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Flash! Grad student discovers how Ctenoides ales, the “disco clam,” flashes

Back in 2010, while diving in Indonesia, Lindsey Dougherty first witnessed the flashing behavior of the so-called “electric clam” or “disco clam,” Ctenoides ales. She decided then and there that the focus of her Ph.D. would be the study of these fascinating bivalve mollusks.

Disco clam flashing

Ctenoides ales caught in the act of flashing. In the photo, it's the silvery white band along the lip of the mantle. Photo by Lindsey Dougherty.

Now, four years later, Dougherty reports in the British Journal of the Royal Society Interface just how the flashing works. A nice description of the mechanism and a video showing the flashing behavior is provided in Robert Sanders’ article on UC Berkeley’s News Center website. Also see The Royal Society’s news blurb (with more video footage) about the study or listen to Lindsey describe her research in a New York Times Science Times podcast on iTunes.

Lindsey on Cal Day

Lindsey Dougherty describes her work with Ctenoides ales to a Cal Day audience. Cal Day is the annual campus-wide open house that takes place every April. Photo by Jenny Hofmeister.

Dougherty is now looking into the reasons for the flashing behavior. Perhaps it attracts prey or serves as a warning to potential predators; or maybe it’s a signal to juveniles of its own species that this is a good substrate on which to settle. We’ll have to wait and see what Dougherty finds out!

Pollen may help solve the mystery of why a pre-Columbian city in Mexico was abandoned

My research focuses on the Holocene geological time period, the last 10,000 years of Earth history. An accurate picture of past climate can help us understand the relationship between past environmental change and ancient societies. In this post, I describe how my summer fieldwork and my broader dissertation project link summer rainfall, microscopic grains of pollen, and an ancient city in Mexico.

The pre-Columbian city of Cantona is an impressive sight, even today. Located near the border of the Mexican states of Puebla and Veracruz, in the Oriental Basin, it covers 12.6 km2 and features a complex network of streets, ball courts, and pyramids. At its peak, between 1,750 and 1,000 calendar years before present, the site was an important Mesoamerican center of trade in obsidian. Archaeological investigations suggest that the city was abandoned abruptly at approximately 1,000 years ago. While the cause is unknown, many have invoked climate change as a possible contributing factor, partially because of the lack of surface water in the region today. This, however, requires an accurate picture of climate change at least 900 years before we had reliable, instrumental measurements of temperature and rainfall.

Cantona ball court

A ball court at the pre-Columbian city of Cantona. Photo by Tripti Bhattacharya.

All is not lost, however. It turns out that past climates leave microscopic traces in lake sediments. A wet climate, for instance, will leave behind different clay minerals than a dry climate. The pollen preserved in lake sediments can also tell us about the regional vegetation at the time the sediments were deposited, which in turn reflects regional climate. Various techniques like radiocarbon dating can be used to establish the age of the sediments. Detailed analysis of pollen composition or sediment geochemistry can therefore provide a long-term perspective on climate change. My research focuses on lake sediments from a volcanic crater lake called Aljojuca that is approximately 30 km south of Cantona. In 2007, a team from the GFZ German Research Centre for Geosciences and Mexico’s Universidad Nacional Autónoma de México took a 12 m sediment core from the lake. Radiocarbon dating suggests that this core contains a continuous, 6,000-year sediment record.

This summer, I collected pollen samples from contemporary vegetation to improve our interpretation of our pollen results from the Aljojuca core. Understanding how vegetation changes along natural gradients of temperature and precipitation (for instance, up the slope of a mountain) can help us interpret the results we see in fossil pollen assemblages. We can even characterize the composition of the pollen created by local vegetation by analyzing the modern pollen preserved in surface soils, small ponds, or even cushions (called polsters) of moss!

Understanding Science in the video spotlight

The California Academy of Sciences produced a video that uses UCMP's Understanding Science website's How Science Works flowchart to map the discovery of a new spider family. UCMP Education and Public Programs team leaders Judy Scotchmoor and Lisa White have starring roles! Watch the video at Science360.

A salute to the Engdahl family

The Engdahl family

From left, Robert, Jane, Duane, and Cathy (Bras) Engdahl. Photo courtesy of Bill Clemens.

The Morris Skinner Award is the Society of Vertebrate Paleontology’s way of honoring those who have added to our knowledge through their contributions to collection of scientifically significant fossils. At its annual meeting in Raleigh, North Carolina, the society honored the Engdahl family of Garfield County, Montana, for their long-term, multi-generational support of paleontological research and education. Students, staff, and faculty associated with UCMP have benefited greatly from the Engdahls’ help and hospitality.

