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Project Lab 

August 9, 2013

Summer Systematics Institute

Systematics: The study of the evolutionary history and diversity of living things and the relationships among these through time.

This week I decided to write about a great program that we have available to undergraduates within our Institute for Biodiversity Science and Sustainability, called the Summer Systematics Institute (SSI).   This program is partially funded by the National Science Foundation’s Research Experience for Undergraduates (REU)  program and the Academy’s Robert T. Wallace endowment.   It is an 8-week paid internship working with an advisor, usually an Academy curator or post-doc.  This summer, the program is in its 18th year and there are 12 participants from all over the country, including a biological illustrator.   During the 8 weeks, the interns learn new techniques and conduct original research, all while attending a series of lectures on themes related to the field such as phylogenetics, collections management, bioinformatics, morphometrics, nomenclature, and biogeography.

SSI taxa compilation

For the past three summers, I have had the wonderful opportunity of helping students in the molecular lab as the Teaching Assistant in the Center for Comparative Genomics.  In this role, I train students how to extract DNA from their specimens and how to use molecular techniques in order to sequence the DNA from those specimens.   The students then use these data to help answer research questions about the evolutionary histories of species or populations.  Not all interns use DNA data as a part of their projects, but since molecular data is commonly used in our field of biology, this is a great opportunity to either learn new techniques or refine techniques that students may have had some exposure to previously.  This year I was able to train some of the interns in the Project Lab, so if you visited in the last few weeks, you may have seen some of them working on their projects!

Yesterday, after a busy 8 weeks, the program culminated in a day where the students gave scientific presentations on their projects.    This year’s projects were quite impressive, and the students worked very hard.  Below are photos of some of the presentations.






To me, the most exciting thing about this program is that the interns get authentic research experience.  I know this to be true because in 2006, I was an SSI intern!  This program really fostered my understanding of and passion for the field of systematics.  If I had not done this program back when I was an undergraduate, I probably wouldn’t be earning a master’s in this field today.  For more information on the SSI program, click here.


Til next time!

Vanessa Knutson

Graduate Student, IZG Dept

Project Lab Coordinator

Filed under: Uncategorized — project_lab @ 12:07 pm

August 1, 2013

Of Sea Monkeys and Fairies

Many folks that I have spoken to in the last week remember the enticing advertisements that used to commonly appear in comic books and kid’s publications, promising amazing experiences with the new pet craze, the Sea Monkey aquarium.  Containing a small plastic aquarium, a packet of dried eggs, some food and minerals, and a magnifying glass, “just add water” and soon you would have a flotilla of tiny, shrimp-like creatures rapidly swimming around on their backs, darting hither and yon around your new instant aquarium.  It sounded great to me as a 10 year old, but I never knew anyone who actually had them.




These tiny creatures bear no resemblance to monkeys, but are in fact small crustaceans commonly referred to as brine shrimp when they are found in salt water or hyper-saline pools, or fairy shrimp when they are found in fresh water.

These are not shrimp at all, but belong to the crustacean class Branchiopoda, in the order Anostraca.  Usually between 6 to 25 mm long, they have paired eyes and from 14 to 16 pairs of legs used both for locomotion and to stir up water currents around their gills to aid breathing.


CASIZ174264_Lat.tif(high contrast).2

Here in California, fairy shrimp are found in vernal pools, also known as ephemeral ponds. These habitats form for only a few months from about December to May, as low lying areas of wetlands fill with water, which then evaporates leaving the pools dry by summer’s end.  Throughout the U.S., wetlands are an endangered habitat closely regulated by the federal government.  Here in California, many vernal pools are found in the Central Valley, often in agricultural areas and places ripe for development.  The delineation of wetlands on private property often causes controversy and clashes between owners, conservationists and the government.




