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Coelacanth: The Fish That Time Forgot

Often called a living fossil, the coelacanth was long believed to have fallen extinct 70 million years ago, until a specimen was recognized in a fish market in South Africa in 1938. The coelacanth has fleshy, lobed fins that look somewhat like limbs, as does the lungfish, an air-breathing freshwater fish.

 

The coelacanth and the lungfish have long been battling for the honor of which is closer to the ancestral fish that first used fins to walk on land and give rise to the tetrapods, meaning all the original vertebrates and their descendants, from reptiles and birds to mammals.

 

The decoding of the coelacanth genome results in a victory for the lungfish as the closer relative to the first tetrapod. But the coelacanth may have the last laugh because its genome — which, at 2.8 billion bp of DNA, about the same size as a human genome — is decodable, whereas the lungfish genome, a remarkable 100 billion DNA units in length, cannot be cracked with present methods. The coelacanth genome is therefore more likely to shed light on the central evolutionary question of what genetic alterations were needed to change a lobe-finned fish into the first land-dwelling tetrapod.

 

The idea of decoding the coelacanth genome began six years ago when Chris Amemiya, a biologist at the University of Washington in Seattle, acquired some samples of coelacanth tissue. He asked the Broad Institute of Harvard and M.I.T., a biological research institute in Cambridge, Mass., to decode the DNA and invited experts in evolutionary and developmental biology to help interpret the results.

 

Dr. Amemiya’s team has sifted through the coelacanth’s genome for genes that might have helped its cousin species, the ancestor to the first tetrapod, invade dry land some 400 million years ago. They have found one gene that is related to those that, in animal species, build the placenta. Coelacanths have no placenta, but they produce extremely large eggs, with a good blood supply, that hatch inside the mother’s body. This gene could have been developed by land animals into a way of constructing the placenta.

 

Another helpful preadaptation is a snippet of DNA that enhances the activity of the genes that drive the formation of limbs in the embryo. The Amemiya team focused on the enhancer DNA sequence because it occurred in the coelacanth and animals but not in ordinary fish. They then inserted the coelacanth enhancer DNA into mice.

 

“It lit up right away and made an almost normal limb,” said Neil Shubin, meaning that the coelacanth gene enhancer successfully encouraged the mouse genes to make a limb. Dr. Shubin, a member of the team, is a paleontologist at the University of Chicago.

 

Present-day coelacanths are ferocious predators that live in a twilight zone about 500 feet deep where light barely penetrates. They lurk in caves during the day and emerge at night to attack surface fish as they descend and deep-sea fish as they rise to the surface. They have no evident need of fins that might help them walk on land.

 

“This is probably an unusual habitat for this lineage,” said Axel Meyer, an evolutionary biologist at the University of Konstanz in Germany and a member of the team. “Other coelacanths lived in more shallow, estuarylike environments 400 million years ago, and you can envisage them using the fins more like walking legs.”

 

The Amemiya team reports evidence that the coelacanth’s genes have been evolving more slowly than those of mammals, possibly because of “a static habitat and lack of predators.” But its environment must have changed quite considerably over the last 400 million years, Dr. Meyer said. Its principal habitat at present is the caves beneath the Comoro Islands in the Indian Ocean, but since these are extinct volcanoes a mere 5 million to 10 million years old, they must be a quite recent home for the coelacanth.

 

The Amemiya team does not possess a full coelacanth — these are endangered species — and decoded the genome from tissues obtained from Rosemary Dorrington of Rhodes University in South Africa. Dr. Dorrington supplied DNA kits to the Comoro Islands fishermen who occasionally snag coelacanths by accident. When a coelacanth was captured in 2003, they preserved blood and tissues, which were given to Dr. Dorrington and kept frozen, Dr. Amemiya said.

 

The specimen was preserved in Moroni, the capital of the Comoro Islands, but Dr. Amemiya has been unable to find out where it is now because of the constant state of civil war in the islands, he said.

 

Can he be certain, then, that the tissue came from a coelacanth? “Oh, no question,” Dr. Amemiya said. “We have DNA from several other coelacanths, from Africa and Indonesia, which is very similar to this one.” The one caught in 2003 was identified as a coelacanth by Said Ahamada, a South African expert, Dr. Amemiya said.

 

Because the original specimen is not available and the DNA sequencing is incomplete, the Amemiya team does not know its sex.

