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Archive for the ‘Research’ Category.

Grad student's artwork graces journal cover

“There are great color reconstructions of dinosaurs, so why not a plant?” thought Department of Integrative Biology and UCMP grad student Jeff Benca when he set out to reconstruct the appearance of a 375-million-year-old Devonian plant. Using Adobe Illustrator CS6 software, he constructed a striking three-dimensional, full-color portrait of a stem of the lycopod Leclercqia scolopendra, or centipede clubmoss. This was no small feat, considering that the fossil plant Jeff was illustrating was a two-dimensional compression.

Jeff Benca and journal cover

Left: Jeff Benca with museum visitors on Cal Day 2014. Photo by Pat Holroyd. Right: Jeff's artwork on the cover of the March 2014 issue of the American Journal of Botany.

The illustration appears in a paper by Jeff and coauthors Maureen Carlisle, Silas Bergen, and UCMP alum Caroline Strömberg in the March 2014 issue of the American Journal of Botany. Jeff’s illustration graces the cover of the issue (see photo above).

Read more about Jeff and his work with fossil and living lycopods at the UC Berkeley Newscenter. Read the abstract for the paper, "Applying morphometrics to early land plant systematics: A new Leclercqia (Lycopsida) species from Washington State, USA."

Werning co-authors paper on growth in Parasaurolophus

Baby Parasaurolophus reconstruction by Tyler Keillor

Artist's restoration of the head of "Joe," the baby Parasaurolophus. Illustration by Tyler Keillor.

Recent Ph.D. grad Sarah Werning, now in a postdoctoral position at the State University of New York at Stony Brook, was a major contributor to a paper released today on ontogeny in Parasaurolophus, a Cretaceous hadrosaurid dinosaur notable for the hollow, bony tube on its skull. The study centers around a remarkable skeleton of a baby Parasaurolophus (nicknamed "Joe") discovered in 2009 by Kevin Terris, a student at The Webb Schools in Claremont, California, in exposures of the 75-million-year-old Kaiparowits Formation, Grand Staircase-Escalante National Monument, Utah. The Webb has been taking students to Grand Staircase-Escalante to prospect for and collect dinosaur bones for several years.

Werning did histologic studies of the six-foot-long specimen and found that the animal was not even one-year old when it died. Sarah reported that "Dinosaurs have yearly growth rings in their bone tissue, like trees. But we didn't see even one ring. That means it grew to a quarter of adult size [25 feet] in less than a year."

Three-dimensional scans of the entire skeleton were made and are freely accessible online. See the paper, along with the 3D scans, in the open-access journal PeerJ. Co-authors on the paper are Andrew Farke of the Raymond M. Alf Museum of Paleontology, Claremont, California, and Webb students Derek Chok, Annisa Herrero, and Brandon Scolieri.

Read more about "Joe" and see photos and video relating to the recovery, preparation, and study of the specimen.

Read more about Sarah's research on her website.

Marshall shows terrestrial mammal extinction due to Red Queen with new work published in Science

By studying 19 groups of Cenozoic mammals Charles Marshall and Tiago Quental tested and confirmed the Red Queen hypothesis. Red Queen is the hypothesis that states that groups must continue to adapt and evolve in response to their environments in order to survive. It's not just extinction events that threaten groups--it's also low rates of origination of new species. The new research (published in Science) shows that these mammal groups have experienced diversity declines in part due to their failure to keep pace with their deteriorating environments.

Read the UC Berkeley News Center story about this work.

Read the Science paper.

Warmer climates can lead to big lizards

A mounted modern lizard alongside the fossil jaw bones.

Pat Holroyd and co-authors describe a new species of giant lizard in the latest issue of Proceedings of the Royal Society B. The fossil jaw bones of this lizard have been in the UCMP collection since the 1970s, but it took a while for them to be recognized as something special. The specimens are from an herbivorous lizard that lived in the warm climate of Asia 40 million years ago. Dubbed Barbaturex morrisoni, this lizard was much bigger than the largest herbivorous lizards alive today. The unique traits of this lizard indicate that a warmer climate may have enabled gigantism via increased floral productivity and metabolic rates.

 

Read the press release at the UC Berkeley Newscenter.

 

Read the full paper at Proceedings of the Royal Society B.