There are several species found throughout California, but this blog focuses on the California Vernal Pool Fairy Shrimp, Branchinecta lynchi, which is federally listed as a threatened species.  These suspension and filter feeders eat unicellular algae, bacteria, and ciliate protists, and also scrape diatoms, algae and protists off of rocks and twigs.  They are an important food source for migrating birds and other organisms using and visiting the pools.  They exhibit sexual dimorphism (physical differences between the male and female), the smaller female recognizable by the attached egg sac, while the male is bigger and more robust, with a pair of large claspers, which are greatly enlarged second antennae, used in mating.  Females of this species lay two different types of eggs.  Summer eggs are soft, and will hatch within the season. Winter eggs have a tough skin, which allows them to form a cyst as they dry. These encysted eggs can survive in soils and sediments for an amazingly long time, up to 10 years!  Winter eggs can be blown long distances, or carried by birds.  This transport from pool to pool increases genetic diversity, aiding species survival.  Pools with lower genetic diversity are more susceptible.  The prevalence of pesticide usage, filling and paving over of wetland areas, and other human activities are the major threats to populations in California, and elsewhere.


The photographs were taken by me with the Big Kahuna digital imaging system, and are voucher specimens from a government survey in the collection of our Invertebrate Zoology department.


Until next time,


Vic Smith

Digital imaging specialist/Invertebrate biologist

Filed under: Uncategorized — project_lab @ 10:28 am

July 27, 2013

Western Screech Owl

A few weeks ago, Laura wrote about the importance of multiple research specimens in a museum collection.  This past weekend I prepared a juvenile Western Screech Owl (Megascops kennicottii) that is a good follow up to the previous blog post for two different reasons – the color morphs or variations and juvenile versus adult plumage.


In the case of the Collared Towhees mentioned in Laura’s blog post, plumage differences sometimes are as subtle as the width of color on the neck.  With other birds such as this Western Screech owl, sometimes the color difference can be a bit more extreme. Western Screech owls have a few different plumage variations that range from grayish to brownish depending on the location.


If our collection were to only have a few specimens of Western Screech owl, the full range of these color morphs may not be represented.  It’s not always clear why some species show a variety of color throughout their range.  Perhaps it is due to environmental factors that allows birds to either stand out or blend in better.  Perhaps it’s a random genetic mutation that has just persisted over time and has no purpose.  We can’t always know the answer to these types of questions until more time has passed and our research collection can provide historical context.


We can also use this specimen to highlight the life stages of the Western Screech owl.  Juvenile plumage is often more subtle than their final adult colors.


This provides the young birds camouflage at a time when they are more susceptible to predation.  The more this juvenile Western Screech owl looks like tree bark, the less likely it will be spotted by a hungry hawk.


Whether we know for sure the reasons why bird plumage can change over time or over geographic space, the research collection can provide a baseline that tells a story of how these birds have lived over long periods of time.  The more data provided, the more accurate the research will be and there’s never any shortage of questions and answers these study skins can provide.


Codie Otte

Curatorial Assistant and Specimen Preparator

Ornithology & Mammalogy Department

Filed under: Uncategorized — project_lab @ 10:06 am

July 18, 2013

Nudi Sex-Ed!

Today, I will discuss nudibranch sex! Nudibranchs are extremely colorful sea slugs whose ancestors lost their shells millions of years ago. “Nudi” in the name nudibranch refers to the loss of a shell. So they are more exposed and naked, than a sea snail, which has a shell. Unlike humans, which are either male or female, nudibranchs and other sea slugs are both! That is, they are hermaphrodites, possessing both male and female reproductive parts. You might ask, why on earth would you need to be both male and female? Well, sea slugs are typically slow moving and very small, so being both male and female increases the chances of finding a mate in the vast expanses of the ocean. When nudibranchs mate they fertilize each other and then both can lay eggs! To do this, they line up their genital pores, the openings on the right sides of their body, and then copulate.


Photo 1


Recently, it was discovered that the nudibranch, Goniobranchus reticulatus, detaches its penis after mating and regrows another in 24 hours! Scientists think this mating strategy has evolved so the sperm of rival nudibranchs stored in the vagina of their mate will not accidentally get passed on to future mates. Sea slug sex is very bizarre!


