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 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 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.

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.

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!

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)

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.

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:

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.

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").

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).

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.

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!

And then, we wait …

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!

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.

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.

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.

Twenty-two scientists including lead author Tony Barnosky urge us to understand the danger of global environmental tipping points in their review paper in the June 7 issue of Nature. They examine data from past global environmental changes, compare it to how humans are changing the planet today, and discuss what that could mean for our future. They conclude that if we continue at our current rates of environmental destruction and resource use there will be dramatic impacts on the quality of life for coming generations.

For more information on the paper, including a video interview with Barnosky and a summary of how this research ties to The Berkeley Initiative in Global Change Biology, read the full press release at the UC Berkeley News Center.

UCMP's Cindy Looy is leading a project to collect 130,000 years worth of sediment data from Clear Lake in order to better understand how life has adapted to climate change. Along the way, members of her team will report back to us with all the progress and drama from the field. Here's our first set of dispatches.

Assembling the barge

From Ivo Duijnstee:

Thu, April 26

First mud
It has begun. Except for some minor delays, the Clear Lake drilling expedition had a relatively smooth start. When our seven-headed UC Berkeley team arrived on site in Lakeport California, six members of the not-for-profit drilling company DOSECC had already assembled the large drilling barge to the point that it was almost good to go. Not much later, three sediment core curators of the National Lacustrine Core Facility (LacCore) arrived; completing the drill team in charge of the first days of this enterprise.

Fri, April 27

Today, a boat pushed the barge to its first drilling position in the southeastern part of the northern branch of the lake. This is in a part of the lake with a thick continuous sediment package. The deeper layers date back at least to the warm part of the previous interglacial (~130,000 years ago), a period we are very much interested in, as it may provide an analog for the current climate change in California.

Sat, April 28

From our Rocky Point base camp on the other side of the water, we can barely make out the barge’s position, as the sizeable drilling barge is reduced to a mere speck on the horizon. The inconspicuousness changes dramatically when night falls and the needle in the haystack turns into a beacon of light, as soon as the flood lights on the barge are switched on.

Tonight, the night crew (on the barge everyone works in two 12-hour shifts) made their way to the barge in the former county fire boat. This boat was made available for the crews’ semidiurnal commute by our collaborators of the Lake County Water Resources Department. Around 11PM, word reached base camp that the DOSECC drillers hoisted the first sediment core up on deck.

The barge has been moved out to the drill site.

Sun, April 29

This morning the night crew brought the uppermost 28 meter (93 ft) of sediment cores ashore, so the Holocene is taken care of. Let’s dig deeper into the Pleistocene!

Cindy Looy with the first core sample.

We have some cores!

So far, things are going smoothly on the drill platform. The day crew is off to their 12 hour shift, and the night crew is heading to bed. At the house in Rocky Point — our base camp — we are starting our pile of sediment-filled transparent tubes in the garage.

Mon, April 30

It’s media day!

Almost all day, camera crews, radio journalists, newspaper photographers and reporters were buzzing around, interviewing UCB/UCMP’s Cindy Looy and Liam Reidy, DOSECC Director of Operations Chris Delahunty and LacCore scientist Ryan O’Grady as they made visits to our floating drill site. We’ve had so much attention already, and the UCB press release is yet to come!

Chris Delahunty being interviewed for KQED radio.

The timing of the media is perfect: just like the weather, everyone in the team is in a sunny mood since the team has reached a greater depth than the USGS did at the same location during its 1973 Clear Lake drilling program. That means that the teams first target (115 m, or 377 ft) has been reached, and there is more to come.

Gravel.

At about 140 m (460 ft) into the sediment, it’s over with the monotonously greenish grey playdough that has filled the plastic core linings so far. In the dark, the night crew has struck gravel, making it impossible to get anything out of the lake bed. Fortunately, the drillers have some tricks up their coverall sleeves. For now they are mixing a special kind of mud that the day shift will use to get through the gravel layer. They will pump the muddy mixture into the borehole so that the gaps between the chunks of gravel will be filled with sticky goo; enabling the drillers to get the loose gravel out.

Tue, May 1

Alas, despite the fact the DOSECC team successfully crossed the gravel layer, things are not going well. Beyond the gravel layer there is sand and more gravel. Now things are going this slow, we decide that it is better to stop drilling at this site, and get started on a second hole nearby. As the two drillers prepare the drilling equipment for the move to the next hole, the scientific part of the night shift gets to spend an unexpected night in the house, where it is warm and couches are comfy... perhaps a bit to comfy when you are trying to stick to the nocturnal routine of the graveyard shift...

Renske with an armload of cores.

Wed, May 2

*S*  hifts are 12 hours long and days start incredibly early

*C*  ores are covered in mud and so are we

*I*  ncessant noise of the generators, shrouding the barge in heavy diesel fumes

*E*  very day starts at 5.45am

*N*  o matter what happens, the entire crew is always in great spirits

*C*  lear Lake is a neat location and the weather is close to perfect

*E*  asily one of the coolest projects I have ever been part of!

See more text, audio, and video coverage of the Clear Lake drilling project here.

What are bug-men and how did their existence benefit UCMP? Watch and listen to this slideshow about an obscure link recently discovered by UCMP micropaleontologist Ken Finger.

Click cover page below to download the full article.

