UCMP's partnership with Point Reyes National Seashore (National Park Service) has resulted in the discovery and collection of an important marine mammal specimen. This specimen is currently being prepared by UCMP Research Associate Robert Boessenecker, and will be reposited at UCMP. Lillian Pearson, a Geoscientist-in-the-Park intern, is setting up protocols for the long-term monitoring of paleontological resources (fossils) at Point Reyes. Erica Clites did this type of work for the National Park Service before coming to UCMP, and has been advising Lillian on the project. For more information, read the full story.
Archive for the ‘Research’ Category.
A morphological study of living and fossil Quercus (oak) pollen from California using scanning electron microscopy
California has more than 26 oak (Quercus) species, many of which have widespread distributions and different habitats. For example, the California black oaks (Q. kelloggii) are distributed in foothills and low mountains (altitude ~4750 feet), while the Coast live oak (Q. agrifolia; altitude ~830 feet) lives near the coast. Palynologists study the distribution of plant pollen and spores in space and time, and changes in their assemblages reflect changes in regional and local vegetation.
In the study of past climates, palynologists have used oak pollen as an indicator of relatively warm environments. But in the examples given above, we see that the range of different oak species varies, so the temperatures in their respective habitats must vary as well. If palynologists treat all the oak species the same — as indicators of a "warm environment" — could this lead to wrong interpretations of the environmental conditions? If the answer is yes, why do palynologists still treat all the oak species the same?
This question could be answered if we resolve a basic problem in pollen taxonomy: how to distinguish between the pollen of different oak taxa. All oak pollen have similar characteristics: three colpi (furrows) and a verrucate surface (small surface features under two microns). Even the ratio of length and width of each species overlaps. These nearly uniform morphological features make identifying oak pollen very difficult at the species level, at least using Light Microscopy (LM).
I am studying pollen samples from Clear Lake to understand climate and vegetation change in California during the last interglacial period (~120-80 kyr ago). See earlier blogs: Dispatches from Clear Lake, part 1 and part 2; California pollen taphonomy and pollen trap study in Clear Lake, California. After studying the lower part of a 150-meter-long lake core that includes sediments from the interglacial period I'm interested in, I found two distinct oak pollen numerical peaks. Before categorizing all oak pollen in the samples as "indicators of warm environments," I would like to know which species of oak they represent. Since it's so difficult to detect morphological differences using Light Microscopy, I wondered if I could identify more diagnostic features on pollen grains using Scanning Electron Microscopy (SEM). Serendipitously, a paper was published on how to use SEM and quantitative analysis to identify grass pollen at the species level. Like oak pollen, grass pollen is also difficult to differentiate using LM identification. Thinking that the methods described in the article could be applied to oak pollen identification, I decided to take SEM images of California oak pollen to see if a systematic identification method could be developed. Then, I'd use quantitative analysis methods to identify the oak species in my Clear Lake interglacial samples and see if there were particular taxa appearing and/or disappearing in the area during times of climate change.
Last summer (July, 2014) I visited Dr. Luke Mander, author of the grass pollen paper, at the University of Exeter, UK, to investigate the possibility of identifying oak pollen using SEM and computer statistics. In an SEM lab, I took 70 images of pollen from 23 extant California oak taxa and 150 images of fossil California oak pollen.
A preliminary analysis has already revealed that at least three pollen wall morphotypes, two of which represent habitat-specific oak types, can be recognized in extant California oak species. Most specimens in Type-1 represent shrub oaks, adapted to dry environments. Type-3 pollen neatly matches specific phylogenetic lineages. We were able to assign the fossil oak pollen from Clear Lake to the three categories of extant California oak pollen. Interestingly, the change in oak pollen groups in Clear Lake sediments suggests species replacement during the start of the interglacial period. I have found that more precise and objective identification of oak pollen types is possible using automated digital image analysis algorithms and a larger training set of SEM photographs of pollen from known species, so I will be working on that in the Fall. I hope to amass more detailed vegetation analyses for past periods of climate change.