Werning blogs at PLOS about the fossils of the Sierra Nevada

In her latest post over at the Public Library of Science blog The Integrative Paleontologists Sarah Werning writes about about what the fossil history of California can teach us about climate change. UCMP is teaming up with other Berkeley natural history museums on the Berkeley Initiative in Global Change Biology to strive for a comprehensive picture of the effects of climate change on past, present, and future life.

Read Sarah's post here.

The Looy Lab paleo detectives: Dori and Cindy at the NMNH

Cissites

A Cissites harkerianus leaf from Ellsworth County, Kansas, collected by Charles Sternberg in the late 1800s, and identified by Leo Lesquereux. Specimen from the Department of Paleobiology, National Museum of Natural History. (photo by Dori Contreras)

Tuesday morning, February 12, 2013, Dori Contreras and Cindy Looy woke before dawn to catch a cross-country flight to Washington, DC, for a two-week visit to the Smithsonian’s National Museum of Natural History (NMNH). Originally, Cindy was going to attend a biannual workshop of the Evolution of Terrestrial Ecosystem Program. However, after Dori obtained a Sigma Xi grant to study a fossil leaf collection housed in the NMNH’s paleobotanical collections, they teamed up and turned it into a joint research excursion filled with an array of activities.

Dori: My main goal was to collect data for a study on the leaf characteristics of early flowering plants from a warm wet climate approximately 100 million years ago. And just to clarify, what I mean by "data" is photographs — lots and lots of high-resolution photographs of individual fossil leaves preserved in rock. The specific fossils that I was interested in come from the Fort Harker locality in Kansas. They were collected over a roughly 30-year period (1860s through 1890s) as a part of the US Geological Survey’s explorations of the geology of the Western Interior of the United States.

I wasn’t exactly sure how many specimens I would find in the museum "stacks," which consist of rows and rows of floor-to-ceiling cabinets filled with drawers of fossils. Based on Leo Lesquereux’s publications from the late 19th century, I was expecting somewhere around 100 specimens. However, after two days of opening wooden drawers I located just over 300 Fort Harker specimens! Many have never been figured or mentioned in publications, and most have not been reevaluated in over 100 years.

Dori with the camera setup

Dori photographing the Cretaceous Fort Harker flora. (photo by Cindy Looy)

I knew that it would be a major task to photograph them all in the detail needed for study, so I went right to work. The museum's imaging room had an impressive setup of top-notch, stand-mounted cameras connected to computers for remote shooting. Most of my time was spent carting specimens back and forth between the stacks and imaging room and doing nonstop photography. The trickiest part of imaging for data collection was getting the lighting angle and brightness just right to pick up the three-dimensional (and often obscure) features of each leaf. At least magnification wasn't an issue — the resolution of the camera I used was so high that a microscope was not necessary!

Inga

Inga cretaceum, another fossil leaf collected by Charles Sternberg and identified by Leo Lesquereux. Specimen from the Department of Paleobiology, National Museum of Natural History. (photo by Dori Contreras)

Ultimately, I was able to photograph almost every specimen in the collection, totaling a whopping 50 gigabytes of images. Now I look forward to the next tasks: naming and organizing all those files, followed by detailed measuring of key ecological leaf characteristics for each specimen. Luckily ,a new Undergraduate Research Apprentice Program (URAP) student just joined "Team Contreras." We hope this study will provide insight into the structure and function of plant communities in warm, wet climates during the early radiation of flowering plants.

Cindy: Last year, members of the NMNH's Evolution of Terrestrial Ecosystem Program received good news from NSF: their Research Coordination Network proposal, "Synthesizing deep time and recent community ecology," was funded. This means that over the next five years a group of paleo- and "extant" ecologists will meet semiannually to study the assembly and disassembly of biological communities in the past and present. Attending this winter's edition of our meeting series was my main goal of this museum trip. Our workshop consisted of three days of presentations, data gathering and subsequent analyses in a friendly and inspiring atmosphere.

