Viruses detected on plants chewed by primates

New research has discovered a noninvasive way to test primates for viruses. Collaboration between UC Davis and Gorilla Doctors has shown that the plants mountain gorillas (Gorilla beringei beringei) and golden monkeys (Cercopithecus mitis kandti) consume and discard can be collected and analyzed to determine what viruses the animals have. Blood samples and oral and rectal swabs all require the researcher to anesthetize the animal, something that is not done with critically endangered mountain gorillas unless absolutely necessary.

Thus, this new noninvasive method will allow researchers to detect viruses simply by following the animals at a distance and collecting any bits of chewed bark, leaves, or fruit the individual discards. For this study, Smiley Evans and colleagues (2016) spent almost a year collecting these vegetation discards from 294 gorillas from 26 different family groups across the Volcanoes National Park, Bwindi Impenetrable Forest, and Mgahinga Gorilla Park.

The authors also looked at golden monkeys, collecting plant samples on three different dates in order to determine if their methods could be used on other primate species. Samples were collected from 18 individuals. For both species, researchers observed the animals, collected disregarded plant parts, and sampled from plants with visible bite marks and saliva.

It was possible to collect samples from nearly every individual in a family, including infants who may not consume the plants but still bite and chew them. DNA and RNA viruses were both successfully detected using this method with minimal disruption. Compared to other methods, Smiley Evans and colleagues were able to sample more individuals with less risk and little behavioral disruption. Using this method, the researcher easily knows the age of the sample because close behavioral observation is required.

Golden monkeys proved more challenging than mountain gorillas because they are arboreal and handle food less with their mouths when compared to mountain gorillas. However, it is still possible to collect samples, but researchers should prepare to collect fewer samples per visit.

This research is especially important for mountain gorillas because infectious diseases are one of the greatest threats to this species, and as wildlife increasingly comes into contact with humans, breakthroughs in disease ecology have the potential to positively impact these gentle giants. Roughly 60% of the remaining 880 mountain gorillas are habituated to humans (Gray et al., 2011; Robbins et al., 2011), meaning they encounter humans, whether tourists, researchers, or others, on a regular basis and are accustomed their presence.

Links of possible interest: 

IUCN mountain gorilla page

Gorilla Doctors

Mountain gorilla genome sequenced

Works cited:
Gray, M., Fawcett, K., Basabose, A., et al., (2011). Virunga Massif Mountain Gorilla Census 2010 Summary Report. International Gorilla Conservation Programme.

Robbins, M. M., Roy, J., Kato, R., Kabano, P., Basabose, A., Tibenda, E., ... & Gray, G. (2011). Bwindi Mountain Gorilla Census 2011-Summary of Results. Uganda Wildlife Authority, 28.

Smiley Evans, T., Gilardi, K. V., Barry, P. A., Dsebide, B. J., Kinani, J. F., Nizeyimana, F., ... & Mazet J. A. (2016). Detection of Viruses Using Disregarded Plants from Wild Mountain Gorillas and Golden Monkeys. American Journal of Primatology.

Questions every biologist should ask before starting research

It's getting to be that magical time of year again! No, it's not Christmas. I'm talking about the time of year when most professors and students have time off from coursework and can venture out to do fieldwork! Whether you're spending the better part of a full day traveling to Madagascar or driving a few minutes from home to your field site, field work is arguably the best part of being a biologist. That said, there are a few things I've learned from my own experiences that I think are worth sharing. Here are ten questions I think everyone should ask themselves before they head to the field.

1. What's the point? No really, what is the significance of your research? This matters because you're probably going to have to include a significant portion of your write-up, whether it's a thesis, academic paper, or paper for class, to what makes your research matter. Knowing the significance of your research also helps you if you're applying for any type of grant or funding because it will definitely be a major factor when considering if your research is worth funding.

Photo credit: US Fish and Wildlife

2. What are the applications of your research? Can anyone use your results? If you're working in a national or state park, are those officials going to use what you've learned in their practices? Or will your results make a difference to future research projects?

