This week, May 7^th to May 13^th, the Academy of Sciences celebrates International Migratory Bird Day.  Although it was originally slated as the second Saturday in May, the birds don’t always recognize our time schedule, and in some places, migratory birds had already left the area so the single day celebration was extended to an entire week.

Here at the Academy, the Ornithology and Mammalogy department’s research collection aids researchers in studying bird migration. Often times migration can be shrouded in mystery-exact migration routes of species can be little known or unknown altogether! By analyzing stable isotopes, or chemical compounds, in feathers of our study skin collection, researchers can determine geographical locations visited by the migrating birds on their long flight. But why migrate at all?

Many birds use migration as a tactic to ensure secure food supplies all year round, especially around breeding time.  Generally, in the Northern Hemisphere, birds will fly north to more temperate spring/summer breeding grounds and then head back down south when winter approaches their northerly breeding habitat.  This allows them to take advantage of warm weather year round, effectively securing their food source consistently for their own stomach and the young they raise.  Some migration journeys take months and some take days depending upon the distance and flight of the bird.

Arctic Terns have one of the longest distances to travel of any birds; they travel 12,000 miles from Antartica in the southern hemisphere’s summer to their Arctic breeding grounds during the northern hemisphere’s summer.  This journey from pole to pole takes this 13-inch bird only a few months to complete!

Instead of migrating for a few months, Bar-tailed Godwits migrate in a little over a week.  This is despite the fact that Bar-tailed Godwit has one of the longest continuous migrations.  They often journey 11,000 miles from New Zealand to their breeding grounds in Alaska in one trip.  A trip to Hawaii from San Francisco is around 2300 miles.  Imagine flying to Hawaii and back four and a half times without stopping!

These long migrations are not limited to larger birds either.  Allen’s hummingbirds also migrate from parts of Southern Mexico up the coast to southern California, a trip of 1500-2400 miles!

For all birds, migration can be a dangerous, exhausting time.  Since one of the driving factors is food, some birds choose not to migrate if they are fed all year round by an outside source like bird feeders or if they land somewhere that has a temperate climate all year.  Some hummingbirds will choose to stick around if they have access to bird feeders and a subspecies of one of our San Francisco residents, the White-crowned Sparrow will not migrate and choose to breed along the coastline.

Bird migration is a truly awesome feat of stamina!  Come check out the Project Lab during Migratory Bird week for some specimens of migratory birds on display. We also will be having specimen preparation during Nightlife on May 10th as well as our collections manager, Maureen Flannery, discussing bird migration!

You can also visit the official International Bird Day website here: http://www.birdday.org/birdday.

Codie Otte
Curatorial Assistant and Specimen Preparator
Ornithology & Mammalogy Department

The Project Lab was recently visited by two botanists from Madagascar: Rokiman (Roki) Letsara, the Botanical Coordinator at the Madagascar Biodiversity Center; and Jacqueline Razanatsoa, a botanist at the National Herbarium of the Parc Botanique et Zoologique de Tsimbazaza. Roki and Jacqueline are currently here at the Academy working with curator Dr. Frank Almeda, who leads the Academy’s botany research at the Madagascar Biodiversity Center in Antananarivo, Madagascar.

Madagascar, the fourth largest island on Earth, is among one of the world’s biodiversity hotspots where the California Academy of Sciences is actively doing research. Not only is Madagascar’s wildlife incredibly diverse, but over 80% of its species are endemic to the island (i.e. they are found nowhere else on Earth). This remarkable level of endemism is a result of the island’s 88 million years of isolation, which has led to the evolution of a unique diversity of plants and animals. However, today, Madagascar’s ecosystems are experiencing habitat destruction, which threatens undo these millions of years of evolution in, relatively speaking, the blink of an eye. Recognizing the urgent conservation needs in Madagascar, the Academy established the Madagascar Biodiversity Center in the nation’s capital, Antananarivo, in 2007. The MBC provides research and training facilities for Malagasy and international scientists to study the biodiversity of the island and to apply this information to conservation planning.

Roki and Jacqueline have come to CAS to share their knowledge of Malagasy flora as well as to progress in their research and training. They are helping to identify and describe some of the Malagasy specimens that are now in the Academy’s herbarium (plant specimen collection). These specimens include species belonging to the families Melastomataceae and Acanthaceae, and the genera Kalanchoe and Aloe.

To help better describe some of these plant species, Roki and Jacqueline are learning how to use their genetic information in order to compare them with other previously described species. In the Project Lab, Roki and Jacqueline are being trained in plant DNA extraction with the help from Dr. Gilberto Ocampo, a post-doctoral fellow in the Botany department. With their plant tissue samples, they go through a series of steps, which involve pipetting chemical buffers, spinning and vortexing tubes and transferring solutions – a much more complex process than the strawberry DNA extractions that you might have seen in the Project Lab’s “Sweet Side of DNA” demonstration. The plant DNA extracted by Roki and Jacqueline will then be analyzed using the lab and computing facilities in the Academy’s Center for Comparative Genomics.