All photos courtesy of Winnie Hsiung.
It's April 18, 2015, and I am sitting in a room at the Charles Motel in Truth or Consequences, New Mexico, the same apartment-style room that I have stayed in during the past four years of field work. Time sure has passed by quickly; from my first paleontological dig as an undergraduate at Texas State University-San Marcos under Dr. Gary Upchurch, to my ambitious inaugural self-guided field trip as a first-year graduate student at Berkeley, to last year's even longer field excursion, and finally to this short trip with my advisor, Cindy Looy. What keeps bringing me back to this area is an exceptional Late Cretaceous flora in the Jose Creek Member of the McRae Formation—this flora is the foundation of my dissertation work.
I am interested in the functional diversity (the range of plant ecological strategies) of Cretaceous forests in warm-wet climates. Cretaceous floras often contain a mix of plants that are no longer seen in association today. The Jose Creek assemblage, for example, includes both palms and redwoods. These non-analog communities can be difficult to understand from the perspective of community ecology, because we cannot make inferences about their ecology based on similarities in taxonomic composition with modern floras. The difficulty of understanding past communities is compounded by the paucity of fossil deposits preserving a "snapshot" of a forest in relative growth position. This is precisely why the Jose Creek deposit is so unique—it contains a flora preserved in a volcanic ash airfall. During my 2013 field season, we traced a single-horizon ash layer for approximately 1.2 km (see previous blog). Such an extensive deposit makes reconstruction of the forest, including lateral variation in forest structure, possible. Because the volcanic ashes are fine-grained and deposited rapidly, the plant parts (leaves, fruits, flowers, seeds, cones, etc.) are very well preserved. I am using morphological features of these plant fossils—and an explicit ecological and spatial sampling scheme—to reconstruct the forest. My ultimate goal is to evaluate the ecological diversity of the community, and to understand how forests in warm-wet climates have changed since the Late Cretaceous.
This is what brings me to Truth or Consequences this April—a continuation of my quest to describe this incredible flora. This trip is a short one—only four days—with two simple missions: (1) "cherry picking" well-preserved leaf specimens to use for trait measurements (for inferences of their ecology), and (2) hunting for cones to finish a whole-plant description of an extinct redwood that is abundant in the deposit.
Last June's trip (2014) was more intensive. I drove to New Mexico with two undergraduates—James Buckel and Negin Sarami—and recent IB graduate/Looy Lab veteran, Stephanie Ranks. We spent two weeks working at the site, establishing new collecting quarries and re-sampling the 12 small exploratory quarries from the previous year, effectively doubling their size. All in all, we have now established 17 quarries that span the length of the exposure! We successfully employed a new data collection method in the field, which had several advantages over the previous year. During the 2013 collecting trip, we collected and brought back to the UCMP all of the specimens excavated from each quarry. This generated a large amount of material very quickly—the maximum that our extra-long SUV could carry. In contrast, during the 2014 trip we looked at all our excavated specimens, comparing them with a leaf morphotype guidebook of over 120 different leaf types that I created from the previous collections. Using the book as a guide, we were able to record the number of occurrences of each morphotype, as well as their percent cover of the rock surfaces, without having to bring every specimen back to the museum. Of course, we did collect the specimens that were very well-preserved or that represented new morphotypes. By adopting this method in the field, we were able to collect far more data than would have been possible by only making collections and still bring back a full load of really nice specimens to the museum.
The flora has proven to be extremely diverse, with new morphotypes being found every day. The variation in morphotype composition from quarry to quarry also suggests a very structurally diverse flora. This is an incredible site to work, never a dull moment! I am really looking forward to the next big trip, and consider myself extremely lucky to receive the support of so many organizations, especially the UCMP and its amazing community of researchers, staff, and donors. Now, back to the field site before I lose any more daylight—Cindy and I still have a day of "wow" moments ahead of us before we return to Berkeley!
