Great white shark genome decoded


This 18 February 2019 video says about itself:

Scientists claim SHARK DNA could contain the secret to longer life in humans

Great white sharks may prove unlikely saviours of human lives thanks to their huge and extraordinary genome, scientists have discovered. The first “map” of the creature’s DNA has uncovered a plethora of mutations that protect against cancer and other age-related diseases, as well as enhanced wound healing.

Experts believe understanding more about the way the great white has evolved to keep its genome stable and resist disease could lead to new life-preserving human treatments. Study co-leader Dr Mahmood Shivji, director of the Save Our Seas Foundation Shark Research Centre at Nova Southeastern University in Florida, US, said: “Genome instability is a very important issue in many serious human diseases. “Now we find that nature has developed clever strategies to maintain the stability of genomes in these large-bodied, long-lived sharks. “There’s still tons to be learned from these evolutionary marvels, including information that will potentially be useful to fight cancer and age-related diseases, and improve wound healing treatments in humans, as we uncover how these animals do it.” Cracking the great white genetic code also revealed the large size of the apex predator’s genome. It contains an estimated 4.63 billion “base pairs”, the chemical units of DNA, making it one-and-a-half times bigger than its human counterpart.

From Nova Southeastern University in the USA:

Great white shark genome decoded

Huge genome reveals sequence adaptations in key wound healing and genome stability genes tied to cancer protection

February 18, 2019

Summary: In a major scientific step to understand the biology of this iconic apex predator and sharks in general, the entire genome of the white shark has now been decoded in detail.

The great white shark is one of the most recognized marine creatures on Earth, generating widespread public fascination and media attention, including spawning one of the most successful movies in Hollywood history. This shark possesses notable characteristics, including its massive size (up to 20 feet and 7,000 pounds) and diving to nearly 4,000 foot depths. Great whites are also a big conservation concern given their relatively low numbers in the world’s oceans.

In a major scientific step to understand the biology of this iconic apex predator and sharks in general, the entire genome of the white shark has now been decoded in detail.

A team led by scientists from Nova Southeastern University’s (NSU) Save Our Seas Foundation Shark Research Center and Guy Harvey Research Institute (GHRI), Cornell University College of Veterinary Medicine, and Monterey Bay Aquarium, completed the white shark genome and compared it to genomes from a variety of other vertebrates, including the giant whale shark and humans.

The findings are reported in the ‘Latest Articles’ section of the journal Proceedings of the National Academy of Sciences.

Decoding the white shark’s genome revealed not only its huge size — one-and-a-half times the size of the human genome — but also a plethora of genetic changes that could be behind the evolutionary success of large-bodied and long-lived sharks.

The researchers found striking occurrences of specific DNA sequence changes indicating molecular adaptation (also known as positive selection) in numerous genes with important roles in maintaining genome stability ¬¬- the genetic defense mechanisms that counteract the accumulation of damage to a species’ DNA, thereby preserving the integrity of the genome.

These adaptive sequence changes were found in genes intimately tied to DNA repair, DNA damage response, and DNA damage tolerance, among other genes. The opposite phenomenon, genome instability, which results from accumulated DNA damage, is well known to predispose humans to numerous cancers and age-related diseases.

“Not only were there a surprisingly high number of genome stability genes that contained these adaptive changes, but there was also an enrichment of several of these genes, highlighting the importance of this genetic fine-tuning in the white shark,” said Mahmood Shivji, Ph.D., director of NSU’s Save Our Seas Foundation Shark Research Center and GHRI. Shivji co-led the study with Michael Stanhope, Ph.D., of Cornell University College of Veterinary Medicine.

Also notable was that the white shark genome contained a very high number of “jumping genes” or transposons, and in this case a specific type, known as LINEs. In fact this is one of the highest proportions of LINEs (nearly 30%) discovered in vertebrates so far.

“These LINEs are known to cause genome instability by creating double stranded breaks in DNA,” said Stanhope. “It’s plausible that this proliferation of LINEs in the white shark genome could represent a strong selective agent for the evolution of efficient DNA repair mechanisms, and is reflected in the positive selection and enrichment of so many genome stability genes.”

