Computer rendering: Graduate student brings extinct plants ‘back to life’

Jeff Benca is an admitted über-geek when it comes to prehistoric plants, so it was no surprise that, when he submitted a paper describing a new species of long-extinct lycopod for publication, he ditched the standard line drawing and insisted on a detailed and beautifully rendered color reconstruction of the plant. This piece earned the cover of March’s centennial issue of the American Journal of Botany

Benca described this 400-million-year-old fossil lycopod, Leclercqia scolopendra, and created a life-like computer rendering. The stem of the lycopod is about 2.5 millimeters across.
“Typically, when you see pictures of early land plants, they’re not that sexy: there is a green forking stick and that’s about it. We don’t have many thorough reconstructions,” said Benca, a graduate student in the Department of Integrative Biology and Museum of Paleontology at UC Berkeley. “I wanted to give an impression of what they may have really looked like. There are great color reconstructions of dinosaurs, so why not a plant?”
Benca’s realistic, full-color image could be a life portrait, except for the fact that it was drawn from a plant that lay flattened and compressed into rock for more than 375 million years.
Called Leclercqia scolopendra, or centipede clubmoss, the plant lived during the “age of fishes,” the Devonian Period. At that time, lycopods — the group Leclercqia belonged to — were one of few plant lineages with leaves. Leclercqia shoots were about a quarter-inch in diameter and probably formed prickly, scrambling, ground-covering mats. The function of Leclercqia’s hook-like leaf tips is unclear, Benca said, but they may have been used to clamber over larger plants. Today, lycopods are represented by a group of inconspicuous plants called club mosses, quillworts and spikemosses.
Both living and extinct lycopods have fascinated Benca since high school. When he came to UC Berkeley last year from the University of Washington, he brought a truckload of some 70 different species, now part of collections at the UC Botanical Garden.
Now working in the paleobotany lab of Cindy Looy, Berkeley assistant professor of integrative biology, Benca continues to establish a growing list of living lycopod species, several of which will eventually be incorporated into the UC and Jepson Herbaria collections.
Visualizing plant evolution
Benca and colleagues wrote their paper primarily to demonstrate a new technique that is helping paleobotanists interpret early land plant fossils with greater confidence. Since living clubmosses share many traits with early lycopods, the research team was able to test their methods using living relatives Benca was growing in greenhouses.
Early land plant fossils are not easy to come by, but they can be abundant in places where rocks from the Devonian Period form outcrops. But a large portion of these are just stem fragments with few diagnostic features to distinguish them, Benca said.
“The way we analyzed Leclercqia material makes it possible to gain more information from these fragments, increasing our sample size of discernible fossils,” he said.
“Getting a better grip on just how diverse and variable Devonian plants were will be important to understanding the origins of key traits we see in so many plants today.” Looy said. Benca’s co-authors are Maureen H. Carlisle, Silas Bergen and Caroline A. E. Strömberg from the University of Washington and Burke Museum of Natural History and Culture, Seattle.

Rare leafcutter bee fossils reveal Ice Age environment at the La Brea Tar Pits

Concerns about climate change and its impact on the world around us are growing daily. New scientific studies at the La Brea Tar Pits are probing the link between climate warming and the evolution of Ice Age predators, attempting to predict how animals will respond to climate change today.

The La Brea Tar Pits are famous for the amazing array of Ice Age fossils found there, such as ground sloths, mammoths, and predators like saber-toothed cats and powerful dire wolves. But the climate during the end of the Ice Age (50,000-11,000 years ago) was unstable, with rapid warming and cooling. New research reported here has documented the impact of this climate change on La Brea predators for the first time.

