rhino tooth Archives - Rhino Review

A 1.7-million-year-old rhino tooth revises their family tree (The Republic of Georgia)

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Gemma Tarlach, Discover | December 19, 2019

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A really old rhino tooth has opened a new path toward understanding the tree of life — including, potentially, our own branch.

In September, researchers detailed in Nature how, using the tooth of a 1.77-million-year-old rhino from the Republic of Georgia, they were able to revise its family tree. The team’s success has implications far beyond rhino ancestry: It’s proof of concept that it’s possible to map out evolutionary relationships between species, with confidence and on a molecular level, without DNA.

Instead, the team extracted and sequenced proteins preserved in the rhino’s tooth enamel.

“Protein sequences are the best proxy [for DNA],” says University of Copenhagen’s Enrico Cappellini, lead author of the study. Cappellini is a specialist in paleoproteomics, the study of ancient proteins preserved in fossils. “In a way, you can read [proteins] like a text. If you retrieve only a few words, you can’t read the story. If you retrieve more words, you start to understand. And if you have the ancient and the modern text side by side, you can see the differences between them.”

Each protein is a unique chain of amino acids arranged in a specific order. Like DNA, over time these complex chains accumulate small changes that can provide clues to the evolution of a species. Unlike fragile DNA, ancient proteins can last for millions of years in fossilized tissues, including bones and teeth.

Illustration as published by Discover Magazine. (Credit: Mauricio Anton)

For years, researchers have been able to extract and broadly identify these ancient proteins. More recently, however, they have been able to read the protein sequences on a much finer scale, finding subtle differences on an amino acid level. It’s similar to the way geneticists work with DNA, only instead of genomes, they’re reconstructing ancient proteomes.

Previous paleoproteomic work focused on the protein collagen, extracted from ancient bones rather than tooth enamel. Collagen, however, doesn’t change much between species, and it’s only a single protein. The tooth enamel proteome provides information on multiple proteins, and, as Cappellini puts it, “better chances to find a text we can read.”

And although the approach is destructive — tiny chips of enamel are pulverized and fed into a mass spectrometer — teeth are among the most common finds in the fossil record.

Paleoproteomics does have limitations. For example, proteomes are much smaller than genomes, so they provide fewer data points, and the extraction and sequencing of ancient proteins is difficult work. Still, the rhino tooth study shows that it’s possible to study organisms on a molecular level well beyond ancient DNA’s expiration date — theoretically including early members of our own family tree.

“I’m always fascinated to see something invisible become visible,” says John Hawks, a paleoanthropologist at the University of Wisconsin-Madison.

While he stressed that he admires the careful, thoughtful work of Cappellini and his colleagues, Hawks cautions that their success may have unintended consequences.

“The reality is that there is a bone rush,” Hawks says. “Copycats will come around to [museum collection curators] and say, ‘I’ll give you a paper in Nature … just give me some teeth to grind up.’ ”

For now, Cappellini is focused on refining the method to obtain more detailed proteomes, from potentially even older fossils.

“We don’t know how far back we can go,” says Cappellini. “I’m looking forward to finding out.”


Genetic data from 1.77 million-year-old rhino tooth could solve some of the biggest mysteries in evolution

By Archeology, Science and technology No Comments
The University of York / SciTech Daily | November 23, 2019

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New research on ancient rhino tooth could unlock evolution mysteries.

Scientists from the University of York were involved in a project to extract original proteins providing genetic data from a 1.77 million-year-old rhino tooth.

It marks a breakthrough in the field of ancient biomolecular studies by allowing scientists to accurately reconstruct evolution in mammals from further back in time than ever before – offering the potential to solve some of the biggest mysteries of animal and human development.

Researchers identified an almost complete set of proteins in the dental enamel of the rhino, the largest genetic data-set older than one million years to ever be recorded.

Original illustration as published by SciTechDaily: Artistic reconstruction of Stephanorhinus in its natural environment. (Credit: Mauricio Anton)

Tooth Enamel

Researchers at the University of York played a vital role ensuring that the proteins recovered were authentic and not contaminated. Dr. Marc Dickinson and Dr. Kirsty Penkman, both from the Department of Chemistry, have been developing a method for isolating protein trapped within fossil tooth enamel, and they applied this to the rhino tooth as well as other fossils from the site.

Dr. Dickinson said: “It was exciting to see such clear evidence from our data that the proteins within the tooth enamel were original, which enables the genetic data derived from them to be used with confidence.”

Professor Enrico Cappellini, a specialist in Palaeoproteomics at the Globe Institute, University of Copenhagen, and first author on the paper, said: “This new analysis of ancient proteins from dental enamel will start an exciting new chapter in the study of molecular evolution.

“Dental enamel is extremely abundant and it is incredibly durable, which is why a high proportion of fossil records are teeth.”

Shift in Understanding

The fossil of the rhino tooth was found in Georgia at a site called Dmanisi, an important archaeological site with the oldest human fossils outside of Africa.