The international research team, which also included scientists from California State University, Monterey Bay, Clemson University, University of Porto, Portugal, and the Theodosius Dobzhansky Center for Genome Bioinformatics, Russia, also found that many of the same genome stability genes in the white shark were also under positive selection and enriched in the huge-bodied, long-lived whale shark.

The discovery that the whale shark also had these key genome stability adaptations was significant because theoretically, the risk of developing cancer should increase with both the number of cells (large bodies) and an organism’s lifespan — there is statistical support for a positive relationship of body size and cancer risk within a species. Interestingly, this does not tend to hold up across species.

Contrary to expectations, very large-bodied animals do not get cancer more often than humans, suggesting they have evolved superior cancer-protective abilities. The genetic innovations discovered in genome stability genes in the white and whale shark could be adaptations facilitating the evolution of their large bodies and long lifespans.

“Decoding the white shark genome is providing science with a new set of keys to unlock lingering mysteries about these feared and misunderstood predators — why sharks have thrived for some 500 million years, longer than almost any vertebrate on earth” said Dr. Salvador Jorgensen, a Senior Research Scientist at the Monterey Bay Aquarium, who co-authored the study.

But the innovations did not end there.

The shark genomes revealed other intriguing evolutionary adaptations in genes linked to wound healing pathways. Sharks are known for their impressively rapid wound healing.

“We found positive selection and gene content enrichments involving several genes tied to some of the most fundamental pathways in wound healing, including in a key blood clotting gene,” said Stanhope. “These adaptations involving wound healing genes may underlie the vaunted ability of sharks to heal efficiently from even large wounds.”

The researchers say they have just explored the “tip of the iceberg” with respect to the white shark genome.

“Genome instability is a very important issue in many serious human diseases; now we find that nature has developed clever strategies to maintain the stability of genomes in these large-bodied, long-lived sharks,” said Shivji. “There’s still tons to be learned from these evolutionary marvels, including information that will potentially be useful to fight cancer and age-related diseases, and improve wound healing treatments in humans, as we uncover how these animals do it.”

Decoding the white shark genome will also assist with the conservation of this and related sharks, many of which have rapidly declining populations due to overfishing,” said Steven O’Brien, a conservation geneticist at NSU, who co-conceived this study. “The genome data will be a great asset for understanding white shark population dynamics to better conserve this amazing species that has captured the imagination of so many.”

This research was funded by NSU’s Save Our Seas Foundation, the Guy Harvey Ocean Foundation, the Hai Stiftung/Shark Foundation, the Monterey Bay Aquarium, and in-kind support from Illumina, Inc., and Dovetail Genomics.

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Megalodon and great white shark updates


Megalodon extinction timeline, credit: Robert Boessenecker

From the University of Wisconsin Oshkosh in the USA:

Giant ‘megalodon‘ shark extinct earlier than previously thought

Prehistoric beast not killed off by a supernova

February 13, 2019

Summary: ‘Megalodon‘ — a giant predatory shark that has inspired numerous documentaries, books and blockbuster movies — likely went extinct at least one million years earlier than previously thought, according to new research. This is a substantial adjustment as it means that O. megalodon likely went extinct long before a suite of strange seals, walruses, sea cows, porpoises, dolphins and whales all disappeared sometime about 1-2.5 million years ago.

Megalodon — a giant predatory shark that has inspired numerous documentaries, books and blockbuster movies — likely went extinct at least one million years earlier than previously thought, according to new research published Feb. 13 in PeerJ — the Journal of Life and Environmental Sciences.

Earlier research, which used a worldwide sample of fossils, suggested that the 50-foot-long, giant shark Otodus megalodon went extinct 2.6 million years ago. Another recent study attempted to link this extinction (and that of other marine species) with a supernova known to have occurred at about this time.

However, a team of researchers led by vertebrate paleontologist Robert Boessenecker with the College of Charleston, Charleston, South Carolina, noted that in many places there were problems with the data regarding individual fossils in the study estimating the extinction date.

