustrates the close family relations between extinct raptorial dinosaurs and living dinosaurs: the birds. Most modern bird skeletons are highly specialised for powered flight, yet many of their characteristic adaptations in particularly the shoulder are absent in the Bavarian fossils of Archaeopteryx. Although its feathered wings resemble those of modern birds flying overhead every day, the primitive shoulder structure is incompatible with the modern avian wing beat cycle.

“The cross-sectional architecture of limb bones is strongly influenced by evolutionary adaptation towards optimal strength at minimal mass, and functional adaptation to the forces experienced during life”, explains Prof. Jorge Cubo of the Sorbonne University in Paris. “By statistically comparing the bones of living animals that engage in observable habits with those of cryptic fossils, it is possible to bring new information into an old discussion”, says senior author Dr. Sophie Sanchez from Uppsala University, Sweden

Archaeopteryx skeletons are preserved in and on limestone slabs that reveal only part of their morphology. Since these fossils are among the most valuable in the world, invasive probing to reveal obscured or internal structures is therefore highly discouraged. “Fortunately, today it is no longer necessary to damage precious fossils”, states Dr. Paul Tafforeau, beamline scientist at the ESRF. “The exceptional sensitivity of X-ray imaging techniques for investigating large specimens that is available at the ESRF offers harmless microscopic insight into fossil bones and allows virtual 3D reconstructions of extraordinary quality. Exciting upgrades are underway, including a substantial improvement of the properties of our synchrotron source and a brand new beamline designated for tomography. These developments promise to give even better results on much larger specimens in the future.”

Scanning data unexpectedly revealed that the wing bones of Archaeopteryx, contrary to its shoulder girdle, shared important adaptations with those of modern flying birds. “We focused on the middle part of the arm bones because we knew those sections contain clear flight-related signals in birds”, says Dr. Emmanuel de Margerie, CNRS, France. “We immediately noticed that the bone walls of Archaeopteryx were much thinner than those of earthbound dinosaurs but looked a lot like conventional bird bones”, continues lead author Dennis Voeten of the ESRF. “Data analysis furthermore demonstrated that the bones of Archaeopteryx plot closest to those of birds like pheasants that occasionally use active flight to cross barriers or dodge predators, but not to those of gliding and soaring forms such as many birds of prey and some seabirds that are optimised for enduring flight.”

“We know that the region around Solnhofen in southeastern Germany was a tropical archipelago, and such an environment appears highly suitable for island hopping or escape flight”, remarks Dr. Martin Röper, Archaeopteryx curator and co-author of the report. “Archaeopteryx shared the Jurassic skies with primitive pterosaurs that would ultimately evolve into the gigantic pterosaurs of the Cretaceous. We found similar differences in wing bone geometry between primitive and advanced pterosaurs as those between actively flying and soaring birds”, adds Vincent Beyrand of the ESRF.

Since Archaeopteryx represents the oldest known flying member of the avialan lineage that also includes modern birds, these findings not only illustrate aspects of the lifestyle of Archaeopteryx but also provide insight into the early evolution of dinosaurian flight. “Indeed, we now know that Archaeopteryx was already actively flying around 150 million years ago, which implies that active dinosaurian flight had evolved even earlier!” says Prof. Stanislav Bureš of Palacký University in Olomouc. “However, because Archaeopteryx lacked the pectoral adaptations to fly like modern birds, the way it achieved powered flight must also have been different. We will need to return to the fossils to answer the question on exactly how this Bavarian icon of evolution used its wings”, concludes Voeten.

It is now clear that Archaeopteryx is a representative of the first wave of dinosaurian flight strategies that eventually went extinct, leaving only the modern avian flight stroke directly observable today.


How turtles got their shells, video

This video from the USA says about itself:

How the Turtle Got Its Shell

12 March 2018

Where did turtles come from? And how did the they get their shells? The answers to these questions would eventually cause scientists to rethink the entire history of reptile evolution.


Pre-Cambrian worm discoveries in Mongolia

Reconstruction of the late Ediacaran (ca. 550 million years ago) sea floor with burrows of a worm-like animal.This was the first discovery of such deeply penetrating burrows. Credit: © Nagoya University

From Nagoya University in Japan:

Digging up the Precambrian: Fossil burrows show early origins of animal behavior

March 12, 2018

Researchers led by Nagoya University discover penetrative trace fossils from the late Ediacaran of western Mongolia, revealing earlier onset of the “agronomic revolution”.

In the history of life on Earth, a dramatic and revolutionary change in the nature of the sea floor occurred in the early Cambrian (541–485 million years ago): the “agronomic revolution.” This phenomenon was coupled with the diversification of marine animals that could burrow into seafloor sediments. Previously, the sea floor was covered by hard microbial mats, and animals were limited to standing on, resting on, or moving horizontally along those mats. In the agronomic revolution, part of the so-called Cambrian Explosion of animal diversity and complexity, vertical burrowers began to churn up the underlying sediments, which softened and oxygenated the subsurface, created new ecological niches, and thus radically transformed the marine ecosystem into one more like that observed today.