 


Via Dr. Stefan Gruenwald
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Travel Through Deep Time With This Interactive Earth

Travel Through Deep Time With This Interactive Earth | NetGeology | Scoop.it
Explore key moments in Earth’s transformative history as continents drift and climate fluctuates over 4.6 billion years
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What's Really Warming the World?

What's Really Warming the World? | NetGeology | Scoop.it

Climate deniers blame natural factors; NASA data proves otherwise


Via Peter Phillips
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Peter Phillips's curator insight, January 21, 3:06 AM
Excellent set of graphs and explanations provide clarity by contrasting natural and human effects on climate change.
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Compression can expand energy storage

Compression can expand energy storage | NetGeology | Scoop.it

The answer to powering Earth lies in renewables and hot air


Via Catherine Russell
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Study is first to map Earth's hidden groundwater

Study is first to map Earth's hidden groundwater | NetGeology | Scoop.it
Groundwater: it's one of the planet's most exploited, most precious natural resources. It ranges in age from months to millions of years old. Around the world, there's increasing demand to know how much we have and how long before it's tapped out.

Via Catherine Russell
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breanna mae johnson's curator insight, December 2, 2015 9:57 AM

This map may help people understand how much groundwater we actually have remaining. This could influence a better perception of water preservation and conservation. With the growing demand of water, people need to know how important it is to use our water wisely for the well-being of future generations.

 

                                                                                       BJ

Violet Knight's curator insight, December 2, 2015 9:59 AM

I believe that this is an important discovery. Now we will be able to conserve enough water to last us until our water supply is replenished. 

Raven Stroud's curator insight, December 3, 2015 10:20 AM

I think that if we do not limit ourselves when it comes to using groundwater, we could end up running out of it and that would cause many problems with the human race and with the environment. -R.S.

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Mystery of how snakes lost their legs solved by reptile fossil

Mystery of how snakes lost their legs solved by reptile fossil | NetGeology | Scoop.it
Fresh analysis of a reptile fossil is helping scientists solve an evolutionary puzzle -- how snakes lost their limbs. The findings show snakes did not lose their limbs in order to live in the sea, as was previously suggested.

 

The 90 million-year-old skull is giving researchers vital clues about how snakes evolved. Comparisons between CT scans of the fossil and modern reptiles indicate that snakes lost their legs when their ancestors evolved to live and hunt in burrows, which many snakes still do today.

The findings show snakes did not lose their limbs in order to live in the sea, as was previously suggested.

 

Scientists used CT scans to examine the bony inner ear of Dinilysia patagonica, a 2-meter long reptile closely linked to modern snakes. These bony canals and cavities, like those in the ears of modern burrowing snakes, controlled its hearing and balance. They built 3D virtual models to compare the inner ears of the fossils with those of modern lizards and snakes. Researchers found a distinctive structure within the inner ear of animals that actively burrow, which may help them detect prey and predators. This shape was not present in modern snakes that live in water or above ground.

 

The findings help scientists fill gaps in the story of snake evolution, and confirm Dinilysia patagonica as the largest burrowing snake ever known. They also offer clues about a hypothetical ancestral species from which all modern snakes descended, which was likely a burrower.

 

Reference:

H. Yi, M. A. Norell. The burrowing origin of modern snakes. Science Advances, 2015; 1 (10): e1500743 DOI: 10.1126/sciadv.1500743

 


Via Dr. Stefan Gruenwald
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Volcanic Rock Hints at Source of Earth's Water

Volcanic Rock Hints at Source of Earth's Water | NetGeology | Scoop.it
Hydrogen isotopes suggest that some water was present when the planet formed
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World's longest continental volcanic chain has been discovered in Australia - ScienceAlert

World's longest continental volcanic chain has been discovered in Australia - ScienceAlert | NetGeology | Scoop.it

Three times longer than the Yellowstone hotspot.


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Soil is a non-renewable resource. Its preservation is essential for food security and our sustainable future

Soil is a non-renewable resource. Its preservation is essential for food security and our sustainable future | NetGeology | Scoop.it
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Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus

Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus | NetGeology | Scoop.it

The genus Microbotryum includes plant pathogenic fungi afflicting a wide variety of hosts with anther smut disease. Microbotryum lychnidis-dioicae infects Silene latifolia and replaces host pollen with fungal spores, exhibiting biotrophy and necrosis associated with altering plant development.

