Hughes Mentor:  Irby Lovette

Department: Ecology and Evolutionary Biology

More Information

A Day in the Life of an Undergrad in the Lovette Lab

The alarm rings at seven in the morning. I drag myself from my nice, comfortable bed, and get ready for another day in the Evolutionary Biology Lab at the Lab of Ornithology. I leave the house, and head down toward campus to catch the shuttle to the Lab of Ornithology. By 9 o’clock, I am sitting behind my computer, figuring out what I need to do for the day. Some days will find me behind a computer all day, analyzing data, or behind the lab bench, transforming tubes with minute quantities of clear colorless liquid into data that will let me see into the genetics of Barn Swallows.

But, before I go any further, a bit of background on my project. One evening, while at a dinner at my advisor’s house, Gernot Huber, a graduate student, approached me and asked me if I wanted to work on a research project. Gernot studies a strange population of Barn Swallows that has decided to nest in Argentina, in South America, when, up until that time, they had only ever nested in North America. He wanted to know more about the population, specifically whether that group of birds are descended from a single group of North American individuals that decided to start nesting in a new place, or whether northern birds constantly join the population. I can do this by comparing the genetics of the North American birds and the South American birds, and determining if there are any major differences.

Now, in order to get to the point where I can look for genetic differences, I need to go through many tedious steps. First, I start with blood taken from a Barn Swallow. I then add some blood to some reagents that break down the blood cells, releasing the DNA. I then filter the DNA from everything else, so I end up with just DNA. From that point, I take the DNA I got from the blood, and I run a PCR reaction, which stands for Polymerase Chain Reaction. What this does, is it takes a small part of the DNA, and makes millions of copies of that small part, allowing us to compare that specific part across many different individuals, and different populations, and also different species. Differences we see can help us to understand the history of those organisms (in my case, the history of the South American Barn Swallows).

From that point, I take the PCR product and I run that in a sequencer, which arranges my products by size. On Genemapper, a computer program that allows me to see my product, alleles appear as peaks at a given size. Any individual can only have two alleles, or versions of a gene, for any one marker. It is then my task to sort through the data, and make sure the computer program made the right decisions based on the diagrams that are generated. Aside from running some computer programs and other analyses, this constitutes much of my work in the lab.

And so ends my day in the Lovette Lab (or rather, four or five days).

A Day in the Life of an Undergraduate in the Lovette Lab

The day starts waiting outside of Corson-Mudd hall for the 8:45am shuttle to the Lab of Ornithology. There is a familiar group of several heading to work. Loretta the shuttle driver greets us warmly, and we ride off to work chatting lightly about Lab gossip, news, our weekends, and the radio programs she listens to. The morning in Irby’s Lab finds lab tech Amanda making coffee and getting set up for the day’s work. Grad students filter in and out, Irby and lab manager Laura arrive, greetings exchanged and people slowly work into the day’s groove.

I head to my favorite computer workstation and look over the day’s activities. I am sequencing several genes from two Hispaniolan bird species, the Palm-Tanagers. These genes are standards in avian molecular work, so I already have my primers and conditions designed and ready, and I can stick to a simple work flow of extraction, PCR, sequencing, and data clean-up.

I benefit again from previous work with the extraction process. DNA from birds is most often extracted from blood, because unlike in mammals, birds have nucleated red blood cells. I am working from a large bank of blood samples collected by the grad student I am working with, and another student working with her has already extracted DNA from most of the samples I need.

The next step is PCR, the Polymerase Chain Reaction. I combine small (microliter) quantities of my DNA extractions with primers, reagents, and nucleotides. This mix goes into a thermocycler which takes it through the PCR. The thermocycler takes the DNA through temperature-guided cycles that alternatingly denature the DNA, allow the primers to anneal, allow new complementary strands to form, and to again denature, so that copies of the DNA strand between the primers are formed. The number of copies grows by a power of two with every cycle, so that a very large number of copies is created by the end of 30 or so cycles. This amplifies a small DNA fragment, my selected genes, for further use. I confirm that the PCR worked by running the DNA out by gel electrophoresis, then purify the PCR products. This process generally takes a whole day, with the morning for setup, several hours to run the PCR, and the afternoon for gels and purification.

The next day, I take a sample of my PCR products, and add it to another mixture of reagents and fluorescent-dyed nucleotides. Another run through the thermocycler binds the fluorescent-dyed nucleotides to the DNA fragments, and then we send the plate to Biotech to have it sequenced, where they read the fluorescent labels along the strand, and send us the raw data back.