This event has long been considered to have occurred in the early Cambrian Period. However, new evidence obtained from western Mongolia shows that the agronomic revolution began in the late Ediacaran, the final period of the Precambrian, at least locally.

A team of researchers, primarily based in Japan, surveyed Bayan Gol Valley, western Mongolia, and found late Ediacaran trace fossils in marine carbonate rocks. They identified U-shaped, penetrative trace fossils, called Arenicolites, from 11 beds located more than 130 meters below the lowermost occurrence of Treptichnus pedum, widely recognized as the marker of the Ediacaran–Cambrian boundary. The researchers confirmed the late Ediacaran age of the rocks, estimated to be between 555 and 541 million years old, based on the stable carbon isotope record.

“It is impossible to identify the kind of animal that produced the Arenicolites traces,” lead author Tatsuo Oji says. “However, they were certainly bilaterian animals based on the complexity of the traces, and were probably worm-like in nature. These fossils are the earliest evidence for animals making semi-permanent domiciles in sediment. The evolution of macrophagous predation was probably the selective pressure for these trace makers to build such semi-permanent infaunal structures, as they would have provided safety from many predators.”

These Arenicolites also reached unusually large sizes, greater than one centimeter in diameter. The discovery of these large-sized, penetrative trace fossils contradicts the conclusions of previous studies that small-sized penetrative traces emerged only in the earliest Cambrian.

“These trace fossils indicate that the agronomic revolution actually began in the latest Ediacaran in at least one setting,” co-author Stephen Dornbos explains. “Thus, this revolution did not proceed in a uniform pattern across all depositional environments during the Cambrian radiation, but rather in a patchwork of varying bioturbation levels across marine seafloors that lasted well into the early Paleozoic.”


Ancient reptiles detached tails to escape

This 2015 video is called Treasure Trove of Permian Fossils Discovered | Prehistoric News.

From the University of Toronto in Canada:

Ancient reptile Captorhinus could detach its tail to escape predator’s grasp

March 6, 2018

Summary: A new study shows how a group of small reptiles who lived 289 million years ago could detach their tails to escape the grasp of their would-be predators — the oldest known example of such behavior.

Imagine that you’re a voracious carnivore who sinks its teeth into the tail of a small reptile and anticipates a delicious lunch, when, in a flash, the reptile is gone and you are left holding a wiggling tail between your jaws.

A new study by the University of Toronto Mississauga research team led by Professor Robert Reisz and PhD student Aaron LeBlanc, published March 5 in the open source journal, Scientific Reports, shows how a group of small reptiles who lived 289 million years ago could detach their tails to escape the grasp of their would-be predators — the oldest known example of such behaviour. The reptiles, called Captorhinus, weighed less than 2 kilograms and were smaller than the predators of the time. They were abundant in terrestrial communities during the Early Permian period and are distant relatives of all the reptiles today.

As small omnivores and herbivores, Captorhinus and its relatives had to scrounge for food while avoiding being preyed upon by large meat-eating amphibians and ancient relatives of mammals. “One of the ways captorhinids could do this,” says first author LeBlanc, “was by having breakable tail vertebrae.” Like many present-day lizard species, such as skinks, that can detach their tails to escape or distract a predator, the middle of many tail vertebrae had cracks in them.

It is likely that these cracks acted like the perforated lines between two paper towel sheets, allowing vertebrae to break in half along planes of weakness. “If a predator grabbed hold of one of these reptiles, the vertebra would break at the crack and the tail would drop off, allowing the captorhinid to escape relatively unharmed,” says Reisz, a Distinguished Professor of Biology at the University of Toronto Mississauga.

The authors note that being the only reptiles with such an escape strategy may have been a key to their success, because they were the most common reptiles of their time, and by the end of the Permian period 251 million years ago, captorhinids had dispersed across the ancient supercontinent of Pangaea. This trait disappeared from the fossil record when Captorhinus died out; it re-evolved in lizards only 70 million years ago.

They were able to examine more than 70 tail vertebrae — both juveniles and adults — and partial tail skeletons with splits that ran through their vertebrae. They compared these skeletons to those of other reptilian relatives of captorhinids, but it appears that this ability is restricted to this family of reptiles in the Permian period.

Using various paleontological and histological techniques, the authors discovered that the cracks were features that formed naturally as the vertebrae were developing. Interestingly, the research team found that young captorhinids had well-formed cracks, while those in some adults tended to fuse up. This makes sense, since predation is much greater on young individuals and they need this ability to defend themselves.

This study was possible thanks to the treasure trove of fossils available at the cave deposits near Richards Spur, Oklahoma.