From dinosaur age mammal to human, new research


Placental mammal family tree

Numbers on red branches from the first eutherian ancestor to Homo sapiens are the numbers of breakpoints in reconstructed ancestral chromosome fragments. Breakpoints are locations where a chromosome broke open, allowing for rearrangements. The number of breakpoints per million years is in parentheses. A total of 162 chromosomal breakpoints were identified between the eutherian ancestor and the formation of humans as a species.
Credit: Harris Lewin, UC Davis

From the University of California – Davis in the USA:

Reconstruction of ancient chromosomes offers insight into mammalian evolution

June 21, 2017

Summary: Researchers have gone back in time, at least virtually, computationally recreating the chromosomes of the first eutherian mammal, the long-extinct, shrewlike ancestor of all placental mammals.

What if researchers could go back in time 105 million years and accurately sequence the chromosomes of the first placental mammal? What would it reveal about evolution and modern mammals, including humans?

In a study published this week in Proceedings of the National Academy of Sciences, researchers have gone back in time, at least virtually, computationally recreating the chromosomes of the first eutherian mammal, the long-extinct, shrewlike ancestor of all placental mammals.

“The revolution in DNA sequencing has provided us with enough chromosome-scale genome assemblies to permit the computational reconstruction of the eutherian ancestor, as well as other key ancestors along the lineage leading to modern humans,” said Harris Lewin, a lead author of the study and a professor of evolution and ecology and Robert and Rosabel Osborne Endowed Chair at the University of California, Davis.

“We now understand the major steps of chromosomal evolution that led to the genome organization of more than half the existing orders of mammals. These studies will allow us to determine the role of chromosome rearrangements in the formation of new mammal species and how such rearrangements result in adaptive changes that are specific to the different mammalian lineages,” said Lewin.

The findings also have broad implications for understanding how chromosomal rearrangements over millions of years may contribute to human diseases, such as cancer.

“By gaining a better understanding of the relationship between evolutionary breakpoints and cancer breakpoints, the essential molecular features of chromosomes that lead to their instability can be revealed,” said Lewin. “Our studies can be extended to the early detection of cancer by identifying diagnostic chromosome rearrangements in humans and other animals, and possibly novel targets for personalized therapy.”

Descrambling chromosomes

To recreate the chromosomes of these ancient relatives, the team began with the sequenced genomes of 19 existing placental mammals — all eutherian descendants — including human, goat, dog, orangutan, cattle, mouse and chimpanzee, among others.

The researchers then utilized a new algorithm they developed called DESCHRAMBLER. The algorithm computed (“descrambled”) the most likely order and orientation of 2,404 chromosome fragments that were common among the 19 placental mammals’ genomes.

“It is the largest and most comprehensive such analysis performed to date, and DESCHRAMBLER was shown to produce highly accurate reconstructions using data simulation and by benchmarking it against other reconstruction tools,” said Jian Ma, the study’s co-senior author and an associate professor of computational biology at Carnegie Mellon University in Pittsburgh.

In addition to the eutherian ancestor, reconstructions were made for the six other ancestral genomes on the human evolutionary tree: boreoeutherian, euarchontoglires, simian (primates), catarrhini (Old World monkeys), great apes and human-chimpanzee. The reconstructions give a detailed picture of the various chromosomal changes — translocations, inversions, fissions and other complex rearrangements — that have occurred over the 105 million years between the first mammal and Homo sapiens.

Rates of evolution vary

One discovery is that the first eutherian ancestor likely had 42 chromosomes, four less than humans. Researchers identified 162 chromosomal breakpoints — locations where a chromosome broke open, allowing for rearrangements — between the eutherian ancestor and the formation of humans as a species.

The rates of evolution of ancestral chromosomes differed greatly among the different mammal lineages. But some chromosomes remained extremely stable over time. For example, six of the reconstructed eutherian ancestral chromosomes showed no rearrangements for almost 100 million years until the appearance of the common ancestor of human and chimpanzee.

Orangutan chromosomes were found to be the slowest evolving of all primates and still retain eight chromosomes that have not changed much with respect to gene order orientation as compared with the eutherian ancestor. In contrast, the lineage leading to chimpanzees had the highest rate of chromosome rearrangements among primates.

