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Project Lab 

March 27, 2012

The Frog Swabbers


Currently, the Herpetology department is acting as a detective, seeking the origin of the Chytrid fungus, a pathogen responsible for huge declines in amphibian populations around the world. Under an internal grant from the Hagey Research Venture, the collaborative team of Dr. Dave Blackburn (CAS) and Dr. Vance Vredenburg (SFSU) is utilizing the Project Lab to investigate the origin of Chytrid fungus, Batrachochytrium dendrobatidis (Bd), its geographical spread, and the diversity of strains. “We are using the museum collections to walk back in time,” says Dr. Blackburn.  “We are repurposing the use of the collections to more directly affect conservation.”

Dr. Blackburn explained the frustration that this pathogen presents to conservation efforts. There are three main ways in which we lose species: climate change, habitat destruction, and disease. If we protect the land, and work towards decreasing human impact, we still have to face the fact that frogs are dying from Chytrid fungus. But how has Chytrid fungus become so widespread?

As of now, they are exploring the hypothesis that Chytrid originated in Africa and was unleashed around the world via the African Clawed Frog, which was being exported beginning in the 1920’s for medical research. The CAS team has ascertained the shipping dates from a primary breeding facility in South Africa and is checking native species of frogs for Chytrid before and after the recorded importation of African Clawed Frog. Further support for the possibility that the lineage is of African origin is the lack of major population declines or mortality of frogs despite widespread evidence of the pathogen, perhaps signifying an immunity or evolutionarily acquired tolerance.

In the Project Lab, Sonia Ghose, a CAS researcher, and the Frog Swabbers, her team of student volunteers from San Francisco State University, are testing this hypothesis. Through a meticulous process of swabbing frog specimens, from some of the 300,000 amphibian specimen in the CAS’s collections, they are gathering DNA for Dr. Vredenburg’s creative PCR technique to ascertain the presence of Bd on even the oldest formaldehyde fixed and ethanol soaked specimens. Unlike the typical histology technique that is hugely time consuming, damaging to specimens, and less likely to thoroughly note the presence or absence of Chytrid, the swabbing is comparably efficient and effective. They swab each specimen 30 times, ten on each side of the underside and five times on each hindfoot, to check the most likely places where the Chytrid may have bred. Chytrid is an aquatic fungus and needs damp places to grow. It propagates in the outermost layer of a frog’s skin, inhabiting keratinized cells and often killing the frog by interrupting necessary exchanges of water, electrolytes, and air.


Sonia extracts DNA for a quantitative PCR test, which is basically a presence-absence test that also records the intensity of the Chytrid infection if it is present. They will soon move on to sequencing the DNA in search of a hyper virulent strain of Bd, perhaps evidence of a looming conservation crisis. Dr. Blackburn explained the possibility of a “super bug,” a Y2K-esque pathogen that could have been born from the recombination of different lineages of Chytrid.

Sonia and the Frog Swabbers will be in the Project Lab some Mondays and Fridays if you are interested in watching the research in progress. Attacking the research from a variety of angles, the CAS team is hoping to piece together the history of the Chytrid fungus in an effort to change its future effects on amphibian species. Uncovering the history, geographical path and virulence of existing strains will help direct conservation efforts and stop the shipping of potential host species.

Page McCargo
Project Lab blogger

Filed under: Uncategorized — project_lab @ 11:10 am

March 23, 2012

What’s in a name? A scientific name, that is.

What’s in a name? According to Juliet, “That which we call a rose by any other name would smell as sweet.” But for a taxonomist, the answer is not so simple and perhaps not so romantic. Taxonomy is the scientific discipline of describing, classifying and naming organisms. At the Academy, a major goal of our research aims to study the diversity of life, and part of this includes discovering, describing and naming new taxa (e.g. species, genera, families).

So, for example, how does one describe and name a new species?

Describing a species involves studying the characters of a certain organism (e.g. its morphology, genetics, ecology, behavior), comparing it with other closely related species and placing it within a classification system based on its relationship to other species. Finally, this work needs to be presented in a peer-reviewed publication. This is no trivial task, and it requires expert knowledge of the particular group of organisms being studied.

A species name is based on an organism’s biological classification and follows the system of binomial nomenclature. A name consists of two words: the generic name and the specific epithet. The generic name is the genus to which the species belongs, and the specific epithet refers to the species within that genus. For example, in the name Homo sapiens, Homo is the genus and sapiens is the specific epithet. There are very specific codes about how to name a species, and these codes are regulated by international organizations such as the ICZN. There are also unofficial rules. For example, you should never name a species after yourself, or else you’ll seem arrogant!