3. What's the minimum you need to accomplish this research? Stuff goes wrong. Plans fail. Something you never could have imagined happens and completely changes your plan. Can your research survive? What part of your methods is essential?

4. How much data do you want to collect? What's the least amount of data you need to collect in order for your project to be successful?

5. Who can you rely on for help? You'll likely have questions. Maybe something will go terribly wrong or maybe you'll think of a great idea while in the field. You might not have the time or resources to research that new idea or alternative plan fully, so who can you call? Who can you email for advice? Are there experts out there you haven't met personally, but who may be worth mustering up the courage to shoot an email to? I'm a big fan of collaboration and scientists helping scientists. Chances are, if you're polite and the person you're requesting help from isn't a total jerk, that person will extend a hand or point you in the direction of someone who can answer your question.

6. How excited you are about this research? Because you're going to encounter bumps in the road,
you're probably going to work on this project more than you ever imagined, and your project is going to be questioned and scrutinized, so you better love it. You better be invested. You're going to have a much harder time if this was really your advisor's idea and it's not your baby, it might be a long road.

Me observing sifakas
Photo credit: Saotra Rakotonomenjanahary

7. How can you connect with nonprofits and conservation organizations to make your research have a significant impact? Yes, your research probably has a very important indirect effect on conservation biology. Sure, studying the reproduction of the Vences' chameleon will help us understand more about the species, thus conserving it. But wouldn't it be better if you could pair with WWF for example and attach a more direct conservation project to your research, collaborate with a partner outside of academia, and make more of a difference?

8. What's the best way to collect data, knowing you're going to eventually enter it all into an Excel sheet and run statistical analyses on it? Think about how you're going to analyze your data. Think about how you're going to arrange your observation sheets and your field notebook so that it's painless (relatively) to enter it all into your computer. You also want your data to go smoothly from your Excel or FileMaker Pro or whatever to a statistical software package. Reformatting your data because you didn't take the time to think about it beforehand is painful and can be very time-consuming. If you're not sure about your statistics or data entry, go talk to a statistician (your advisor should also be able to help you with this).

9. Think about how you're going to present your final product and what details you might want to collect or note while you're doing research that aren't essential to your research question, but that might be nice to have. For example, it's hard to show a slide with a photo of everyone in your lab if you never took that photo. For your study on behavior and daily activity budget, it's impossible to determine if humidity might have had an effect on how much time your giraffes spent resting if you didn't measure humidity. Think about the little things.

10. What photos are you going to wish you had taken when you return home/finish your research? There's always at least one...

Research experience as an undergraduate student (or earlier)

Courtesy: National Science Foundation

Whether you're an undergraduate biology major or a high-school student figuring out whether or not you want to be a biology major, getting research experience is a wise idea. In fact, it's arguably even essential, depending on what stage of your education/career you're in.

More people are getting their undergraduate degree than ever before. Many students do well in terms of grades and have excellent recommendation letters from their professors. By gaining research experience, you set yourself apart from the majority in a competitive field. You show that you can use all of the knowledge from the books and apply it, and moving beyond the book smarts is important. I think it's in most (if not all) students best interest to gain research experience before graduating.

There are multiple ways to do this: choose coursework that includes independent research as part of the course, do an independent study with a professor in your department or a department you're interested in, do an undergraduate thesis if you're really willing to take on the work load, or gain your research experience over the summer.

Many universities have research experience for undergraduates (REU) programs that take place over the summer. These are programs specifically designed with undergrads in mind. They typically don't require any previous research experience, although some may require certain coursework or that you be in you junior or senior year of your degree. You'll work with a faculty member and you'll be paid to do research. Housing is also usually provided.

Courtesy: National Science Foundation

The experience you have in an REU will depend on the project itself and the faculty member running the project. You may find yourself working under the guidance of a graduate student on a daily basis or you may find that you do your assigned work and check in with the faculty member every few days or so. Most REUs accept only ten or so students and they can be quite competitive. Check out this PDF from the University of Wisconsin-Madison on what an REU is, applying for one, and why you should do one.