“When chromosomes rearrange, new genes and regulatory elements may form that alter the regulation of expression of hundreds of genes, or more. At least some of these events may be responsible for the major phenotypic differences we observe between the mammal orders,” said Denis Larkin, co-senior author of the study and a reader in comparative genomics at the Royal Veterinary College at the University of London.

The chromosomes of the oldest three ancestors (eutherian, boreoeutherian, and euarchontoglires) were each found to include more than 80 percent of the entire length of the human genome, the most detailed reconstructions reported to date. The reconstructed chromosomes of the most recent common ancestor of simians, catarrhini, great apes, and humans and chimpanzees included more than 90 percent of human genome sequence, providing a structural framework for understanding primate evolution.

‘Ghostbusters’ ankylosaur dinosaur discovery


This video from Canada says about itself:

10 May 2017

3D animation of the retrodeformed skull of Zuul crurivastator. The original skull was crushed during fossilization, and this animation shows how the skull may have looked beforehand.

Scientists from the Royal Ontario Museum (ROM) have identified and named a new species of anklylosaurid or armoured dinosaur, Zuul crurivastator (Zool CRUR-uh-vass-TATE-or). Its skeleton is one of the most complete and best preserved skeletons of this group of dinosaurs ever found, which includes a complete skull and tail club, and preserved soft tissues.

From Science News in the USA:

New dinosaur resurrects a demon from Ghostbusters

Found in Montana, the skeleton is the most complete ankylosaur unearthed to date

By Laurel Hamers

5:00am, June 12, 2017

Zuul is back. But don’t bother calling the Ghostbusters. Zuul crurivastator is a dino, not a demon. A 75-million-year-old skeleton unearthed in Montana in 2014 reveals a tanklike dinosaur with a spiked club tail and a face that probably looked a lot like its cinematic namesake.

The find is the most complete fossil of an ankylosaur, a type of armored dinosaur, found in North America, researchers report May 10 in Royal Society Open Science. It includes a complete skull and tail club, plus some preserved soft tissue, says study co-author Victoria Arbour, a paleobiologist at the Royal Ontario Museum in Toronto. “It really gives us a good idea of what these animals looked like.”

The bones reveal that Z. crurivastator had spikes running all the way down its tail, not just on the club itself. That arrangement means the weaponry was more than just a “massive sledgehammer,” Arbour says. The club was a formidable weapon. The term crurivastator comes from the Latin for “shin destroyer.”

Arbour previously created mathematical models to calculate the force with which similar ankylosaurs might have swung their tails. These appendages provided a winning combination: good at absorbing impacts and able to smack an opponent hard enough to hurt, she says. Despite their armor and fearsome tail, ankylosaurs were plant eaters. So they probably used their tails to smack predators or compete with other ankylosaurs.

Arbour and museum colleague David Evans plan to investigate the thin sheet of fingernail-like material covering the bony plates on the tail, along with other details of the fossil that are typically lost in such old specimens. The rare preserved soft tissue might even let scientists extract ancient proteins, Arbour says, providing insight into how these building blocks of life have changed since the days of dinos.

Having all this material in hand, she says, “kind of pushes the envelope about what we can identify in the fossil record.”

This music video from the USA is called Ray Parker Jr. – Ghostbusters.

Tyrannosaurus had scales, not feathers everywhere


This video says about itself:

Scientists Confirm T. Rex Didn’t Have Feathers

9 jun. 2017

Since humans knew about dinosaurs, we have speculated that they were reptiles with scaly skin. Then in 2011, there were dinosaur fossils found in amber that had feathers on them. That started a debate on whether Jurassic Park and Jurassic World got it wrong for having dinosaurs in the movies without feathers. Now scientists want the world to know that the T. rex did not have feathers.

From Biology Letters:

Tyrannosauroid integument reveals conflicting patterns of gigantism and feather evolution

Phil R. Bell, Nicolás E. Campione, W. Scott Persons, Philip J. Currie, Peter L. Larson, Darren H. Tanke, Robert T. Bakker

Published 7 June 2017

Abstract

Recent evidence for feathers in theropods has led to speculations that the largest tyrannosaurids, including Tyrannosaurus rex, were extensively feathered.