Organizations that have generously supported this work include:
— UCMP Graduate Student Award, University of California Museum of Paleontology, 2013 and 2014
— Geological Society of America Graduate Student Research Grant, 2014
— Integrative Biology Graduate Research Fund, 2014
— Sigma Xi Grants-in-Aid of Research, UC-Berkeley Chapter, 2014
— Mid-American Paleontological Society (MAPS) Outstanding Student Research Award, 2013
— GRAC Research Funds, UC-Berkeley Integrative Biology Department, 2013
Occurrences of green tides have been on the rise in recent years worldwide. The most impressive have been reported off the coast of China in the Yellow Sea. In August 2014, the Monterey Bay area experienced a green tide that resulted in the accumulation of the macroalgae, Ulva, on its beaches. Algal blooms often make the headlines in spring and summer yet they are not a new phenomenon. In fact, toxic algal blooms may have been responsible for bird, fish and marine mammal die-offs recorded in the fossil records of Chile's Neogene and Gulf Coastal Florida's Pliocene. Blooms are typically considered to be an indication of decreased ocean health and pollution but there are many other factors that contribute to algal blooms. While Ulva itself doesn't produce toxic chemicals as it grows, the bacteria that decompose the alga once it begins to die can suck the oxygen from the surrounding seawater, suffocating other marine life.
Environmental factors necessary to generate an algal bloom include:
— High nutrients
— Calm water
— Few grazers or predators
I've been interested in learning more about why we see green tides when we do. To do this, I've been focusing on the microscopic reproductive stages of the green-tide-forming algae, Ulva. In July 2014 I began collecting two liters of seawater every month from San Francisco Bay. I divide the water into culture flasks, add nutrients important to algal growth—such as nitrate, phosphate, ammonium, trace metals and vitamins—and culture it in environmental chambers on the UC Berkeley campus. These chambers are set to simulate summer conditions (16°C, 12-hour days) and every week I replace the seawater with fresh nutrient-enriched seawater. After four weeks I find young Ulva blades and tubes growing on the bottom of my culture flasks. Since I know the volume of the water I originally put into the flasks, I can estimate the number of propagules per liter that were present at the time of collection. I've been repeating this sampling at an additional four locations within San Francisco Bay once every season to estimate variation in spatial distribution of these reproductive stages.
Every cell in adult Ulva (blade or tube) has the potential to become reproductive, releasing up to 16 swimming spores from each cell. The cells along the margins of the blades usually become reproductive first; you can see the difference in color between the reproductive cells and vegetative cells in the image at right, below.
Along with the help of some UC Berkeley undergraduates, I am also tracking the settlement of young Ulva at my field site in Tiburon. We have attached settling plates made of resin to rocks in the intertidal zone near the Romberg Tiburon Center. These settling plates are submerged at high tide and exposed at low tide. Each month we return to the intertidal at low tide to collect the plates covered in algae and replace them with sterilized plates. Once back at the lab we use a dissecting microscope to estimate the amount of young Ulva growing on the plates. Now we are working on comparing the amount of young Ulva that grows in the cultures to the patterns of young Ulva we are seeing on the settling plates.
All photos courtesy of Rosemary Romero.
If you have taken the elevator to the top of Sather Tower, aka the Campanile, perhaps you've heard that some of the floors of the tower are filled with fossils. This is not a campus myth, it's fact!
The Campanile is celebrating its 100th anniversary this year and its very first occupants — moving in before the tower was even completed — were fossils. At that time, the museum and Department of Paleontology were in Bacon Hall, just east of the Campanile, so as a storage facility, the tower was conveniently located. Although the museum has moved several times over the past century, the fossils in the Campanile have not.
