Category Archives: Integrative Biology

Go With The Flow

If you get the chance to meet Emily Khazan, you’ll probably learn a thing or two about damselflies. You can think of them as smaller versions of dragonflies whose wings can fold back

Emily attempting to collect ants off of baited trees in Costa Rica

Emily attempting to collect ants off of baited trees in Costa Rica

when they perch. They need bodies of water to breed and live, and sometimes, water caught in the leaves of a plant is all that’s needed for survival. For her Masters degree, she worked with damselflies that lived in old growth forests in Costa Rica. She would wade through thick underbrush, collecting data, trying to understand how damselflies were affected by a highly impacted landscape throughout a biological corridor that was designed for restoration of habitat for a large-bodied, strong-flying bird.


These days, you’ll find her stooped over the bank of a river in the desert, collecting the various insect inhabitants that live there. Working in the David Lytle lab, she wants to understand how these aquatic invertebrate communities are affected by climate change by seeing how they respond to the changing river flow. Why does it matter? Because aquatic invertebrates not only serve as a food source for fish, and a good indicator for water quality, but because our world is interconnected, biodiversity matters.


One of Emily's current study sites: the lower Salt river outside of Phoenix, AZ

One of Emily’s current study sites: the lower Salt river outside of Phoenix, AZ

So, how does one go from research in the tropics to the arid lands of the American southwest? For Emily, its a story where she continuously reinvents herself as she moves across the landscape. This Sunday, you can hear her journey from her first ecology course at the University of Michigan, to persevering through an underfunded Masters degree fueled by her weird love of damselflies and their environment, to leading a research station in Costa Rica, and finally coming to OSU to study aquatic invertebrates.

Tune in Sunday, June 12, 2016 at 7PM PST on KBVR 88.7FM or stream live at

View of the Costa Rican coast line from the Caño Palma Biological Station (

Intertidal Interdependence and Environmental Change


Low tide in the rocky intertidal ecosystem, near Depoe Bay Oregon. At the edge of the water is the “low zone”, where plants and algae thrive. Photo: Allie Barner

When you say “ecosystem”, most people think of a food chain. There are links in the chain, and each species is a link that keeps the chain together. This encourages a view of the world in which we see the importance of individual species. Traditionally, this means that when we try to understand how an ecosystem might react to a sudden environmental change we look at how individual species might react.

For Allie Barner, however, an ecosystem is more like a web. Each strand in the web is supported not just by one or two others, but by every other strand. In an ecosystem, the relationships between all species present are often just as important as any individual species’ role. This view, focusing on the ways in which species rely on one another to survive in their environment, is called community ecology. To better understand what it takes to keep an ecosystem healthy, Allie believes we need to move past a “who eats who” perspective and start thinking about communities of species as a whole. Losing even one species due to environmental change might destabilize an entire ecology.


While the tide is out, Allie and company rush to install an experiment that excludes all herbivorous animals to try to understand how animals that graze on plants and algae affect entire ecosystems. Photo: J. Robinson/PISCO

Allie, a graduate student in Oregon State’s Integrative Biology program studying under Bruce Menge and Sally Hacker, explores this at the Oregon coast. Out at the beach, Allie inspects the intertidal zones,  the areas that are sometimes submerged at high tide and sometimes exposed to the open air at low tide. Here a wide array of species are dependent on one another for survival, and they form an ecological web that is very sensitive to changes in the environment.

The rocky intertidal ecosystem in Oregon is incredibly diverse: in this picture there are dozens of species, from the greenish-yellow sponge, to the lettuce-like leafy red algae, to the large drooping kelp.

The rocky intertidal ecosystem in Oregon is incredibly diverse: in this picture there are dozens of species, from the greenish-yellow sponge, to the lettuce-like leafy red algae, to the large drooping kelp. Photo: Allie Barner

Today a pressing issue, especially in marine environments, is climate change. Ocean acidification, caused by excess Carbon Dioxide in the atmosphere, is having a profound effect on many species and increasing water temperatures are quickly altering ecosystems that have existed in relative stasis for many thousands of years.

Allie’s goal is not only to understand how climate change might affect intertidal ecologies, though. Allie hopes to use her data to understand how ecosystems react to change in a more general sense. By seeing the similarities across ecosystems, even from something as small as an intertidal kelp bed and as large as a tropical forest, Allie believes we can begin to understand the deeper rules that govern the environment we live in. Only then can we begin to more deeply understand our impact on it.

To learn more about Allie’s research and her journey to graduate school, tune in this Sunday at 7PM, PST! You can stream the show live online, or listen to the interview live on the air at 88.7 KBVR FM, Corvallis!

James and the Giant Beetle Question

A very handsome beetle.

A very handsome beetle. credit: Carabidae of the World

James Pflug, fourth year PhD student, grew up in rural Missouri turning over rocks, catching and collecting insects. Messin’ with bugs is his favorite activity, and his parents encouraged him to pursue this passion as a career. Good thing too, because James is now working at Oregon State University Department of Integrative Biology with advisor David Maddison. In the Maddison Lab, James studies carabid beetles (ground beetles), specifically vivid metallic ground beetles. According to James, this beetle group is composed of the “most handsome” beetles. James is one of many scientists, phylogeneticists, around the world working to sort out the family tree of this group. This is not just a who-is-related-to-who question, but really a how is subgroup A of beetles related to subgroup B, and how do subgroups A and B related to other beetle subgroups?