In the new study, the researchers reported every fossil occurrence of O. megalodon from the densely sampled rock record of California and Baja California (Mexico) in order to estimate the extinction.

Besides Boessenecker, the research team included Dana Ehret, of New Jersey State Museum; Douglas Long, of the California Academy of Sciences; Morgan Churchill, of the University of Wisconsin Oshkosh; Evan Martin, of the San Diego Natural History Museum; and Sarah Boessenecker, of the University of Leicester, United Kingdom.

They found that genuine fossil occurrences were present until the end of the early Pliocene epoch, 3.6 million years ago. All later fossils either had poor data provenance and likely came from other fossil sites or showed evidence of being eroded from older deposits. Until 3.6 million years ago, O. megalodon had a continuous fossil record on the West Coast.

“We used the same worldwide dataset as earlier researchers but thoroughly vetted every fossil occurrence, and found that most of the dates had several problems-fossils with dates too young or imprecise, fossils that have been misidentified, or old dates that have since been refined by improvements in geology; and we now know the specimens are much younger,” Boessenecker said.

“After making extensive adjustments to this worldwide sample and statistically re-analyzing the data, we found that the extinction of O. megalodon must have happened at least one million years earlier than previously determined.”

This is a substantial adjustment as it means that O. megalodon likely went extinct long before a suite of strange seals, walruses, sea cows, porpoises, dolphins and whales all disappeared sometime about 1-2.5 million years ago.

“The extinction of O. megalodon was previously thought to be related to this marine mass extinction-but in reality, we now know the two are not immediately related,” Boessenecker said.

It also is further unclear if this proposed mass extinction is actually an extinction, as marine mammal fossils between 1 and 2 million years old are extraordinarily rare-giving a two-million- year-long period of “wiggle room.”

“Rather, it is possible that there was a period of faunal turnover (many species becoming extinct and many new species appearing) rather than a true immediate and catastrophic extinction caused by an astronomical cataclysm like a supernova,” Boessenecker said.

The researchers speculate that competition with the newly evolved modern great white shark (Carcharodon carcharias) is a more likely reason for megalodon’s extinction.

Great whites first show up with serrated teeth about 6 million years ago and only in the Pacific; by 4 million years ago, they are finally found worldwide.

“We propose that this short overlap (3.6-4 million years ago) was sufficient time for great white sharks to spread worldwide and outcompete O. megalodon throughout its range, driving it to extinction-rather than radiation from outer space,” Boessenecker said.

A new study has documented unexpected consequences following the decline of great white sharks from an area off South Africa. The study found that the disappearance of great whites has led to the emergence of sevengill sharks, a top predator from a different habitat. A living fossil, sevengill sharks closely resemble relatives from the Jurassic period, unique for having seven gills instead of the typical five in most other sharks: here.

Why Megalodon sharks were so big


This November 2017 video says about itself:

Sharks are cartilaginous fishes, what’s that? It means sharks don’t really have real bones. Size of sharks vary from species to species, from small shark size like Port Jackson sharks to medium size like whitetip reef and up to large size of the great white species and gigantic size of the basking shark species. Comparison of sharks are done against a grid and diver silhouette. Comparison and size of these shark species are taken from Wikipedia.

From Swansea University in Wales:

What it takes to be a giant shark

January 24, 2019

Summary: Have you ever wondered why the Megalodon shark became to be so big? Or wondered why some other sharks are much smaller?

In a paper published by Evolution, research led by Swansea University’s Dr Catalina Pimiento and co-authored by an international team of scientists from the UK, Europe and the USA examined the biological traits of all sharks and rays before running a series of evolutionary models to seek how gigantism evolved over time.

The results showed that for a shark to be giant, it would need to first evolve adaptations that enhance feeding such as the ability to control — at least to some degree — their own body temperature or become a filter feeder.

One of the most famous giant sharks, Megalodon — the topic of 2018 Hollywood film The Meg — was an active predator that could measure up to 18 metres in length and became extinct around two million years ago.

Meanwhile, the whale shark — which is still around today — can also reach 18 metres but isn’t an active predator. Instead, it is a filter feeder and eats tiny plankton from the sea.

