WFS News: Tooth Loss Precedes the Origin of Baleen in Whales

@WFS,World Fossil Society,Riffin T Sajeev,Russel T Sajeev

Rivaling the evolution of feathers in dinosaurs, one of the most extraordinary transformations in the history of life was the evolution of baleen — rows of flexible hair-like plates that blue whales, humpbacks and other marine mammals use to filter relatively tiny prey from gulps of ocean water. The unusual structure enables the world’s largest creatures to consume several tons of food each day, without ever chewing or biting. Now, Smithsonian scientists have discovered an important intermediary link in the evolution of this innovative feeding strategy: an ancient whale that had neither teeth nor baleen.

(A–G) Dorsal (A) and ventral (B) views of the holotype skull; lateral (C) view of the right mandible; dorsal (D), lateral (E), medial (F), and ventral (G) views of left tympanic bulla.

(A–G) Dorsal (A) and ventral (B) views of the holotype skull; lateral (C) view of the right mandible; dorsal (D), lateral (E), medial (F), and ventral (G) views of left tympanic bulla.

In the Nov. 29 issue of the journal Current Biology, scientists at the Smithsonian’s National Museum of Natural History and colleagues describe for the first time Maiabalaena nesbittae, a whale that lived about 33 million years ago. Using new methods to analyze long-ago discovered fossils housed in the Smithsonian’s national collection, the team, which includes scientists at George Mason University, Texas A&M University and the Burke Museum of Natural History and Culture in Seattle, have determined that this toothless, 15-foot whale likely had no baleen, showing a surprising intermediary step between the baleen whales that live today and their toothed ancestors.

Figure illustrates a composite phylogeny including results from this analysis (Figure S4) and recently published analyses [5, 7, 8]. (A) Time calibrated simplified phylogeny, with collapsed clade resolution for Mammalodontidae, Aetiocetidae and Eomysticetidae, and crown Mysticeti. (B–E) Colored bars indicate groups figured; gray bars indicate groups not figured. Panels (b–e) represent 3D models of select specimens in lateral view with artistic reconstructions of their feeding modes: (B) Basilosaurus isis; (C) Coronodon havensteini; (D) Maiabalaena nesbittae; and (E) Balaenoptera musculus. These panels illustrate the loss of a functional dentition, the intermediate phase with neither teeth nor baleen, and the subsequent origin of baleen. Illustrations are original artwork by Alex Boersma (www.alexboersma.com).

Figure illustrates a composite phylogeny including results from this analysis (Figure S4) and recently published analyses [5, 7, 8].
(A) Time calibrated simplified phylogeny, with collapsed clade resolution for Mammalodontidae, Aetiocetidae and Eomysticetidae, and crown Mysticeti.
(B–E) Colored bars indicate groups figured; gray bars indicate groups not figured. Panels (b–e) represent 3D models of select specimens in lateral view with artistic reconstructions of their feeding modes: (B) Basilosaurus isis; (C) Coronodon havensteini; (D) Maiabalaena nesbittae; and (E) Balaenoptera musculus. These panels illustrate the loss of a functional dentition, the intermediate phase with neither teeth nor baleen, and the subsequent origin of baleen. Illustrations are original artwork by Alex Boersma (www.alexboersma.com).

“When we talk about whale evolution, textbooks tend to focus on the early stages, when whales went from land to sea,” said National Museum of Natural History’s curator of fossil marine mammals. “Maiabalaena shows that the second phase of whale evolution is just as important for evolution over big scales. For the first time, we can now pin down the origin of filter-feeding, which is one of the major innovations in whale history.”When whales first evolved, they used teeth to chew their food, just like their land-dwelling ancestors. As time went on, many descendants of these early whales continued to chew their food, inheriting this trait from their predecessors. But as the oceans around them changed and animals evolved, entirely new feeding strategies arose, including baleen filter feeding, says National Museum of Natural History predoctoral fellow Carlos Mauricio Peredo, the lead author of the study who analyzed the Maiabalaena fossils.

Whales were the first mammals to evolve baleen, and no other mammal uses any anatomical structure even remotely similar to it to consume its prey. But frustratingly, baleen, whose chemical composition is more like that of hair or fingernails than bone, does not preserve well. It is rarely found in the fossil record, leaving paleontologists without direct evidence of its past or origins. Instead, scientists have had to rely on inferences from fossils and studies of fetal-whale development in the womb to piece together clues about how baleen evolved.

As a result, it has not been clear whether, as they evolved, early baleen whales retained the teeth of their ancestors until a filter-feeding system had been established. An early initial assumption, Peredo said, was that ocean-dwelling mammals must have needed teeth or baleen to eat — but several living whales contradict that idea. Sperm whales have teeth in their bottom jaw, but none on the top, so they cannot bite or chew. Narwhals’ only teeth are their long tusks, which they do not use for feeding. And some species of beaked whales, despite being classified as toothed whales, have no teeth at all.

Because of its age, Peredo said, paleontologists suspected Maiabalaena might hold important clues about baleen’s evolution. The fossil comes from a period of massive geological change during the second major phase of whale evolution, around the time the Eocene epoch was transitioning to the Oligocene. With continents shifting and separating, ocean currents were swirling around Antarctica for the first time, cooling the waters significantly. The fossil record indicates that whales’ feeding styles diverged rapidly during this timeframe, with one group leading to today’s filter-feeding whales and the other leading to echolocating ones.

Consequently, Maiabalaena had received plenty of scrutiny since its discovery in Oregon in the 1970s, but the rock matrix and material that the fossil was collected in still obscured many of its features. It was not until Peredo finally cleaned the fossil and then examined it with state-of-the-art CT scanning technology that its most striking features became clear. Maiabalaena‘s lack of teeth was readily apparent from the preserved bone, but the CT scans, which revealed the fossil’s internal anatomy, told the scientists something new: Maiabalaena‘s upper jaw was thin and narrow, making it an inadequate surface from which to suspend baleen.

“A living baleen whale has a big, broad roof in its mouth, and it’s also thickened to create attachment sites for the baleen,” Peredo said. “Maiabalaena does not. We can pretty conclusively tell you this fossil species didn’t have teeth, and it is more likely than not that it didn’t have baleen either.”

While Maiabalaena would not have been able to chew or to filter feed, muscle attachments on the bones of its throat indicate it likely had strong cheeks and a retractable tongue. These traits would have enabled it to suck water into its mouth, taking up fish and small squid in the process. The ability to suction feed would have rendered teeth, whose development requires a lot of energy to grow, unnecessary. The loss of teeth, then, appears to have set the evolutionary stage for the baleen, which the scientists estimate arose about 5 to 7 million years later.

Peredo and Pyenson see studying whale evolution as key to understanding their survival in today’s rapidly changing oceans. Like the emergence of baleen, tooth loss in whales is evidence of adaptability, suggesting that whales might be able to adapt to challenges posed in the ocean today. Still, Peredo cautions, evolutionary change may be slow for the largest whales, which have long life spans and take a long time to reproduce.

