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Project Lab 

March 27, 2013

Preserving Slugs

Last time I wrote about how we collect nudibranchs in the field. This time I want to tell you a little bit about the preservation process.

First, I’d like to explain briefly why we make collections at all. Here at the Academy, and other natural history museums around the world, we have a library of life— preserved specimens collected from different locations and different times. We have everything from plants to insects to fish to my favorite- nudibranchs. These collections allow biologists to study the biodiversity of our planet and to study how populations and species of living things change over time. This is an aspect of the Academy that you may not see directly when you visit, but behind the museum walls, there are about 28 million specimens and several biologists that study them.

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Different groups of organisms have different methods of preservation. If you were to visit the collections, you would find pinned insects, dry shells, bird and mammal skins and many specimens in jars. The method of preservation depends on the nature of the animal (Does it have a soft body? A hard exoskeleton? Does it have parts that will dissolve in a certain kind of preservative?), the history/tradition of research on that organism and the preferences or convenience of the people doing the collecting. The nudibranchs on our shelves are mostly initially preserved (fixed) in ethanol (ethyl alcohol, the same stuff as in drinking alcohol), formalin (a solution of formaldehyde, which is a gas), or Bouin’s solution (a solution of picric acid, acetic acid and formaldehyde). Each preservation method has pros and cons, depending on what you need from the specimen.

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Many of our older nudibranch specimens were initially preserved in formalin or Bouin’s solution. These preservation methods are great for preserving soft tissues, which make dissection a lot easier. This is useful when we are interested in looking at the internal differences or similarities between species. However, these solutions can degrade DNA. Because I use DNA as a tool for my research, I need specimens that have been preserved in ethanol. Unfortunately, because many of the older specimens were preserved in formalin or Bouin’s solution, I cannot use them in my DNA study. However, these specimens are far superior for dissection, so either preservation method involves some compromise.

So how do we preserve them?

As just about anyone who has ever seen a nudibranch will tell you, nudibranchs are BEAUTIFUL creatures. Some refer to them as the butterflies of the sea because they are so charismatic and colorful. Unfortunately, no matter what solution we preserve them in, they lose their color (we sure wish this wasn’t the case, as they’d be a lot more exciting to show the public if they still had color!). This means that it is essential to document what these animals look like while they are still alive. This is why photography is so important for what we do. Without a photo, we have no way to know what the animal looked like when it was alive.

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After we photograph the animals, we put them to sleep (anaesthetize them) using a solution of magnesium chloride and seawater. How long it takes for them to drift off into dreamland depends on the size of the animal- the larger the animal, the longer it takes. I’ve spent several nights up until ungodly hours waiting for these slugs to become anaesthetized. Once the nudibranchs stop moving, we place them in the preservative (ethanol, formalin, or Bouin solution).

If the animal is preserved in alcohol, it should be good to go for DNA extraction. Unfortunately, these alcohol-preserved specimens become very brittle, which makes dissection very challenging. The bodies also tend to become a lot more distorted when preserved in ethanol. One alternative is to take a small piece of the animal to store in ethanol, while the rest gets preserved in formalin or Bouin’s solution. However, a problem with this method is that if you run out of the DNA extraction, you can’t extract any more DNA!

Ultimately, each method of preservation comes with some sort of compromise, but the ultimate goal is to preserve these specimens to better understand life on our planet.

That is all for this week. Till next time!

Vanessa Knutson

Project Lab Coordinator and Graduate Student

Department of Invertebrate Zoology and Geology


Filed under: Uncategorized — project_lab @ 9:41 am

March 21, 2013

Type Specimen Photography in the Project Lab

One of the important jobs taking place in the Project Lab is the imaging of specimens from the Academy’s type collection. Over the past several years I have been actively working to photograph some of the Academy’s type specimens of insects and arachnids, and other workers have been documenting type specimens of reptiles, amphibians and fish. The Entomology Department alone has about 18,000 type specimens, of which only a small fraction has been imaged (good job security for me!).

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So, what is a type specimen, and why are they important?

When a researcher thinks they have found an undescribed and unnamed species, the first thing they have to do is make sure that it hasn’t already been named. This can be quite a problem in itself, as much of the scientific exploration of the world took place from the mid 1700’s to the late 1800’s, when sovereign nations sent out explorers in ships to find out what was in the world. These folks did not have iphones, the internet, or even a postal system with which to communicate, and as a consequence, many species got described and named multiple times. According to the rules established by the international committee on species naming, it is the earliest published description that has the valid name. Fortunately, today, we do have the internet and phone resources that allow us to do the detective work to determine if the species is undescribed.

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Once the researcher has determined they are working with a new species, they will go through the process of carefully describing the organism, paying special attention to the similarities and differences between the new species and all known similar species, and noting the characteristics that make it distinct from all other species. They will also place the new species within a taxonomic hierarchy, such as order, family, and genus.

This description is then submitted for review by anonymous peers, who evaluate the work and suggest strengths and possible weaknesses for revision. Once evaluation and revision are completed, the paper may be accepted for publication, and a new species has been officially named and recorded! But, there is one more step to make the process complete and official. The researcher must designate a type specimen called a holotype. This is often the specimen from which the description was actually made. The holotype serves as the placeholder for the species name, and is deposited in a museum like the California Academy of Sciences. Because there is only one holotype for each species, different museums all around the world have different holotypes in their collections.