These two subjects formed key parts of the research, which centred on the tree of life for sharks, where the authors mapped characteristics relating to body size, like their thermo-regulatory capacity, feeding mechanism and diet.

Researchers then found that sharks could become giants by following one of two possible evolutionary pathways; the mesothermic pathway, which consists of evolving the ability to self-control the temperature of their most important organs — or the filter-feeding pathway, which consists of evolving the ability to feed on microscopic plankton.

The mesothermic adaptation allows sharks to live in different types of habitats — including cold waters — and also hunt more effectively. The filter-feeding adaptation allows sharks to eat the most abundant food in the ocean — plankton.

However, there are risks involved for any shark following the evolutionary pathways that lead to gigantism. The mesothermic species need to consume big prey to maintain their high energetic demands, but when these prey are scarce, giant sharks are more susceptible to extinction. The scarcity of large prey in times of rapid climatic change was the most likely cause of the extinction of Megalodon.

While the filter feeders have shown more resilience, they are at risk of eating large volumes of toxic micro plastics that now can be found in the world’s oceans — thus threatening their extinction.

Dr Catalina Pimiento, lead researcher and Postdoctoral fellow at Swansea University, said:

“Sharks provide an ideal case study to understand the evolutionary pathways leading to gigantism in the oceans because they display contrasting lifestyles and adaptations, and because they have an evolutionary history of at least 250 million years.”

Dinosaur age shark discovery


One of the tiny fossilized teeth recovered from Galagadon, so named for the shape of its teeth, which resemble the spaceships in the video game Galaga. Credit: Copyright Terry Gates

From North Carolina State University in the USA:

Ancient carpet shark discovered with ‘spaceship-shaped’ teeth

January 21, 2019

The world of the dinosaurs just got a bit more bizarre with a newly discovered species of freshwater shark whose tiny teeth resemble the alien ships from the popular 1980s video game Galaga.

Unlike its gargantuan cousin the megalodon, Galagadon nordquistae was a small shark (approximately 12 to 18 inches long), related to modern-day carpet sharks such as the “whiskered” wobbegong. Galagadon once swam in the Cretaceous rivers of what is now South Dakota, and its remains were uncovered beside “Sue”, the world’s most famous T. rex fossil.

“The more we discover about the Cretaceous period just before the non-bird dinosaurs went extinct, the more fantastic that world becomes,” says Terry Gates, lecturer at North Carolina State University and research affiliate with the North Carolina Museum of Natural Sciences. Gates is lead author of a paper describing the new species along with colleagues Eric Gorscak and Peter J. Makovicky of the Field Museum of Natural History.

“It may seem odd today, but about 67 million years ago, what is now South Dakota was covered in forests, swamps and winding rivers,” Gates says. “Galagadon was not swooping in to prey on T. rex, Triceratops, or any other dinosaurs that happened into its streams. This shark had teeth that were good for catching small fish or crushing snails and crawdads.”

The tiny teeth — each one measuring less than a millimeter across — were discovered in the sediment left behind when paleontologists at the Field Museum uncovered the bones of “Sue”, currently the most complete T. rex specimen ever described. Gates sifted through the almost two tons of dirt with the help of volunteer Karen Nordquist, whom the species name, nordquistae, honors. Together, the pair recovered over two dozen teeth belonging to the new shark species.

“It amazes me that we can find microscopic shark teeth sitting right beside the bones of the largest predators of all time,” Gates says. “These teeth are the size of a sand grain. Without a microscope you’d just throw them away.”

Despite its diminutive size, Gates sees the discovery of Galagadon as an important addition to the fossil record. “Every species in an ecosystem plays a supporting role, keeping the whole network together,” he says. “There is no way for us to understand what changed in the ecosystem during the mass extinction at the end of the Cretaceous without knowing all the wonderful species that existed before.”

Gates credits the idea for Galagadon’s name to middle school teacher Nate Bourne, who worked alongside Gates in paleontologist Lindsay Zanno’s lab at the N.C. Museum of Natural Sciences.