If an REU isn't for you, there are still plenty of other options. Doing an independent study for a semester or two allows you to work one-on-one with a professor and assist with his/her research. You can develop a deep understanding of a specific topic, learn about what the research process is like, and earn a grade and credits for your efforts. If you play your cards right and enjoy the experience, that professor you work with can also be a great reference, as he/she will really get to know you over the time.

There are many parts of the research process: the initial design, applying for funding, preliminary data collection, experiment design, redesign, data analysis, and writing up your results. Try and get experience in as many of these areas as possible or talk to your professors or supervisors about their experiences. This is a time in your life when you can gain experience and learn a lot from your supervisors and other project mentors. It may seem a bit intimidating, but everyone knows you're an undergraduate, a newbie. The point is to contribute and learn. 

Whether you choose to do an REU, an independent study, a larger undergraduate thesis, or purposefully enroll in courses with research as a component, there is nothing like gaining hands-on experience. You'll discover whether or not you like working in a lab or want to work in the field. You'll find out if you're great at designing your own projects or if you're better at following directions. A career as a research scientist is not for everyone just as fieldwork is not for everyone or lab work. The only way you will find any of this out is by exploring it yourself. Having these experiences will set you apart and make you more unique as an applicant for jobs or graduate programs. I don't think it's a stretch to say that you need to have some sort of research experience to be a competitive applicant for graduate programs, as more and more people are pursing post-graduate degrees. Potential graduate advisors want to know that you can do the research you're applying to work with them for. They don't want to send you out to the field and find out you can't stand the bugs and want to come home! Regardless of whether you want to apply to grad school, you should gain some research experience because you'll leave university with a better understanding of the work you are best at and the work you enjoy.

This is around the time when some REU applications are due. I've listed some REUs below, some of which are funded through the National Science Foundation (NSF).

NSF-funded project with the Enchinacea Project with opportunities for undergraduates, recent graduates, or even graduate students.
Experience for high-school student, undergraduates, and even teachers with Rocky Mountain Biological Laboratory.
REU with Models in Evolution, Ecology, and Systematics through Kent State.
Aquatic Chemical Ecology REU through Georgia Tech sponsored by NSF.
NSF-sponsored ten week program for undergraduates to do independent and collaborative research in the Chihuahuan Desert

For more REUs, check out the NSF website.

Citizen science-What it is and how almost anyone can get involved

Watch birds in your own yard with Cornell

Citizen science is a type of scientific research where part or all of the project is done by amateur
scientists. It's a great way to get involved with research, broaden your knowledge, and make a difference. Practically anyone can get involved with a project these days if you have internet access: school children, busy professionals, retirees, stay-at-home parents, undergraduates looking for experience, or anyone else with an interest in nature. You don't have to be an expert, and you'll learn along the way. There are projects you can participate in without ever leaving your house and projects where you definitely get to go far from home!

Take for example what I would argue is one of the most well-known citizen projects: The Cornell Ornithology's FeederWatch . Count the birds you see at your feeder from November to April for FeederWatch and your data will be used by researchers at Cornell to track species distribution and abundance. More than 20,000 people from across North America participate in FeederWatch and the project has been around for decades. Another citizen science project out of Cornell is NestWatch. With NestWatch, participants record any nests they find and monitor the birds in those nests. Scientists then use this data to study reproductive success. Cornell has quite a few options if you're looking to get involved and watch birds.

Keep track of pollinators for The Sunflower Project

If birds aren't your thing, help scientists keep track of pollinators with The Sunflower Project. You'll pick a spot in your yard or in a public place, record the common name or species of the plant, and watch for pollinators for at least five minutes (if you sit for 10 minutes and don't see any pollinators, that's still data). If you're really a go-getter, you can use their resources to learn to identify different pollinators, which will help The Sunflower Project out even more. Given that many pollinator population numbers are in decline, projects like this are more important than ever.

