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Evo in the news: Making sense of ancient homonin DNA

Denisova-Cave-2

Denisova Cave, where the fossil finger was discovered. Photo provided by ЦуваевНиколай at ru.wikipedia and shared via Creative Commons.

When archaeologists discovered a 40,000 year old pinky bone in a Siberian cave, everyone wondered who the bone belonged to. Researchers extracted DNA from the fossil and used it to construct an evolutionary tree to see how the pinky bone's owner was related to modern day humans and Neanderthals. Scientists were surprised by what they found — read more about it in this month's Evo in the news: Making sense of ancient homonin DNA.

Each month, the UCMP's Understanding Evolution website features an Evo in the news article, which focuses on the evolutionary aspects of a popular news story. Click here to browse the Evo in the news archive!

Congratulations Tim White!

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Tim White. Photo: Discovery Communications, LLC.

Congratulations are due to Tim White, Director of the Human Evolution Research Center and Faculty Curator at the UCMP! Tim was selected by Time Magazine as one of The 100 Most Influential People in the World. Tim receives this recognition for his work on human evolution. This past fall, Tim and his colleagues published numerous papers on Ardipithecus ramidus, the oldest and most complete skeleton of a human ancestor. Congratulations, Tim!

Highlights from Understanding Evolution

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Map and photos: Tom Devitt

Ring species are often touted as examples of speciation in action — and the Ensatina salamander, which forms a ring around California's Central Valley, is a classic example. Biologists discovered this ring species back in the 1950s, and investigations of Ensatina continue today. Learn more about Ensatina in this research profile of biologist Tom Devitt, on the UCMP's Understanding Evolution website. Tom is a graduate student in Integrative Biology here at UC Berkeley. The profile follows him from the field to the lab, from studying the morphology to investigating the molecules. Tom even does some exciting experiments on Ensatina mating behavior — be sure to check out this research profile!

Creatures from the black lagoon

Lake Merritt

Lake Merritt, Oakland, California.

Very little was known about wetland ecology back in 1869, when Samuel Merritt dammed a former tidal slough and began developing its surrounding wetland as his "Jewel of Oakland." By restricting the flow of waters in and out of the newly created tidal lagoon, a.k.a. Lake Merritt, silt and algae were allowed to accumulate and within a few years the lake had become a bit of an environmental disaster. Nevertheless, part of it was designated by Teddy Roosevelt as our nation's first wildlife refuge, protecting more than 90 species of migrating waterfowl. Lake Merritt serves as a drainage basin for the regional flood control system, receiving urban runoff from a 4,650-acre watershed through 60 storm drain outfalls. Four creeks drain into this 145-acre lagoon from the east, while tidegates regulate flow to the south through a narrow channel that connects it with Oakland Inner Harbor and San Francisco Bay. The lagoon is also polluted by illegal dumping of substances such as paints, solvents, and oil, which are highly toxic to marine life. In addition to mechanical harvesting of its widgeon grass, 1,000 to 7,000 pounds of trash are removed from the lagoon every month. Merritt’s short-lived dream as a spectacular swimming hole in downtown Oakland is, in reality, more accurately described as a very large recreational sewer.

Despite all of its tarnish, the Jewel of Oakland has been a haven for some organisms that thrive on an abundant supply of bacteria and algae and tolerate the tidal, seasonal, and anthropogenic changes of this stressed environment. Among them are a few species of microscopic foraminifera (think of sand-sized shelled amoebas) that are being monitored by Ken Finger, Jere Lipps, and Dawn Peterson. Recent studies have shown that foraminifera might be useful environmental indicators of pollution. Lake Merritt presents an opportunity to study how they will respond to the remediation measures planned by the City of Oakland. Currently, only the shoreline of the lake supports living populations of foraminifera, while the deeper lake bottom is a dead zone of black mud stinking of methane. Why is that, you ask? Well, all of the algae, widgeon grass, bird droppings, and other organic waste that escapes harvest sinks to the bottom, and the process of their bacterial decomposition depletes the dissolved oxygen in the stagnant water just above. In contrast, wind-driven circulation keeps the surface waters and shallow margins circulating and aerated, enabling fish, invertebrates, plants, and foraminifera to survive.