Two new studies published by research associates at of the Page Museum document significant change over time in the skulls of both dire wolves and saber-toothed cats. “Different tar pits at La Brea accumulated at different times,” said F. Robin O’Keefe of Marshall University, lead author on the dire wolf study. “When we compare fossils deposited at different times, we see big changes. We can actually watch evolution happening.”
After the end of the last Ice Age, La Brea dire wolves became smaller and more graceful, adapting to take smaller prey as glaciers receded and climate warmed. This rapidly changing climate drove change in saber-toothed cats as well. “Saber-toothed cats show a clear correlation between climate and shape. Cats living after the end of the Ice Age are larger, and adapted to taking larger prey,” said Julie Meachen of Des Moines University, lead author on the sabertooth study.
The two scientists discuss their work in a video here:
“We can see animals adapting to a warming climate at La Brea,” said O’Keefe. “Then humans show up and all the big ones disappear. We haven’t been able to establish causality there yet. But we are working on it.”
The emerging links between climate change and evolution needs further study. There are many unanswered questions; such as why predators change in the ways that they do, the importance of factors other than climate, and whether the arrival of humans played a role in the mass extinction at the end of the Ice Age. “There is much work to be done on the specimens from the tar pits. We are working actively to bring together the researchers and resources needed to expand on these discoveries,” says John Harris, chief curator at the Page Museum. “Climate change is a pressing issue for all of us, and we must take advantage of what Rancho La Brea can teach us about how ecosystems react to it.”

Rare fossilized embryos more than 500 million years old found

The Cambrian Period is a time when most phyla of marine invertebrates first appeared in the fossil record. Also dubbed the “Cambrian explosion,” fossilized records from this time provide glimpses into evolutionary biology when the world’s ecosystems rapidly changed and diversified. Most fossils show the organisms’ skeletal structure, which may or may not give researchers accurate pictures of these prehistoric organisms. Now, researchers at the University of Missouri have found rare, fossilized embryos they believe were undiscovered previously. Their methods of study may help with future interpretation of evolutionary history.

“Before the Ediacaran and Cambrian Periods, organisms were unicellular and simple,” said James Schiffbauer, assistant professor of geological sciences in the MU College of Arts and Science. “The Cambrian Period, which occurred between 540 million and 485 million years ago, ushered in the advent of shells. Over time, shells and exoskeletons can be fossilized, giving scientists clues into how organisms existed millions of years ago. This adaptation provided protection and structural integrity for organisms. My work focuses on those harder-to-find, soft-tissue organisms that weren’t preserved quite as easily and aren’t quite as plentiful.”
Schiffbauer and his team, including Jesse Broce, a Huggins Scholar doctoral student in the Department of Geological Sciences at MU, now are studying fossilized embryos in rocks that provide rare opportunities to study the origins and developmental biology of early animals during the Cambrian explosion.
Broce collected fossils from the lower Cambrian Shuijingtuo Formation in the Hubei Province of South China and analyzed samples to determine the chemical makeup of the rocks. Soft tissue fossils have different chemical patterns than harder, skeletal remains, helping researchers identify the processes that contributed to their preservation. It is important to understand how the fossils were preserved, because their chemical makeups can also offer clues about the nature of the organisms’ original tissues, Schiffbauer said.
“Something obviously went wrong in these fossils,” Schiffbauer said. “Our Earth has a pretty good way of cleaning up after things die. Here, the cells’ self-destructive mechanisms didn’t happen, and these soft tissues could be preserved. While studying the fossils we collected, we found over 140 spherically shaped fossils, some of which include features that are reminiscent of division stage embryos, essentially frozen in time.”
The fossilized embryos the researchers found were significantly smaller than other fossil embryos from the same time period, suggesting they represent a yet undescribed organism. Additional research will focus on identifying the parents of these embryos, and their evolutionary position.
Schiffbauer and his colleagues published this and related research in a volume of the Journal of Paleontology which he co-edited.

Ancient whodunit may be solved: Methane-producing microbes did it!