Workshop attendees

The NMNH’s Evolution of Terrestrial Ecosystems Program workshop attendees. Cindy is ninth from the left. (photo by Dori Contreras)

It is always a treat to return to the NMNH, smack in the middle of the National Mall in DC. From 2004 to 2008 I worked as a research fellow in the Paleobiology Department of this bigger sister of the UCMP and being at the NMNH always instills a special feeling. It could be the 325,000 square feet of exhibition space, the 20,000 daily visitors from all over the globe, or the 126,000,000 documented specimens in the museum's collections. Perhaps it is the illusion of being in the "center of the world," with the close proximity of the NMNH to the White House. But still, I know how lucky I am to be at the west coast equivalent of the NMNH. The UCMP public exhibits may be primarily online, but with the Department of Integrative Biology, the UCMP boasts something that the NMNH lacks altogether and something that presidential fly-bys can never compensate for: a pack of fabulous graduate and undergraduate students!

Outside of the meeting I had plenty of time to catch up with friends and work with former colleagues. Fellow-paleobotanist Bill DiMichele and I spent quite a bit of time in the museum's paleobotany collections. During the past 20 years, Paleozoic paleobotanists from the NMNH (Bill DiMichele, Dan Chaney, and Serge Mamay) have intensively sampled latest Pennsylvanian, Early Permian and Middle Permian sites in Texas. More than 360 collections of compression fossils were assembled using sampling strategies appropriate for the reconstruction of plant communities. Bill and I pulled out numerous conifers for morphotyping. We are trying to get a grip on how diverse early Permian Euramerican forests were, and how seed-plant dominated assemblages changed through time. Working our way through all the cabinets took quite some time, but that's nothing compared to all the imaging and measuring that still needs to be done. Ah well, that’s what is great about being a scientist: the work is never completed. Every question answered raises plenty of new, interesting questions.

Bill and Cindy

Cindy and Bill DiMichele working in the paleobotanical collections. (photo by Dori Contreras)

Both: Additionally, we got to present our work to east coast paleontologists and geologists at the annual Penn-Smithsonian Geobiology Symposium. It's always good to foster cross-talk on the continental scale and represent the paleontological force that is the UCMP!

Cindy and Dori sample pie

If you ever find yourself in DC, we highly recommend breakfast at Paul's French bakery ("Bonjour Madame!"). Here we test some of their pies for Cindy’s birthday. (photo by Bill DiMichele)

The Looy Lab paleo detectives

Solving the mysteries of the past and present one rock at a time

East of the Berkeley campus, we see the beautiful, green Berkeley Hills, the golden letter "C" and a somewhat classy-looking, dome-shaped building on the Lawrence Berkeley National Laboratory campus. This houses the ALS, or Advanced Light Source. Personally, I find the name a bit silly because it doesn't seem to capture the awesomeness of this giant machine. It's like calling the Space Shuttle a Progressive Flying Tool.

synchotron at LBL

Photo from newscenter.lbl.gov

The ALS is a synchrotron, a particular type of particle accelerator. The particles are sped up by a shifting magnetic field within a closed circuit. The shape of this circuit is an almost circular polygon and since the building was specifically designed for the synchrotron, the building is round. But what happens inside?

Each time when the particle beam is bent at each of the polygon's corners, light is produced — primarily ultraviolet and x-rays. The x-rays are not your ordinary dental office x-rays, but much "harder" x-rays. Unlike the relatively harmless photo at the tooth doctor, this beam would kill you before you could say "¿qué?"

But what can paleontologists and paleobotanists do with this advanced light? Hard x-rays allow us to see fossils while they are still inside the rock. This means that you don't have to crack open the rocks, clear away rock matrix and run the risk of damaging precious fossils. In some cases, the material is simply too fragile to be prepared; it would not hold up. Scanning the rock allows us to make 3D reconstructions of fossils hidden inside the rock without damaging them.

We've been scanning all kinds of really old fossils: horsetails from the Carboniferous (~300 million years ago, or Ma), kelp holdfasts from the Oligocene (~30 Ma), tiny (3 mm or ~1/8 inch) and not so tiny (7 cm or ~2¾ inch) pine cones, early land plants from the Devonian (~390 Ma), and pollen cones of extinct redwoods from the Cretaceous (~70 Ma). The size of the fossils is limited by the size of the protective shielding enclosure that keeps the scientists safe while using these lethal x-rays.