But the foraminifera have a higher coincidence of malformed shells in Lake Merritt than in San Francisco Bay, which could be related to their stressed environment, where temperature, salinity, and oxygen levels change regularly. Studies elsewhere suggest that these micro-mutants result from high levels of contaminants, heavy metals, industrial pollution, and domestic sewage. In 2002, Oakland passed a bond measure that will clean up and improve the health of the lake by increasing tidal flow and installing aeration units. With these changes, will the shell deformities become less severe or more infrequent? Will living foraminifera begin to colonize the deeper parts of the lake? We hope to answer these and other intriguing questions as we continue to collect and analyze these minute “creatures from the black lagoon.”

Lake Merritt Dawn Peterson Ammonia tepida - normal Ammonia tepida - deformed Ammonia tepida

Fossils found fortuitously

Whale Excavation INot all fossils are discovered by paleontologists combing the earth on special expeditions. Many fossils are found by accident — particularly during construction projects. Impressive fossils, like whales, mammoths, and sloths, have been found while digging foundations for buildings, leveling land for highways, and excavating subway tunnels. This spring, the UCMP blog will take you on a tour of Bay Area construction sites, past and present, to show you some of the fossils underfoot in the region.

This week, Dave Haasl, a former Museum Scientist at the UCMP, tells us about his work with PaleoResource Consultants, a consulting firm that performs what is known as mitigation paleontology. If fossils are found on public lands during construction, the law requires that they be preserved. The fossils need to be excavated quickly, so that construction can carry on. And, the fossils need to be excavated by trained paleontologists, so they are properly preserved for future scientific study. This is a job for mitigation paleontologists! As Dave explains, "we need to mitigate the impact [of construction] to scientifically important resources. This includes fossils, as well as archaeological specimens."

There are two parts to mitigation paleontology. First, the paleontologists do pre-construction field surveys. "We look at the stratigraphy of the area, and plot the potential fossil localities," says Dave. Then, when those areas are dug up, workers know to be on the lookout for fossils. The second part of paleo mitigation is monitoring, which occurs throughout a construction project. Construction workers may not recognize fossils when they come across them, so it's important to have a trained paleontologist on site. If fossils are found, the monitors halt construction and quickly excavate the fossils. They call in a network of paleontologists, and typically they are able to excavate the fossils within a few days.

Recently, two marine mammal skeletons, a whale and a dolphin, were found during the construction of a sea wall along the California coastline. Santa Cruz County is building a sea wall between Santa Cruz and Capitola, to protect the cliffs and buildings from large waves. However, the sea wall will block access to that section of the coastline, preventing any future paleontological exploration of the area. Paleontologists were asked to survey the area before the wall was built, to see if any fossils were present.

An amateur paleontologist had seen vertebrae protruding from the sandstone — these vertebrae belonged to a small whale that lived in the late Miocene, about 5 million years ago. PaleoResource Consultants excavated the specimen, wrapped it in plaster to protect it during transport, and brought it back to their offices in Auburn, California, where it is now being prepared.

A second skeleton, a dolphin, was found by Robert Boessenecker, a graduate student at Montana State University studying marine vertebrate fossils in California. The dolphin, now extinct, is also from the late Miocene, and is related to the Chinese river dolphin. "Marine mammals were much more diverse at that time," says Dave.

While Dave's career path as a paleo mitigation consultant may seem unusual, there is a real need for trained paleontologists in this field. "There is more paleo work in the West than paleontologists who can do it," he says. "Often, archaeologists do the work, because paleontologists are not available." And this work is important. As a result of big construction projects, fossil material is collected that otherwise would still be in the ground. These specimens are then used in scientific research. Says Dave, "This is our historic heritage. If it's destroyed or sealed off, we're losing something of potential scientific value. Yeah, we need roads, we need power plants. But we're going to try to preserve as much of our past as we can."

Learn more about fossils found during construction projects in upcoming blogs!