James spends many days identifying boxes of ground beetles.

James spends many days identifying ground beetles.

How do you figure out how beetles are related to each other? Well, DNA of course! Just as you could have your own genome analyzed to understand your ancestry, James is collecting beetles from around the world, analyzing their genomes, and interpreting their ancestry. Scientists have already developed a variation assay to tell you what percent European, Asian, or Native American you may be, and James is working to develop the same thing for ground beetles! This will be a huge step forward for beetle phylogenetics AND think of all the beetles who will now know where their family originates! Just kidding about the latter, but you get the idea.

James started getting serious about bug study during his time as an undergraduate working in the Enns Entomology Museum at the University of Missouri. Almost as though he was in the right place at the perfect time, a position presented itself in the research lab of the museum’s curator, Robert Sites. Together with Arabidopsis researcher, Chris Pires, Sites was interested in the phylogenetics of biting water bugs, and they needed James to work in the lab. James got hands on experience extracting DNA from insects and performing next-generation genome sequencing and analysis. This experience, in time, was his ticket into the Maddison Lab at OSU where he is currently using next-generation sequencing techniques to understand the evolutionary history of ground beetles.

James performing DNA Isolation in the lab.

James performing DNA Isolation in the lab.

In addition to unpacking and reassembling the genome of ground beetles, James is committed to science communication. James knows that good science communicators are good teachers and they attract people to science and instill excitement for topics that might seem a bit dull on the surface, like beetle family trees. From personal experience, James is a captivating speaker who makes beetle phylogenetics thrilling and aesthetically pleasing. Fuzzy carabid beetles are handsome. Check out James’ blog,, to learn more about this stunning group of beetles. They are truly diverse in habitat, appearance, and diet!

Tune you radio to 88.7 FM KBVR Corvallis this Sunday, May 1 at 7 PM to hear more about James’ research and journey to graduate school. Not from ‘round here? Stream the show live!

Whosits & Whatsits Galore: What do larval fish eat, and who eats them?

20150402_HatfieldGradStudentMiram_HO-4675  Tonight on Inspiration Dissemination, Miram Gleiber (a 1st year PhD student in Integrative Biology) discusses her passion for ‘le poisson’. Working underneath Su Sponaugle and Bob Cowan, Miram first got into the piscine when she was a little girl, investigating tide pools in Victoria, British Columbia. “When you take a scoop of water from the ocean you don’t realize what’s in it,” Miram muses, “… it’s a whole other world.”

Figure 1  Figure 2

Above: Larval Fish captured in the Straits of Florida (Photos by: Cedric Guigand) on the left, and on the right, Copepods captured in the western Antarctic Peninsula: Clockwise from top left are Calanus propinquus, Paraeuchaeta antarctica, Metridia gerlachei, Calanoides acutus (Photos by: Miram Gleiber)

Because Larval fish grow up to be reef fish, which are good for biodiversity and tourism, obtaining accurate numbers of wild stock that survive the larval stage and understanding what conditions promote survival is valuable knowledge. The fish first hatch and “hang out” for thirty days in the open ocean before coming back to the reef, during which time they subsist largely on patches of zooplankton and phytoplankton that float around in the open ocean. Miram’s current research at OSU aims to understand how these patches of tiny biodiversity contribute to the growth and survival of the small fishes that eventually make their way into the view of our camera lenses and photo albums, and sometimes to our plates, as well.

To learn more about Miram and her adventures on the open sea, join us at 7pm Pacific on 88.7 FM KBVR Corvallis, or stream the talk live here!

ARSV Laurence M. Gould, a 230-foot Antarctic research vessel.

ARSV Laurence M. Gould, a 230-foot Antarctic research vessel.

From Systems Bio and Symbiosis to Nepovirus and Nematodes

There are perhaps a many as one million species of nematodes. Some parasitic varieties can grow to a meter in length, but most are microscopic in size. They inhabit almost every environment imaginable, from salt water to soil, and even human bodies. But it isn’t the symbiosis between a parasitic nematode like hookworm and a human that Danielle Tom is interested in, her research in the Department of Integrative Biology at OSU concerns a particular nematode called Xiphinema americanum.

51XyTEl0Y1L Despite the fact that nematodes cover most of the planet’s surface and there are probably billions of them thriving on the earth at any given moment, surprisingly little is still known about the worms. Xiphinema americanum, for instance, carries a bacteria specially designed to live inside it called Xiphinematobacter. Studying the evolutionary genomics of these species can help elucidate the phylogenetic, or evolutionary, history of both. This work is important to the United States Department of Agriculture, because Xiphinema americanum is a potential carrier for nepovirus, which can infect important crops like grapes, raspberries, and tobacco via these plants’ root systems, which the worm also exists in a symbiotic relationship with. This sort of an analysis, of an animal and its relationship to its environment at multiple levels of scale and with regard to multiple other species, is called systems biology.

Danielle works under Dee Denver, associate professor and director of the the Molecular Cellular Biology program (MCB), and she will be joining us on the show tonight at 7pm pacific time.

To learn more about this exciting research and her personal journey into genomics and biology, tune into 88.7 FM to listen, or stream the show live here!