Because the cyclotron basically runs 24/7, the scanning time slots are generally 24 hours long and scanning rocks can take a while. Here's the general process that we go through for each scan:

Cindy and Ivo

Left: First, we select a fossil. Right: Then we mount it on a stand (improvising a la MacGyver). These and the rest of the photos are by Cindy Looy and Dori Lynne Contreras.

Orienting a fossil on the stand

Next we orient the fossil on the stand just right to get the best quality scan of the target specimen (which surprisingly takes a bit of work and "expert guess-timation").

The hutch

Once ready, the mount and fossil are placed in a "hutch" made of radiation shielding. Left: This is the hutch, a big container that protects everyone around from the harmful x-rays. Right: Inside the hutch there is a normal optical camera (at ~9 o'clock), the stand on which the fossil is mounted, and the x-ray detector (the big black box at the right).

The hutch doors and camera

To start the scanning process a number of safety procedures have to be followed, otherwise the beamline will not open. Left: The doors of the hutch have to be closed, and while an ominous alarm sounds, you have to press certain buttons to actually allow the x-ray to come into the hutch. Once it does, a red rotating emergency light comes on and the doors cannot be opened. Right: Once the sample is in the hutch we use the normal camera to focus in on the sample.

Adjusting the settings and set to go

Left: As each fossil sample is different, adjustments to the settings are needed. For instance, thicker rocks generally need a higher dose of x-rays than thin ones. Right: And we are good to go! It's scanning time!

Waiting for the scan to finish

And then, we wait …

Data analysis and celebration

Left: Actually, there is not a whole lot of sitting about going on, because the data that the x-ray collector gathers has to be analyzed. This takes up quite a bit of time (note the ridiculous amount of caffeine) and a LOT of computing power. Luckily, the computers at Lawrence Berkeley National Lab are up to the task! Right: Then we celebrate our success!

Caldwell's rare octopus research makes headlines

Roy Caldwell has been working with Richard Ross of the California Academy of Sciences to study a rare, beautiful, and so far unnamed species of octopus. Their work, along with some of Roy's photos, is the subject of a feature article in the San Francisco Chronicle.

Plants have a lot to tell us about the past …

Jeff Benca is a welcome addition to the Department of Integrative Biology and UCMP’s highly active paleobotany group as a member of Cindy Looy’s lab.  However, Jeff also spends a lot of his time “up the hill” at the UC Botanical Garden, where he has been given space for his astonishing collection of lycopods that he brought with him from his days at the University of Washington. This ancient vascular plant group (along with rare carnivorous plants and orchids) actually caught his interest while he was still a high school student in Seattle, but since those days, he has not only found ways to cultivate the plants, but is conducting research on both modern and extinct members of the lineage. Jeff hopes to discover how members of the lycopod group survived and thrived through the End-Permian extinction, 252 million years ago.

Both his research focus and unabashed enthusiasm caught the attention of National Geographic’s Explorers Journal and UC Berkeley’s News Center.

A collaborative grant to examine what triggers megafauna extinction

Tony Barnosky has received an NSF grant that will support a highly collaborative research program to test the synergistic effects of climate change and human population growth in magnifying extinction intensity.  South America offers a natural site to test these effects.  Barnosky and graduate students Emily Lindsey and Natalia Villavicencio hypothesize that if human impacts were significant in causing extinctions, then the last records for taxa should be found only after humans arrived on the continent, and that the geographic pattern of extinction should follow the sequence of human colonization and population increase in different regions. If climate alone drove extinction, taxa should disappear during the most pronounced climate changes, but not necessarily coincident with first human appearance and population increase. If synergy intensifies extinction, then extinction should accelerate dramatically when increased human population pressures and rapid climate change coincide.

The data from South America will provide an ideal way to examine the role of synergy in triggering extinction. For that reason, the project team proposes to:

  • Provide radiocarbon dates needed to determine the chronology of extinction for a broad spectrum of South American megafauna
  • Contribute to the international cooperation needed to analyze the extinction chronology
  • Provide a web-accessible database of the Quaternary fauna of South America, similar to NEOMAP and NEOTOMA
  • Use the information to better characterize the extent to which the looming threats of rapid climate change and growing human population can intensify extinction potentials
  • Develop effective outreach programs and scientific strategies to help minimize future extinctions.