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Assistant director reunites with UCMP alumni in Ethiopia to investigate Mesozoic ecosystems

Assistant director Mark Goodwin is in Ethiopia for several weeks as part of a collaborative project with UCMP alums Greg Wilson (University of Washington) and Randall Irmis (Utah). Together with colleagues from the University of Oklahoma, Addis Ababa University, and Mekelle University in Ethiopia, the team is investigating non-marine Mesozoic ecosystems from the Northwestern Plateau, Ethiopia.

Mark reports "we had great success in the Late Jurassic units and it is gratifying working with Ethiopian students and staff from the Earth Sciences Dept at Addis Ababa University. In the late Jurassic Mugher Mudstone, in addition to turtles, fish, croc teeth and verts, we found a partial crocodile skull with brain case and parietals, partial lower jaw, many allosauroid-like theropod teeth at almost every site and finally some large dinosaur bones - still fragmentary but we're getting there - and very rich micro vertebrate localities that just have to have mammals - collected some bags of sediment from each. Working with the Earth Sciences Dept at Addis Ababa University has been great and hopefully a model for future work and lots of opportunity for collaboration, including informal science."

This collaborative research project, "US-Ethiopia planning visit for the investigation of non-marine Mesozoic ecosystems from the Northwestern Plateau, Ethiopia," is funded by the National Science Foundation grant NSF-CNIC-1444238.

Group pic at the top of the flood basalts that cap the steep sided canyons of the Blue Nile Gorge, near Fiche, Ethiopia. From L to R: Tadesse Berhanu (PhD student, Oklahoma State); Connie Rasmussin (PhD student, Utah); Keegan Melstrom, PhD student, Utah); Randy Irmis (Utah); Greg Wilson (Washington); Mark Goodwin (UCMP); Dave Demar (Postdoc, Washington); Million Mengesha and Samuel (Earth Sciences Dept., Addis Ababa University).

Group pic at the top of the flood basalts that cap the steep sided canyons of the Blue Nile Gorge, near Fiche, Ethiopia. From L to R: Tadesse Berhanu (PhD student, Oklahoma State); Conny Rasmussin (PhD student, Utah); Keegan Melstrom, PhD student, Utah); Randy Irmis (Utah); Greg Wilson (Washington); Mark Goodwin (UCMP); Dave Demar (Postdoc, Washington); Samuel Getachew and Million Mengesha  (Earth Sciences Dept., Addis Ababa University).

Bones in the Belltower, a Berkeley Science Review feature by Sara ElShafie

fall_2015_elshafie_featureThe Fall 2015 issue of the Berkeley Science Review features an article by Sara ElShafie, a UCMP graduate student in the Padian Lab, on the McKittrick tar seep fossils that have been stored in the Campanile since the 1930s. The convergence of an Institute of Museum and Library Services grant to the UCMP to clean and catalogue more the 12,000 specimens in the collection and the centennial celebration of the Campanile in 2015 shined a spotlight on these unique fossils.

In interviews with UCMP graduate students Eric Holt and Ashley Poust, and UCMP staff Lisa White and Pat Holroyd, Sara details the work performed to preserve history and scientific significance of the McKittrick collection. Over 3,000 collective hours spent by more than a dozen students will improve the accessibility to the collection for future research and a rich digital archive facilitates sharing with the education community.

The Berkeley Science Review is a graduate student-run magazine showcasing research conducted UC Berkeley in a variety of disciplines.

Humans began altering natural world 6,000 years ago

Egyptian farmers in the Neolithic period 5,000-6,000 years ago.

Egyptian farmers in the Neolithic period 5,000-6,000 years ago.

Scientists have found an abrupt change about 6,000 years ago in how terrestrial plant and animal species coexisted, right about the time human populations were ballooning and agriculture was spreading around the world.

The findings suggest that human activity had reached a tipping point where hunting and farming were impacting the natural world in irreversible ways — changes that have continued to increase to this day.

The researchers, including UC Berkeley’s Cindy Looy, an assistant professor of integrative biology, will report their findings in the Dec. 17 issue of the journal Nature.

The scientists looked at fossil data on how species coexisted over the past 307 million years, specifically how often a particular pair of plant or animal species is found within the same community. Out of all possible combinations of two species in a certain region and time interval, the proportion of pairs of species that co-occurred remained relatively stable until 6,000 years ago. At that time, the chances of co-occurrence dropped significantly, suggesting that humans were creating some barrier to the dispersal of plants or animals.

"This tells us that humans have been having a massive effect on the environment for a very long time," said lead author S. Kathleen Lyons, a paleobiologist in the Evolution of Terrestrial Ecosystems (ETE) program at the Smithsonian Institution's National Museum of Natural History in Washington, D.C.

Analyses of modern communities of plants and animals have found that for most pairs of species, the presence of one species within a community does not influence whether the other is present or absent. For pairs where there is an association, most occur within the same community less frequently than expected, suggesting some influence keeps them apart.

But when Lyons, Looy and their colleagues investigated the composition of ancient communities using fossil data, they found exactly the opposite. Their analysis showed that from 307 million years ago, the time known as the Carboniferous period, to about 6,000 years ago, in the Holocene epoch, there was a pattern of pairs of species occurring together within communities rather than being segregated.

"The proportion of co-occurring species pairs was relatively stable from the late Paleozoic until 6,000 years ago, even during periods of major climate change and mass extinction and despite the appearance of many new players in the terrestrial ecosystems, such as mammals and flowering plants," Looy said. "The decline of coupled species pairs in the Holocene also cannot be explained by the transition from the last glacial to the current interglacial at the end of the Pleistocene, as this happened too early. Instead, it is more likely caused by an increase in human population size and the resulting land use and agriculture."