These steps are the basis of my molecular work, but are a relatively simple matter. It is very important to keep all samples accurately labeled, to be well organized while setting up reactions, and to pipette carefully. When I begin analyzing my raw data with a program called Sequencher, it becomes clear whether I was careful enough during setup. With luck, the sequence data appears as clean peaks colored as each representative nucleotide in the sequence. If I am not so lucky, some contamination in the setup results in messy sequence, where background squiggles of color obscure the true peaks. Sometimes sequences will fail entirely, with the cause never really known. If I’m really unlucky, more serious problems occur.

I have encountered a few of those problems, and that is where accurate record keeping comes into play. I have discovered while reading my sequence data, that a sample that was one species should actually have been another species. Careful analysis of my records and results revealed an error in pipetting: at one point I accidently switched two rows of samples. I have done even worse, though, when I discovered several sequences of one gene, in a batch of data that should only have been another gene. Despite stepping back through my entire work flow, I could locate no source of the misplaced gene. The inability to figure out a source of the contamination meant completely scrapping the data set and re-starting from scratch.

These kind of screw-ups are generally met with a mixture of laughs and good-natured curses, and are followed by long days of catch-up to fix the mistakes. Irby takes these times to stress the importance of keeping good details on everything you do while doing molecular work. He also makes the point of having a work flow while pipetting that allows you to catch your own mistakes before they get sequenced, and to help prevent those mistakes from occurring.

At the end of the day, counters are cleaned, samples are refrozen, data is entered into my lab notebook, and I head home. It can be very exhausting, especially after a really long day. Despite the hard work, I return each day because I am eager to delve back into the project.

A Day in the Life of an Undergraduate in the Lovette Evolutionary Biology Lab at the Lab of Ornithology

You have to really want to work here. That is the very first condition. Professor Irby Lovette knows that the key to successful research is self-motivation and he accepts no substitutes. Those who are excited by their projects and interested in this field of biology are the people who can overcome setbacks in the lab and push on through the frustration that inevitably comes with doing research.

Finding the right fit was the first challenge for me in my quest for a new lab this spring. I already had some research experience and wanted to find a lab that did research in my areas of interest. I spent a lot of time reading about different professorsí research online. I compulsively e-mailed professors asking them about opportunities in their labs. I set up appointments to meet with them and discuss their research. In the end, however, I found that it was a lot easier to approach professors who already had an idea of who I was; professors I had taken a course from or knew independently. I had gone to Kenya with Irbyís Tropical Field Ecology and Behavior course the summer before I approached him about research. I knew I was interested in the work he did in his lab and he knew that I was self-motivated and able to work independently.

There is a diverse range of projects that go on in this lab. Some studies use genetic variability to determine phylogenic relationships. Other projects involve population genetics. Paternity studies and other behavioral projects are possible with the genotyping that goes on in the lab. Other people are sequencing genes. Iím working on determining the relationships between mosquitoes and their host species. Many of the projects in the lab involve birds, we do live in the Lab of Ornithology after all, but others involve species of insects or fish. Because mosquitoes eat pretty much everything my project necessitates blood or tissue samples from species of birds, mammals, reptiles, and amphibians. While the research that goes on in this lab spans a whole range of fields and interests the tools and techniques most commonly used are surprisingly similar.

This last month the PCR block and I have become very tight. Little by little I have been optimizing my way to its heart and it has certainly found its way into mine. I had read about them in my genetics textbook and heard about it in Biochemistry but nothing has solidified my understanding of the polymerase chain reaction techniques like the first-hand laboratory experience Iíve accrued over this last month. Another popular piece of equipment in this lab is the sequencing and genotyping machine. It is one of the more complicated and expensive machines in the lab. Other techniques that everyone in the lab is familiar with include extractions and gel electrophoresis. These methods are used daily by almost everyone.

Surprisingly, however, the research that occurs in this lab entails more than just lab work. Sometimes I spend whole afternoons working on the computer analyzing data or designing primers. I spend mornings reading papers by other evolutionary biologists, hoping to gain insight into my own work. Once or twice Iíve taken field trips to collect specimens. When Iíve collected enough data Iíll begin spending some time working with a statistics program to see if my results are significant. And of course there are times when I find myself at loose ends waiting for a PCR to finish or a gel to run. This is the time I usually spend checking e-mail or surfing the Facebook. Itís important to attend to such important business when thereís down time.

Thereís a lot of freedom in this lab. I do not have anyone looking over my shoulder or asking me about my progress regularly. I have acquired the skills to work independently and I set my own schedule. I have the space I need to be creative. Designing primers is an art as much as it is a science. I have daily exercises in abstract thinking and trouble-shooting is a way of life in the lab. If something fails the first time giving up simply does not occur to me. However, I am not expected to figure out everything on my own. There are many nice and knowledgeable people around including lab technicians, graduate students, lab managers, and post-docs. And while Professor Lovette is busy he is always willing to make time to talk.