We describe fossil integument from Tyrannosaurus and other tyrannosaurids (Albertosaurus, Daspletosaurus, Gorgosaurus and Tarbosaurus), confirming that these large-bodied forms possessed scaly, reptilian-like skin.

Body size evolution in tyrannosauroids reveals two independent occurrences of gigantism; specifically, the large sizes in Yutyrannus and tyrannosaurids were independently derived. These new findings demonstrate that extensive feather coverings observed in some early tyrannosauroids were lost by the Albian, basal to Tyrannosauridae. This loss is unrelated to palaeoclimate but possibly tied to the evolution of gigantism, although other mechanisms exist.

According to Dutch paleontologist Anne Schulp, it is possible that tyrannosaurs had a few feathers as ornament at places where no scales were found.

Dinosaur age baby bird discovered in amber


This video says about itself:

Stunning fossil reveals prehistoric baby bird caught in amber

9 June 2017

Amber hunters in Burma dug up a remarkably complete bird hatchling that dates to the time of the dinosaurs. The bird’s side, almost half of its body, was dipped in tree sap, which hardened around the neck bones, claws, a wing and its toothed jaws.

Scientists identified the animal as a member of the extinct group called enantiornithes, and published their discovery in the journal Gondwana Research this week.

The chick died young and fell into a pool of sap. It died halfway through its first feather molt, suggesting that the animal broke out of its egg just a few days before it perished. Its life began in the moist tropics beneath conifer trees. It ended near a puddle of conifer gunk, called resin, which fossilized into amber. Burmese diggers uncovered the amber 99 million years later.

Enantiornithines are close relatives to modern birds, and in general, they would have looked very similar. However, this group of birds still had teeth and claws on their wings,” said Ryan McKellar, a paleontologist at Canada’s Royal Saskatchewan Museum. This animal lived during the Cretaceous Period, which came to a cataclysmic close 65.5 million years ago and took the non-bird dinosaurs with it.

The enantiornithes, due to their distinct hip and ankle bones, may have flown differently than modern birds. But they were capable fliers. (If you are wondering whether this bird relative was more bird or winged dinosaur, well, consider it both: Birds are avian dinosaurs, after all.)

Entombed in amber were details as fine as the hatchling’s eyelid and the outer opening of its ear. The resin recorded no sign of a struggle. “The hatchling may have been dead by the time it entered” the resin pool, McKellar said. “One of the leg bones has been dragged away from its natural position, suggesting that the corpse may have been scavenged before it was covered by the next flow of resin.”

Evidence suggests that enantiornithes received little in the way of parental care, unlike more doting modern birds. The ancient chicks, born on the ground, had to scamper into trees to avoid being eaten. Scampering enantiornithes got stuck in resin fairly frequently, McKellar said, though this fossil is far more comprehensive than typical specimens.

Its 99-million-year-old claws appear almost as detailed as chicken feet you’d find in a supermarket. The foot, presumed at first to be a lizard‘s by the amber miner who found it, was covered in golden scales and just under an inch long. “The preserved skin surface allows us to observe the feet in great detail,” McKellar said.

The resin trapped one of the bird’s wings as well. Despite its young age, the animal already had brown flight feathers on its wings. McKellar said it also had “a sparse coat of fluffy pale or white feathers across most of its belly, legs, and tail.”

McKellar and his colleagues probed the fossil using several types of imaging technology, including light microscopes and X-ray micro-CT scanning. The researchers discovered that the feathers on the enantiornithes’ wings were quite similar to modern bird feathers. But its tail and legs were covered by what McKellar described as tufts similar to “proto-feathers” or “dino-fuzz.”

Recent amber discoveries offer strikingly detailed, if orange-tinted, windows into ancient worlds. Sap trapped not only birds but lizards, bugs and bits of non-bird dinosaurs, too. In December, McKellar and his colleagues announced they’d found a dinosaur tail trapped in amber also excavated from a mine in Burma (also known as Myanmar).

