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Project Lab 

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.

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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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