Whale Excavation I Whale Excavation II Whale Excavation III Whale Prep - edited

Lupé's story, part 2: Prototyping the mammoth exhibit

LupeSkullUCMP graduate student Kaitlin Maguire is working with the Children’s Discovery Museum in San Jose to develop a new exhibit about the life of Lupé, a mammoth fossil that was found in the nearby Guadalupe River.  This is the second in a series of blogs about Lupé and the new exhibit. Read Kaitlin’s first Lupé blog here.

Development of the Lupé Story Exhibition is moving along quickly as exhibit ideas come to life in prototyping labs, in which the development team at the Children’s Discovery Museum (CDM) sets up preliminary exhibits and opens them up to the public for feedback. Prototyping labs are an important aspect of developing an exhibition; the prototyping labs show how children interact with the exhibits and if the exhibits are successful in teaching the children something about Lupé, paleontology, and the process of science. Maureen Callanan, a professor at UC Santa Cruz, is also interested in the prototyping labs because it gives her and her graduate students a chance to study how children learn and interact with their parents and caregivers.  Maureen and her students then provide additional feedback to the CDM team from a cognitive psychology perspective. Preliminary exhibits in the first prototyping lab included bone puzzles, play dioramas of the Pleistocene, and sifting for fossils. The most popular exhibit in the first prototyping lab was the dig site where some children spent hours using wooden tools to dig out fossils of Pleistocene mammals.

In December, we all got the chance to meet Roger Castillo, the San Jose citizen who found the Lupé fossils as he was walking his puppy along the Guadalupe River. Hearing Roger tell his story about the discovery was inspirational. As a citizen scientist, he is invested in the health of the Guadalupe River and all it has to offer, including fossils. Growing up in San Jose, he has monitored the river his entire life. Specifically, he has looked at salmon populations in the river, changes in the level of the river, and erosion caused by the river.

Upon hearing Roger enthusiastically describe how he discovered the fossils, the CDM team decided to focus on recreating the “discovery moment” for children to experience at the museum. The next prototyping lab will contain exhibits designed to create an experience of discovery, excitement, and curiosity. Children will discover fossils on a riverbank, uncover them, and ask questions about the fossils much in the way Roger did. This prototyping lab will be open through the spring. A third prototyping lab will open in the fall and final production of the exhibition will start afterward leading up to the grand opening in the spring of 2011.

DigPit BonePuzzle Sifter

Conifer evolution workshop

ConiferIf there were a Guinness Book of World Records for conifers, California would be one of the top record holders: the Golden State has the tallest conifer, the most massive conifer, and the oldest conifer. Learn much more than just conifer trivia at an upcoming workshop, The Origin and Evolution of Conifers, co-hosted by the UCMP and The Jepson Herbarium. Through talks, discussions, and a hands-on lab, you'll learn all about the origin, evolution, and diversification of this unique plant group. Museum Scientist Diane Erwin, Faculty Curator Cindy Looy, and UCMP Post-doc Lenny Kouwenberg will lead the workshop. It will be held on Saturday, February 6, from 9am to 4pm. For more info on the workshop, including registration information, click here.

Genetics and Evolution of the Skeleton Research Initiative conference

gesriThe Genetics and Evolution of the Skeleton Research Initiative recently had its semiannual meeting in San Francisco. Organized by UCMP Faculty Curator Leslea Hlusko, the focus for this year’s meeting was Development, Diseases, and Evolution of Mineralized Tissues. Two graduate students from the Hlusko lab, Theresa Grieco and Sarah Amugongo, give us these snapshots from the conference:

Highlights from the conference, by Theresa Grieco:

The GESRI meeting draws bone biologists from all over the Bay Area — UC Berkeley, UC San Francisco, UC Davis, Stanford, and Lawrence Livermore National Lab. The speakers and attendees work in a variety of contexts, including biomed, EvoDevo, paleontology research, and veterinary/clinical research. It is great that this meeting is able to draw together a diverse group that is willing to talk across field boundaries and present their findings to the broader scientific community. We heard talks about fracture repair, bone mineralization and its changes during fossilization, osteoarthritis, tooth bioengineering, and how bones and teeth can be used to infer life history traits.