Some of the first fossils to be moved into the tower were vertebrate bones from John C. Merriam's excavations at the Rancho La Brea tar pits. These bones, collected prior to 1914, occupy four of the five floors devoted to fossil storage. But the Campanile houses several other collections too. There are bones collected in the 1930s from asphalt deposits in McKittrick (about halfway between San Luis Obispo and Bakersfield) and nearby Maricopa; mammoth bones, teeth, tusks, and other miscellaneous Pleistocene fossils; modern whale bones; a few blocks containing ribs of the plesiosaur Hydrotherosaurus alexandrae; crates containing plaster casts of dinosaur footprints and trackways that were made by Sam Welles while doing field work in the Kayenta Formation of Arizona; petrified wood from the Petrified Forest; fossil plants; invertebrate fossils, including collections moved to the Campanile from McCone Hall and some from Triassic rocks in Nevada; Upper Cretaceous leaves from Bryce Canyon, Utah; oil company collections of microfossils (bulk samples) and invertebrates; casts of mastodont skulls; an ichthyosaur skull; some sculptural reconstructions (including a glyptodont); and cases of reprints. A conservative estimate of the number of fossils stored in the Campanile, excluding the microfossils, is 300,000.
During this year-long celebration of the Campanile, it is only fitting that the fossils housed there receive some attention too. We will periodically post blogs throughout the year to discuss some of the ongoing research projects that involve the Campanile's fossils. For instance, UCMP Curator and Associate Professor of Integrative Biology Leslea Hlusko and her lab have two projects underway and Eric Holt, an undergrad in Tony Barnosky's lab, is looking at wolf morphometrics. And back in September we announced the grant award from the Institute of Museum and Library Services to curate the Campanile's McKittrick fossils. To date, more than 2,500 specimens have been cleaned and cataloged, and more than 500 images of 273 specimens have been added to CalPhotos.
Stay tuned for more about the Campanile's fossil treasures!
What’s the first thing that comes to mind when you think of Africa? Probably a lot of big animals, right? Elephants and lions, zebras and cheetahs, hippos and rhinos, giraffes, and enormous herds of wildebeest moving across the savannah.
Well, what a lot of people don’t realize is that for most of the past 50 million years, most of the world looked a lot like Africa! Not that long ago, Europe, Asia, and North and South America all hosted relatives of elephants, zebras, and lions inhabiting ecosystems that looked a lot like today's African savannah. There were rhinos roaming the Riviera, wooly mammoths wandering Wyoming, and Glyptodons (a kind of giant armadillo) gallivanting in Guyana. Here in California we had mammoths and mastodons (another elephant relative), horses and tapirs, oxen and antelopes, jaguars and lions, saber-toothed cats (our state fossil!), giant wolves, giant bears, giant bison, and (my favorite) giant sloths. South America had rodents the size of cows. Australia had wombats the size of hippos. Even relatively small islands had giant mammals, although not quite as giant as on the continents, because big animals tend to get smaller (and small animals bigger) on islands. There were giant lemurs on Madagascar, pygmy hippos in the Mediterranean, dwarf giant sloths in the Caribbean, and pygmy mammoths on California’s Channel Islands.
Scientists call these giant animals “megafauna” (mega = big, and fauna = animals). We still have megafauna in the world, but there used to be a whole lot more of it. In fact, it appears that having a large number of large-bodied animals in an ecosystem is actually the normal state for our planet, at least for the geologic era we are living in today, the Cenozoic (or “Age of Mammals”) . But sometime in the past 50,000 years (very recent geologically), everywhere except for Africa, most of those large animals became extinct. And we still aren’t sure why!
People often ask me, “Why was everything bigger in the past?” But I think the question should really be the other way around — “Why is everything so small now?” As a paleontologist studying the extinction of the megafauna, this is a question I ask on a daily basis.
Basically, there are two main ideas about why these large animals went extinct. One hypothesis is that the extinctions were actually due to us — to humans. The scientists who peg people as the culprits point to several lines of evidence: For one thing, in most of the places where the extinctions happened, large animals tend to disappear from ecosystems right about the same time that humans arrive for the first time (we know this from radioisotopic dating, scientific techniques that allow us to determine the exact age of fossils and the sediments they are found in). Also, in a few places, we actually have evidence of humans hunting extinct megafauna, such as mammoths. Finally, we know from modern situations that humans can have a major impact on animals, both directly (like hunting) and indirectly (like burning forests, fragmenting habitats, and causing erosion) .