“Given the scale and rate of changes in the ocean today, we don’t exactly know what that will mean for all of the different species of filter-feeding whales,” he said. “We know that they’ve changed in the past. It’s just a matter of whether they can keep up with whatever the oceans are doing — and we’re changing the oceans pretty quickly right now.”

  1. Carlos Mauricio Peredo, Nicholas D. Pyenson, Christopher D. Marshall, Mark D. Uhen. Tooth Loss Precedes the Origin of Baleen in WhalesCurrent Biology, 2018; DOI: 10.1016/j.cub.2018.10.047
Source: Smithsonian. “Whales lost their teeth before evolving hair-like baleen in their mouths: Newly described fossil whale in museum collections reveals a surprising intermediate step in their evolution.” ScienceDaily. ScienceDaily, 29 November 2018. <www.sciencedaily.com/releases/2018/11/181129142423.htm>.
@WFS,World Fossil Society,Riffin T Sajeev,Russel T Sajeev

Seismic analysis reveals huge amount of water dragged into Earth’s interior

Slow-motion collisions of tectonic plates under the ocean drag about three times more water down into the deep Earth than previously estimated, according to a first-of-its-kind seismic study that spans the Mariana Trench.

The observations from the deepest ocean trench in the world have important implications for the global water cycle, according to researchers in Arts & Sciences at Washington University in St. Louis.

“People knew that subduction zones could bring down water, but they didn’t know how much water,” said Chen Cai, who recently completed his doctoral studies at Washington University. Cai is the first author of the study published in the Nov. 15 issue of the journal Nature.

“This research shows that subduction zones move far more water into Earth’s deep interior — many miles below the surface — than previously thought,” said Candace Major, a program director in the National Science Foundation’s Division of Ocean Sciences, which funded the study. “The results highlight the important role of subduction zones in Earth’s water cycle.”

“Previous estimates vary widely in the amount of water that is subducted deeper than 60 miles,” said Doug Wiens, the Robert S. Brookings Distinguished Professor in Earth and Planetary Sciences in Arts & Sciences and Cai’s research advisor for the study. “The main source of uncertainty in these calculations was the initial water content of the subducting uppermost mantle.”

To conduct this study, researchers listened to more than one year’s worth of Earth’s rumblings — from ambient noise to actual earthquakes — using a network of 19 passive, ocean-bottom seismographs deployed across the Mariana Trench, along with seven island-based seismographs. The trench is where the western Pacific Ocean plate slides beneath the Mariana plate and sinks deep into the Earth’s mantle as the plates slowly converge.

The new seismic observations paint a more nuanced picture of the Pacific plate bending into the trench — resolving its three-dimensional structure and tracking the relative speeds of types of rock that have different capabilities for holding water.

Rock can grab and hold onto water in a variety of ways.

Ocean water atop the plate runs down into the Earth’s crust and upper mantle along the fault lines that lace the area where plates collide and bend. Then it gets trapped. Under certain temperature and pressure conditions, chemical reactions force the water into a non-liquid form as hydrous minerals — wet rocks — locking the water into the rock in the geologic plate. All the while, the plate continues to crawl ever deeper into the Earth’s mantle, bringing the water along with it.

Previous studies at subduction zones like the Mariana Trench have noted that the subducting plate could hold water. But they could not determine how much water it held and how deep it went.

“Previous conventions were based on active source studies, which can only show the top 3-4 miles into the incoming plate,” Cai said.

He was referring to a type of seismic study that uses sound waves created with the blast of an air gun from aboard an ocean research vessel to create an image of the subsurface rock structure.

“They could not be very precise about how thick it is, or how hydrated it is,” Cai said. “Our study tried to constrain that. If water can penetrate deeper into the plate, it can stay there and be brought down to deeper depths.”

The seismic images that Cai and Wiens obtained show that the area of hydrated rock at the Mariana Trench extends almost 20 miles beneath the seafloor — much deeper than previously thought.

The amount of water that can be held in this block of hydrated rock is considerable.

For the Mariana Trench region alone, four times more water subducts than previously calculated. These features can be extrapolated to predict the conditions under other ocean trenches worldwide.

“If other old, cold subducting slabs contain similarly thick layers of hydrous mantle, then estimates of the global water flux into the mantle at depths greater than 60 miles must be increased by a factor of about three,” Wiens said.

And for water in the Earth, what goes down must come up. Sea levels have remained relatively stable over geologic time, varying by less than 1,000 ft. This means that all of the water that is going down into the Earth at subduction zones must be coming back up somehow, and not continuously piling up inside the Earth.

Scientists believe that most of the water that goes down at the trench comes back from the Earth into the atmosphere as water vapor when volcanoes erupt hundreds of miles away. But with the revised estimates of water from the new study, the amount of water going into the earth seems to greatly exceed the amount of water coming out.

“The estimates of water coming back out through the volcanic arc are probably very uncertain,” said Wiens, who hopes that this study will encourage other researchers to reconsider their models for how water moves back out of the Earth. “This study will probably cause some re-evaluation.”

Moving beyond the Mariana Trench, Wiens along with a team of other scientists has recently deployed a similar seismic network offshore in Alaska to consider how water is moved down into the Earth there.

“Does the amount of water vary substantially from one subduction zone to another, based on the kind of faulting that you have when the plate bends?” Wiens asked. “There’s been suggestions of that in Alaska and in Central America. But nobody has looked at the deeper structure yet like we were able to do in the Mariana Trench.”

Source: www.sciencedaily.com

Massive impact crater from a kilometer-wide iron meteorite discovered in Greenland

An international team lead by researchers from the Centre for GeoGenetics at the Natural History Museum of Denmark, University of Copenhagen have discovered a 31-km wide meteorite impact crater buried beneath the ice-sheet in the northern Greenland. This is the first time that a crater of any size has been found under one of Earth’s continental ice sheets. The researchers worked for last three years to verify their discovery, initially made in the 2015. The research is described in a new study just published in the internationally recognized journal Science Advances.

Map of the bedrock topography beneath the ice sheet and the ice-free land surrounding the Hiawatha impact crater. The structure is 31 km wide, with a prominent rim surrounding the structure. In the central part of the impact structure, an area with elevated terrain is seen, which is typical for larger impact craters. Calculations shows that in order to generate an impact crater of this size, the earth was struck by a meteorite more than 1 km wide. Credit: The Natural History Museum of Denmark

Map of the bedrock topography beneath the ice sheet and the ice-free land surrounding the Hiawatha impact crater. The structure is 31 km wide, with a prominent rim surrounding the structure. In the central part of the impact structure, an area with elevated terrain is seen, which is typical for larger impact craters. Calculations shows that in order to generate an impact crater of this size, the earth was struck by a meteorite more than 1 km wide.
Credit: The Natural History Museum of Denmark

The crater measures more than 31 km in diameter, corresponding to an area bigger than Paris, and placing it among the 25 largest impact craters on Earth. The crater formed when a kilometre-wide iron meteorite smashed into northern Greenland, but has since been hidden under nearly a kilometre of ice.