Around the time co-occurrence patterns changed, humans were becoming increasingly dependent on agriculture, a cultural shift that physically altered the environment and would have introduced artificial barriers to dispersal never seen before. Even at low levels of agriculture and other human impacts, there was a detectable shift in co-occurrence structure, indicating that species were not able to migrate as easily as they did for the previous 300 million years.

For more details about the study, see this story on the Smithsonian's website.

This post was originally published online in the UC Berkeley News Center

See also:

National Fossil Day website features research by UCMP and partners

The UCMP partnership with Point Reyes National Seashore and the National Park Service continues to thrive and fossil discoveries made as a result of this partnership are highlighted in a previous post. Lillian Pearson, who works part-time with Museum Scientist Erica Clites cataloging specimens from the Point Reyes National Seashore, is the lead author on an article posted in honor of National Fossil Day (October 14, 2015) describing Cenozoic life and landscape features.

National Fossil Day article summarizes the research here.


Robert Boessenecker (College of Charleston), Lillian Kennedy Pearson (GeoCorps Intern at Point Reyes National Seashore), Sarah Boessenecker, and Erica Clites (University of California, Musuem of Paleontology), are excavating the partial skeleton of an extinct porpoise. The skeleton was excavated from the Purisima Formation on Drakes Beach and includes a nearly complete skull, ribs, several vertebrae, and a humerus. Photo by Kathleen Zoehfeld.

Landscapes change forever when large mammals disappear

An African elephant grazing among trees.

An African elephant grazes. Photo credit: Tony Barnosky

Research on the extinction of large mammals by members of the Barnosky Lab and their colleagues highlights how entire landscapes are affected when modern elephants and their extinct relatives, mastodons and mammoths, disappear.  From plants that are no longer grazed to fewer nutrients in soils, the loss of megafauna significantly impacts ecosystems in a dramatic fashion as detailed in recent articles and interviews.

Learn more about this recent research:


New research shows how mammals became smaller in response to dramatic climate warming

Lead author Brian Rankin holds jaws of two species of 50 million year old horses.  Measurements of their teeth were used to study how global change can affect how mammals evolve.

Lead author Brian Rankin holds jaws of two species of 50 million year old horses. Measurements of their teeth were used to study how global change can affect how mammals evolve.

Fifty-six million years ago the Earth underwent a dramatic warming event, with temperatures increasing by as much as 7° Celsius over a span of just 100,000 years. Many mammals responded to this temperature increase by becoming much smaller. How these changes happened, however, is poorly understood. Identifying and measuring the mechanisms that drove these changes was the focus of a new study by University of California Museum of Paleontology researchers Brian Rankin and Pat Holroyd, and colleagues from University of Calgary and Western University of Health Sciences.

Lead author Brian Rankin, the newest postdoctoral scholar of University of California Museum of Paleontology, explains "When temperatures get warmer, we see a wide range of mammals become smaller. Determining what evolutionary processes are responsible for these changes and how much each contribute to this pattern has been very uncertain. We chose the evolution of mammals at the Paleocene-Eocene boundary because it is a time of dramatic global warming when many different types of animals became dwarfed and the fossil record of this time is incredibly rich."

In a new paper published in Proceedings of the Royal Society B, these researchers present a new method to separate and quantify body size change due to selective extinction vs. change within lineages to determine which is the most important way in which evolution takes place during times of global warming. They found that that some evolutionary mechanisms (i.e., species selection) might act differently during global warming events, favoring mammals that increase in size rather than decrease. The methods developed in the paper can now be broadly applied to look at evolutionary change during other times of global change.

Partnership with Point Reyes National Seashore leads to important discovery of marine specimen

ptreyes-fossilUCMP'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.

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.

Oak pollen

Oak pollen grain

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.

Winnie with SEM

Winnie using the Scanning Electron Microscope.

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.

Pollen wall morphotypes

The three pollen wall morphotypes.

All photos courtesy of Winnie Hsiung.

Building a forest: The adventures continue in the Jose Creek Member

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.

Leaf specimens and Dori

Assorted leaf specimens found at the Jose Creek site, and Dori, happy to have found a cone attached to conifer foliage. Leaf photos by Dori Contreras; photo of Dori by Stephanie Ranks.

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.

Negin wrapping and labeling

Negin wrapping and labeling fossils to take back to UCMP. Photo by Dori Contreras.

Dori, Stephanie, and James

The field crew: Dori, Stephanie, and James (Negin not pictured). Photo by CJ at the Charles Motel and Hot Springs.

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

Do green tide algae reproduce all year?

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:

— Sunlight
— High nutrients
— Calm water
— Few grazers or predators
— Temperature
— Salinity

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.

Collecting water samples

I collect monthly water samples from the San Francisco Bay at the Romberg Tiburon Center. Each season I visit four additional locations within the bay to estimate spatial variation in reproductive stage abundances.

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.

Left: These algae (<1cm) grew from reproductive cells of Ulva, also known as sea lettuce. Right: There is a color difference between reproductive and vegetative cells in Ulva. The former are the lighter ones along the margins.

Left: These algae (<1cm) grew from reproductive cells of Ulva, also known as sea lettuce. Right: There is a color difference between reproductive and vegetative cells in Ulva. The former are the lighter ones along the margins.[/caption] 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.

[caption id="attachment_3955" align="aligncenter" width="470"]Algae established on a settling plate A quantity of algae has established itself on this settling plate.

All photos courtesy of Rosemary Romero.