The second hypothesis for why the megafauna went extinct is that the climate changed too much (or too fast), and the animals could not adapt to their new environments. We know that climate was changing at the time that the megafauna disappeared in many parts of the world, and in some places (including Ireland and northern Europe and Asia) the extinctions seem to be correlated with changes in vegetation and stress that can be directly linked to climate. Scientists who favor this hypothesis also point out that given all the fossils we have of extinct megafauna, only a handful show any evidence of hunting by humans.
Finally, there are some scientists — including myself and many of my colleagues — who think that most of the global megafauna extinctions probably resulted from a combination of both climate and human impacts. While there appear to be some places where extinctions may have been caused by climate change alone, and others where humans were the sole culprit, it seems that more species went extinct faster in regions where both of these factors came into play simultaneously. Whatever the answer, scientists all over the world are working to learn more about why our world looks so different today than it did in the past.
Why do we care about what caused the megafauna extinctions? Aside from the “wow” factor of reimagining these past ecosystems, large mammals constitute many of the world’s most currently endangered species, and so understanding how these animals are affected by climate changes and human activities might help us prevent the megafauna that are still alive today from disappearing too. This is important not only because it would be sad to have a world with no elephants, tigers, or polar bears, but also because losing these big animals could spell trouble for a lot of other species, including humans. Megafauna have major impacts on Earth’s ecosystems: they affect what plants grow where, how often and long forest fires burn, and how rich the soil is. They are important transporters of nutrients and seeds, and they can create and destroy habitat for smaller species. Megafauna are so important, in fact, that some scientists have proposed reintroducing them to habitats where they once lived — either by actually cloning extinct species, or by bringing in their closest living relatives from (where else?) Africa.
While these measures may help restore some natural areas, they are no substitute for maintaining healthy ecosystems in the first place. Hopefully, the research being done by scientists like me and my colleagues today can be used in conservation efforts, to help prevent the next big megafauna extinction.
• South American megafauna image from jqjacobs.net.
Ninety-six percent of marine and 70% of terrestrial species died in the Permian mass extinction, which began about 252 million years ago and lasted for over 20,000 years. Geochemistry tells us that this extinction coincided with a severe and rapid change in the Earth’s carbon cycle, but this alone could not have been the cause of the extinction. Initially it was thought that carbon dioxide released by Siberian volcanism explained this change in the carbon cycle but the volcanic outgassing was not large enough to have been responsible for this big a disruption. So if not volcanoes, what could have produced so much carbon in the atmosphere?
A new study shows that the speed and exponential growth of carbon had to be of biological origin. The study proposes that the emergence of a new group of microbes, Methanosarcina, was responsible for producing the methane in the atmosphere that led to the extinctions. At around 250 million years ago, these microbes acquired fancy new machinery, or a new metabolic pathway through lateral gene transfer that made them capable of taking advantage of the large amounts of marine carbon produced at the time and converting it to methane. This also required large amounts of nickel that was released by the volcanoes. The new source of nickel, a limiting resource in the ocean, combined with increases in marine carbon created a feeding frenzy of bacteria. Following the production of methane by Methanosarcina, other microbes, anaerobic methanotrophs, turned the methane into carbon dioxide further lowering oxygen levels in the ocean.