In science we are often confined to studying processes that occur on local scales. This is a natural place to begin and there is great value in understanding local events and processes, but the ultimate goal, at least in my mind, is to synthesize all these smaller snapshots of how living things interact and respond to their environments into a cohesive, whole-world portrait. This kind of comprehensive understanding is particularly important in light of global climate change, which demands that we develop conservation strategies that address broader issues than conservation has in the past. The "Holy Grail," in this regard, would be data covering the whole earth and all taxa, throughout the history of life. Regretfully, this is unlikely to ever be fully realized; however, there has been a recent blossoming of databases, containing all kinds of biological data from across the globe that begins to build toward this overarching ambition. Of particular relevance to paleontologists is the Neogene Mammal Mapping Portal (NeoMap), which holds records of mammalian fossils from the last 30 million years in North America.

NeoMap unifies two free-standing, open-access databases—the Miocene Mammal Mapping Project (MioMap)², hosted by the UCMP, and the Quaternary Faunal Mapping Project (FAUNMAP)^3,4—and enables the user to access and download any published (and some unpublished) data on fossil mammals (along with complete metadata), to map the localities where these fossils were collected, and to generate tables of species abundances (minimum number of individuals). These tables can be easily modified for more specific purposes, for example, to estimate species/area relationships or to assemble a taxonomic list for an entire region during a given period of time. This means that research addressing a wide variety of macro-scale questions is now possible using NeoMap—previously, these kinds of projects were prohibitively laborious, because they required extensive and exhaustive literature searches followed by painstaking data standardization.

A recent example of the utility of NeoMap is described in a book chapter by Tony Barnosky (UCMP), Marc Carrasco (UCMP), and Russell Graham: Collateral mammal diversity loss associated with late Quaternary megafaunal extinctions and implications for the future (chapter in "Comparing the Geological and Fossil Records: Implications for Biodiversity Studies"¹). This paper explores whether all of the biodiversity loss exhibited by mammals at the end of the Pleistocene can be explained by extinction of megafauna. The authors found that over and above the loss of large mammals that went extinct, there was local and regional loss of diversity because geographic ranges of species got smaller. That "collateral diversity loss" resulted in an additional 6-51% diversity reduction, depending on location, that was on top of species loss by extinction. This collateral loss affected small mammals even more than large mammals¹. The bottom line is that extinction is only one symptom of diversity loss, and local or regional extirpations compound and intensify the massive ecological changes that take place during biodiversity crises like the one we are experiencing today.

This project illustrates two tools that make NeoMap so powerful: paleo-areas were drawn and measured in NeoMap using the BerkeleyMapper utility, and species presence/absence tables were generated using the MioMap EstimateS Web Service, which queries all the points selected in BerkeleyMapper and returns the data as a sites-by-species table. In my own work, fellow UCMP grad student Michael Holmes and I have used NeoMap to study how the distribution of species in different body size and diet functional groups has changed through time in the Northern Great Plains. Our analysis has shown remarkable stasis in the relative number of species in each functional group across millions of years, except during two periods of rapid climate change: the end of the Mid-Miocene Climatic Optimum, and the Pleistocene/Holocene transition⁵.

To use the database, learn more about it, or read about other examples of research using NeoMap, go to http://www.ucmp.berkeley.edu/neomap/.

References:
1. Barnosky, A.D., Carrasco, M.A., Graham, R.W., 2011, Collateral mammal diversity loss associated with late Quaternary megafaunal extinctions and implications for the future. Comparing the Geological and Fossil Records: Implications for Biodiversity Studies. Geological Society, London, Special Publications. 358:179-189

2. Carrasco, M.A., Kraatz, B.P., Davis, E.B., Barnosky, A.D., 2005. Miocene Mammal Mapping Project (MIOMAP). University of California Museum of Paleontology http://www.ucmp.berkeley.edu/miomap/

3. FAUNMAP Working Group, 1994. FAUNMAP: a database documenting late Quaternary distributions of mammal species in the United States. Illinois State Museum Scientific Papers 25(1-2):1-690.
4. Graham, R.W., and E.L. Lundelius, Jr., 2010. FAUNMAP II: New data for North America with a temporal extension for the Blancan, Irvingtonian and early Rancholabrean. FAUNMAP II Database, version 1.0.

5. Stegner, M.A. & Holmes, M., 2011. Using paleontological databases to assess spatial and temporal conservation of mammalian community structure as an aid to conservation planning. Society of Vertebrate Paleontology Meeting, Las Vegas, NV.

The Berkeley Initiative in Global Change Biology (BiGCB) was recently awarded a $2.5 million dollar grant by the Gordon and Betty Moore Foundation.  The grant funds seven major projects and involves the participation of faculty members in eight departments and four of the Berkeley Natural History Museums on Berkeley's campus, including UCMP and IB faculty Cindy Looy, Tony Barnosky, and Charles Marshall.  Projects focus on using novel methods to understand the past, present, and future of the biosphere, ranging from obtaining a high resolution record of climate change using lake cores to applying theory-based metrics to analyze biological change.

Established in November 2009, BiGCB is an initiative bringing together over 100 Berkeley faculty and researchers to collaborate in the field of global change biology.  The Initiative is focused on integrating multiple disciplines to better predict how the biosphere will be affected by global changes through careful understanding of these changes in the past and present.