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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.

gymnodoris-ceylonica-comparison

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.

terry-photographing

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:

unidentified-rat

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.

neotoma_tray

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.

rattus-specimens

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

February 28, 2013

Collecting Slugs

Last time I gave you a taste of what it is like to participate in a major expedition. This time I’m going to explain how we actually find and collect nudibranchs and other sea slugs.

First of all, sea slugs can be found just about anywhere in the world’s oceans from the shallow intertidal down to the deep sea, and from the cold polar regions to the warm tropics. Depending on what type of habitat we are trying to sample, we may use different techniques.

No matter what technique we use, one thing that is particularly important to our lab is to make sure that we leave a minimal impact on the habitats that we sample. This means that if we turn over a rock or a dead coral boulder, we make sure to turn it back to the way that it was. We do this because there are many kinds of animals that live on the bottom of or underneath rocks and rubble (like certain kinds of sponges). If you turn over a rock and don’t put it back the way it was, those animals lose their habitat and may not survive. Because of this, we do our best to leave habitats in the same condition as we found them.


under_rock

Intertidal

For species that are found in the intertidal, we go out during a low tide and wade around and look for slugs. The lower the tide, the better. When I was at Kings Beach in Queensland, Australia, I surveyed the intertidal by wading and turning rocks. I found this technique very effective for this habitat and most of the slugs that I found at this site were hiding under rocks.

Terry SCUBA diving

Subtidal

While we occasionally sample in the intertidal, most of our sampling happens subtidally (below the low tide mark). The main technique we use to survey for nudibranchs subtidally is SCUBA diving. In Madang, Papua New Guinea we would do about 2 to 3 dives nearly every day. While diving, we turn over rocks or dead coral boulders. It’s really amazing what you can find living under these! Most of the slugs that live on a coral reef are found hiding under coral rubble. For this reason, I get really excited when I find a dive site with a lot of coral rubble!  I will also mention that some slugs are only found at night, so to find these, we SCUBA dive at night. Many of the slugs I study are found at night over a sandy bottom. To find these, you want to survey as much of the bottom as possible during the night dive.

coral_rubble

Another technique we may use as an alternative to SCUBA is snorkeling or free-diving. At one of my sites in Australia, I looked for nudibranchs while snorkeling. This is a little bit more difficult than SCUBA for me because I’m not able to hold my breath for that long. This made it challenging to turn larger rocks and requires a lot more energy to be constantly free-diving down to the bottom. However, in some ways snorkeling is more convenient and less expensive than SCUBA diving.

Collection

Once we find a slug, we need to get it into a container. This can be a bit tricky because the slugs are very soft, often slippery and usually squishy. It becomes even more challenging if you are working with a very small slug (the size of a grain of rice, or a sesame seed!) and if you have currents in the water. There is nothing worse than a tiny slug floating off in the currents! Typically, I will pick up the slug with my fingers and do my best to place it in a plastic jar underwater. Other people often use plastic bags, but I find the hard containers easier to manage. After the slug is in the jar, I place it in my mesh collecting bag, and go off to find the next slug!

collecting

Finding slugs can be quite challenging, but extremely satisfying! Check back in a few weeks to hear about the preservation process!

Vanessa Knutson

Project Lab Coordinator and Graduate Student

Department of Invertebrate Zoology and Geology


Filed under: Uncategorized — project_lab @ 1:33 pm

February 21, 2013

Vic’s Nudibranch Addiction

Most people who see me in the Project Lab know me as the bug and spider guy, taking pictures of and talking about the arthropods with whom we share the planet. But I have a secret past in which I studied the butterflies of the sea, those fascinating sea slugs known as nudibranchs!

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For those of you who follow the project lab blogs, you are aware that 2 different graduate students working in the Project Lab are doing projects on nudibranchs for their degrees. Each of them is studying a different group of these fascinating and beautiful animals, defining their evolutionary relationships, and probably finding new species along the way.

I became involved with nudibranchs in the mid-90’s here at the Academy’s Summer Systematics Institute (SSI), where I worked with Terry Gosliner. I was hooked, and soon returned as a graduate student at San Francisco State University, with Terry and Gary Williams (our coral expert) as my in-house research advisors. I spent much of my time studying the family Tritoniidae, who feed on soft corals, so Gary was able to provide valuable expertise on their prey species. At the time, the majority of our museum holdings of this family had been collected and preserved in a way that made DNA analysis impossible, so without much fresh material, I was confined to a morphological approach.