But amber containing dino DNA, as popularized by “Jurassic Park” and its ancient mosquitoes swollen with dinosaur blood, appears to remain in the realm of science fiction. “Unfortunately, DNA seems to be ‘off the menu’ for specimens such as this one,” McKellar said. “To the best of our current understanding, DNA has a half-life of around 500 years and cannot be recovered in meaningful quantities from amber pieces that are more than a few million years old.”

From LiveScience:

100-Million-Year-Old Amber Holds Tiny, Feathery Chick

By Mindy Weisberger, Senior Writer

June 9, 2017 11:20am ET

Much of the body of a wee Cretaceous-era chick was preserved in incredible detail in a piece of Burmese amber, and bears “unusual plumage,” according to the researchers who described the unique find in a new study.

Excavated from a mine in what is now northern Myanmar, the precious lump of fossilized tree sap is estimated to be about 98 million years old, and holds the most complete specimen to date representing a group of extinct toothed birds called enantiornithines (eh-nan-tee-or-NITH’-eh-neez), which died out at the end of the Cretaceous period (about 145 million to 65.5 million years ago).

Body proportions and plumage development in the tiny specimen indicated that it was very young, while details in the feathers’ structures and distribution highlighted some of the key differences between these ancient avians and modern-day birds, the scientists wrote in the study. [See Stunning Photos of the Cretaceous Chick in Amber]

Though scientists had previously found specimens of this bird group in amber, the new find included features never seen before, such as the ear opening, the eyelid and skin on the feet.

Its body measured about 2.4 inches (6 centimeters) in length, from the tip of its beak to the end of the truncated tail. The scientists used micro-CT scans and digital 3D reconstruction to further analyze the specimen — processes that took nearly a year to complete, study co-author Jingmai O’Connor, a professor with the Institute of Vertebrate Paleontology and Paleoanthropology at the Chinese Academy of Sciences, told Live Science in an email.

The amber chunk — which measured around 3.4 inches (8.6 cm) long, 1.2 inches (3 cm) wide and 2.2 inches (5.7 cm) thick— had been divided down the middle into two pieces. Unfortunately, this cut sliced through the specimen’s skull, damaging some of the bones and relegating the chick’s beak to one amber fragment and the braincase and neck to the other, the researchers reported.

Even so, the body was near-complete, with the amber containing the tiny bird’s head and neck, part of its wings, feet and tail; and plenty of soft tissue and attached feathers. The bird was undergoing its first molt when it became caught in the sticky tree sap; there was only a light covering of plumage on its body. But it already had a full set of flight feathers on its wings, suggesting that birds in this group were highly independent from an early age, the study authors wrote.

In recent years, amber fossils have revealed fascinating glimpses of life from many millions of years ago — from ant-termite warfare and a daddy longlegs’ long-lasting erection to a spider attacking prey in its web and a bug that jumped out of its skin.

And when it comes to birds, fossils’ exceptional preservation of plumage helps paleontologists understand the diversity of feathers and the role they played for early avians, O’Connor said in the email.

“Feathers can never be well understood in normal fossils,” O’Connor said. “But in amber, we get crystal-clear views of what primitive feathers were like, and they reveal all sorts of bizarre morphologies,” she said.

The findings were published online June 6 in the journal Gondwana Research.

World’s oldest fossil mushroom discovery in Brazil


This video says about itself:

7 June 2017

The world’s oldest fossilized mushroom, dating from 115 million year ago, has been discovered in Brazil and is being called a ‘scientific wonder’. The mushroom fell into a river and began its journey in becoming a fossil at the time when Earth’s supercontinent Gondwana was breaking apart.

It made its way into a highly saline lagoon, sank through the stratified layers of salty water, and was covered in layers of fine sediment, in time becoming a fossil. The world’s oldest fossil mushroom was preserved in limestone, an extraordinarily rare event, researchers say.

From the University of Illinois at Urbana-Champaign in the USA:

World’s oldest fossil mushroom found

June 7, 2017

Roughly 115 million years ago, when the ancient supercontinent Gondwana was breaking apart, a mushroom fell into a river and began an improbable journey. Its ultimate fate as a mineralized fossil preserved in limestone in northeast Brazil makes it a scientific wonder, scientists report in the journal PLOS ONE.