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These holotype collections are of great importance to researchers, who often compare the named types to specimens they are working on, to see if they have found new species. It is the responsibility of museums like ours to make these type specimens available to researchers, and in the past, the only way to share was by sending out the actual specimen. This always involved a certain amount of risk on the part of the lender, with the possibility that the specimen would be retained, lost, damaged or destroyed in transit. By taking a series of high quality images that show the important features of the organism, as well as recording the original labels, it is often possible to give researchers the information they need without having to send the specimen. In addition, all of these photographs will be posted on the Academy website, where they are viewable to the public (Entomology Types). At present, our collection of robber flies, (family Asilidae), and our types of scorpions are available on the web, as well as Coleoptera (beetle) types. Our entire collection of spider types is soon to be completed, and some of the other insect orders have spotty representation as images.

Now it is time for me to get back to work creating images, so until next time…

Vic Smith

Curatorial Assistant and Imaging Specialist.


Filed under: Uncategorized — project_lab @ 12:32 pm

March 14, 2013

The (Bird) Eyes Have It

This weekend I prepared a Barred Owl (Strix varia) for the Ornithology and Mammalogy collection and it got me thinking about sclerotic rings.

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Sclerotic rings are a bony structure found surrounding the eyeball of many vertebrates, such as fish and birds. Since vision is so important to birds from finding food to watching for predators, or being able to judge distance for a smooth landing, having this bony ring keeps their vision as sharp as possible. The eye rings also hold the eyeball into place, preventing movement of the eye within the socket. We humans, as mammals, do not have sclerotic rings and it’s hard to imagine what it would be like. Luckily owls are known for the head turning abilities!

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The shape and size of the eye ring can tell us more about what kind of lifestyle the bird had. For example, a flatter eye ring versus a tubular eye ring can tell us the time of day a bird may be most active. As a nocturnal animal, the Barred Owl’s sclerotic ring looks a bit different from that of most other birds. Their eyes are wide in diameter but also long and tubular to enhance the owl’s night vision. Having a larger corneal diameter allows more control over the amount of light reaching the retina. Other nocturnal owls such as the Great-Horned Owl (Bubo virginianus) have large tubular eye rings as well. Comparatively, this Western Gull (Larus occidentalis) has flatter sclerotic rings since they are active during the day.

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At the Academy, we prepare the sclerotic rings along with any bird skeleton. Gathering additional data on avian behavior and skeletal structure enhances the knowledge that we can use to conserve these amazing birds!

Codie Otte
Curatorial Assistant and Specimen Preparator
Ornithology & Mammalogy Department


Filed under: Uncategorized — project_lab @ 12:09 pm

March 6, 2013

Aw, Rats!

I recently prepared a study skin of a rat that needed its species identified. It got me thinking about how difficult mammal species can be to distinguish from each other. Like an earlier blog I wrote about the Rock Hyrax and identifying mammals by skulls, I thought I’d take another opportunity to walk through the steps we sometimes have to go through to figure out what species we’re working on, but this time by external characteristics only. Consider this a “Local Rats 101” of sorts.

To start off, I feel the need to make the disclaimer that I love rodents. I think they’re absolutely adorable, as are the majority of all small mammals (well, most mammals in general, really). With that out of the way, let’s get started.

Here’s the rat that I prepared:

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It was given to us by one of our usual donors who finds birds and mammals throughout Northern California and brings them in to us. He, however, is a bird specialist, and isn’t as confident with his mammal identification. He guessed that this rat species was the Dusky-footed Woodrat, Neotoma fuscipes. Woodrats are a native to North America, unlike the Old World rats that I’ll mention shortly. They’re very soft and fluffy and have large ears and hairy tails. True to their name, they collect wood debris and pile it into huge nests that can be 3-8 feet across and up to 6 feet high. These nests are used as shelter by other rodents, as well as reptiles and amphibians. You can sometimes find nests while hiking or mountain biking along trails with lots of oak trees.

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If you compare the rat that I prepared to a woodrat, you can already see that they look quite different. The woodrat fur is longer and softer, the ears are much bigger, and the tail is hairy (though that might be difficult to tell from the pictures). So, Neotoma fuscipes is ruled out, but it was a good guess by this collector!

We’ll move on to the two common Old World rat species: the Black Rat or Roof Rat (Rattus rattus) and the Brown Rat or Norway Rat (Rattus norvegicus). Both of these species are thought to have originated in Asia and have since spread throughout the world to become two very common species. They look very similar but have two key differences: ear size and tail length.

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Rattus rattus have larger ears and long tails that are longer than half of their total length (tip of nose to tip of tail). Rattus norvegicus have smaller ears and shorter tails that are less than half of their total length. This is one reason why it’s so important that we take measurements of all birds and mammals that we are about to prepare for the collection; having the original measurements can help distinguish different species, especially since their measurements might be slightly altered during the preparing process. Bodies can stretch out or shrink, making an animal deceptively larger or smaller than it originally was.

From this information, we can go back to the rat that I prepared. The measurements that I wrote down were: ear length 22 millimeters (mm), total length 380 mm, and tail length 175 mm. Since the tail is less than half the total animal length along with the small ears, this is Rattus norvegicus, the Brown Rat.

I always love a chance to use my powers of deduction when “mystery” specimens get donated to us. Next time you see a rat scurrying around (hopefully outside and not in your kitchen), take a moment to consider it as the cute mammal it really is – you might get a new appreciation for rodents!

Laura Wilkinson

Curatorial Assistant and Specimen Preparator

Ornithology and Mammalogy


Filed under: Uncategorized — project_lab @ 12:36 pm

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