This close collaboration between CAS and Malagasy scientists, like Roki and Jacqueline, is crucial for the exchange of knowledge and experience, and together, we will be able to better understand the unique diversity of Madagascar and advance conservation efforts to protect the island’s critical habitats.

Barbara is a facial reconstructionist. She laughs as she says this, and gently reconnects the hinges of the jawbone of a baby sea otter. I find Barbara immersed in her Tuesday routine - neatly numbering bones and gluing skulls together. Barbara has been volunteering at the California Academy of Sciences, one day a week, ever since her retirement 15 years ago. She has worked in all three CAS’s: the original museum in Golden Gate Park, the Howard Street location and the current renovated museum. And now, stationed in the Project lab, she seems at once an adept puzzle solver and creative artist, dipping her finger in Elmer’s glue to adhere a bone fragment back to the cranium of an adult male Sea Otter.

She shares some of the things she never thought she would learn, “See this bone,” she says. It is a long straight bone, which seems disproportionately big to connect to the skull in her hands. “This is a baculum, a penis bone. It is kept with the skulls to differentiate their sex.” She moves on to tell me the other notable species she has numbered: Kangaroo, hippo, giraffe, to name a few. “Not the entire skeletons,” she explains, “but you certainly learn things you never thought you would.”

Barbara likes the interactive function of the Project lab where she has recently been working. She digs through the pile of boxes on her left and pulls out a baby skull to show me where you can see the baby teeth coming through. She says, “I can’t help but wonder, do they get toothaches?” She loves the opportunities she gets to share her curiosities with the public. “It’s interesting for young people to see that other baby animals go through the same process of losing their teeth. It’s something they can relate to, and maybe even get a better idea of how things work in their own bodies.” She runs her hand over the half grown tooth and puts it back in the pile of finished skulls.

Barbara also gets a window into more serious ailments we share with Sea Otters and other species. She remembered the challenge of dealing with a Sea Lion skeleton with Osteoporosis. One of the amazing gifts of having the collections is the opportunity for knowledge, not just about specific species, but also about shared diseases and our interconnectivity.

She has been working on Sea Otters for close to ten years. “But no,” she says “the work has not become redundant; it changes all the time.” She gets in her zone and it can be meditative. “I like to make it a leisurely day,” she says, “I come early and sit with a scone and some coffee and watch the public.” Barbara is an avid birder, one of many reasons she was interested in volunteering for the CAS. She also used to be a librarian and worked in Silicon Valley for a company, which shared databases between libraries. Her passion for sharing is evident and the Project lab provides a great opportunity to see her at work and ask her questions about the creatures she has helped document for CAS over the last decade and a half.

Page McCargo
Project Lab blogger

Many of us know what a Raven looks like, and have probably heard the haunting poem by Edgar Allan Poe.  I’ve heard them calling from my rooftop at all hours of the day and clacking their bills when I pass by, hardly moving out of the way whenever there’s a passerby.  These gregarious birds belong to one of the smartest avian families-the Corvid family, which includes Ravens, Crows, Jays, and Magpies amongst others.

Today, I am preparing a Common Raven, Corvus corax, for the Ornithology and Mammalogy research collection.  This specimen will enter into our collection of more than 30,000 study skins used for scientific research on avian populations and systematics.

Although Common Ravens can oft be seen down at Ocean Beach or in Golden Gate park, it might be surprising to learn they were not always such a ubiquitous presence in the Bay Area until the late 1970s to early 1980s. While it’s not clear what has caused the increase in Raven populations, they don’t seem to mind the co-habitation!  Carrion eaters by trade, Common Ravens are able to take advantage of human settlements and the trash we leave behind, scavenging their meals from our bins. Since the Raven doesn’t have a hooked bill to pry flesh from dead carrion, it usually has to wait for larger predators or vultures to take the first bite before moving in, but humans leave behind plenty of scrumptious morsels for the Raven to feast with relatively little effort on their part.

Another member of the Corvid family, American Crows (Corvus brachyrhinchos) have also benefited from their relationships with humans.  Crows have been seen dropping nuts onto the road and waiting for cars to crush the shell leaving the Crow with a healthy snack.  If a car tire misses the nut, Crows were seen re-positioning the nut during the lull between cars.  Pretty smart!

One of the most recognized studies involved Betty, a Caledonian Crow (Corvus moneduloides).  When faced with a vertical tube containing a morsel of food and a piece of wire, Betty was able to bend the straight wire into a hook and fish out the food with the bent end of wire.  Betty was able to do this with no previous presentation of this type of problem to solve.  This was one of the first experiments to demonstrate a bird’s ability to improvise tool making.

Whether scavenging our trash, using our cars as nutcrackers or just plain stealing our chips right out of the beach bag, Corvids have found a place in San Francisco.  Now if only I had a second bag of chips for myself…

Codie Otte
Curatorial Assistant and Specimen Preparator
Ornithology & Mammalogy Department

What has five eyes, a pair of wings, spiked legs with sharp grasping claws, and a scabbard with a stabbing beak inside? It’s a magnificent predator known as the robber fly! Robber flies (family Asilidae) are a large group of flies found all over the world in and near forests. They are among the most effective and terrifying predators on the planet.