“The crater is exceptionally well-preserved, and that is surprising, because glacier ice is an incredibly efficient erosive agent that would have quickly removed traces of the impact. But that means the crater must be rather young from a geological perspective. So far, it has not been possible to date the crater directly, but its condition strongly suggests that it formed after ice began to cover Greenland, so younger than 3 million years old and possibly as recently as 12,000 years ago — toward the end of the last ice age” says Professor Kurt H. Kjær from the Center for GeoGenetics at the Natural History Museum of Denmark.

Giant circular depression

The crater was first discovered in July 2015 as the researchers inspected a new map of the topography beneath Greenland’s ice-sheet. They noticed an enormous, but previously undetected circular depression under Hiawatha Glacier, sitting at the very edge of the ice sheet in northern Greenland.

“We immediately knew this was something special but at the same time it became clear that it would be difficult to confirm the origin of the depression,” says Professor Kjær.

In the courtyard at the Geological Museum in Copenhagen just outside the windows of the Center for GeoGenetics sits a 20-tonne iron meteorite found in North Greenland not far from the Hiawatha Glacier.

“It was therefore not such a leap to infer that the depression could be a previously undescribed meterorite crater, but initially we lacked the evidence,” reflects Associate Professor Nicolaj K. Larsen from Aarhus University.

The crucial evidence

Their suspicion that the giant depression was a meteorite crater was reinforced when the team sent a German research plane from the Alfred Wegener Institute to fly over the Hiawatha Glacier and map the crater and the overlying ice with a new powerful ice radar. Joseph MacGregor, a glaciologist at NASA, who participated in the study and is an expert in ice radar measurements adds:

“Previous radar measurements of Hiawatha Glacier were part of a long-term NASA effort to map Greenland’s changing ice cover. What we really needed to test our hypothesis was a dense and focused radar survey there. Our colleagues at the Alfred Wegener Institute and University of Kansas did exactly that with a next-generation radar system that exceeded all expectations and imaged the depression in stunning detail. A distinctly circular rim, central uplift, disturbed and undisturbed ice layering, and basal debris. It’s all there.”

In the summers of 2016 and 2017, the research team returned to the site to map tectonic structures in the rock near the foot of the glacier and collect samples of sediments washed out from the depression through a meltwater channel.

“Some of the quartz sand washed from the crater had planar deformation features indicative of a violent impact, and this is conclusive evidence that the depression beneath the Hiawatha Glacier is a meteorite crater, ” says Professor Larsen.

The consequences of the impact on the Earth’s climate and life

Earlier studies have shown that large impacts can profoundly affect Earth’s climate, with major consequences for life on Earth at the time. It is therefore very resonable to ask when and how and this meteorite impact at the Hiawatha Glacier affected the planet.

“The next step in the investigation will be to confidently date the impact. This will be a challenge, because it will probably require recovering material that melted during the impact from the bottom of the structure, but this is crucial if we are to understand how the Hiawatha impact affected life on Earth,” concludes Professor Kjær.

Source: www.sciencedaily.com

Ancient DNA reveals history of extinct Caribbean monkey

Analysis of ancient DNA of a mysterious extinct monkey named Xenothrix — which displays bizarre body characteristics very different to any living monkey — has revealed that it was in fact most closely related to South America’s titi monkeys (Callicebinae). Having made their way overwater to Jamaica, probably on floating vegetation, their bones reveal they subsequently underwent remarkable evolutionary change.

The research published today in Proceedings of the National Academy of Sciences (12 November 2018) and carried out by a team of experts from international conservation charity ZSL (Zoological Society of London), London’s Natural History Museum (NHM), and the American Museum of Natural History in New York, also reveals that monkeys must have colonised the Caribbean islands more than once. The study reports an incredible discovery of how the unusual ecology of islands can dramatically influence animal evolution.

Xenothrix, unlike any other monkey in the world, was a slow-moving tree-dweller with relatively few teeth, and leg bones somewhat like a rodent’s. Its unusual appearance has made it difficult for scientists to work out what it was related to and how it evolved. However, the scientific team have successfully extracted the first ever ancient DNA from an extinct Caribbean primate — uncovered from bones excavated in a Jamaican cave and providing important new evolutionary insights.

Professor Samuel Turvey from ZSL, a co-author on the paper, said: “This new understanding of the evolutionary history of Xenothrix shows that evolution can take unexpected paths when animals colonise islands and are exposed to new environments. However, the extinction of Xenothrix, which evolved on an island without any native mammal predators, highlights the great vulnerability of unique island biodiversity in the face of human impacts.”

Professor Ian Barnes, whom runs the NHM’s ancient DNA lab, and co-author said: “Recovering DNA from the bones of extinct animals has become increasingly commonplace in the last few years. However, it’s still difficult with tropical specimens, where the temperature and humidity destroy DNA very quickly. I’m delighted that we’ve been able to extract DNA from these samples and resolve the complex history of the primates of the Caribbean.”

It is likely that Xenothrix‘s ancestors colonised Jamaica from South America around 11 million years ago, probably after being stranded on natural rafts of vegetation that were washed out of the mouths of large South American rivers. Many other animals, such as large rodents called hutias (Capromyidae) that still survive on some Caribbean islands today, probably colonised the region in the same way.

Ross MacPhee of the American Museum of Natural History’s Mammalogy Department, a co-author of the study, said: “Ancient DNA indicates that the Jamaican monkey is really just a titi monkey with some unusual morphological features, not a wholly distinct branch of New World monkey. Evolution can act in unexpected ways in island environments, producing miniature elephants, gigantic birds, and sloth-like primates. Such examples put a very different spin on the old cliché that ‘anatomy is destiny.'”

What Xenothrix may have looked like has been greatly debated, with suggestions that it looked like a kinkajou (Potos) or a night monkey (Aotus). Living titi monkeys are small tree-dwelling monkeys found across tropical South America, with long soft red, brown, grey or black fur. They are active during the day, extremely territorial and vocal, and live up to 12 years in the wild, with the father often caring for the young.

Though the Galapagos Islands are famous for inspiring Charles Darwin’s theory of evolution, the islands of the Caribbean have also been home to some of the most unusual and mysterious species to have ever evolved. However, the Caribbean has also experienced the world’s highest rate of mammal extinction since the end of the last ice age glaciation, likely caused by hunting and habitat loss by humans, and predation by invasive mammals brought by early settlers.

Source: www.sciencedaily.com

Citation: Zoological Society of London. “Primates of the Caribbean: Ancient DNA reveals history of mystery monkey: Weird evolution revealed in now-extinct monkey which inhabited Jamaica until a few hundred years ago.” ScienceDaily. ScienceDaily, 12 November 2018. <www.sciencedaily.com/releases/2018/11/181112191645.htm>.

