Category Archives: Integrative Biology

Beetle-Seq: Inferring the Phylogeny of Clivinini

“Species Scape” by Francis Fawcett. A digital version of the original design drawn by Francis Fawcett and prepared by Quentin Wheeler.

We humans are far outnumbered by organisms that are much smaller and “less complex” than ourselves. The cartoon above depicts representatives of major groups of organisms, and each organism is drawn such that its size reflects the number of species contained within its group. The bird, the fish, and the trees look as expected, but you may notice the enormous beetle. No, beetles are not generally larger than trees or elephants, but there are more species of beetles than any other group of organisms. Beetles are a wonderful representative of the biodiversity of the earth because they can be found in almost every terrestrial and non-marine aquatic environment!

Examples of carabid beetles of the tribe Clivinini (top row; photos with ‘HG’ – Henri Goulet, otherwise – David Maddison). Male genitalia of a clivinine species, Ardistomis obliquata, with possible ‘copulatory weapons’ (right) and several examples of clivinine female genitalia (bottom row) modified from Zookeys 2012;(210):19-67 shared under CC BY 3.0.

Our guest this week, Antonio Gomez from the Department of Integrative Biology, studies a group of beetles called clivinines (pronounced kliv-i-nīnz) which has 1,200 species, and potentially more that have yet to be discovered. Antonio is also particularly interested in the morphological diversity and evolution of clivinine beetle sperm. Antonio wants to know: What is the evolutionary history of clivinine beetles? What is the pattern of morphological diversity of sperm in clivinine beetles, and how are sperm traits evolving? The objective is to collect beetles, study their form, sequence their DNA, and understand their diversification.

Several examples of sperm conjugates (cases where two or more sperm are physically joined and travel together) in carabid beetles. Conjugation is considered rare, but in carabid beetles, it’s the rule and not the exception to it. In many carabids, sperm leave the testis but do not individualize. Instead, they remain together and swim as a team.

This is no small task, but Antonio is well equipped with microscopes to dissect and describe beetle anatomy, a brain geared to pattern recognition, and some fresh tools for genome sequencing. All of this is used to build an evolutionary tree for beetles. This is kind of like a family tree, but with species instead of siblings or cousins. Antonio and other students in the lab of David Maddison are adding knowledge to the vastness of the beetle unknown, bit by bit, antenna by antenna, gene by gene.

Antonio Gomez collecting beetles near a really bright light (a mercury vapor light trap) near Patagonia, Arizona.

Like many of our graduate students at Oregon State, a group of great mentors can make all the difference. Before working with Dr. Kelly Miller at University of New Mexico, he never knew beetle phylogenetics meant exploring exotic locations around the world to collect and potentially discover new species. As an undergraduate, Antonio even named a species of water beetle, Prionohydrus marc, after the undergraduate research program that go him started as a beetle systematist, the Minority Access to Research Careers (MARC) program. Pretty amazing. That was not his first or last research project with insects before he joined ranks at Oregon State, he also was participated in a Research Experience for Undergraduate program at the California Academy of Sciences and completed a Master’s at University of Arizona. Now he has ample experience working with beetles and is maybe a little overwhelmed but still excited by the unknown beetle tree of life. Next on his list of questions: did the ancestor of all clivinines likely have sperm conjugation?

You’ll have to tune in on Sunday April, 16 at 7 pm to hear more about that evolutionary arms race!
Not in Corvallis? No sweat! Stream the show live.

Can’t get enough? Follow this link to learn about Stygoprous oregonensis, a blind subterranean diving beetle that had not been seen in 30 years. Recently, a team of researchers that included Antonio Gomez reported the discovery of more specimens, which allowed them to place Stygoporus in an evolutionary tree.

Corals need someone in their corner

Katherine holding all nine of the coral species she is studying for one chapter of her dissertation.

Climate change has begun to show its effects around the world in the form of warming temperatures, increased major weather events, and shrinking global sea ice. Unfortunately, one of the hardest hit species on earth is likely to be the corals, a marine animal, yes I said animal, whose beauty is well documented. Ocean acidification is limiting calcification, a process used for coral growth, and warming ocean temperatures is causing bleaching of once vibrant coral reefs. However, there is good news for everyone who appreciates tropical oceans, the diversity of ocean life, or just plain old natural beauty. Although it’s still uncertain how corals will be able to adapt to the rapidly changing ocean environment, coral scientist Katherine Dziedzic is optimistic about the future of coral.