We determined the haploid genome sequence for M. lychnidis-dioicae and analyzed whole transcriptome data from plant infections and other stages of the fungal lifecycle, revealing the inventory and expression level of genes that facilitate pathogenic growth. Compared to related fungi, an expanded number of major facilitator superfamily transporters and secretory lipases were detected; lipase gene expression was found to be altered by exposure to lipid compounds, which signaled a switch to dikaryotic, pathogenic growth. In addition, while enzymes to digest cellulose, xylan, xyloglucan, and highly substituted forms of pectin were absent, along with depletion of peroxidases and superoxide dismutases that protect the fungus from oxidative stress, the repertoire of glycosyltransferases and of enzymes that could manipulate host development has expanded. A total of 14 % of the genome was categorized as repetitive sequences. Transposable elements have accumulated in mating-type chromosomal regions and were also associated across the genome with gene clusters of small secreted proteins, which may mediate host interactions.

 

The unique absence of enzyme classes for plant cell wall degradation and maintenance of enzymes that break down components of pollen tubes and flowers provides a striking example of biotrophic host adaptation.


Via Francis Martin
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Fossils rewrite history of penetrative sex

Fossils rewrite history of penetrative sex | NetGeology | Scoop.it
The history of sex may have to be rewritten thanks to a group of unsightly, long-extinct fish called placoderms. A careful study of fossils of these armour-plated creatures, which gave rise to all current vertebrates with jaws, suggests that their descendants — our ancient ancestors — switched their sexual practices from internal to external fertilization, an event previously thought to be evolutionarily improbable.
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World's Earliest Flower may Date back 162 million Years

World's Earliest Flower may Date back 162 million Years | NetGeology | Scoop.it
The world's first typical flower may date back to 162 million years ago, more than 37 million years earlier than previously thought, Chinese researchers reported in a new study.


The fossil flower, named Euanthus panii, was found in western Liaoning Province, according to the study, which was published in the recent edition of the UK-based Historical Biology, an international journal of paleobiology.
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Geology IN: What caused the Nepal earthquake?

Geology IN: What caused the Nepal earthquake? | NetGeology | Scoop.it
Geology IN is a geological website, has the latest geology news, best Minerals gallery, useful information about rocks, dinosaurs, field works, minerals, fossils, books, stratigraphy, and volcanoes
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Fossil reveals terror bird’s power

Fossil reveals terror bird’s power | NetGeology | Scoop.it
Bones of a new terror bird confirm the creatures used their beaks to hatchet their prey but also raise questions about what drove the birds extinct.
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Quest to drill into Earth’s mantle restarts

Quest to drill into Earth’s mantle restarts | NetGeology | Scoop.it
Indian Ocean expedition resumes a six-decade campaign to bore right through the planet’s crust.

Via Catherine Russell
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Tiny Welsh therapod is world's earliest Jurassic dinosaur

Tiny Welsh therapod is world's earliest Jurassic dinosaur | NetGeology | Scoop.it

Newly-classified therapod Dracoraptor hanigani is the oldest known dinosaur from the Jurassic period


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Curiosity Rover Continues to Gather Martian Soil Samples

Curiosity Rover Continues to Gather Martian Soil Samples | NetGeology | Scoop.it

NASA's Curiosity Mars Rover continues its campaign to study active sand dune on Mars, scooping and analyzing samples.

At its current location for inspecting an active sand dune, NASA's Curiosity Mars rover is adding some sample-processing...


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Earth’s mineralogy unique in the cosmos

New research from a team led by Carnegie's Robert Hazen predicts that Earth has more than 1500 undiscovered minerals and that the exact mineral diversity of ...

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Scientists on a mission to drill a hole deep enough to reach the Earth's crust

Scientists on a mission to drill a hole deep enough to reach the Earth's crust | NetGeology | Scoop.it

Scientists will set out this week to drill a hole into the Indian Ocean floor to try to get below the Earth's crust for the first time.

 

They want to sample rock from the planet's mantle - its deep interior. In the process, the researchers hope to check their assumptions about the materials from which the crust itself is made. It will probably take several years to drop the full 5 to 5.5km, says co-team leader, Prof Chris MacLeod. This is in addition to the 700m of water between the drilling ship, the Joides Resolution (JR), and the seabed.

 

"In total, we think it will take three expeditions," the Cardiff University geologist told BBC News. "The science is approved and we have funding for this initial two-month investigation. But we will need to come back and we may not complete the task until the 2020s."

 

There have been several attempts to drill into the mantle, but none has yet succeeded. This latest effort may fare better, however, because faulting and erosion have already thinned the crust at the targeted drill site, known as Atlantis Bank on the South West Indian Ridge of the Indian Ocean.