The mushroom somehow made its way into a highly saline lagoon, sank through the stratified layers of salty water and was covered in layer upon layer of fine sediments. In time — lots of it — the mushroom was mineralized, its tissues replaced by pyrite (fool’s gold), which later transformed into the mineral goethite, the researchers report.

“Most mushrooms grow and are gone within a few days,” said Illinois Natural History Survey paleontologist Sam Heads, who discovered the mushroom when digitizing a collection of fossils from the Crato Formation of Brazil. “The fact that this mushroom was preserved at all is just astonishing.

“When you think about it, the chances of this thing being here — the hurdles it had to overcome to get from where it was growing into the lagoon, be mineralized and preserved for 115 million years — have to be minuscule,” he said.

Before this discovery, the oldest fossil mushrooms found had been preserved in amber, said INHS mycologist Andrew Miller, a co-author of the new report. The next oldest mushroom fossils, found in amber in Southeast Asia, date to about 99 million years ago, he said.

“They were enveloped by a sticky tree resin and preserved as the resin fossilized, forming amber,” Heads said. “This is a much more likely scenario for the preservation of a mushroom, since resin falling from a tree directly onto the forest floor could readily preserve specimens. This certainly seems to have been the case, given the mushroom fossil record to date.”

The mushroom was about 5 centimeters (2 inches) tall. Electron microscopy revealed that it had gills under its cap, rather than pores or teeth, structures that release spores and that can aid in identifying species.

Fungi evolved before land plants and are responsible for the transition of plants from an aquatic to a terrestrial environment,” Miller said. “Associations formed between the fungal hyphae and plant roots. The fungi shuttled water and nutrients to the plants, which enabled land plants to adapt to a dry, nutrient-poor soil, and the plants fed sugars to the fungi through photosynthesis. This association still exists today.”

The researchers place the mushroom in the Agaricales order and have named it Gondwanagaricites magnificus.

Japan’s biggest ever dinosaur discovery


The bones of the dinosaur Mukawaryu which have been cleaned so far. These likely represent more than half of the bones the dinosaur had

From Hokkaido University in Japan:

Japan’s largest complete dinosaur skeleton discovered

June 6, 2017

Summary: The complete skeleton of an eight-meter-long dinosaur has been unearthed from marine deposits dating back 72 million years at Japan’s northern island of Hokkaido, making it the largest dinosaur skeleton ever found in Japan.

Excavations to uncover a fossilized duck-billed dinosaur (Hadrosauridae) in the Hobetsu district of Mukawa Town have been underway since 2013. It is the third time a complete skeleton of a Hadrosaurid from a marine stratum has ever been discovered, according to the research team from Hokkaido University and Hobetsu Museum in Mukawa.

Hadrosaurids, or duck-billed dinosaurs, were common herbivores during the Late Cretaceous Period (about 100 million to 66 million years ago) and thrived on the Eurasian, North and South American continents as well as at Antarctica. Complete hadrosaur skeletons have been unearthed on these continents, but it is extremely rare for a complete skeleton of a land dinosaur to be discovered in a marine stratum.

In 1936, a complete hadrosaur skeleton was unearthed from a marine stratum in Sakhalin and named Nipponosaurus by Professor Takumi Nagao of Hokkaido Imperial University (predecessor of Hokkaido University). It had been the only such fossilized dinosaur from a marine stratum that was assigned a name. The latest discovery of the fossilized skeleton, nicknamed “Mukawaryu” (Mukawa dragon), represents the third such discovery in the world, including a complete skeleton of an undescribed specimen.

If a complete skeleton is defined as a skeleton containing more than 50 percent of the bones, Mukawaryu represents the second complete dinosaur skeleton unearthed in Japan after Fukuivenator, a 2.5-meter carnivore from the Early Cretaceous Period (about 145 million to 100 million years ago) discovered in Katsuyama City, Fukui Prefecture. Mukawaryu is the first complete skeleton of a herbivore from the Late Cretaceous Period and from a marine stratum in Japan.

Dr. Yoshitsugu Kobayashi of the research team said “We first discovered a part of the fossilized Mukawaryu skeleton in 2013, and after a series of excavations, we believe we have cleaned more than half of the bones the dinosaur had, making it clear that it is a complete skeleton.”