Demise of Indus Valley civilization could have been a result of climate change.

More than 4,000 years ago, the Harappa culture thrived in the Indus River Valley of what is now modern Pakistan and northwestern India, where they built sophisticated cities, invented sewage systems that predated ancient Rome’s, and engaged in long-distance trade with settlements in Mesopotamia. Yet by 1800 BCE, this advanced culture had abandoned their cities, moving instead to smaller villages in the Himalayan foothills. A new study from the Woods Hole Oceanographic Institution (WHOI) found evidence that climate change likely drove the Harappans to resettle far away from the floodplains of the Indus.

Beginning in roughly 2500 BCE, a shift in temperatures and weather patterns over the Indus valley caused summer monsoon rains to gradually dry up, making agriculture difficult or impossible near Harappan cities, says Liviu Giosan, a geologist at WHOI and lead author on the paper that published Nov. 13, 2018, in the journal Climate of the Past.

“Although fickle summer monsoons made agriculture difficult along the Indus, up in the foothills, moisture and rain would come more regularly,” Giosan says. “As winter storms from the Mediterranean hit the Himalayas, they created rain on the Pakistan side, and fed little streams there. Compared to the floods from monsoons that the Harappans were used to seeing in the Indus, it would have been relatively little water, but at least it would have been reliable.”

Evidence for this shift in seasonal rainfall — and the Harapans’ switch from relying on Indus floods to rains near the Himalaya in order to water crops — is difficult to find in soil samples. That’s why Giosan and his team focused on sediments from the ocean floor off Pakistan’s coast. After taking core samples at several sites in the Arabian Sea, he and his group examined the shells of single-celled plankton called foraminifera (or “forams”) that they found in the sediments, helping them understand which ones thrived in the summer, and which in winter.

Once he and the team identified the season based on the forams’ fossil remains, they were able to then focus on deeper clues to the region’s climate: paleo-DNA, fragments of ancient genetic material preserved in the sediments.

“The seafloor near the mouth of the Indus is a very low-oxygen environment, so whatever grows and dies in the water is very well preserved in the sediment,” says Giosan. “You can basically get fragments of DNA of nearly anything that’s lived there.”

During winter monsoons, he notes, strong winds bring nutrients from the deeper ocean to the surface, feeding a surge in plant and animal life. Likewise, weaker winds other times of year provide fewer nutrients, causing slightly less productivity in the waters offshore.

“The value of this approach is that it gives you a picture of the past biodiversity that you’d miss by relying on skeletal remains or a fossil record. And because we can sequence billions of DNA molecules in parallel, it gives a very high-resolution picture of how the ecosystem changed over time,” adds William Orsi, paleontologist and geobiologist at Ludwig Maximilian University of Munich, who collaborated with Giosan on the work.

Sure enough, based on evidence from the DNA, the pair found that winter monsoons seemed to become stronger — and summer monsoons weaker — towards the later years of the Harappan civilization, corresponding with the move from cities to villages.

“We don’t know whether Harappan caravans moved toward the foothills in a matter of months or this massive migration took place over centuries. What we do know is that when it concluded, their urban way of life ended,” Giosan says.

The rains in the foothills seem to have been enough to hold the rural Harapans over for the next millennium, but even those would eventually dry up, likely contributing to their ultimate demise.

“We can’t say that they disappeared entirely due to climate — at the same time, the Indo-Aryan culture was arriving in the region with Iron Age tools and horses and carts. But it’s very likely that the winter monsoon played a role,” Giosan says.

The big surprise of the research, Giosan notes, is how far-flung the roots of that climate change may have been. At the time, a “new ice age” was settling in, forcing colder air down from the Arctic into the Atlantic and northern Europe. That in turn pushed storms down into the Mediterranean, leading to an upswing in winter monsoons over the Indus valley.

“It’s remarkable, and there’s a powerful lesson for today,” he notes. “If you look at Syria and Africa, the migration out of those areas has some roots in climate change. This is just the beginning — sea level rise due to climate change can lead to huge migrations from low lying regions like Bangladesh, or from hurricane-prone regions in the southern U.S. Back then, the Harappans could cope with change by moving, but today, you’ll run into all sorts of borders. Political and social convulsions can then follow.”

Also collaborating on the study was Ann G. Dunlea, Samuel E. Munoz, Jeffrey. P. Donnelly, and Valier Galy of WHOI; William D. Orsi of Ludwig-Maximilians-Universität MuÌ?nchen; Marco Coolen and Cornelia Wuchter of Curtin University in Australia; Kaustubh Thirumalai of Brown University; Peter D. Clift of Louisiana State University; and Dorian Q. Fuller of University College, London.

The work was supported by the National Science Foundation’s Division of Ocean Sciences and internal WHOI funds.

Citation: Woods Hole Oceanographic Institution. “Climate change likely caused migration, demise of ancient Indus Valley civilization.” ScienceDaily. ScienceDaily, 14 November 2018. <www.sciencedaily.com/releases/2018/11/181114234855.htm>.

evolution of animal ecosystem on islands

Islands have been vital laboratories for advancing evolutionary theory since the pioneering work of Charles Darwin and Alfred Russel Wallace in the 19th century.

Now, a new paper appearing in PLOS ONE from an international team of investigators describes two new fossil relatives of marsupials that shed light on how a unique island ecosystem evolved some 43 million years ago during the Eocene.

A reconstruction of the Eocene of Turkey, where the small marsupial was found. Besides the marsupials, the fauna includes embrithopods (the rhino-like animals of the background, more related to elephants and sea cows), pleuraspidotheriids (primitive ungulates with a deer/dog look), a group of primates called omomyids, bats, tortoises and crocodiles. Credit: Oscar Sanisidro | University of Kansas

A reconstruction of the Eocene of Turkey, where the small marsupial was found. Besides the marsupials, the fauna includes embrithopods (the rhino-like animals of the background, more related to elephants and sea cows), pleuraspidotheriids (primitive ungulates with a deer/dog look), a group of primates called omomyids, bats, tortoises and crocodiles.
Credit: Oscar Sanisidro | University of Kansas

“Evolution in many ways is easier to study in an island context than on a large continent like North America because it’s a simpler ecosystem,” said coauthor K. Christopher Beard, Distinguished Foundation Professor of Ecology and Evolutionary Biology at the University of Kansas and senior curator with KU’s Biodiversity Institute and Natural History Museum. “Evolutionary biologists have been focusing on islands ever since Darwin and Wallace independently formulated their ideas about evolution based on their observations of plants and animals living on the Galapagos and the Malay archipelago, which is modern Indonesia.”

However, Beard said a poor fossil record for animals living on islands through “deep time,” or across a multimillion-year time frame, has hampered our understanding of exactly how island ecosystems are assembled. The new paper describes two new fossil species, identified from their teeth, that inhabited the Pontide region of modern-day north-central Turkey.