Looking to head further from home? Away from your backyard? Then a great organization with multiple project options is Earthwatch Institute. There are opportunities specifically for families, teens, or you can join an expedition on your own. You can study caterpillars and climate change in Costa Rica for nine days, lions and their prey in Kenya for two weeks, Darwin's finches in the Galapagos, or choose something more local, such as wetlands in South Carolina. These expeditions aren't cheap, but this is an excellent institution. No unorganized field trips, unanswered emails or phone calls when you have questions, or leaders with little experience or who are poor teachers. Earthwatch was founded in 1971 and is respected in the scientific world. You'll learn a lot and it will look great on your resume.

For more opportunities, check out SciStarter, a website where you can search for projects based on topic or on location/time (projects at night, projects at home, entirely online, and so forth).

A lack of results, it happens.

Earlier this month, I attended the American Society of Primatologists annual meeting to present a paper. One of the talks I attended that I really quite enjoyed was given by Jessica Rothman, "Within-Species Variability in the Microhabitats of Mountain Gorillas (Gorilla beringei): Implications for Nutrient Balancing."  As I'm sure you've guessed from the talk title, Rothman, a nutritional ecologist at the CUNY in NYC, studies mountain gorillas, the fuzziest of the gorillas. Mountain gorillas are primarily folivores, meaning their diet is composed largely of leaves and herbaceous matter. There are very few mountain gorillas left in the wild and there are none in captivity, so of course Rothman studies the ones remaining in the wild.

Male mountain gorilla

Rothman noticed that the gorillas would sometimes bypass or ignore foods that they would stop and feed on at other times. She wanted to know why. Why would the gorillas pass up foods in one instance only to stop and feed on the same type of food in other instances? Some days gorillas will feed on these plants all day and other times they will travel right by them. That seems a little odd, doesn't it?

Sounds like a great question to me! To answer her question, Rothman collected lots of plant samples and recorded information about the microhabitat in which those samples were found. Variables she looked at included altitude, slope angle, topographic position, and areas of the park zoned for human use. She looked to see if gorillas stopped to consume plants at say a lower altitude for example and ignored the ones at a higher altitude, or if perhaps gorillas ignored foods in human-use areas and stopped to feed on the same plants outside of these areas.

Next, foods were analyzed for their nutritional value. The amount of sugar, protein, and fiber in each sample was determined as what the amount of tannins, bitter tasting compounds produced by plants that deter animals from feeding on the plant. Perhaps foods found in areas outside of human use are of higher nutritional quality than foods found inside areas that humans frequent.

Unfortunately, there were no real significant differences in any of the nutrients or tannins with respect to the microhabitat variables Rothman and colleagues looked at, especially when one considers what gorillas would be able to detect in terms of nutrients. 

Photo by Dylan Walters

Rothman found lots of nutritional variability within microhabitats, including variability within a single month, but as Rothman said, we're not yet able to explain this variability or were not asking the right questions.

This may seem like a disappointing result, and in ways it is. Of course as scientists, we like to ask questions and then have a concrete answer. We want to be able to say, "Gorillas are avoiding plants in high altitudes because the nutritional content of those plants is lower" for example, but that's not what was found. The reality is that sometimes we can't find a correlation, a connection or relationship between two or more things showing interdependence (note this connection or relationship is not necessarily causation), or an answer to our original question. Maybe we're looking at the wrong variables, maybe we're missing some key part of the puzzle, maybe there isn't a link there at all, or maybe our methodology isn't quite the best way to answer the question we're asking. This happens to all scientists regardless of the field.

A lack of correlations or findings is not a waste of time or complete loss though. New questions can present themselves or a new approach may suddenly become clear. And it's important to remember that we do learn from studies where no correlations are found. Scientist still need to publish their results and share them with others.




Food for thought: Why do scientists still need to publish studies where no correlations are found? Why is it important to share these results?

More food for thought: Can you think of how Rothman might use different methods to answer this question? What else might be causing gorillas to pass the same foods at some points in time and stop and feed on them at other times?