Katherine is a fourth year PhD student in Integrative Biology. Her research in the Meyer lab is helping to pinpoint some bright spots in coral adaptation. With the help of many collaborators around the world, Katherine is trying to find the survivors in the coral community, identify the genes theses corals are using to adapt, and then “teach” the rest of the corals how to thrive in a warmer ocean. Katherine is using a research method first developed for human disease studies called genome wide association studies (GWAS) to determine the genetic variants that are most highly correlated with bleaching corals . Recent results have been promising and Katherine is hoping to narrow in on a potential gene, or genes, of interest. Unfortunately, progress to save the coral is slow going because much of the coral research has not been translated into action, despite the reefs’ charismatic depiction in nature documentaries.

Katherine diving in Bocas del Toro, Panama collecting samples for her acclimation experiment.

A well-functioning national research program should function as a giant cycle to support government policy. Research improves knowledge, knowledge informs policy decisions, policy decisions lead to new areas of research. However, there are often large gaps between the scientific community, the policy makers, and the general public. Katherine hopes to help bridge the gap between science and policy decisions once she finishes her PhD work. She has completed a graduate certificate in marine resource management and plans to use her knowledge base in coral research to help governmental organizations take better care of our precious ocean resources.

If you want to hear about how Katherine got into coral research, you can listen to Katherine’s episode of Inspiration Dissemination from about two years ago. However, this time we’ll talk to Katherine about what she’s discovered about coral adaptation and her ongoing transition from PhD student to science policy advisor. Tune in Sunday, 12/4 at 7pm (PST) on KBVR-FM!

Paul does it all: Is there hope for the amphibian taxa?

Everyday there is a constant battle between healthy immune systems and parasites trying to harass our bodies. In the case of buffalos in South Africa they cannot simultaneously fight off a tuberculosis infection and a parasitic worm. Their immune system has to choose which of the adversaries it will fight; this decision has consequences for the individual and the health of the entire population of buffalos it encounters. This situation is not unlike those for humans. We are not fighting one immunological disease at a time, but many at once and they can interact to influence how we feel. Our guest this evening specializes in disease ecology, which focuses on how the spread of pathogens interacts with humans and non-human organisms.

Paul while working as the Ezenwa Lab manager at the University of Georgia

Paul Snyder has worked on tiny ticks in New York to wild buffalo in South Africa, but he’s had a very colorful life before beginning his studies at OSU. Even though he loved everything science and technology growing up, there was limited exposure to those fields in high school and he never thought of being a scientist as a career path. To put things in perspective, he wasn’t allowed to buy any video games growing up; instead he programmed his first working computer game at the ripe age of 6, yes six, years old! Paul continued his illustrious career as a 13-year old paperboy, then burger flipper, and eventually working his way up through the ranks to the manger of a Toys R Us store. He realized he wanted to focus on science and pursued his schooling at University of South Florida doing research on the interaction of parasites and tadpoles, then New York counting ticks, and finally University of Georgia as a lab manager. Oh yeah, somewhere in-between he successfully mastered the bass guitar with his band mates and learned how to program virtual reality simulations, but I digress.

In his downtime Paul works on virtual reality apps for us to enjoy

Back in the world of science, Paul is working with Dr. Blaustein’s Integrative Biology lab group in the College of Science that he first became aware of from his work with South African buffalo’s. Rather than beginning his disease ecology research with human trials, Paul is focusing on the #1 declining vertebrate taxa in the world. Amphibians have been sharply declining since the 1980’s and there have been no shortage of guesses, but sadly few answers as to why this is happening. Paul’s current project has identified a species-virus interaction (e.g. the number of species present impacts how the infection spreads). But Paul’s real interest and ongoing research lies in the very young field of ecoimmunology: how do the immune systems of organisms change over time in response to the environment they experience.

You’ll have to tune in to hear how he plans to rectify the molecular-scale view of immunology, with the large-scale controls from the environment. You can listen tonight September 18^th 2016 at 7PM on the radio at 88.7FM KBVR Corvallis, or stream live at 7PM.

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

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

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 http://kbvr.com/listen

View of the Costa Rican coast line from the Caño Palma Biological Station (http://www.coterc.org/)

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. 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. 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.

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, Beetlefacts.org, 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?

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.”

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.

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.

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!