During the Eocene the Pontide region was an island in a larger version of the modern Mediterranean Sea called Tethys. At that time, Africa and Eurasia were not connected as they are today in the Middle East, but Africa was drifting northward due to plate tectonics and would eventually collide with Eurasia millions of years later. The Pontide region was sandwiched between these converging continents. This geological setting makes the Pontide region similar to the island of Sulawesi in the Indonesian archipelago, which is similarly sandwiched between the converging continents of Asia and Australia.

“No other ecosystem on the face of the planet from any time period matches what we’re finding in the Eocene of Turkey — it’s a completely unique mammalian ecosystem much like Madagascar is today,” he said. “But how did this island biota develop over time? You need fossils and time depth to see that. We’re able here to study in great detail how this ancient island evolved — where the different animals came from, how they got there and when they got there. Once they got there, some of these mammals, including one of the new marsupial lineages we’ve discovered, were able to diversify on the island. Most of the Eocene mammals on the Pontide island seem to have gotten there by swimming or rafting across parts of the Tethys Sea, instead of getting stranded on the island when it got separated from adjacent parts of Eurasia.”

Beard’s collaborators in the research were Grégoire Métais of the Museum national d’Histoire naturelle in Paris, John R. Kappelman of the University of Texas, Alexis Licht of the University of Washington, Faruk Ocakog?lu of Eskis?ehir Osmangazi University in Turkey, and KU’s Pauline M.C. Coster and Michael H. Taylor.

In the Pontide marsupial fossils — which have no living descendants — the team found evidence that distinctive forms of life that develop on islands are ill-fated in general, given enough time.

“One thing we know for sure is that the incredibly interesting and unique Eocene biota that occurred on this island in what is now Turkey at some point was totally eradicated,” Beard said. “It was eradicated when the island was reconnected to mainland Eurasia and more cosmopolitan animals were able to access it for the first time, driving the weird island biota to extinction. The message for conservation biology today is that island ecosystems are inherently ephemeral on the grand scale of macroevolutionary time. Today, conservation biologists are concerned about many endangered taxa on islands. The ugly truth that paleontology provides is that, given enough time, most island faunas are doomed to extinction. They’re cul-de-sacs of evolution — even though they’re wonderful places to study processes of evolution.”

Beard said the two newly described fossil marsupials — Galatiadelphys minor and Orhaniyeia nauta — lived near the top of the food chain on the Pontide of the Eocene, because mammalian carnivores were unable to reach the small island.

“One of weirdest things about the island fauna from the Pontides is that there are no true mammalian carnivores,” he stated. “There was nothing related to cats, dogs, bears or weasels — no modern mammalian predators. They couldn’t get to the Pontide terrain because it was a little island. So, these marsupials ecologically are taking their place at the top of the food chain.”

According to the KU researcher, the newly discovered fossils demonstrate geological context has a huge influence on how ecosystems are assembled on any given island.

“Current ideas about island evolution are based on some fairly simplistic, yet fairly effective, models,” Beard stated. “These models propose that organisms colonize islands based on two main factors — how big is the island and how far away is it from nearby continental landmasses? A bigger island makes a bigger target and hosts a greater diversity of habitats, making it easier for organisms to colonize the island and once they get there they have a better chance of surviving and maybe even diversifying.”

Based on his team’s findings from the Pontide region, Beard said that geological context was at least as important as an island’s size or distance from colonizing animals’ source territory.

“All men may have been created equal, but all islands were not. The geological context of the island — here it’s in a region of active tectonic convergence — we think is swamping these other factors, size and distance to mainland,” he said. “The oddest thing about the Pontide mammal fauna is that it contains a unique mixture of animals coming from Europe, Africa and Asia. Even our two new marsupials show different evolutionary roots in the north and the south. This makes sense because the Pontide island was being sandwiched between Eurasia and Africa, and animals were arriving there from multiple directions. We can make an interesting analogy with the modern island of Sulawesi in Indonesia, which like the Pontide terrain has a mixed fauna. It mainly hosts animals like tarsiers, pigs and shrews that are clearly related to Asian species, but you also have on Sulawesi species that are obviously related to mammals from New Guinea. If you look at plate tectonics today, Sulawesi is getting sandwiched between Australia and Asia in much the same way the Pontide was being sandwiched between Africa and Asia in the Eocene.”

Beard recently returned from Turkey where he and his team conducted more fieldwork. This research was funded by multiple sources including a major grant from the US National Science Foundation.

Citation: University of Kansas. “Deep-time evolution of animal life on islands.” ScienceDaily. ScienceDaily, 14 November 2018. <www.sciencedaily.com/releases/2018/11/181114144318.htm>.

Rare fossil bird deepens mystery of avian extinctions

During the late Cretaceous period, more than 65 million years ago, birds belonging to hundreds of different species flitted around the dinosaurs and through the forests as abundantly as they flit about our woods and fields today.

But after the cataclysm that wiped out most of the dinosaurs, only one group of birds remained: the ancestors of the birds we see today. Why did only one family survive the mass extinction?

A newly described fossil from one of those extinct bird groups, cousins of today’s birds, deepens that mystery.

Fossilized wishbone or furcula of Mirarce eatoni. The V shape is more like the wishbones of today's birds, which are agile, strong fliers, than the U-shaped wishbones of theropod dinosaurs. Credit: David Strauss photo

Fossilized wishbone or furcula of Mirarce eatoni. The V shape is more like the wishbones of today’s birds, which are agile, strong fliers, than the U-shaped wishbones of theropod dinosaurs.
Credit: David Strauss photo

The 75-million-year-old fossil, from a bird about the size of a turkey vulture, is the most complete skeleton discovered in North America of what are called enantiornithines (pronounced en-an-tea-or’-neth-eens), or opposite birds. Discovered in the Grand Staircase-Escalante area of Utah in 1992 by University of California, Berkeley, paleontologist Howard Hutchison, the fossil lay relatively untouched in University of California Museum of Paleontology at Berkeley until doctoral student Jessie Atterholt learned about it in 2009 and asked to study it.

Atterholt and Hutchison collaborated with Jingmai O’Conner, the leading expert on enantiornithines, to perform a detailed analysis of the fossil. Based on their study, enantiornithines in the late Cretaceous were the aerodynamic equals of the ancestors of today’s birds, able to fly strongly and agilely.

“We know that birds in the early Cretaceous, about 115 to 130 million years ago, were capable of flight but probably not as well adapted for it as modern birds,” said Atterholt, who is now an assistant professor and human anatomy instructor at the Western University of Health Sciences in Pomona, California. “What this new fossil shows is that enantiornithines, though totally separate from modern birds, evolved some of the same adaptations for highly refined, advanced flight styles.”

The fossil’s breast bone or sternum, where flight muscles attach, is more deeply keeled than other enantiornithines, implying a larger muscle and stronger flight more similar to modern birds. The wishbone is more V-shaped, like the wishbone of modern birds and unlike the U-shaped wishbone of earlier avians and their dinosaur ancestors. The wishbone or furcula is flexible and stores energy released during the wing stroke.