Photo 2


The male and female reproductive organs are adjacent to one another inside the slug’s body. The anatomy of the reproductive system varies between species. The female portion of the reproductive system in the slugs I study includes a vagina, receptaculum seminis, and glands that produce different components of the eggs. The receptaculum seminis, is a sac that stores sperm for prolonged periods of time. The male portion of the reproductive system includes the prostate, vas deferens, and ejaculatory duct. As you can see, some of the names for the parts of sea slug reproductive systems are the same as those for humans!


Photo 3



Photo 4


This concludes nudibranch sex-ed! Thanks for checking in!


Carissa Shipman

Graduate Assistant in Public Programs

Department of Invertebrate Zoology and Geology

Filed under: Uncategorized — project_lab @ 10:36 am

July 10, 2013

Why have collections?

One of the most common questions I get here is why we have so many individual specimens of the same species. It’s a valid question, considering that “collecting,” as far as personal collections go, involves obtaining individuals of a set. What we do here, however, is not like collecting baseball cards; we are essentially a library for researchers to reference when studying a particular organism. In order to have an effective sample size for a study, researchers must look at more than one individual of a species.

The way that we explain this to younger visitors when they come in to tour our collections is: if an alien came into your classroom and wanted to study humans but could only pick two of you as a representation of the entire human species, which ones should the alien take? The students quickly realize that, while they’re all the same species (Homo sapiens), no one person is the “ordinary” example of a human. It’s the same for all species.

If you were studying a bird species, such as a Towhee, would you prefer to look in a drawer like this:

photo1 copy


Or like this?


photo2 copy_sm


photo3 copy_sm copy

We clearly have a much larger collection of Collared Towhees than White-throated Towhees. Even though all of these Collared Towhees are the same species, it’s easy to see the variation between each individual. This is why we keep every specimen that is brought to us (given that we know where and what date it was found). Even if not in good enough condition to make a study skin, we can keep the skeleton, a wing, or even the entire specimen stored in ethanol. In fact, we prefer to not make study skins out of every single specimen, or else we wouldn’t have a broad variety of preparations. If a researcher was studying muscle attachments in birds, he/she would want to look at our collection of whole specimens in alcohol. Similarly, if a researcher was interested in studying the leg bones of weasels, he/she would use our skeletal collection instead of study skins.

This is what our collection is all about – having as many reference materials for researchers as possible. Consider how much of research these days relies on DNA and molecular analysis, yet museum curators had no idea about DNA back in the 1800s. Imagine what researchers may be able to do with our research collection 100 years from now that we don’t have a clue about today. It’s exciting to think about how these specimens will be used in the future!

The next time you visit a museum, think about all of the specimens that are kept in collections off of the main floor. While the main floor has a lot of educational material, scientific collections are necessary to further understand life around us.

Laura Wilkinson

Curatorial Assistant and Specimen Preparator

Ornithology & Mammalogy

Filed under: Uncategorized — project_lab @ 10:06 am

July 5, 2013

What do malacologists do on their days off?

Malacology- the study of mollusks (clams, squid, snails, etc.)

WSM opisthobranch symposiumwcap

An important part of being a scientist, is sharing your research with colleagues.  Last week, a few of us from our nudibranch lab took a break from lab and computer work to attend the Annual Meeting of the Western Society of Malacologists in San Diego.  The meeting consisted of three days of oral presentations and a poster session all based on mollusk-related research.  Some talks were about the history of the use of shelled mollusks for food, tools, and adornment. Other talks were about the change in the composition of mollusk species in certain areas over time, which can be heavily influenced by human settlement.  The whole second day of talks was devoted to sea slugs.  Both my labmate Carissa and I presented talks on our graduate research on nudibranchs and our advisor, Terry, presented on some new species of sea slugs (genus Philine).