So a day in my lab isnít any one way really, every day is different. There are times when things get dull or when I get frustrated with my project. But the barrage of challenges Iím met with continuously makes the work exciting. And the satisfaction I get from a clean gel, a new tissue sample successfully extracted, or designing a primer that works consistently makes the difficult times worthwhile. When the school year starts I know that there will be new challenges. Balancing class work with research is complicated. But I think that if I set aside certain blocks of time in my weekly schedule for lab work that I will be able to make time for everything. Research is really just applying what Iíve learned in class. Itís an extension of the education process.

A Hughes Scholar's Guide to Doing Research in the Lovette Lab

I work in the Lovette Lab in the Lab of Ornithology. The Lovette Lab is the evolutionary biology lab, so everyone in it studies evolution in some from, though not everyone in it studies birds. I was lucky because I didn't have to know a lot to get into the lab. Professor Lovette enjoys taking in undergrads with little or no research experience and makes the lab a great place to gain research experience. Most undergrads upon entering are paired with a grad student who shows them the ropes and teaches them the many research techniques they will need to use while doing work in the lab.

I work with graduate student Dana Hawley on the House Finch. I am studying the genetic diversity of the males. I am trying to prove that the less inbred (more genetically diverse) males tend to have brighter red breasts. My day in the lab can vary a lot. Some days I do lab work all day, sometimes many quick processes that need to be done often, or sometimes I spend the day doing one long process. Other days I might spend the entire day in the computer room studying my data and analyzing it.

To do my research there are three main techniques that I use. DNA extraction, in which I get DNA out of samples of bird blood that I have. Polymerase chain reactions, in which I amplify a small sequence of my previously extracted DNA. And genotyping, in which I look at my amplified DNA to see whether the bird was hetero or homozygous for the allele I am looking at. There are many other techniques done in my lab but those are the ones more relevant to my project.

I have learned a lot from this project, both about research and about myself. About research, I have learned that it’s both a lot of fun, potentially very frustrating, but in the end very rewarding. About myself I have learned that I really enjoy lab work, even when things don't work out the way I wanted them too, and that I really enjoy asking people questions about what they do.

Summer research is very different then research, mostly because the disappointment and the rewards get a lot bigger. During the school year I only spent about 10 hours a week in the lab, so I didn't accomplish nearly as much as I did in the summer. When you spend 40 hours a week in the lab and something doesn't work its incredibly frustrating, very different then when you spend 3 hours in a lab and can walk away after. But when something works after that much time spent it feels very very good.

Overall I have really been enjoying my research experience and I am very grateful for the opportunity offered to me by the Lovette Lab.

A Hughes Scholar Guide to Doing Research in the Evolutionary Biology Lab

At the Evolutionary Biology Lab, located at the Cornell Lab of Ornithology, you will find a group of people who care so passionately about what they do that they often spend nights and weekends in the lab trying to move their research forward or take on additional projects. Every day there is a diverse group of graduate and undergraduate students working side by side, using techniques in molecular biology to study the earth’s biodiversity. Everyone is filled with a contagious excitement about his or her own individual project and is always willing to share extensive knowledge of it with you. Dr. Irby Lovette and Laura Stenzler, who both believe strongly in encouraging undergraduates to pursue their own interests and design their own research projects, run the Evolutionary Biology Lab. While students are given a great deal of independence in their research, there is also always an invaluable support network of mentors and friends to provide guidance and bounce ideas off of.

The lab supports many different projects that look at evolutionary relationships among species, the genetic movement of populations, family relationships that occur in social groups of organisms, and even the associations between parasites and their hosts. Most of the projects are associated with ornithology, but students are also working diligently to study whales, lizards and other animals they have an interest in. Research is done using a variety of tools in molecular biology such as PCR, and the genotyping and sequencing of DNA. Information obtained is used to better understand relationships among species and to help conserve the earth’s biodiversity.

I am currently studying the genetic movement of the Florida Scrub-Jay between fragmented habitat patches in order to help devise an effective conservation strategy for this federally threatened species. To do this, I extract DNA from hundreds of blood samples, use PCR to amplify specific portions, genotype the birds at multiple microsatellite loci and then use a computer program to model the dispersal behavior of this species. This means many long hours in the lab sometimes doing very repetitive processes, but obtaining results is always well worth the work. Having the additional time over the summer to generate data for this project has proved invaluable.

Working at the Evolutionary Biology Lab requires a great deal of self-motivation and attention to detail. Genuine interest in the concepts studied here is much more important than being extremely familiar with the topics. I took a one-semester class of evolutionary biology before beginning research in the lab, but learned so much more by just interacting with other lab members than I ever could have from a textbook. Doing research allows you the amazing opportunity of seeing and doing biology in real-world applications and should be a part of any undergraduate’s biology education.