If enantiornithines in the late Cretaceous were just as advanced as modern birds, however, why did they die out with the dinosaurs while the ancestors of modern birds did not?

“This particular bird is about 75 million years old, about 10 million years before the die-off,” Atterholt said. “One of the really interesting and mysterious things about enantiornithines is that we find them throughout the Cretaceous, for roughly 100 million years of existence, and they were very successful. We find their fossils on every continent, all over the world, and their fossils are very, very common, in a lot of areas more common than the group that led to modern birds. And yet modern birds survived the extinction while enantiornithines go extinct.”

One recently proposed hypothesis argues that the enantiornithines were primarily forest dwellers, so that when forests went up in smoke after the asteroid strike that signaled the end of the Cretaceous — and the end of non-avian dinosaurs — the enantiornithines disappeared as well. Many enantiornithines have strong recurved claws ideal for perching and perhaps climbing, she said.

“I think it is a really interesting hypothesis and the best explanation I have heard so far,” Atterholt said. “But we need to do really rigorous studies of enantiornithines’ ecology, because right now that part of the puzzle is a little hand-wavey.”

Atterholt, Hutchison and O’Connor, who is at the Institute of Vertebrate Paleontology and Paleoanthropology in Beijing, China, published an analysis of the fossil today in the open-access journal PeerJ.

Theropod dinosaurs evolved into birds

All birds evolved from feathered theropods — the two-legged dinosaurs like T. rex — beginning about 150 million years ago, and developed into many lineages in the Cretaceous, between 146 and 65 million years ago.

Hutchison said that he came across the fossil eroding out of the ground in the rugged badlands of the Kaiparowits formation in the Grand Staircase-Escalante National Monument in Garfield County, Utah, just inside the boundary of the recently reduced monument. Having found bird fossils before, he recognized it as a late Cretaceous enantiornithine, and a rare one at that. Most birds from the Americas are from the late Cretaceous (100-66 million years ago) and known only from a single foot bone, often the metatarsus. This fossil was almost complete, missing only its head.

“In 1992, I was looking primarily for turtles,” Hutchison said. “But I pick up everything because I am interested in the total fauna. The other animals they occur with tells me more about the habitat.”

According to Hutchison, the area where the fossil was found dates from between 77 and 75 million years ago and was probably a major delta, like the Mississippi River delta, tropical and forested with lots of dinosaurs but also crocodiles, alligators, turtles and fish.

Unlike most bird fossils found outside America, in particular those from China, the fossil was not smashed flat. The classic early Cretaceous bird, Archaeopteryx, was flattened in sandstone, which preserved a beautiful panoply of feathers and the skeletal layout. Chinese enantiornithines, mostly from the early Cretaceous, are equally beautiful and smashed flatter than a pancake.

“On one hand, it’s great — you get the full skeleton most of the time, you get soft tissue preservation, including feathers. But it also means everything is crushed and deformed,” she said. “Not that our fossils have zero deformation, but overall most of the bones have really beautiful three-dimensional preservation, and just really, really great detail. We see places where muscles and tendons were attaching, all kinds of interesting stuff to anatomists.”

Once Hutchison prepared the fossils and placed them in the UC Museum of Paleontology collection, they drew the attention of a few budding and established paleontologists, but no one completed an analysis.

“The stuff is legendary. People in the vertebrate paleontology community have known about this thing forever and ever, and it just happened that everyone who was supposedly working on it got too busy and it fell by the wayside and just never happened,” Atterholt said. “I was honored and incredibly excited when Howard said that I could take on the project. I was over the moon.”

Her analysis showed that by the late Cretaceous, enantiornithines had evolved advanced adaptations for flying independent of today’s birds. In fact, they looked quite similar to modern birds: they were fully feathered and flew by flapping their wings like modern birds. The fossilized bird probably had teeth in the front of its beak and claws on its wings as well as feet. Some enantiornithines had prominent tail feathers that may have differed between male and female and been used for sexual display.

“It is quite likely that, if you saw one in real life and just glanced at it, you wouldn’t be able to distinguish it from a modern bird,” Atterholt said.

This fossil bird is also among the largest North American birds from the Cretaceous; most were the size of chickadees or crows.

“What is most exciting, however, are large patches on the forearm bones. These rough patches are quill knobs, and in modern birds they anchor the wing feathers to the skeleton to help strengthen them for active flight. This is the first discovery of quill knobs in any enantiornithine bird, which tells us that it was a very strong flier.”

Atterholt and her colleagues named the species Mirarce eatoni (meer-ark’-ee ee-tow’-nee). Mirarce combines the Latin word for wonderful, which pays homage to “the incredible, detailed, three-dimensional preservation of the fossil,” she said, with the mythical Greek character Arce, the winged messenger of the Titans. The species name honors Jeffrey Eaton, a paleontologist who for decades has worked on fossils from the Kaiparowits Formation. Eaton first enticed Hutchison to the area in search of turtles, and they were the first to report fossils from the area some 30 years ago.

Thousands of such fossils from the rocks of the Kaiparowits Formation, many of them dinosaurs, contributed to the establishment of the Grand Staircase-Escalante National Monument in 1996.

“This area contains one of the best Cretaceous fossil records in the entire world, underscoring the critical importance of protecting and preserving these parts of our natural heritage,” Atterholt said. “Reducing the size of the protected area puts some of our nation’s most valuable natural and scientific resources at risk.”

Hutchison’s field work was supported by the Annie M. Alexander endowment to the UCMP.

Citation: University of California – Berkeley. “Rare fossil bird deepens mystery of avian extinctions: Most complete North American enantiornithine fossil was aerodynamic equal of modern birds.” ScienceDaily. ScienceDaily, 13 November 2018. <www.sciencedaily.com/releases/2018/11/181113080908.htm>.

WFS News:Evolution of High Tooth Replacement Rates in Sauropod Dinosaurs

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Evolution of High Tooth Replacement Rates in Sauropod Dinosaurs

Citation: D’Emic MD, Whitlock JA, Smith KM, Fisher DC, Wilson JA (2013) Evolution of High Tooth Replacement Rates in Sauropod Dinosaurs. PLoS ONE 8(7): e69235. https://doi.org/10.1371/journal.pone.0069235

Editor: Alistair Robert Evans, Monash University, Australia

Abstract
Background

Tooth replacement rate can be calculated in extinct animals by counting incremental lines of deposition in tooth dentin. Calculating this rate in several taxa allows for the study of the evolution of tooth replacement rate. Sauropod dinosaurs, the largest terrestrial animals that ever evolved, exhibited a diversity of tooth sizes and shapes, but little is known about their tooth replacement rates.