 

The project, which is running under the auspices of the International Ocean Discovery Program (IODP), would give scientists access ultimately to fresh, unaltered peridotite - the rock, rich in olivine minerals, that, because of the size of the mantle, makes up the bulk material of the planet's interior.


Via Dr. Stefan Gruenwald
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The real sea monsters

The real sea monsters | NetGeology | Scoop.it
No known dinosaurs lived in the oceans. But there were lots of big aquatic reptiles that were every bit as ferocious and awesome.
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Mineralogy on Mars

A lecture on the mineralogy of Mars, using the latest data from the Mars rovers and orbiters. Fairly technical.

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Réptil que conviveu com os dinossauros descoberto por equipa de português

Réptil que conviveu com os dinossauros descoberto por equipa de português | NetGeology | Scoop.it
Fóssil recebeu nome de um feitiço que aparece na saga Harry Potter.
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Did dinosaur-killing asteroid trigger largest lava flows Earth ever saw?

Did dinosaur-killing asteroid trigger largest lava flows Earth ever saw? | NetGeology | Scoop.it

The asteroid that slammed into the ocean off Mexico 66 million years ago and killed off the dinosaurs probably rang the Earth like a bell, triggering volcanic eruptions around the globe that may have contributed to the devastation, according to a team of University of California, Berkeley, geophysicists.

 

Specifically, the researchers argue that the impact likely triggered most of the immense eruptions of lava in India known as the Deccan Traps, explaining the "uncomfortably close" coincidence between the Deccan Traps eruptions and the impact, which has always cast doubt on the theory that the asteroid was the sole cause of the end-Cretaceous mass extinction.

 

"If you try to explain why the largest impact we know of in the last billion years happened within 100,000 years of these massive lava flows at Deccan ... the chances of that occurring at random are minuscule," said team leader Mark Richards, UC Berkeley professor of earth and planetary science. "It's not a very credible coincidence."

 

Richards and his colleagues marshal evidence for their theory that the impact reignited the Deccan flood lavas in a paper to be published in The Geological Society of America Bulletin, available online today (April 30) in advance of publication.

 

While the Deccan lava flows, which started before the impact but erupted for several hundred thousand years after re-ignition, probably spewed immense amounts of carbon dioxide and other noxious, climate-modifying gases into the atmosphere, it's still unclear if this contributed to the demise of most of life on Earth at the end of the Age of Dinosaurs, Richards said.

 

Richards proposed in 1989 that plumes of hot rock, called "plume heads," rise through Earth's mantle every 20-30 million years and generate huge lava flows, called flood basalts, like the Deccan Traps. It struck him as more than coincidence that the last four of the six known mass extinctions of life occurred at the same time as one of these massive eruptions.

 

"Paul Renne's group at Berkeley showed years ago that the Central Atlantic Magmatic Province is associated with the mass extinction at the Triassic/Jurassic boundary 200 million years ago, and the Siberian Traps are associated with the end Permian extinction 250 million years ago, and now we also know that a big volcanic eruption in China called the Emeishan Traps is associated with the end-Guadalupian extinction 260 million years ago," Richards said. "Then you have the Deccan eruptions -- including the largest mapped lava flows on Earth -- occurring 66 million years ago coincident with the KT mass extinction.

 

Michael Manga, a professor in the same department, has shown over the past decade that large earthquakes -- equivalent to Japan's 9.0 Tohoku quake in 2011 -- can trigger nearby volcanic eruptions. Richards calculates that the asteroid that created the Chicxulub crater might have generated the equivalent of a magnitude 9 or larger earthquake everywhere on Earth, sufficient to ignite the Deccan flood basalts and perhaps eruptions many places around the globe, including at mid-ocean ridges.


Via Dr. Stefan Gruenwald
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The Nepal Earthquake Made Mt. Everest an Inch Shorter

The Nepal Earthquake Made Mt. Everest an Inch Shorter | NetGeology | Scoop.it
Satellite data gives the first results for the way the land moved during the quake
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A recriação do terramoto de 1755 que se tornou viral

A recriação do terramoto de 1755 que se tornou viral | NetGeology | Scoop.it
Vídeo foi publicado em 2014 pelo Smithsonian Channel
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Geology IN: Study: Yellowstone magma much bigger than thought

Geology IN: Study: Yellowstone magma much bigger than thought | NetGeology | Scoop.it
Geology IN is a geological website, has the latest geology news, best Minerals gallery, useful information about rocks, dinosaurs, field works, minerals, fossils, books, stratigraphy, and volcanoes
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