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Perhaps the coolest part of the work was the job of identifying and describing new species. Dr. Robert Bolland, now retired, is a nudibranch expert, collector and diver who spent much of his time underwater collecting in the Ryukyu Island chain of Japan, providing many specimens to our collection. He collected a beautiful little nudibranch, along with the soft coral he found it on, which the nudibranch appeared to be eating.

The new species was named in honor of the collector. Dissections of the preserved animals provided stomach contents containing tiny skeletal elements from the coral, which we compared to the coral found with the animals, providing evidence that this coral species appeared to be the sole food source for this nudibranch.

Until next time,

Vic Smith

Imaging Specialist /Curatorial Assistant

Entomology Department


Filed under: Uncategorized — project_lab @ 12:13 pm

February 15, 2013

Specimen of the Day: Common Poorwill

Specimen of the Day: Phalaenoptilus nuttallii

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Phalaenoptilus nuttallii is quite a big name for such a small bird! The common name for this bird is the Common Poorwill, although you may have never even seen or heard of this bird before because of its amazing camouflage and nocturnal lifestyle.

The Common Poorwill belongs to a group of birds known as the Nightjars. They are nocturnal birds that can be found on the ground or in low tree branches watching for insects. The calls of the Poorwill are what actually give these birds their name. “Poor-will, poor-will, poor-will” they call at night, often being mistaken for insects or some other animal. The plumage of the Common Poorwill renders them virtually invisible, especially at night, which is why most people may not even know the sound they are hearing is actually a bird!

common-poorwill-specimen1

A special thing about the Common Poorwill is that this bird can enter into a state called “torpor” during the winter. Like mammals, these birds can lower their body temperature to a state resembling hibernation until food becomes more abundant. Unlike hibernation, which can last many, many months, torpor can refer to shorter periods of decreased metabolic activity and heart rate. For example, hummingbirds may bring their body into a state of torpor during the evening when temperatures are lower until the following morning when the temperature rises.

While the Common Poorwill may be new to you, they certainly are an interesting and beautiful bird. If you hear one on a summer night look down on the ground, it may be hiding at your feet!

Codie Otte
Curatorial Assistant and Specimen Preparator
Ornithology & Mammalogy Department


Filed under: Uncategorized — project_lab @ 12:18 pm

February 6, 2013

Venture to the Philippines

In less than a month, I depart for an adventure of a lifetime! I am leaving the Academy for two months to work for the international conservation organization, Project Seahorse, to survey marine protected areas (MPAs) near the Philippine island of Bohol. The long-term monitoring of these areas is important for three main reasons:

  • To inform fishing communities of the health of their reefs
  • To mobilize communities to create and manage more MPA’s
  • To provide data to assess the effectiveness of the establishment of these areas on the recovery of reefs.

Community efforts will include increasing awareness of the value of the marine diversity and educating the people about more sustainable practices for utilizing their marine resources.

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My first two weeks will entail intensive SCUBA training, followed by six weeks of surveys. Our efforts will be centered on documenting the diversity of fishes, seahorses and benthic marine invertebrates, such as coral. Project Seahorse is a world leader for marine conservation and research on seahorses. Seahorses are currently under threat due to habitat loss and their unsustainable usage in Chinese medicine.

I had my first wild seahorse encounter on my last trip to the Philippines. It was a tiny pink pygmy seahorse. Upon first glance, I did not see it, since it looked exactly like the soft coral it was attached to! What a sight to behold!

pygmy_seahorse

I have been attracted to the Philippines, since learning it was home to some of the most spectacular sea slugs. It is also the center of the center of marine diversity in the world. This fact has lead to my continued interest in the Philippines as the prime location to search for anti-cancer compounds within the array of marine slugs found here.

The cure for different types of cancer and other disease could be found in the organisms inhabiting the ocean. This is another reason why conserving our oceans is paramount! To learn more about this, see my prior post: http://www.calacademy.org/blogs/projectlab/?p=1351.

Preparation for my trip has been quite involved since I will be living in a remote village on Jandayan Island where there is no running water and limited electricity. I have roughed it before, but I am anticipating this to be much more rigorous. Despite this, experiencing and protecting the breathtaking beauty of the underwater environment is well worth it!