Methodology/Principal Findings

Dental histology of the sauropod dinosaurs Camarasaurus and Diplodocus. Thin sections of Camarasaurus (A, C) and Diplodocus (B, D) premaxillary teeth showing incremental lines of von Ebner (white arrowheads) in dentin. Teeth are oriented with their long axis horizontal and the occlusal surface directed to the right. A shows the tip of tooth 3iii of Camarasaurus, and B shows the tip of tooth 4iv of Diplodocus. C and D are enlarged images of one ‘limb’ of tooth 3ii and 4iii, respectively. Abbreviations: edj, enamel-dentin junction; en, enamel; pc, pulp cavity. [planned for page width].

Dental histology of the sauropod dinosaurs Camarasaurus and Diplodocus.
Thin sections of Camarasaurus (A, C) and Diplodocus (B, D) premaxillary teeth showing incremental lines of von Ebner (white arrowheads) in dentin. Teeth are oriented with their long axis horizontal and the occlusal surface directed to the right. A shows the tip of tooth 3iii of Camarasaurus, and B shows the tip of tooth 4iv of Diplodocus. C and D are enlarged images of one ‘limb’ of tooth 3ii and 4iii, respectively. Abbreviations: edj, enamel-dentin junction; en, enamel; pc, pulp cavity. [planned for page width].

Cladogram of sauropodomorphs showing the optimization of key features related to elevated tooth replacement rates. The light gray field indicates taxa that have at least three replacement teeth at each tooth position; dark gray field encapsulates taxa that have narrow tooth crowns. Silhouettes along the top of the cladogram show the number and size of replacement teeth in one tooth position. These include (from left to right): Patagosaurus (MPEF-PV 1670), Mamenchisaurus [47], Diplodocus (this study), Nigersaurus [Sereno, Wilson, Witmer, Whitlock, Maga, Ide and Rowe, unpublished data], Camarasaurus (this study), and the Río Negro titanosaur (MPCA-79) [48]. Number of replacement teeth is unknown in Brachiosauridae, but the taxon is optimized to have had at least three. Cladogram based on [30] with the addition of Tazoudasaurus [49] and Bonitasaura [50]. [planned for column width].

Cladogram of sauropodomorphs showing the optimization of key features related to elevated tooth replacement rates.
The light gray field indicates taxa that have at least three replacement teeth at each tooth position; dark gray field encapsulates taxa that have narrow tooth crowns. Silhouettes along the top of the cladogram show the number and size of replacement teeth in one tooth position. These include (from left to right): Patagosaurus (MPEF-PV 1670), Mamenchisaurus [47], Diplodocus (this study), Nigersaurus [Sereno, Wilson, Witmer, Whitlock, Maga, Ide and Rowe, unpublished data], Camarasaurus (this study), and the Río Negro titanosaur (MPCA-79) [48]. Number of replacement teeth is unknown in Brachiosauridae, but the taxon is optimized to have had at least three. Cladogram based on [30] with the addition of Tazoudasaurus [49] and Bonitasaura [50]. [planned for column width].

We present tooth replacement rate, formation time, crown volume, total dentition volume, and enamel thickness for two coexisting but distantly related and morphologically disparate sauropod dinosaurs Camarasaurus and Diplodocus. Individual tooth formation time was determined by counting daily incremental lines in dentin. Tooth replacement rate is calculated as the difference between the number of days recorded in successive replacement teeth. Each tooth family in Camarasaurus has a maximum of three replacement teeth, whereas each Diplodocus tooth family has up to five. Tooth formation times are about 1.7 times longer in Camarasaurus than in Diplodocus (315 vs. 185 days). Average tooth replacement rate in Camarasaurus is about one tooth every 62 days versus about one tooth every 35 days in Diplodocus. Despite slower tooth replacement rates in Camarasaurus, the volumetric rate of Camarasaurus tooth replacement is 10 times faster than in Diplodocus because of its substantially greater tooth volumes. A novel method to estimate replacement rate was developed and applied to several other sauropodomorphs that we were not able to thin section.
Conclusions/Significance

Differences in tooth replacement rate among sauropodomorphs likely reflect disparate feeding strategies and/or food choices, which would have facilitated the coexistence of these gigantic herbivores in one ecosystem. Early neosauropods are characterized by high tooth replacement rates (despite their large tooth size), and derived titanosaurs and diplodocoids independently evolved the highest known tooth replacement rates among archosaurs.

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WFS News: Linking Geology and Microbiology

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Linking Geology and Microbiology: Inactive Pockmarks Affect Sediment Microbial Community Structure

Citation: Haverkamp THA, Hammer Ø, Jakobsen KS (2014) Linking Geology and Microbiology: Inactive Pockmarks Affect Sediment Microbial Community Structure. PLoS ONE 9(1): e85990. https://doi.org/10.1371/journal.pone.0085990

Editor: Hauke Smidt, Wageningen University, Netherlands

Phylum level abundances of representative OTU sequences. The Lowest common ancestor algorithm was used to classify OTU sequences with blastN against the SILVA V108 SSURef database. The phylum Proteobacteria was split to accommodate for the different abundances within the various sub clades. OTUs that did not classify to the proteobacterial subclades were assigned to the taxon Proteobacteria. The group “Not assigned” consists of sequences with significant blast hits but could not be classified using the set LCA parameters. The group “Above phylum” contains OTU sequences assigned to either the kingdom Bacteria or to cellular organisms. Note that only the top 25 taxa are indicated for clarity.

Phylum level abundances of representative OTU sequences.
The Lowest common ancestor algorithm was used to classify OTU sequences with blastN against the SILVA V108 SSURef database. The phylum Proteobacteria was split to accommodate for the different abundances within the various sub clades. OTUs that did not classify to the proteobacterial subclades were assigned to the taxon Proteobacteria. The group “Not assigned” consists of sequences with significant blast hits but could not be classified using the set LCA parameters. The group “Above phylum” contains OTU sequences assigned to either the kingdom Bacteria or to cellular organisms. Note that only the top 25 taxa are indicated for clarity.

Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment.

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WFS News: Synthetic microorganisms and study of evolution

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Scientists at Scripps Research and their collaborators have created microorganisms that may recapitulate key features of organisms thought to have lived billions of years ago, allowing them to explore questions about how life evolved from inanimate molecules to single-celled organisms to the complex, multicellular lifeforms we see today.

By studying one of these engineered organisms-a bacterium whose genome consists of both ribonucleic acid (RNA) and deoxyribonucleic acid (DNA)-the scientists hope to shed light on the early evolution of genetic material, including the theorized transition from a world where most life relied solely on the genetic molecule RNA to one where DNA serves as the primary storehouse of genetic information.

Using a second engineered organism, a genetically modified yeast containing an endosymbiotic bacterium, they hope to better understand the origins of cellular power plants called mitochondria. Mitochondria provide essential energy for the cells of eukaryotes, a broad group of organisms-including humans-that possesses complex, nucleus-containing cells.