A couple of the days (only one for me!), a bunch of us slugsters got up extra early (5AM!) to head out to the tidepools to see what kind of nudibranchs we could find.  We found several species of nudibranchs, including a few that I’ve never seen up here in the Bay Area.  Here are some of the species we encountered:

 Austraeolis stearnsi_1

Cadlina flavomaculata1

Limacia cockerelli_1

Doriopsilla gemela_1

F.porterae singlewcap



That’s all for now.  Till next time!


Vanessa Knutson

Graduate Student, IZG Dept

Project Lab Coordinator

Filed under: Uncategorized — project_lab @ 10:08 am

June 27, 2013

A Tale of Two “Flies

“True” flies belong to the order Diptera, which means two wings, which all true flies possess. The second pair of wings which most other insects have has been reduced to a pair of knob-like structures called halteres, which vibrate rapidly in flight and act like gyroscopic stabilizers. True flies include such creatures as gnats, midges, mosquitoes, crane flies, house flies, horse flies, robber flies, etc. There are, however, quite a few insects referred to as flies, though they do not belong to the Diptera. These include such animals as butterflies, dragonflies, fireflies, and one of the groups I am going to talk about today, the lanternflies.


Lanternflies are part of a group of insects in the suborder Homoptera generally called plant hoppers. These insects use piercing beaks which they stick into stems and twigs to feed on plant juices. The lanternflies often have beautifully colored and patterned wings, and the front of their heads is often expanded into a large bulb or snout. Because of their brilliant colors, it used to be thought that they glowed in the dark, hence their common name. They don’t glow, but they can be extraordinarily beautiful. Lanternflies are active at night, feeding. But why have bright colors if you only are active at night when you can’t be seen? During the daytime, lanternflies rest on the trunks of trees, with their colorful wings folded out of sight. Their bodies blend in well with the colors and patterns of the trunks, but when a predator gets too close, they will suddenly open their wings, and the flash of color acts to startle potential predators.


Now, back to the true flies, which for the most part contain some of the most commonly encountered and familiar insects, like house flies and mosquitoes. There are many thousand species of flies, many of them quite common and easily recognized for what they are, although several groups like the flower flies (Syrphidae) have a tendency to look like bees.  There are, however, some flies that are very odd, and some that are quite rare. The featured fly this week is both extremely odd, and extremely rare.

 Hirsuta profile

Back in the 1930’s, an explorer in Kenya discovered a strange, apparently flightless fly that was covered with dense hair. At first look, they thought it might be a spider.  These creatures and their larvae where in a crack in one single boulder, inhabited by bats, who had deposited their guano. These flies have been found nowhere else in the world, and were not observed again till they where found again at the same location, more than 60 years later! The 2 wings have been reduced to hairy straps, the eyes very small, not at all resembling the normal idea of a fly. This oddity goes by the name Mormotomyia hirsuta.



That’s it for this week’s blog, I will be back in about another month with more things strange and beautiful from the project lab.


Vic Smith, Imaging Specialist.

Filed under: Uncategorized — project_lab @ 11:50 am

June 19, 2013

California Quail in San Francisco

The other week I prepared a California Quail (Callipepla californica) for the O&M research collection and it got me thinking about our beautiful California State bird. Found throughout the West Coast from Baja California to the Pacific Northwest, the California Quail was named state bird in 1931.  Round, charming and distinct these quail are delightful to watch foraging under shrubbery, plumes bobbing with every scratch.



Although common throughout their range, here in San Francisco the quail population has been on the decline for the last few decades. Once inhabiting both Golden Gate Park and the Presidio, the last known covey of quail in San Francisco now hangs on in Golden Gate Park.


Some may wonder, if these birds are so common in the rest of their range, why is local extirpation a problem?  One issue is the urban landscape- a changing landscape in the city is difficult for these birds that mostly travel by foot.  Crossing roads and traversing city streets even just within the park can be dangerous and fatal.


Another factor is increased predator populations that prey on the quail’s young and eggs.  Well-meaning park visitors regularly feed raccoons, rats and feral cats, but this extra food brings in more predators and allows the park to artificially support larger predator numbers that then turn to other local wildlife as a additional food sources.