Carissa Shipman

Graduate Assistant in Public Programs

Department of Invertebrate Zoology


Filed under: Uncategorized — project_lab @ 12:29 pm

February 1, 2013

Taxidermy or not?

A very common question I get when interacting with guests here at the Academy is whether I am a taxidermist. I suppose that in a way, I am, but I consider myself a study skin preparator rather than a taxidermist.

So, what’s the difference? Well, see for yourself!

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Traditionally, taxidermists create “live mounts” – mounted specimens that are posed to look as though they are still alive. They’re posed in life-like ways and have realistic glass eyes. Study skins, on the other hand, aren’t posed in a way that you would find in nature – they are flat and compact, which is typical for specimens in a museum collection. While they may not seem as interesting to look at, study skins are essential to our research collection. These specimens take up much less space than live mounts and are prepared in a standardized way among museums, so it’s much easier for researchers to come through and look at a series of a species. Imagine trying to look at a feature of an animal if they’re all posed in different ways!

So, why do we have so many study skins in our collection? The average visitor might find it strange that we have thousands of bird and mammal skins, but it’s not strange at all. Here at the Academy, we’re a library that houses collections of life rather than books. These study skins are essential for bird and mammal researchers to use for their studies. They may be doing a comparative study about plumage differences in birds, or might take small samples from each skin in order to analyze DNA.

While I have yet to begin preparing live mounts, I love making study skins. The fact that they’ll be a part of the collection for hundreds of years and may help answer scientific questions in the future is very exciting to me. They may not look like they’re still alive, but these study skins have a life of their own in scientific research.

Laura Wilkinson

Curatorial Assistant and Specimen Preparator

Ornithology & Mammalogy


Filed under: Uncategorized — project_lab @ 1:30 pm

January 25, 2013

Tales from an Expedition

So I’ve been back from the field for about a month now, but there is still so much to tell about my experience as a part of the ‘Our Planet Reviewed’ Initiative, Papua New Guinea 2012-2103 Expedition.

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The goal of the expedition was to document as many species as possible from the Madang Lagoon, to get a sense of the level of biodiversity of this part of the Coral Triangle.  Through this kind of fieldwork, not only do we discover new species, but we also collect baseline data to see how diversity can change in a region over time.   I was part of a team that was looking specifically for nudibranchs and other sea slugs.  For four out of six weeks, our opisthobranch (sea slug) team consisted of two graduate students: myself and Jessica Goodheart from Cal Poly Pomona. My advisor Terry Gosliner joined for the last two weeks of the expedition. Though it was only a few of us as the main sea slug collectors, other divers also brought us specimens and were huge help.

Opisthobranch team

Of the three legs of the expedition (terrestrial, shallow water, and deep water), the shallow water marine part (the part we participated in) had about 120 different participants from at least 18 different countries!  About 90 of these were scientists and the rest included photographers, people involved with SCUBA logistics, a scientific illustrator and even a sociologist. The whole expedition involved a HUGE amount of coordination!

As you can imagine, an expedition of this size needs a laboratory so that all of the scientists can observe and process their specimens. This temporary lab space must be able to accommodate many scientists coming and going over 6 weeks. We would spend anywhere from about 6 to 10 hours daily in the lab (others spent longer hours in the lab, but we spent several hours diving everyday in addition to lab time). Here is what our temporary lab space looked like:

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There were lots of stations with the essentials: power outlets and desk lamps, and for many stations, microscopes. Our setup for sea slug collecting was pretty basic. Here is a peak at what our workstation looked like with some notes on the tools of the trade:

nudistationweb

So what was it like to be in this temporary lab space?  HOT!!! The weather in Madang was roughly in the high 80s with high humidity.  It was also apparent that the heat would prefer to hang out in the lab with all the scientists rather than disperse elsewhere.  Imagine trying to take a photo of a slug that is the size of a grain of rice while you have sweat dripping down your face!  Good thing we had a fan, even if it did break during the last week.

That’s all for now.  Stay tuned for more about how we actually collect these slugs and preserve them…

Vanessa Knutson

Graduate Student, Department of Invertebrate Zoology and Geology

Project Lab Coordinator


Filed under: Uncategorized — project_lab @ 12:48 pm
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