In the late 1960s, the late Harley Garbani went to the valley of Hell Creek in northeastern Montana with the goal of collecting skeletons of dinosaurs for exhibit at the Natural History Museum of Los Angeles County. He was particularly successful in his discoveries on the Engdahl Ranch. In addition to two skeletons of Tyrannosaurus rex he discovered the remains of other non-avian dinosaurs, which were collected with the help of Lester Engdahl and his sons, Robert and Larry.

On the Engdahl Ranch, Harley also discovered concentrations of fossils of mammals, lizards, turtles, and other relatively small vertebrates that lived with the dinosaurs. In 1972, Harley, who became a field research associate of UCMP, introduced Bill Clemens and students from our museum to the Engdahls and these rich concentrations of small fossils. This was the beginning of a continuing project to study the evolution of the fauna and flora that lived with the last of the dinosaurs and the survivors of the mass extinction at the end of the Cretaceous. UCMP’s collections now contain extensive samples of fossil plants and animals from this interval of earth history. These continue to be the bases for a wide variety of research projects.

Through the years until his death in 1995 Lester Engdahl supported UCMP field parties. For example, he helped us refurbish a homesteader’s cabin and made it available to our field crews. In the summers the cabin provided a kitchen and shelter from the more than occasional thunderstorms. The rest of the year it served as a secure storage place for field supplies. Lester’s son, Robert Engdahl, his wife Jane, and their children, Duane and Cathy, were particularly supportive and helpful. Jane and her children “caught the bug” and became skilled in prospecting for vertebrate fossils. Many summer field seasons opened with expeditions to collect fossils or evaluate sites that they had discovered.

Field work in Garfield County continues to be more than just collecting old bones, shells, and leaves. Since 1972 over fifty undergraduate and graduate students from Berkeley and other universities have come to Garfield County in the summer to learn collecting and research techniques. Nine of these students from UCMP completed research for their Ph.D. degrees making use of information on the geology and fossils collected in the area. This involvement continues as the Engdahls support the work of field parties from the University of Washington and the Burke Museum led by UCMP alumnus Greg Wilson.

Jane Engdahl and Cathy Engdahl Bras attended the meeting in Raleigh and received the Skinner Award. We add our thanks for all they and their family have contributed to the success of UCMP’s programs of research and education.

Archosaurs: A new online exhibit

UCMP is proud to announce the completion of its web exhibit on archosaurs — I guess you could call it a Diapsida exhibit but we've chosen to focus on the archosaur lineage.

Matt examines the skull of Tomistoma

Matt Wedel examines the skull of Tomistoma, the False Gharial. Photo by Vanessa Graff.

It's roots go back to the end of the spring semester, 2006. Former UCMP grad student John Hutchinson (Ph.D., 2001, now a Professor of Evolutionary Biomechanics at the University of London's Royal Veterinary College) had updated a number of the museum's web pages on dinosaurs, and he was asked whom he'd recommend for writing new material on the archosaur lineage. John suggested that we approach grad student Matt Wedel in the Padian Lab, and that summer the research, reading, and writing began.

Matt sent the bulk of the content for the archosaurs exhibit to me in May of 2007, but that was also the year Matt earned his Ph.D. and got a new job. Between the job and family, it was tough finding time to work on the final bits of archosaurs.

Meanwhile, I tracked down images, formatted the text that I had for the web, and continued to check in with Matt periodically. In May of 2010 Matt sent me the final pieces of archosaurs, the most important being his text on modern crocodilians. For the next several months, I worked with Matt to resolve some issues surrounding the archosaur phylogeny and I continued to hunt down images. By November, the exhibit was finally ready … except navigating among the numerous pages within the exhibit was quite difficult, so we decided to postpone its launch until UCMP Webmaster, Josh Frankel, could implement a solution. With the navigation issue resolved, archosaurs is now up and ready for the public. It only took us about six years!

The museum appreciates not only Matt's expertise, but his dedication — he was determined to complete the archosaurs exhibit no matter how long it took. And now it's finally “done” … although as Matt will be the first to tell you, the perceived relationships between organisms — particularly extinct ones — are always in a state of flux (due to new evidence and interpretations). So maybe Matt isn't completely done with archosaurs after all ….

Matt Wedel is currently Assistant Professor of Anatomy at the Western University of Health Sciences in Pomona, California.

Lessons for today in ancient mass extinctions

This month's Evo in the News on Understanding Evolution looks at the work of incoming UCMP faculty curator Seth Finnegan. Seth is the lead author on a paper published in Proceedings of the National Academy of Sciences showing that the end of the Ordovician marked a true mass extinction caused by habitat loss due to falling sea levels and cooling of the tropical oceans. The Evo in the News feature explains and discusses the significance of this research, and includes additional links, resources, and questions for use in classrooms.

Read Evo in the News: Lessons for today in ancient mass extinctions.