Finally, when a specific population of any species disappears, it also takes its genetic information with it.  Loss of genetic variability overtime can cause a species to become vulnerable to changes in its environment.  If one population is susceptible to the same stressor (disease, bacteria, viruses, etc.), there is less chance that population can survive an outbreak without large losses.  Due to its small population, San Francisco’s quail residents are struggling with low genetic variability and inbreeding, which produces less fit young.  This puts them at further risk.



So how do the Academy’s research specimens fit into this story?The research collection’s specimen database is a helpful resource in tracking the historical distribution of California Quail within San Francisco.  Combining this information with current avian surveys provides useful information for restoration plans to provide habitat for quail.  Hopefully San Francisco won’t lose its last quail residents just yet!


Codie Otte

Curatorial Assistant and Specimen Preparator

Ornithology & Mammalogy Department

Filed under: Uncategorized — project_lab @ 11:34 am

June 13, 2013

What is a species?

Did you know there are 26 different species concepts (Wilkins, 2002)? This is just mindboggling! You may have thought the definition of a species was settled long ago, but the reality is, the concept of a species is still under intense debate. The most commonly accepted and taught definition of a species is “a population or group of populations whose members have the potential to interbreed in nature and produce viable, fertile offspring, but do not produce viable, fertile offspring with members of other such groups” (Campbell, 2008).



This question is extremely relevant to my graduate project, which is looking at the diversity and relationships of nudibranch sea slugs in the family Dotidae from the Indo-Pacific and North Atlantic. For my project, I am describing five new species from the Indo-Pacific and another from South Africa, originally thought to be a N. Atlantic species. How do I know these are distinct from all other sea slugs ever named and described? Well, since the specimens used in my project are no longer living, I first look at living photographs of the slugs, which will most of the time help me determine whether the species I am naming and describing is in fact completely new. In cases where it is not clear whether the individual in the living photograph is new, we compare its photo to the description of the species most similar to it. This methodology helps determine if the individual in question is a morpho-species, which is one of the 26 species concepts (Wilkins, 2002). A morpho-species is considered a species based on its distinctive physical appearance and morphological features. Below are three photographs of un-described species from the Indo-Pacific Nudibranchs and Sea Slugs. They have been designated as new since they look so different from anything that has already been described.


To be more certain that an individual is altogether new, sequencing their DNA is essential. This DNA is then compared to all the others that have been sequenced, and are accessible in a database or from your own work, to see if its DNA is different enough. For my project, I sequenced three separate genes from my slugs. The gene most commonly used to determine whether an individual is a new species is the gene cytochrome c oxidase subunit 1 (CO1). For animals, this is considered the barcoding gene. The CO1 gene is like a UPC sticker, since it is usually distinctive enough to be used to identify new species, just as a UPC sticker helps identify a particular product being purchased in the checkout line of a store.



This gene is then statistically compared between pairs of individuals to give a number known as a pair-wise distance. Below is a list of hypothetical CO1 pair-wise distances, which are in decimals, between four separate pairs of individuals considered to be different species. This decimal number is multiplied by 100 to create a percent. The higher this percent, the greater the differences in the two gene sequences being compared. The methods used here, help us determine if a species is new based on the genetic species concept (Wilkins, 2002).


Doto sp. 20 sequence Doto sp. 21 sequence 0.18
Doto sp. 20 sequence Doto sp. 22 sequence 0.15
Doto sp. 20 sequence Doto sp. 23 sequence 0.14
Doto sp. 20 sequence Doto sp. 24 sequence 0.13





So what happens if the CO1 distance is not great enough between individuals suspected of being different? In these instances, it is best to look at the distances of another gene. In the case of my project, I looked at the gene 16S. If the distances of both genes agree with one another, than you can be more certain that what you are looking at is completely new or not new. When comparing the distances between two genes, the relative rates of evolution in those genes, must also be taken into account. Since CO1 is a much more quickly evolving gene than 16S, its distances are much greater. By using both living photographs and genes we can usually determine if an individual is a new species.