When most people think of scary predators they think of things such as sharks, lions, tigers and wolves, but the robber fly is right up there with them. Like all flies, it has two wings (Diptera, the name for the group containing flies and mosquitoes means 2 wings). The powerful muscles in the enlarged thorax allow the robber fly to be a very strong and rapid flyer.  To see where it is going and what it is hunting for, the robber fly uses its 2 large compound eyes, which enable it to see ahead, to the sides and behind all at the same time. A second set of 3 simple eyes on a bump on its ‘forehead’ sees only light, shadow and movement. but helps the fly not to be easily caught or attacked.  Six long, spiny legs ending with grasping claws allow the fly to capture and hold prey, often when both fly and prey are in flight.

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

How many of you have walked by the Project Lab and noticed some pretty strange things, and maybe even gross things, happening inside? There’s a good chance that you’ve seen a staff member or volunteer from the Ornithology and Mammalogy department preparing dead birds and mammals for our research collection. The majority of what we do in here is preparing study skins, our main method of preserving specimens.

Study skins are just what their name implies – skins that are studied by researchers. In order to keep just the skin of a bird or mammal, we have to remove any soft parts from the inside that could rot over time. I start by making an incision down the front of the specimen, and slowly separate the muscle from the skin. I’ll continue this process until the whole body is separate from the skin of the animal, severing at the limbs and tail as I go along. This is generally the part that gets the best round of Eeewwwwws  from the visitors watching outside the lab. You can see in the picture above that I already have all of the muscle and the body removed from this hawk, circled in blue. It looks just the same as when you get a chicken or turkey at the grocery store!

I now have just the skin of the bird with its feathers attached. In birds we leave a few bones in the wings, legs, feet, and the skull to give the skin some structure. In mammals, there are typically only a few toe bones left inside. Now I can stuff the skin with some cotton and a wooden dowel, shown in this picture of a Varied Thrush. The cotton serves as a body to replace the one I removed, while the dowel helps give additional structure. Once the specimen is stuffed, I’ll sew up the incision.

Each animal is then pinned onto a board. We pin them in a specific position so that, when the specimen is dry, it will forever be in this shape. This part is a bit different from traditional taxidermy, where animals are positioned into life-like poses. Researchers don’t need specimens to look life-like in order to take any measurements or samples that they might need, plus it would take up too much space! That’s what study skins are designed to do: create a compact library for researchers to reference.

The next time you walk by the Project Lab and see one of us preparing a study skin, stop and watch! It may seem a little gross, but it’s a cool process that’s been around for over 100 years and is essential for us to continue building our library of life here at the Academy.

Laura Wilson

Curatorial Assistant & Specimen Preparator

Department of Ornithology and Mammalogy

Note: Refer to previous blog posted 2/22/12 for additional information

As a part of my masters research, I am studying the nudibranch Doto coronata, which is found in the Northeast Atlantic from Iceland to Scandinavia, and to Iberia and the Mediterranean. Doto coronata is the type species for the genus Doto, meaning that it is the representative species for the genus. I am particularly interested in examining D. coronata because it is also a “species complex,” a group of closely related species that are difficult to delineate due to recent reproductive isolation. Since D. coronata is a type species, it is important to know which specimen/species within the complex actually represents the genus as a whole.

The Doto within this species complex are a challenge to tell apart since their morphologies are so similar. It is thought that there are many species within D. coronata since several specimens have been found feeding on distinctive hydroids. It is still uncertain whether hydroid prey can be utilized as a taxonomic character for the Doto. If the hydroid prey is found to be a reliable character for the species complex of D. coronata, it may be possible to use it to identify other cryptic Doto species.

So, how many species are thought to be within the species complex of D. coronata?  In 1976, Lemche identified four cryptic species within D. coronata. He acknowledged that the four he described had the potential to be divided into even more species. (Morrow et al, 1992). Later on, two distinct morphs within this complex were described by Morrow et al.  One of these morphs was collected from the hydroid Hydrallmania falcata and the other from Sarsia eximia (Morrow et al, 1992).

Since a great deal of confusion still exists with regards to which specimen represents D. coronata, a neotype has never been assigned. A neotype is a type specimen that has been designated following the original holotype.  It is created in the event that the holotype is either lost or when the original description does not cite the specimen.

Several specimens suspected to be D. coronata have been examined in the Project Lab to provide greater clarity on this species complex. These include specimens collected from three distinct hydroids from Wales, UK, one from Maine and another from South Africa. Comparisons of the Automontage photographs of these specimens and their DNA will help sort out if there are additional species within this complex. The photographs of these specimens indicate there is distinguishable variation in the shape of the cerata and tubercles. These photographs and their gene sequences will assist in determining if these small morphological differences observed are due to intraspecific or interspecific variation.

Carissa Shipman

Invertebrate Zoology & Geology graduate student

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

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

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.

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