 A genetically modified yeast containing an endosymbiotic bacterium. Credit: Scripps Research

A genetically modified yeast containing an endosymbiotic bacterium.Credit: Scripps Research

The researchers report engineering the microbes in two papers, one published October 29, 2018 in the Proceedings of the National Academy of Sciences (PNAS) and another published August 30, 2018 in Journal of the American Chemical Society (JACS).

“These engineered organisms will allow us to probe two key theories about major milestones in the evolution of living organisms-the transition from the RNA world to the DNA world and the transition from prokaryotes to eukaryotes with mitochondria,” says Peter Schultz, PhD, senior author on the papers and president of Scripps Research. “Access to readily manipulated laboratory models enables us to seek answers to questions about early evolution that were previously intractable.”

The origins of life on Earth have been a human fascination for millennia. Scientists have traced the arc of life back several billion years and concluded that the simplest forms of life emerged from Earth’s primordial chemical soup and subsequently evolved over the eons into organisms of greater and greater complexity. A monumental leap came with the emergence of DNA, a molecule that stores all of the information required to replicate life and directs cellular machinery to do its bidding primarily by generating RNA, which in turn directs the synthesis of proteins, the molecular workhorses in cells.

In the 1960s, Carl Woese and Leslie Orgel, along with DNA pioneer Francis Crick, proposed that before DNA, organisms relied on RNA to carry genetic information, a molecule similar to but far less stable than DNA, that can also catalyze chemical reactions like proteins. “In science class, students learn that DNA leads to RNA which in turn leads to proteins-that’s a central dogma of biology-but the RNA world hypothesis turns that on its head,” says Angad Mehta, PhD, first author of the new papers and a postdoctoral research associate at Scripps Research. “For the RNA world hypothesis to be true, you have to somehow get from RNA to a DNA genome, yet how that might have happened is still a very big question among scientists.”

One possibility is that the transition proceeded through a kind of microbial missing link, a replicating organism that stored genetic information as RNA. For the JACS study, the Scripps Research-led team created Escherichia coli bacteria that partially build their DNA with ribonucleotides, the molecular building blocks typically used to build RNA. These engineered genomes contained up to 50 percent RNA, thus simultaneously representing a new type of synthetic organism and possibly a throwback to billions of years ago.

Mehta cautions that their work so far has focused on characterizing this chimeric RNA-DNA genome and its effect on bacterial growth and replication but hasn’t explicitly explored questions about the transition from the RNA world to the DNA world. But, he says, the fact that E. coli with half its genome comprised of RNA can survive and replicate is remarkable and seems to support the possibility of the existence of evolutionarily transitional organisms possessing hybrid RNA-DNA genomes. The Scripps Research team is now studying how the mixed genomes of their engineered E. coli function and plans to use the bacteria to explore a number of evolutionary questions.

For instance, one question is whether the presence of RNA leads to rapid genetic drift-large changes in gene sequence in a population over time. Scientists theorize that massive genetic drift occurred quickly during early evolution, and the presence in the genome of RNA could help explain how genetic change occurred so quickly.

In the paper published in PNAS, the researchers report engineering another laboratory model for an evolutionary milestone thought to have occurred more than 1.5 billion years ago. They created a yeast dependent for energy on bacteria living inside it as a beneficial parasite or “endosymbiont.” This composite organism will allow them to investigate the ancient origins of mitochondria-tiny, bacteria-like organelles that produce chemical energy within the cells of all higher organisms.

Mitochondria are widely thought to have evolved from ordinary bacteria that were captured by larger, single-celled organisms. They carry out several key functions in cells. Most importantly, they serve as oxygen reactors, using O2 to make cells’ basic unit of chemical energy, the molecule ATP. As crucial as mitochondria are to cells, their origins remain somewhat mysterious, although there are clear hints of descent from a more independent organism, widely assumed to have been a bacterium.

Mitochondria have a double-membrane structure like that of some bacteria, and-again, like bacteria-contain their own DNA. Analyses of the mitochondrial genome suggest that it shares an ancient ancestor with modern Rickettsia bacteria, which can live within the cells of their hosts and cause disease. Stronger support for the bacterial origin of mitochondria theory would come from experiments showing that independent bacteria could indeed be transformed, in an evolution-like progression, into mitochondria-like symbionts. To that end, the Scripps Research scientists engineered E. coli bacteria that could live in, depend upon, and provide key assistance to, cells of Saccharomyces cerevisiae, also known as baker’s yeast.

The researchers started by modifying E. coli to lack the gene encoding thiamin, making the bacteria dependent on the yeast cells for this essential vitamin. At the same time, they added to the bacteria a gene for ADP/ATP translocase, a transporter protein, so that ATP produced within the bacterial cells would be supplied to their yeast-cell hosts-mimicking the central function of real mitochondria. The team also modified the yeast so that their own mitochondria were deficient at supplying ATP. Thus the yeast would be dependent on the bacteria for normal, mitochondria-based ATP production.

The team found that some of the engineered bacteria, after being modified with surface proteins to protect them from being destroyed in the yeast, lived and proliferated in harmony with their hosts for more than 40 generations and appeared to be viable indefinitely. “The modified bacteria seem to accumulate new mutations within the yeast to better adapt to their new surroundings,” says Schultz.

With this system established, the team will try to evolve the E. colito become mitochondria-like organelles. For the new E. coliendosymbiont, adapting to life inside yeast could allow it an opportunity to radically slim its genome. A typical E. coli bacterium, for example, has several thousand genes, whereas mitochondria have evolved a stripped-down set of just 37.

The Scripps Research team rounded out the study with further gene-subtraction experiments, and the results were promising: they found they could eliminate not just the E. coli thiamin gene but also the genes underlying the production of the metabolic molecule NAD and the amino acid serine, and still get a viable symbiosis.

“We are now well on our way to showing that we can delete the genes for making all 20 amino acids, which comprise a significant part of the E. coli genome,” says Schultz. “Once we’ve achieved that, we’ll move on to deleting genes for the syntheses of cofactors and nucleotides, and within a few years we hope to be able to get a truly minimal endosymbiotic genome.”

The researchers also hope to use similar endosymbiont-host systems to investigate other important episodes in evolution, such as the origin of chloroplasts, light-absorbing organelles that have a mitochondria-like role in supplying energy to plants.

Journal References:Angad P. Mehta, Yiyang Wang, Sean A. Reed, Lubica Supekova, Tsotne Javahishvili, John C. Chaput, Peter G. Schultz. Bacterial Genome Containing Chimeric DNA–RNA SequencesJournal of the American Chemical Society, 2018; 140 (36): 11464 DOI: 10.1021/jacs.8b07046

  1. Angad P. Mehta, Lubica Supekova, Jian-Hua Chen, Kersi Pestonjamasp, Paul Webster, Yeonjin Ko, Scott C. Henderson, Gerry McDermott, Frantisek Supek, Peter G. Schultz. Engineering yeast endosymbionts as a step toward the evolution of mitochondriaProceedings of the National Academy of Sciences, 2018; 201813143 DOI: 10.1073/pnas.1813143115

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