Survival of the fittest

Baobab tree

“Survival of the fittest” is a phrase most people have heard of. Some people may even attribute it to Charles Darwin, although he actually adopted it from someone else. Many people don’t understand what the fittest means in terms of biology. An individual’s fitness is their ability to successfully produce offspring that survive to adulthood. I have a fitness of zero because I have no children. My sister has a fitness of two because she has two children. A primate mother who gives birth to twins, but only one infant survives to adulthood would have a fitness of one. An individual’s fitness is related to its adaptations, or traits that make an individual or a species better suited to the environment.

Introduced Brown Lemur on Trail

I am attempting to adapt by changing my project. I originally proposed to study four troops of sifakas. I wanted two troops in the spiny forest and two groups in the gallery forest. However, upon my arrival, I learned from my Malagasy assistant that there are only three groups total in the spiny forest, and each had one lactating female. We were able to locate two groups in our first few days but only one still had a lactating female. Given the scarcity of lactating females in the spiny forest, I have adapted to my environment and am only studying three troops in the gallery forest. I have five lactating mothers total, which is less than I wanted but this is the reality of the situation. We all have to adapt to our surroundings. A species may be perfectly well-adapted to it’s environment, but if a large change comes about, say humans start hunting that species, well then that species better adapt. Those most able to adapt to change are usually the ones most able to survive. Humans aren't exempt from change. 

Brown lemurs were introduced to Berenty, meaning they are not native to this area. The only diurnal primates at Berenty should be ring-tailed lemurs (Lemur catta) and Verreaux's sifakas. However, brown lemurs were introduced in 1975 and I have seen far more of them than sifakas. Clearly they have adapted to their new environment. They seem to be thriving as far as I can tell! The species of brown lemur at Berenty is actually a hybrid of two, genetically distinct species that bred together. They range wherever there is food, although they are a bit more timid than ring-tailed lemurs, the species of lemur Berenty is well-known for. The ring-tailed lemurs often steal food from the tourists and show up to breakfast for any table scraps left behind. Certain troops of ring-tailed lemurs have creatively adapted to the tourists here.

Critical thinking: Can you think of other examples of animals adapting due to their close relationship with humans?

Finding primates

 A question I often get asked is how we find the animals. Well, the short answer is we look. We walk around the forest, using trails if they’re available, with our heads craned up to see the highest branches. (Yes, it eventually hurts your neck a lot to do so much looking up). If we can’t find them using the trails, we start going into the woods. (If you’re lucky, you’ve got a machete to cut your way through-we didn’t.) Spider webs inevitably cling to your face. Thankfully, I have yet to find any large spiders clinging to me. You can also wave a stick in front of where you walk, like a magic wand, so that the spider webs cling to the stick and not your face. I do this often. Anyways, we search, and we search, and we search, and we listen. Sometimes you can hear the primates moving or hear them foraging. They drop leaves or they may break a twig and it falls to the forest floor. If you’re lucky, they vocalize. Primates are not entirely silent creatures.

Sifaka in gallery forest

In the beginning, when you’re new to a troop of primates you’re studying, there can be a lot of searching. You can spend hours of your week walking around, stopping and looking for the slightest movement. But there are some tricks to finding primates. If it’s first thing in the morning, they’re likely eating somewhere. If it’s cold out, they’re probably high up in the branches sunning themselves. If it’s the middle of the day and really hot, they’re probably resting in a shaded spot. Think like a primate! If it’s starting to get dark, they’re probably moving to their sleeping trees. Once you’ve followed the same troop for a few occasions, you start to know the area they cover and they’re habits. Maybe they have a particular sleeping site they often return to. Perhaps there’s one or two species of tree they really enjoy eating, so you search for those trees.

Can you spot the sifaka?

I think someone should do a study where they have radio-collared troops whose locations are always known, and then send a bunch of primatologists into the forest looking for primates. I bet you anything the primatologists walk right by the primates a few times. I think my assistant and I walked by the group we were trying to find at least twice today. Maybe three times. How hard is it to find seven white, sifakas in a green and brown forest? Well, if the sifakas aren’t moving and the bright sun is making everything look even whiter, it’s not a piece of cake.