Today we see similar short-lived low oxygen events in the ocean, but these are driven by algal blooms. Marine algae (i.e., marine plants) are responsible for most of the photosynthesis that occurs on the planet and the resulting oxygen and marine organic carbon. Just like the plants that grow in your garden, these algae rely on nutrients to grow and reproduce. When there’s a new source of otherwise limiting nutrients, they often grow rapidly and we call this a “bloom.” As the algae use up the nutrient source, they begin to die and microbial decomposition begins. These microbes consume oxygen in the water as they feed on the algae and release hydrogen sulfide gas as they have their own population explosion. Just as scientists have observed in the fossil record for the Permian extinction, we see low oxygen levels in areas of the ocean following algal blooms and increases in microbial digestion. The hydrogen sulfide gases released during decomposition of modern algal blooms often produce mass die-offs of marine animals.I study microscopic life history stages of modern bloom-forming algae, green seaweeds in particular. These life stages are similar to invertebrate larvae in that they are released into the ocean by adults and can be carried long distances by waves and currents. Last spring I set out to learn how to detect these life stages in coastal waters using their genetic code, or DNA. I was hoping that I could use this method to predict when these seaweed blooms were more likely to happen. My first challenge was to find out if I could extract DNA from these life stages. I went to the rocky intertidal at the Romberg Tiburon Center (RTC) and collected some specimens of adult Ulva, the alga responsible for most of the worlds green seaweed blooms. I brought the algal specimens back to the lab and kept them dry, dark, and cold for a week. When I submerged the algae in artificial seawater they began to release what looked like green ooze. Upon closer investigation under a microscope this ooze proved to be microscopic swimmers, Ulva's tiny planktonic life history stage! I filtered this solution of swimmers to concentrate them and stored them in the freezer for DNA extraction at a later time. Just to make sure my procedure for DNA extraction would work for green algae, I extracted DNA from as many morphologically different specimens of adult Ulva I could find at RTC. These included specimens taken in small volume from the solution of swimmers and I filtered them on the the same day. After the extraction procedure I used a method called gel electrophoresis to test if I had successfully extracted DNA from my samples. This method works by adding a fluorescent dye that will bind to any DNA present and produce a glowing band under UV light. Unfortunately, the first four times I tried this, no glowing bands resulted. After taking a few more classes and working with other scientists that have experience extracting DNA from algae, I finally had a breakthrough. I successfully extracted DNA from the adult Ulva specimens I collected in December 2013. I’m still tying to figure out what went wrong with the filters, but I went back to RTC in April 2014 to do another survey of Ulva species. By the end of this spring I will be able to test for changes in Ulva species composition across different seasons.
In July 2013, I visited the Denver, Colorado, area to collect data from two collections housed at United States Geological Survey (USGS) facilities and the University of Colorado (CU) Museum of Natural History. The USGS collections are housed in the Core Research Center on the Denver Federal Center campus. The building is also a repository for a large collection of soil samples and approximately 1.7 million feet of drilled rock, sediment, and ice cores. The Museum of Natural History is located at the University of Colorado campus in scenic Boulder, Colorado.
Though these collections cover a wide range of organisms from all over the world, my purpose there was to visit the fossil collections from the Western Interior Seaway. The Western Interior Seaway was a widespread shallow sea that flooded the North American continent from the Gulf of Mexico to the Arctic Ocean during the Late Cretaceous Period (about 100 to 65 million years ago). My work focuses on the faunal dynamics associated with invasion into these shallow sea environments. By more closely examining natural experiments in the past when biota encountered widespread novel physical conditions, we can better inform our predictions of how organisms will respond to the rapid global change happening today.
To that extent, I was interested in photographing and documenting a portion of the vast numbers of ammonites the two institutions have amassed over the years. Ammonites are a completely extinct group of hard-shelled cephalopods, related to the modern-day squid, octopus, and nautilus. Their fossils are often sold in rock shops because their beautiful undulating suture lines make them aesthetically pleasing items. They were incredibly diverse and abundant during the time the Western Interior Seaway existed, and so are an ideal study group to explore the dynamics of this system.
The large collection of Cretaceous bivalves, gastropods, and ammonites kept in the USGS collection is primarily the result of work done by USGS geologists, such as William Cobban, who collected and published on the Western Interior throughout the late 20th century and is still at the USGS facilities in Denver today. The collection contains drawer upon drawer of specimens. With the generous help of curator Kevin “Casey” McKinney, I photographed hundreds of ammonites, including many unpublished specimens. These photographs will be used to identify morphological features that may have influenced the degree to which ammonites were able to invade or adapt to the seaway. It was an adventure exploring the dusty cabinets, where every drawer held a surprise.