For me personally, it is a great way to meet and keep in touch with local mentors and colleagues and get fresh ideas. It’s really the best way to find out about potential resources and collaborations for research projects. It was also great to see a presentation by a biochemist or embryologist drawing questions from practicing MDs or bioengineers, and to see such different people getting excited about each other's work. One thing that I thought was interesting was that sometimes questions would be misunderstood, usually because people trained in different fields catch on to very different aspects of your research than the ones you’ve been trained to look at. Talking about these kinds of questions in a little more detail can reveal significant implications of your research in other arenas, or where the methods or data collected from another field could make your research better.

A highlight of the day was one of our plenary speakers, Dr. David Kingsley, who gave a talk about why he developed the stickleback fish as a model system for EvoDevo and a case study about pelvic reduction and hindlimb loss in these fish. Through genetic mapping, his lab identified a set of chromosome deletions in the regulatory region of a gene called Pitx1. These deletions have been selected for in many different stickleback populations around the world. These deletions only affect the molecular switch for Pitx1 expression in the hindlimb, allowing the rest of the gene’s vital functions to be preserved. He then showed us how similar phenotypes can be seen evolutionarily, with hindlimb loss and pelvic reduction in snakes, manatees, and in mice missing the Pitx1 gene. Dr. Kingsley then brought us into the clinic with case studies of club foot in humans. Wow!

A sampling of GESRI talks, by Sarah Amugongo:

Though only in its infant stages, GESRI has already become very popular among bone biologists in the Bay Area and beyond. I was astounded by the turnout, especially from the un-registered members. The range of topics covered was quite impressive: from basic bone biology, to clinical application, to evolutionary history of bone mineralization.

Here are a few of the talks that were given at the conference:

  • One talk focused on the repair of fractures. A high oxygen level was demonstrated to be very important for the healing of fractures. Interestingly, the process of fracture repair is different from the process of normal bone development in several ways. The source of bone cells is different, and the processes that regulate cell fate are different too.
  • The inverse relationship between osteoarthritis and osteoporosis was also notably interesting. With the loss of cartilage, there is an up-regulation of bone growth as demonstrated by research on osteoarthritis of the hip.
  • The growth hormones TGF-beta and IGF-1 have different signaling pathways, but both have been demonstrated to be important to the skeleton as they regulate osteoblast differentiation and proliferation. Osteoblasts are cells that are responsible for bone formation.
  • In addition to studying the extant organisms, learning that soft tissue is also preserved in the fossil record through the study of dinosaur fossils was really amazing. It made me wonder what else we’ve been missing by just focusing on bones. This might open a whole new area of research in paleo!

View the full meeting program here.

The Year of Science Zine-a-thon Contest

Science Zines

How do you learn fun new information about science?

a) Newspaper

b)  TV

c) The Internet

d) The Science Zine that I found on a bench while I was waiting for the bus

If answer d) seems totally strange and you have no idea what a Science Zine is, or even how to pronounce it, read on!

A zine (pronounced zeen) is a little magazine. Science Zines are a cool way to convey scientific knowledge — a fusion of art and science that fits in the palm of your hand. Check out The Small Science Collective for some examples — this website has lots of Science Zines that you can print out, read, and then leave in public places for random strangers to enjoy.

You don't have to limit yourself to reading Science Zines — you can create your own! The Year of Science 2009 is sponsoring a Zine-a-thon Contest, awarding prizes for the best Science Zines.

First come up with a science topic — your topic can be anything, but it should fit in with one of the Year of Science themes. Next, make a zine by folding an 8 ½ x 11 sheet of paper into little book with 8 mini-pages. (Folding is easy, no origami experience required! Check out the easy folding instructions.) Then, be like da Vinci and combine art and science! Zines must be sent in and postmarked by November 1, 2009. For more info, visit the Zine-a-thon Contest website.

I'm going to write a Science Zine version of my dissertation — I'll squeeze 6 years of research onto those 8 tiny pages. Look for it on a bus stop bench near you!