When a new species is being described, the specimen that the description is based on becomes the type specimen, and the scientific name of the species is formally attached to this specimen. In the Project Lab, I have been photographing amphibian and reptile type specimens from the Herpetology research collection. This collection contains around 400 type specimens that were collected in the USA as well as from all over the world. In the future, these images will be put online and made available to the public. By making our type specimen collection accessible, the Academy can help the wider scientific community in defining taxonomic groups and in better understanding biodiversity.


However, definitions of taxa are not fixed in stone; the classification and validity of certain taxonomic groups are not always agreed upon by all scientists, and sometimes, a re-examination may lead to changes in scientific names. So, for a taxonomist who has put in all the hard work into describing a certain species, that same organism by any other name might not sound as sweet!

Tinya Hoang, Project Lab Coordinator

Filed under: Uncategorized — project_lab @ 5:02 pm

March 13, 2012

Small mammals of the Presidio


Quick, how many different species can you name that live in the Presidio?  I think of Red-tailed Hawks, Common Ravens, Red and Grey Foxes, and thorny Blackberry bushes to name a few.  But what about all those small animals you may not see?  How do we find out what lives in the Presidio?

In 1994, the area now known as the Presidio Trust was handed over to the National Parks Service and since then, major restoration projects have been underway to revert the coastal habitat back to its original state.  One way to evaluate the success of the habitat restoration is to survey animal populations and determine what species call the Presidio home now compared to a decade ago.

Every three months from December 2010 to July 2011, the Academy of Sciences sent out interns and volunteers working under the direction of our Field Technician, Liz Carlen, to survey the small mammal population of the Presidio.  Some of the species found include California Voles (Microtus californicus), Deer Mice (Peromyscus maniculatus), and various Shrew species (Sorex spp.).  Many of us would never notice these small mammals on a sunny stroll through Crissy Field or through Lobos Dunes, but they still play a vital role in the ecological health of the area.

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In the Project Lab, I’ve been preparing some of the California Voles and Deer Mice that were found dead during the survey.  The Ornithology and Mammalogy research collection can use these study skins in several different ways.  The study skin can be used for physiological, morphological and genetic research, while the location and date that the specimen was found can give geographic and spatial information about population change.  Armed with this new information, the Presidio Trust can determine what steps of their restoration have been the most successful and any further restoration that may need to be done.

That’s a lot of information to get from a small brown mammal!  The next time you see something scurry across your path, think about what that small little guy can tell you!

Codie Otte
Curatorial Assistant and Specimen Preparator
Ornithology & Mammalogy Department

Filed under: Uncategorized — project_lab @ 12:05 pm

March 5, 2012

Imaging at the Project Lab

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The 21st century could be characterized as the digital age, and modern museums have responded whole-heartedly with efforts to produce digital images of their specimen holdings. Researchers throughout the California Academy of Sciences produce huge numbers of digital images that add value to our research collections. Some of this imaging takes place in our Project Lab, where we have some top-notch equipment for producing exquisite, detailed images of our specimens. Among my projects is the imaging of type specimens. In addition to their normal specimen collections, each department at the Academy also keeps collections of type specimens. These specimens are the placeholders and representatives of what a particular species actually is. When a new species is named by a researcher, it is a requirement for them to designate a Holotype, often the specimen from which the species has been described. These specimens can be extremely important to researchers, and it is the Academy’s responsibility as a world class museum to make them available to qualified researchers around the world. High quality digital images often make it possible for researchers to share our specimens without them having to leave the building. It is also a goal of the Academy to make these images available to the public, and many are or will be available on our website.

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I have been involved in imaging our type collections of robber flies and scorpions. Robber flies are among nature’s top predators, using strong wings, long claws, sharp eyesight and a stabbing beak to catch other insects in flight and eat them! Nearly 400 species of robber fly types collected from all over the world are now available for viewing. Here is a link: http://research.calacademy.org/redirect?url=http://researcharchive.calacademy.org/research/entomology/typesDB/default.asp. Under Family, select Asilidae from the pull down menu. Soon, our large and important collection of American and worldwide scorpion types will also be posted. Scorpions are not often seen in the daylight, but they are important predators found all over the world, wherever there is soil or leaf litter. Looking closely at the natural world is thrilling to me, and I am continually amazed at its complexity and beauty.

Vic Smith
Invertebrate biologist, curatorial assistant and imaging specialist
Department of Entomology

Filed under: Uncategorized — project_lab @ 6:17 pm

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