There are instances, where the genetic data cannot tell us either way whether an individual is clearly distinct or not. This is the case for several individuals sequenced in my project.  The most logical explanation for these individuals is they are in the process of turning into distinct species. As species evolve into new species, their genes reflect a continuum from separate populations to new species. For instance in my project, a COI pair-wise distance between two individuals of 0.0015 (.15% difference) is considered the same species, while a distance of 0.10 (10% difference) is great enough to consider the two individuals as separate species. If the distance falls somewhere between these two values, such as 0.03 (3%), it can be said, that perhaps these two individuals are in the process of undergoing speciation. I am certain, that some of the species in my project are in the middle of speciation since many of their distances reflect intermediate values. I am witnessing evolution!

Doto sp. 13 ?, 12mm, 20m


As you can see, trying to determine whether a sea slug is new to science is a complex process, requiring multiple methodologies. The methods used here help us determine a new species based on the genetic and morpho- species definition of a species (Wilkins, 2002).




Wilkins, J (2002), Summary of 26 Species Concepts, http://researchdata.museum.vic.gov.au/forum/wilkins_species_table.pdf


Campbell, Neil, et al. Biology. San Francisco: Pearson Benjamin Cummings, 2008. Print.


Carissa Shipman

Graduate Assistant in Public Programs

Department of Invertebrate Zoology and Geology

Filed under: Uncategorized — project_lab @ 10:04 am

June 5, 2013

Fossorial Species: Not Just Pests!

I recently prepared two specimens that are both examples of fossorial species. Although this word is similar to “fossil” (both words are derived from the latin word fossa, which means “ditch”), fossorial animals are not remains that have been preserved in rock, but are actually animals who are adapted for digging and living underground. Many people consider these particular species pests, but they’re very interesting animals: the Broad-footed Mole (Scapanus latimanus) and the Botta’s Pocket Gopher (Thomomys bottae).

photo1 copy


Both species have typical fossorial features: reduced eyes and ears (less areas for dirt to get in) along with large claws for digging.

photo2 copy

The Broad-footed Mole is in the family Talpidae, an insectivorous family that is closely related to shrews (Soricidae). Moles are completely subterranean, meaning they live entirely underground. Their front feet are made for digging and are permanently turned outward to help push dirt away from them. Because of their subterranean life, their eyes are very small and they do not have external ears, meaning that they rely on their sense of touch from their face, legs, and tail. They eat worms and insects that they find in the dirt. It’s difficult to find a photo of a live mole, since they spend the majority of their time underground. This photo is of a live European Mole, which has the same features as our Broad-footed Mole.

photo3 copy

The Botta’s Pocket Gopher is typically the bane of gardeners. An herbivorous rodent, the gopher eats plants by pulling them into burrows by their roots. This obviously is not helpful when trying to keep your garden thriving, but burrowing animals actually help aerate the soil. Gophers have eyes that are a bit larger than moles’ and they have small external ears (the ears of this particular specimen were 9mm), but they still have large claws that aid in digging.

photo4 copy

From a previous post that I wrote about mammal skulls, you can see that the skulls of these two animals are completely different: moles have flatter, elongated skulls with rows of sharp teeth (for eating worms and insects), while gophers have typical rodent skulls with two enlarged incisors (for cutting through plants, with molars for breaking down the plant material.)

photo5 copy

While these fossorial mammals may seem like pests in your garden, remember that they each have specific purposes and fill important environmental roles. If you feel that you have to remove the ones in your garden, please do not use poisons. These toxic chemicals can make their way up the food chain and kill larger predators such as snakes, hawks, owls, and even house cats. You wouldn’t want someone poisoning your food, so don’t do the same thing to the wildlife!

Next time you see evidence of a fossorial animal, think about all of the unique adaptations they have to live underground, and try to appreciate them for what they are: cool animals!.

Laura Wilkinson

Curatorial Assistant and Specimen Preparator

Ornithology & Mammlogy

Filed under: Uncategorized — project_lab @ 10:41 am
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