There are more than 50 kinds of dinosaurs in the hadrosaurid dinosaurs, which is grouped into two groups: uncrested (Hadrosaurinae) and crested members (Lambeosaurinae). “Although Mukawaryu has some characteristics of both groups, our preliminary analysis indicated it might belong to the Hadrosaurinae. Further cleaning of the fossils and detailed research should make it clearer which group the Mukawaryu skeleton belongs to,” says Kobayashi.

Bus-sized pliosaur discovery in Russia


This video says about itself:

26 May 2017

Scientists have discovered a “highly unusual” new species of extinct sea-dwelling reptile in Russia.

Similar in appearance to a river dolphin or gharial crocodile, the fish-eating sea-beast would have had a long beak-like snout.

Related to the top predators who ruled the ocean during the dinosaur age, its lengthy “rostrum” set it apart from its relatives who had large and powerful toothed jaws.

The “pliosaur Luskhan itilensis” is estimated to have measured about 6.5m (21.3ft) – the size of a small bus.

It would have had four large flippers which evolved from feet over a long period of time, and an oar-like tail.

The marine reptile‘s skull was unearthed from the bank of the Volga River near the Russian city of Ulyanovsk.

The skull alone, with its long and slender snout, measured 1.5m (5ft) – the average height of a 13 year old boy.

Scientists believe that the animal’s unusual beak suggests that this family of marine reptiles – called plesiosaurs – colonised a much wider range of ecological niches than previously believed.

From the University of Liège in Belgium:

New species of bus-sized fossil marine reptile unearthed in Russia

May 25, 2017

Summary: A new species of a fossil pliosaur (large predatory marine reptile from the ‘age of dinosaur[s]’) has been found in Russia and profoundly change[s] how we understand the evolution of the group, says an international team of scientists.

A new species of a fossil pliosaur (large predatory marine reptile from the ‘age of dinosaur[s]’) has been found in Russia and profoundly change[s] how we understand the evolution of the group, says an international team of scientists.

Spanning more than 135 Ma during the ‘Age of Dinosaurs‘, plesiosaur marine reptiles represent one of longest-lived radiations of aquatic tetrapods and certainly the most diverse one. Plesiosaurs possess an unusual body shape not seen in other marine vertebrates with four large flippers, a stiff trunk, and a highly varying neck length. Pliosaurs are a special kind of plesiosaur that are characterized by a large, 2m long skull, enormous teeth and extremely powerful jaws, making them the top predators of oceans during the ‘Age of Dinosaurs’.

In a new study to be published today in the journal Current Biology, the team reports a new, exceptionally well-preserved and highly unusual pliosaur from the Cretaceous of Russia (about 130 million years ago). It has been found in Autumn 2002 on [the] right bank of the Volga River, close to the city of Ulyanovsk, by Gleb N. Uspensky (Ulyanovsk State University), one of the co-authors of the paper. The skull of the new species, dubbed “Luskhan itilensis,” meaning the Master Spirit from the Volga river, is 1.5m in length, indicating a large animal. But its rostrum is extremely slender, resembling that of fish-eating aquatic animals such as gharials or some species of river dolphins. “This is the most striking feature, as it suggests that pliosaurs colonized a much wider range of ecological niches than previously assumed” said Valentin Fischer, lecturer at the Université de Liège (Belgium) and lead author of the study.

By analysing two new and comprehensive datasets that describe the anatomy and ecomorphology of plesiosaurs with cutting edge techniques, the team revealed that several evolutionary convergences (a biological phenomenon where distantly related species evolve and resemble one another because they occupy similar roles, for example similar feeding strategies and prey types in an ecosystem) took place during the evolution of plesiosaurs, notably after an important extinction event at the end of the Jurassic (145 million years ago). The new findings have also ramifications in the final extinction of pliosaurs, which took place several tens of million years before that of all dinosaurs (except some bird lineages). Indeed, the new results suggest that pliosaurs were able to bounce back after the latest Jurassic extinction, but then faced another extinction that would — this time — wipe them off the depths of ancient oceans, forever.