After four days in the suburbs of Denver, I took a bus up to beautiful Boulder, Colorado, just 45 minutes outside of Denver proper. After winding my way through the University of Colorado-Boulder campus, I arrived at the Bruce Curtis Building where the museum collections were housed. Collection manager Talia Karim greeted me and helped me get set up before showing me around the collections housed in the basement. Here, there were not as many specimens as at the USGS, but they were no less impressive. During the next three days, I photographed about a hundred more beautifully prepared specimens before I had to say goodbye to the Denver area.
The richness of the collections were such that, no matter how often I visit, there will always be much more to discover. I have plans to return in the near future to continue my explorations of these amazing and underused resources.
As a graduate student affiliated with the UCMP, there are many resources readily available to me. Not only does the museum have the largest university research collection, but the curators, museum scientists, and staff are some of the most knowledgeable and helpful anywhere. UCMP is recognized for taking care of its graduate students, and one of the ways they do it is by providing multiple funding opportunities. I applied to UCMP for funding last year in order to conduct museum travel for my research and I was fortunate to get an award from the Welles Fund.
One major aspect of my research focuses on looking at shape differences in the skulls of monitor lizards. Monitor lizards, or varanids, are generally thought of as being fairly large lizards (e.g., Komodo dragon), but some may be no longer than a pencil. Although there are many extinct species and genera within this group, there are approximately 70 living species in the single genus Varanus. They live in Africa, Southern Asia, and Australia, and are ecologically versatile, with some being strictly terrestrial, arboreal, or even semi-aquatic. Fossil varanids from Asia may be as much as 90 million years old; varanid fossils are also found in North America and Europe.
Thanks to my Welles Fund award, last year I was able to visit the American Museum of Natural History in New York, The Yale Peabody Museum in New Haven, CT, and the Australian Museum in Sydney, Australia. At these museums I photographed the skulls of over 300 modern varanid skulls, getting top, side, and bottom views of each. I use these photos for a technique called Geometric Morphometrics. Morphometrics (greek “morphe” or shape, and “metria” or measurement) is a general term used for describing the quantification of shape. Many fields within biology use this technique to study numerous questions, like changes from juvenile to adult morphologies, how ecology influences shape, and in my case, comparing species from different regions to each other and to those in the fossil record. Geometric Morphometrics is a technique that uses landmarks (coordinates) placed on photos of specimens that can be regarded as a a similar point in each specimen in the study. There are various ways of analyzing the data, but essentially the locations of the landmarks on different specimens are compared and quantified. One main analysis conducted with this data is called Principal Component Analysis which tells you where the maximum amount of variation in your specimens happens to be. This allows the researcher to determine how much shape difference exists in their specimens of interest. In my case, museum visits are essential since they allow for adequate sample sizes to compare the species found in different locations of this group.
I was able to analyze the data to answer various questions, and one of the most interesting discoveries was that the varanids in Africa, where there are only about six species, are almost as morphologically variable as those in, for example, Australia where there are approximately 30 species (depending on where you designate certain groups). I am continuing to analyze and collect data, but I am thankful to the UCMP for providing the finanical assistance necessary for me to complete a large portion of my dissertation project. As a side benefit, traveling to distant museums allowed me to visit interesting and beautiful locations!
Pollen analysis (or palynology) has been used to study Quaternary changes in vegetation and climate in North America since the nineteenth century. Palynologists generally compare plant assemblages in spatial-time frames instead of focusing on particular plant species. These changes in plant assemblages across landscapes through time are a good indication of vegetation shifts caused by environmental changes. Besides using pollen assemblages to reconstruct parent plant communities in a particular area, certain species, which are sensitive to changes in temperature or precipitation, are of special interest. By comparing assemblages of plant communities and these indicative species through time and space, we can infer how regional flora responded to environmental changes such as changes in climate.