Bay Area Field Guide: Point Reyes

Point Reyes and the surrounding area in Marin County is a beautiful place to visit and learn about local geology, paleontology, botany and zoology. Marin County contains large outcrops of the Franciscan Complex rocks. These rocks, mostly Cretaceous in age, are a mélange of rocks that originated to the west and accreted to the California coast as the Pacific Plate subducted beneath the North American Plate.  The Franciscan Complex includes metamorphics, chert, greywacke, shale and pillow basalts. The pillow basalts formed on the ocean floor 100 to 200 million years ago, thousands of miles to the west at a spreading center or a hotspot.

Point Reyes is on the western side of the San Andres Fault, a large fault system that runs along the coast of California. The geological layers that make up Point Reyes originated further south and are traveling north (about 1.6 inches per year) along the fault line.  The basement rock of Point Reyes is 350 to 450 million year old granite and the sedimentary rocks the granite metamorphosed. Overlying these rocks are a series of Tertiary sedimentary deposits including the Pt. Reyes Conglomerate, Laird Sandstone, Monterey Shale and “Drake’s Bay Formation”. This last formation, Miocene in age, has been subdivided into the Santa Margarita Sandstone, Santa Cruz Sandstone and the Purisima Formation. All three of these formations outcrop further south in the East Bay, Santa Cruz and at the San Gregorio Beach, respectively, providing evidence that Point Reyes is traveling north. The Purisima Formation outcrops at Drake’s Beach where several whale fossils have been found by UCMP researchers along with several invertebrate fossils.

Photos courtesy of Nick Matzke, Jenna Judge, and Lucy Chang.

Please note that a collecting permit and official permission is required to collect, or even pick up, any vertebrate fossil or fossil fragment in any of California's State and National Parks. Other public lands, including city parks and open spaces, may have similar regulations. Best to check in with the appropriate land use office wherever your adventures take you to inquire where the best spots are to see fossils in the field and what is and is not permitted while hiking and exploring our fossil heritage in these natural preserves.

Understanding Evolution and Understanding Science February updates

The UCMP's Understanding Evolution and Understanding Science websites have been updated for February with the following features:

Bay Area Field Guide: Tilden Park

I think it took us all by surprise to learn that Tilden Park contains several fossil localities and has a rich history with the UCMP. Don Savage, a former professor of paleontology and past chair of the Department of Paleontology at Cal, found a gomphothere jaw by Inspiration Point off Nimitz Way in 1961 and John C. Merriam collected the type specimen of Eucastor lecontei from deposits near Vomer Peak.

Underlying the beautiful rolling hills of the park are terrestrial deposits of the Miocene. The oldest of these deposits are the Claremont Formation containing chert and siliceous shale layers deposited 14 to 16 million years ago in a deep marine basin. Overlying this formation are the alluvial-fluvial mudstone, sandstone and conglomerate deposits of the Orinda Formation that originated from a higher, mountainous region west of the East Bay. You can see clear views of the Orinda Formation just east of the Caldecott Tunnel on Highway 24. The Moraga Formation overlies the Orinda Formation. This basaltic flow erupted from a volcano at Round Top in the Robert Sibley Volcanic Regional Preserve, just south of the Caldecott Tunnel, about 9-10 million years ago.

There are a number of lava flows visible from Highway 24, east of the Caldecott Tunnel, that are several feet thick. Many of them have a red zone or baked contact at their base where the hot lava contacted with the wet and cool alluvial deposits of the Orinda Formation, oxidizing the sediments. These volcanic deposits are resistant and now form the ridges of the Berkeley Hills and San Pablo Ridge. Some of the lava flows dammed rivers causing the formation of lakes. Deposits from these lakes formed the Siesta Formation composed of fine-grained light gray sediments. These soft rocks are easily eroded and have resulted in several landslides. Capping these deposits is another lava flow called the Bald Peak Basalt (9 million years old), visible at Vomer Peak in Tilden Park. All of these rock layers were folded due to tectonic activity. This created a large north to south plunging syncline that encompasses Tilden Park.

Photos courtesy of Nick Matzke, Tony Huynh, and Lucy Chang.

Please note that a collecting permit and official permission is required to collect, or even pick up, any vertebrate fossil or fossil fragment in any of California's State and National Parks. Other public lands, including city parks and open spaces, may have similar regulations. Best to check in with the appropriate land use office wherever your adventures take you to inquire where the best spots are to see fossils in the field and what is and is not permitted while hiking and exploring our fossil heritage in these natural preserves.