This rearranging of the evolutionary lineage of a single species may seem like a small adjustment, but identifying changes in numerous extinct mammals and humans could lead to massive shifts in our understanding of the way nature has evolved.

The team of scientists is already implementing the findings in their current research. The discovery could enable scientists across the globe to collect the genetic data of ancient fossils and to build a bigger, more accurate picture of the evolution of hundreds of species, including our own.

Reference: “Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny” by Enrico Cappellini, Frido Welker, Luca Pandolfi, Jazmín Ramos-Madrigal, Diana Samodova, Patrick L. Rüther, Anna K. Fotakis, David Lyon, J. Víctor Moreno-Mayar, Maia Bukhsianidze, Rosa Rakownikow Jersie-Christensen, Meaghan Mackie, Aurélien Ginolhac, Reid Ferring, Martha Tappen, Eleftheria Palkopoulou, Marc R. Dickinson, Thomas W. Stafford Jr, Yvonne L. Chan, Anders Götherström, Senthilvel K. S. S. Nathan, Peter D. Heintzman, Joshua D. Kapp, Irina Kirillova, Yoshan Moodley, Jordi Agusti, Ralf-Dietrich Kahlke, Gocha Kiladze, Bienvenido Martínez-Navarro, Shanlin Liu, Marcela Sandoval Velasco, Mikkel-Holger S. Sinding, Christian D. Kelstrup, Morten E. Allentoft, Ludovic Orlando, Kirsty Penkman, Beth Shapiro, Lorenzo Rook, Love Dalén, M. Thomas P. Gilbert, Jesper V. Olsen, David Lordkipanidze and Eske Willerslev, 11 September 2019, Nature.

DOI: 10.1038/s41586-019-1555-y


Ancient rhinos roamed the Yukon

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University of Colorado at Boulder, Phys.Org | October 31, 2019

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In 1973, a teacher named Joan Hodgins took her students on a hike near Whitehorse in Canada’s Yukon Territory. In the process, she made history for this chilly region.

While exploring the tailings left behind by a now-defunct copper mine, Hodgins and her students stumbled across a few fragments of fossils—bits and pieces of what seemed to be teeth alongside pieces of bone.

The ancient fragments of teeth were so small and in such bad shape that “most paleontologists may not have picked them up,” said Jaelyn Eberle, a curator of fossil vertebrates at the University of Colorado Boulder’s Museum of Natural History.

But Hodgins did. Now, more than 40 years after the teacher’s fateful hike, an international team led by Eberle used modern technology to identify the origins of those enigmatic fossils.

In a study published today, Eberle and her colleagues report that the fossil tooth fragments likely came from the jaw of a long-extinct cousin of today’s rhinoceroses. This hefty animal may have tromped through the forests of Northwest Canada roughly 8 to 9 million years ago.

And it’s a first: Before the rhino discovery, paleontologists had not found a single fossil vertebrate dating back to this time period in the Yukon.

“In the Yukon, we have truckloads of fossils from ice age mammals like woolly mammoths, ancient horses and ferocious lions,” said Grant Zazula, a coauthor of the new study and Yukon Government paleontologist. “But this is the first time we have any evidence for ancient mammals, like rhinos, that pre-date the ice age.”

Original photo as published by Phys.org: An artist’s imagining of an ancient relative of today’s rhinoceroses splashing through a stream next to turtles and fish in the Yukon. (Credit: Julius Csotonyi)

It’s a gap in the fossil record that scientists have been keen to fill.

To understand why, imagine the Earth during the Tertiary Period, a span of time that began after the dinosaurs went extinct and ended about 2.6 million years ago. In that age, a land bridge called Beringia connected what are today Russia and Alaska.

Paleontologists believe that animals of all sorts, including mammoths and rhinos, poured over that bridge.

There’s just one problem: The geology and environment of the Yukon, which sat at the center of that mass migration route, isn’t conducive to preserving fossils from land animals.

“We know that a land bridge must have been in operation throughout much of the last 66 million years,” Eberle said. “The catch is finding fossils in the right place at the right time.”

In this case, the people at the right place and at the right time was a Yukon schoolteacher and her students.

When Eberle first saw Hodgins’ fossil teeth, now housed in the Yukon Government fossil collections in Whitehorse, she didn’t think she could do much with them.

Then she and her colleagues landed on an idea: Eberle put one of the small pieces under a tool called a scanning electron microscope that can reveal the structure of tooth enamel in incredible detail.

She explained that mammal teeth aren’t all built alike. The crystals that make up enamel can grow following different patterns in different types of animals, a bit like a dental fingerprint. The Yukon tooth enamel, the team found, carried the tell-tale signs of coming from a rhinoceros relative.

“I hadn’t thought that enamel could be so beautiful,” Eberle said.

The method isn’t detailed enough to determine the precise species of rhino. But, if this animal was anything like its contemporaries to the south, Eberle said, it may have been about the same size or smaller than today’s black rhinos and browsed on leaves for sustenance. It also probably didn’t have a horn on its snout.