Evidence left at the crime scene is abundant and global: Fossil remains show that sometime around 252 million years ago, about 90 percent of all species on Earth were suddenly wiped out — by far the largest of this planet’s five known mass extinctions. But pinpointing the culprit has been difficult, and controversial.
Now, a team of MIT researchers may have found enough evidence to convict the guilty parties — but you’ll need a microscope to see the killers.
The perpetrators, this new work suggests, were not asteroids, volcanoes, or raging coal fires, all of which have been implicated previously. Rather, they were a form of microbes — specifically, methane-producing archaea called Methanosarcina — that suddenly bloomed explosively in the oceans, spewing prodigious amounts of methane into the atmosphere and dramatically changing the climate and the chemistry of the oceans.
Volcanoes are not entirely off the hook, according to this new scenario; they have simply been demoted to accessories to the crime. The reason for the sudden, explosive growth of the microbes, new evidence shows, may have been their novel ability to use a rich source of organic carbon, aided by a sudden influx of a nutrient required for their growth: the element nickel, emitted by massive volcanism at just that time.
The new solution to this mystery is published this week in the Proceedings of the National Academy of Sciences by MIT professor of geophysics Daniel Rothman, postdoc Gregory Fournier, and five other researchers at MIT and in China.
The researchers’ case builds upon three independent sets of evidence. First, geochemical evidence shows an exponential (or even faster) increase of carbon dioxide in the oceans at the time of the so-called end-Permian extinction. Second, genetic evidence shows a change in Methanosarcina at that time, allowing it to become a major producer of methane from an accumulation of carbon dioxide in the water. Finally, sediments show a sudden increase in the amount of nickel deposited at exactly this time.
The carbon deposits show that something caused a significant uptick in the amount of carbon-containing gases — carbon dioxide or methane — produced at the time of the mass extinction. Some researchers have suggested that these gases might have been spewed out by the volcanic eruptions that produced the Siberian traps, a vast formation of volcanic rock produced by the most extensive eruptions in Earth’s geological record. But calculations by the MIT team showed that these eruptions were not nearly sufficient to account for the carbon seen in the sediments. Even more significantly, the observed changes in the amount of carbon over time don’t fit the volcanic model.
“A rapid initial injection of carbon dioxide from a volcano would be followed by a gradual decrease,” Fournier says. “Instead, we see the opposite: a rapid, continuing increase.”
“That suggests a microbial expansion,” he adds: The growth of microbial populations is among the few phenomena capable of increasing carbon production exponentially, or even faster.
But if living organisms belched out all that methane, what organisms were they, and why did they choose to do so at that time?
That’s where genomic analysis can help: It turns out that Methanosarcina had acquired a particularly fast means of making methane, through gene transfer from another microbe — and the team’s detailed mapping of the organism’s history now shows that this transfer happened at about the time of the end-Permian extinction. (Previous studies had only placed this event sometime in the last 400 million years.) Given the right conditions, this genetic acquisition set the stage for the microbe to undergo a dramatic growth spurt, rapidly consuming a vast reserve of organic carbon in the ocean sediments.
But there is one final piece to the puzzle: Those organisms wouldn’t have been able to proliferate so prodigiously if they didn’t have enough of the right mineral nutrients to support them. For this particular microbe, the limiting nutrient is nickel — which, new analysis of sediments in China showed, increased dramatically following the Siberian eruptions (which were already known to have produced some of the world’s largest deposits of nickel). That provided the fuel for Methanosarcina’s explosive growth.
The resulting outburst of methane produced effects similar to those predicted by current models of global climate change: a sudden, extreme rise in temperatures, combined with acidification of the oceans. In the case of the end-Permian extinction, virtually all shell-forming marine organisms were wiped out — consistent with the observation that such shells cannot form in acidic waters.
“A lot of this rests on the carbon isotope analysis,” Rothman says, which is exceptionally strong and clear in this part of the geological record. “If it wasn’t such an unusual signal, it would be harder to eliminate other possibilities.”
While no single line of evidence can prove exactly what happened in this ancient die-off, says Rothman, who is also director of MIT’s Lorenz Center, “the cumulative impact of all these things is much more powerful than any one individually.” While it doesn’t conclusively prove that the microbes did it, it does rule out some alternative theories, and makes a strong and consistent case, he says.