Before comparing these past assemblages of plant communities and inferring environmental changes, palynologists carefully consider the processes leading to pollen accumulation. Do their pollen and spore assemblages accurately reflect local or more regional vegetation? Are certain pollen types over- or underrepresented? Does the assemblage include the majority of taxa present in the local plant communities? Pollen assemblages are incorporated in sediments at the end of a long taphonomic pathway, and are affected by temporal and quantitative aspects of pollen and spore production, differential dispersal characteristics, secondary transport, and other taphonomic processes.
How could we get hints of that process throughout geologic time? Wind-pollinated assemblages are most often transported and they are usually produced in large amounts and have wider dispersal ranges. To study the taphonomic process of pollen and spores, palynologists often use surface samples to research the discrepancy between vegetation composition and pollen assemblages. Such analysis also might help to understand the taphonomic conditions in the sample area and provide a reference point for a regional paleopalynological study.
For my dissertation research, I am compiling a California pollen reference collection. Focused on the last interglacial period, I plan to reconstruct the vegetation from a relatively warm period during that time interval. My methods involve extracting pollen from core samples from Clear Lake. Clear Lake is the largest lake in California with a sedimentary record going back at least to the last interglacial period (~130 ka) (see Scientists core into Clear Lake to explore past climate change). The microscopic pollen grains are expected to yield important clues on the history of vegetation communities and the taphonomic process surrounding Clear Lake; data from pollen traps set in different vegetation areas in the vicinity of the lake — forests up to 2 km from the lake, or small, more distant upstream communities — will enable further analysis of modern vegetation types.
The most common pollen in Clear Lake samples is wind-pollinated, mostly pine and oak pollen. An important question is: does this pollen mainly originate from the northwestern forests, the southwestern forests, or other adjacent places? To solve this question, I started to look for appropriate types of pollen traps to collect surface samples and, with the help of my undergrads, Mary Grace Rodriguez and Rebecca Shirsat, we built some traps to position in the field.
After visiting the Clear Lake area a couple of times, I positioned the first 10 pollen traps close to the lake — many thanks to Carolyn Ruttan from Lake County Water Resources who helped me obtain landowners' permits for this.
The first time doing field research is often filled with anticipation. On January 20, I left Berkeley in the early morning. I was so excited — not only because I could finally install my pollen traps, but because it would be only my second time driving through winding mountain roads!
After meeting Carolyn Ruttan I set off to Clear Lake State Park, our first pollen trap site. I selected a rocky corner of the lake that had a gorgeous view. Securing this first pollen trap to the ground was a challenge, but we stabllized the base with pebbles and used a small iron wire to prevent the trap from blowing over in the wind.
The next trap was easier to position, being on soft soil in Anderson Marsh. We only had to avoid picking a spot where weeds might cover the area later in the year.
The Lake County Land Trust’s Rodman Preserve is another one of my research sites. The trust was formed as a non-profit organization in 1994 and it works to protect important land resources, wetlands, forests, etc., in Lake County, CA.
The Elem Indian Colony, near Clearlake Oaks on the eastern shore of Clear Lake, is my fourth research site. It is a Native American colony of Pomo, associated with the Sulphur Bank Rancheria. The residents were friendly and curious about our purpose. I am sure they will help prevent tourists from removing the trap that we placed near a power station.
We then attached pollen traps to railings and floating platforms at three sites. Installation of the first 10 pollen traps was completed on this first trip; we went back two weeks later to complete the west side of the lake.
The most serious threat to my traps is the strong winds around Clear Lake, especially on the northwest side. Strong, seasonal winds can take down deeply-rooted trees and it could damage the pollen traps. Squirrels and birds might also be a problem but hopefully, the iron wires we used will keep them safe from animals. I plan to return to Clear Lake later in the year to replace trap materials and to see what my pollen traps have collected (if the squirrels and birds have not absconded with my trap materials)!