The group also looked at a collection of fossils found alongside the rhino’s tooth chips. They belonged to two species of turtle, an ancient deer relative and a pike fish. The discovery of the turtles, in particular, indicated that the Yukon had a warmer and wetter climate than it does today.

Hodgins, now-retired, is excited to see what became of the fossils she and her students discovered more than 40 years ago: It’s “just so wonderful to learn what has developed with them from long ago,” she said.

Eberle added that the Yukon’s newly-discovered rhino residents are a testament to the importance of museums.

“The fact that these specimens were discovered in the Yukon museum collection makes me really want to spend more time in other collections, including at CU Boulder, looking for these kinds of discoveries that are there but haven’t had the right eyes on them yet,” Eberle said.

More information: Jaelyn Eberle et al, The First Tertiary Fossils of Mammals, Turtles, and Fish from Canada’s Yukon, American Museum Novitates (2019). DOI: 10.1206/3943.1

Provided by University of Colorado at Boulder

1.7-million-year-old rhino tooth provides oldest DNA data ever studied

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Jason Daley, Smithsonian.com | September 12, 2019

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DNA sequencing has revolutionized the way researchers study evolution and animal taxonomy. But DNA has its limits—it’s a fragile molecule that degrades over time. So far, the oldest DNA sequenced came from a 700,000-year-old horse frozen in permafrost. But a new technique based on the emerging field of proteomics has begun to unlock the deep past, and recently researchers extracted genetic information from the tooth enamel of a rhinoceros that lived 1.7 million years ago.

In traditional DNA sequencing, the molecule is run through a machine that amplifies the genetic material and is able to read off the sequence of nucleotides—adenine (A), cytosine (C), guanine (G) and thymine (T)—that make up the DNA strand and encode instructions to make amino acids and proteins. The quality and completeness of a genome depends on how well the DNA is preserved.

Original photo as published by Smithsonianmag.com: The skull of the 1.77-million-year-old Stephanorhinus rhino. (Mirian Kiladze, Georgian National Museum)

The new proteomics approach is essentially reverse engineering. Using a mass spectrometer, researchers look at preserved proteins and are able to determine the amino acids that make them up. Because researchers know what three-letter DNA sequence encodes each amino acid, they can then determine the DNA sequence for the protein.

“It’s reading DNA when you don’t have any DNA to read,” Glendon Parker, a forensic scientist at the University of California, Davis, says in a press release. He and colleagues are developing proteomics techniques that can be used in criminology, evolutionary biology and anthropology. “Protein is much more stable than DNA, and protein detection technology is much better now.”

The most stable protein that we know of is tooth enamel, which can remain intact in fossils for millions of years. Enrico Cappellini of the University of Copenhagen and colleagues focused on this protein in a new study in the journal Nature. The researchers took a miniscule amount of enamel from the tooth of a 1.77-million-year-old Eurasian rhinocerous species called

Stephanorhinus, which was dug up in Dmanisi, Georgia. The DNA had long since degraded, but mass spectrometry allowed the team to retrieve genetic data from the enamel, the oldest ever to be recorded, according to another press release.

“For 20 years ancient DNA has been used to address questions about the evolution of extinct species, adaptation and human migration, but it has limitations. Now for the first time we have retrieved ancient genetic information which allows us to reconstruct molecular evolution way beyond the usual time limit of DNA preservation,” Capellini says. “This new analysis of ancient proteins from dental enamel will start an exciting new chapter in the study of molecular evolution.”

The finding has big implications for evolutionary biology. While DNA is scarce, tooth enamel is plentiful. “[Tooth enamel] seems to protect its protein almost like a little time capsule,” co-author and chemist Kirsty Penkman of the University of York tells David Behrens at The Yorkshire Post. “It’s a step forward from Darwin. He was making his predictions based on the shape of bones—we’re now able to get molecular information from the bone and the teeth. The potential for this to be applied to a huge range of different species, including humans, is enormous.”

Scientists already have a massive amount of material for genetic analysis available at their fingertips. “There are tons of these fossils sitting around in museums and in sediments around the world, and we can now get useful evolutionary information from them,” Penkman says.

One of the potential applications of this technique is sorting out the human family tree. Currently, the oldest DNA researchers have from human ancestors is about 400,000 years old, enough to tell us a little bit about Homo sapiens, Neanderthals and Denisovans. But beyond that, reports Phoebe Weston at The Independent, paleoanthropologists have primarily relied on changes in anatomy to decide if an ancient hominin is our direct ancestor. For instance, there is no direct genetic link between modern humans and Homo erectus, which may be a direct ancestor. Some evidence also suggests that early humans interbred with Homo erectus. A genome from that species would help iron out the relationship.

The new technique has already shaken up the family tree of ancient rhinoceroses. According to the paper, the enamel DNA reveals that the Stephanorhinus rhino is not a direct ancestor of the better known woolly rhino, which survived until the Pleistocene about 10,000 years ago, but is a sister lineage and the two likely evolved from a common ancestor. And this probably isn’t the only branch on the tree of life that will be reshaped by proteomics in the near future.