A Hughes Scholar Guide to Doing Research in the Lovette Lab

I’ve been working in Dr. Irby Lovette’s lab of evolutionary biology since the winter of 2005. Dr. Lovette welcomes any undergraduates that show enthusiasm for evolutionary research, even if they have absolutely no research experience. Everyone in the lab is very welcoming to undergraduates. They all see it as their mission to take new-comers under their wings in guiding them through the ins and outs of avian evolutionary research. As a result, being new to research was only a minor speed bump in the way of starting my own project.

In fact, I was able to start my own project after only a few weeks of learning all of the techniques used in the lab. With superb guidance from both Dr. Lovette and Dr. Hawley I was able to design a project that will unravel the evolutionary history and genetic variation in the house finch through analyzing the mitochondrial gene ND2. The techniques I use for my project are fairly straight-forward. I take DNA that’s been extracted from blood samples and use a restriction enzyme reaction to digest the nuclear pseudogenes, nonfunctional copies of ND2, that exist in the blood cells. I then carry out PCR to amplify the mitochondrial ND2. Finally, I carry out sequencing reactions that allow me to obtain the nucleotide sequence. From start to finish, this is approximately a two day process.

This process sounds very simple but it involves much troubleshooting which makes every day unique and interesting. On top of this, talking to all the other undergraduate and graduate students about their wide range of interesting projects prevents dull moments.

From just the past few months I’ve spent in Dr. Lovette’s lab I’ve learned that research is perfect for me. It appeals to my curious nature and craving to answer interesting questions. I’ve also learned that summer research is much more productive than research during the school year. Its nearly impossible to accomplish any significant research during the school year without sacrificing other things, such as grades. For this reason I urge all prospective undergraduate researchers to begin your projects during the summer.

An Interview with Dr. Irby Lovette

Lovette in Brief:

Professor Lovette came to Cornell University in the Fall of 2001 and he presently holds a joint appointment as an Assistant Professor in Cornell's Department of Ecology and Evolutionary Biology and as the Director of the Evolutionary Biology Program at the Cornell Lab of Ornithology.


His Early Work:

When asked how he chose his profession, Lovette explains that he was always fascinated by Biology. Even as a child before he knew of the field of Ecology and Evolution, he used to study the natural world.

Professor Lovette began his research career as an undergraduate. He took his senior year off to do field work in the Galapagos. There he collected data for the famous study of “Darwin’s finches” that compared the birds’ beak sizes and shapes to the type of food they eat.

Lovette continued to work in tropical ecosystems, both in his doctoral program at the University of Pennsylvania, where he did his thesis work with the Smithsonian Tropical Research Institute in Panama, and as a postdoctoral associate at the Center for Tropical Research in San Francisco. Lovette says that he does not have a particular preference between tropical and temperate ecologies and that each has its advantages and disadvantages; tropical ecologies over a great diversity of species for study, however there is more background knowledge for temperate species.


His Current Endeavors:

While Lovette is involved in many different projects, there were two projects that I specifically asked him about: the Warbler Tree of Life Project and the Florida Scrub Population Genetics project.

For the warbler project, Lovette is working with professors from other universities in order to construct a complete evolutionary tree for all the birds in the warbler family. This tree will have many applications for other studies that will help us better understand the evolutionary history of these birds. For example, one study which Lovette intends to do will show whether drab colorations are found in the females of many different species as a result of a close evolutionary relationship or because they are advantageous for ground-nesting females to avoid predators. Lovette has already completed a first draft of the complete tree and he is beginning to analyze it.

The scrub jay project uses both field observations and DNA analysis to determine the dispersal patterns of this bird. The scrub jay exits in several isolated patches in Florida. This species is being threatened as increasing development has resulted in destruction of their habitats. By determining how the jays disperse between habitat patches, better efforts can be made to conserve the species. This project could even result in the creation of corridors to link together isolated habitat patches.


Academic Involvement:

Professor Lovette teaches Evolutionary Biology and also a field course in Kenya during the Summer and Winter breaks. For the Kenya course, students work in teams to form and investigate their own research hypothesis. Studies done by students this Summer included tracking animal dispersal by location of their dung and determining if the aggressiveness of the ants that inhabit a tree has an effect on whether or not a bird chooses to nest there.


When he’s not in the lab…

Unfortunately, between his duties to the University, his research, and his family, Dr. Lovette has little time for hobbies. When he does have free time, Lovette enjoys spending time with his six year old son. He has even found the time to take him camping this summer! Lovette also enjoys reading on a variety of subjects and one of his favorite authors is Wallace Stegner.