The eternal value of Natural History and the dazzling molecular promise

nescent imageThe advent of highly efficient and low cost sequencing techniques along with increased computing power have been important catalysts for the massive generation of genomic data (Davey et al., 2011). In parallel have come studies of gene expression and regulation, each of which has earned its own field such as "trancriptomics," "proteomics," "metabolomics," etc. (Zhou et al., 2011). In addition, the combination of these disciplines with ideas associated with graph theory has produced a new area of study called Systems Biology (Saito and Matsuda, 2010). Certainly in the last 30 years we have learned more than we ever imagined and unexpected avenues of research have opened. Every day the dream of deciphering the genetic identity of every living organism becomes more and more possible.

However, in the middle of the Post-Genomic Era it has become clear that we have forgotten something. That "something" is what has been fundamental to biology since its inception: Natural History. The great technical complexity, versatility and explanatory power of molecular studies have produced a shadow on the more “traditional” approaches. Some argue that the age of exploration to remote areas and the discovery of new species and detailed monographs with morphological descriptions are part of a distant and romantic past. However, we have described about 1.8 million species and there are calculations that estimate a total of 10 million without considering those present in the fossil record. Is the exercise of the natural history really an anachronistic activity?

The lack of knowledge of the species with which we share our planet is only the tip of the iceberg, because in many cases the knowledge of the biology of those already described is even more precarious. Walking through the shelves of various libraries I have found that most new books address issues associated with genetics and molecular biology, while most of those which are about anatomy or taxonomy are written in brown paper and illustrated in ink. At some point I thought the latter would look good in a museum, but now I have another opinion. Who is capable of replicating that knowledge today? How many students are being instructed in these areas today? To my relief a few names do come to mind, but it’s is a very small number.

Faced with this "molecularization" of biology, those old natural history books take a new value as the sole repository of a discipline that in many cases has not been practiced for years. So those faded pages are the only remnant we have of that knowledge. Not only are the data and descriptions in these books important, but the hypotheses and speculations have enormous value, because they are the products of an integration that emerged from someone who had an extensive knowledge of biodiversity. So despite the lack of molecular understanding these ideas have elements that only someone who has spent years in the field or amongst museum specimens is able to see.

The lack of support for the study of natural history is a critical problem that if left alone will likely reach a tipping point from which recovery would be difficult if not impossible. The lack of master-apprentice continuity in the study of a group of organisms can be fatal, because much of the taxonomic and technical knowledge is simply lost. What is the cause of this trend?

As was the case with positivism, when it was stressed that all of the sciences be quantifiable and models, today molecular biology shines with its own splendor. This glow was won by the large amount of data and the results that have been produced from it. However, it has also shaded the importance of non-molecular studies.

This can be seen not only in major research programs, but also in the training of future biologists. More than once I came to know a great deal of metabolic and genomic data for a particular organism, but had no idea how big it was. Similarly, on several occasions I have seen how the tree of life is reduced to a phylogeny of only "model organisms."

Although the molecular approach can reveal a lot of secrets, there are other secrets that molecular approaches simply cannot reveal. The over-emphasis of techniques, can reduce or even stop the investment of resources in non-molecular studies and close funding opportunities and job positions. In an extreme case, this could make taxonomists swell the lists of endangered species that only they are able to recognize.

The dazzling molecular promise is that by reducing everything to its scale, it would allow an understanding of most biological phenomena. This initially generated great enthusiasm, but it also prohibits considering the existence of unique properties at different levels of organization that are not possible to study from a simple decomposition of the whole into numerous small parts. Molecular tools have opened vast windows in understanding the phenomenon of life, but like all tools, are not able to open them all. It is important to overcome the excitement of a novelty itself and be able to assess the limitations of these powerful techniques.

The eternal value of natural history, on the other hand, relates to the fact that the questions like "What is this?," "Where does it come from?," "What does it eat?" never become outdated. The human capacity to identify and recognize the components of the natural world is the foundation of all our biological knowledge. For hundreds of years the tools of natural history have remained unchanged, and the data produced by these tools is critical for the future as well. Either deep in the forest or collecting along the coast line, whenever the naturalist finds a new organism he/she always returns to the same eternal questions ….

Darko Cotoras Ph.D.(c)
Department of Integrative Biology
University of California, Berkeley

This text will be presented in the blog contest sponsored by National Evolutionary Synthesis Center (NESCent). It is based on: “El eterno valor de la historia natural y la encandilante promesa molecular” uploaded by the author to on 08/04/2011.

Literature cited

Davey J.W., P.A. Hohenlohe, P.D. Etter, J.Q. Boone, J.M. Catchen, and M.L. Blaxter. 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics 12:499-510.

Saito K., and F. Matsuda. 2010. Metabolomics for functional genomics, systems biology, and biotechnology. Annual Review of Plant Biology 61:463–89.

Zhou Z., J. Gu, Y. Du, Y. Li, and Y. Wang. 2011. The -omics era — toward a systems-level understanding of Streptomyces. Current Genomics 12:404-416.