Recently my paper was published at PLoS ONE (yay!). Although, I have published before, this was my biggest paper to date in that it was one that I spearheaded the whole way through. I went to the field, collected the data, processed all of the samples, analyzed all of the data, and wrote it all. I was even my advisor’s first Ph.D. student and the first to work from this field site and on these questions. Of course I had help and guidance from my co-authors and field associates, but in terms of what I gave, this was my largest contribution to science and essentially a better part of the last six years of my life. With a large accomplishment such as this, comes joy, struggle, and insight that can’t be expressed in the scientific method. Here, I share with you some of the behind-the-scenes stories of the process that became that paper.
Okay, there really wasn’t any blood in this research, but there could have been! The park that I worked in, Lopé National Park, Gabon is notorious for having aggressive elephants (for thoughts on why, click here). What this meant for my research was simply slowing things down or having parts of it come to a halt, which of course meant smaller sample sizes. The goal of this research was to collect fresh elephant dung, which was used as a source of DNA, across the largest possible landscape at the population level, but in a short time frame (about one week). I was trying to capture the fine-scale genetic patterns of African forest elephants, so I wanted to cover a lot of ground, but I needed to work within a short time period to make sure the elephants didn’t move around too much. I worked with amazing crews of Gabonese field assistants and tried to get as many assistants as possible given budget (Gabon is surprisingly expensive) and their availability. Each morning, I would create maps and assign teams of two to walk a route looking for fresh dung. We would drop off teams by vehicle within parts of the park for them to hike their route. If there was a grouchy elephant on the trail though, it meant that the whole section had to be abandoned. As elephants can move fast (compared to humans), and the risk of being charged and potentially attacked in Lopé is very real, it was very difficult for a team to start another route that was safe from the elephant and that could be done in that time frame. It was not uncommon for a team to go in and have to backtrack to escape an elephant, therefore leaving the territory largely unsampled for the day.
The sweat portion is similar vein to the blood section. The fieldwork was a race against time – literally. If I were sampling in a park in East or Southern Africa, chances are I could drive across the park and look for samples in those different areas, being able to cover a large extent of the park even in a day. However, in most Central and West African parks, there are no roads. Although Lopé does have roads, they are only located in a small portion of the park. If you want to sample a larger area, you have to do it on foot, which is very slow. I would look at the map and think sure, I can easily get from A to B in a day. Then I would talk to the staff, and find that it would require a one-week camping trip. To take the time to hike in and camp in only one area of the park did not make sense both logistically and financially. I would constantly have to scale down what could be done. Even after sampling an area for a day, coming back exhausted, when looking at the map, the distance covered on the map didn’t seem to match my level of exhaustion. Large hills, deep ravines, and elephants were consistent natural barriers.
Collecting the samples started off slow. The very first day it had started raining intensely, which meant we couldn’t go out. The next day, we got about six samples. If we collected six samples for the next three days, the project wouldn’t work (only 24 samples total for a session). I was starting to lose hope that this wasn’t working. Luckily, things started to pick up and over the course of the four separate one-week sessions, I had about 50 samples per session. During one session, it seemed like the elephants were especially on my side and defecating all over the place. Just driving to sites we would find tens of piles of dung samples (I never thought I would get so excited about dung!). For that session, I had 102 samples. By the time my fieldwork was over, I had collected about 500 samples, of which approximately half were for this fine-scale population genetics study.
After the success of collecting so many samples, came the scariest part – the genetics. The genetics was the scary because it held the “truth.” My biggest fear would be that my sample size was going to be incredibly low. What if I spent all of that time running around the park only to have collected dung from the same few elephants? I had no way of knowing if my samples were from different individuals. As I processed my samples, the results started to come in. The first step was identifying individuals. I worked with ten microsatellites, and needed at least six to amplify successfully to be able to consider the sample an individual. This was probably the saddest part for me, having some samples that did not amplify at a sufficient number of loci, that I was sure were unique individuals, and having to abandon them. Although dung is a great source for collecting DNA, as it is abundant and non-invasive, the quality is overall lower, and therefore there will be a certain percentage of samples that will not work. It was hard to give up on those samples I had worked so hard for to collect.
The next scariest was the analysis. Not doing the analysis itself, but sorting the samples for analysis. Starting with about 50 samples per session, I had to remove males, juveniles, and adult females that had their samples collected more than once. I was interested in females because they are the individuals that have a more structured social system in African savanna elephants. In forest elephants, there is evidence of groups, but we do not fully understand to what extent and what the relationships are. Male forest elephants are solitary except when pursuing mates. Juvenile elephants are dependent on adult females, therefore using their samples would not be independent.
In the end, I worked with what I could given the samples I had. While I would have preferred more samples, my research still provides important information, especially considering how little is known about the species. Also, excitingly, the trends held up. On one day, I actually collected enough samples allowing me to do an analysis within a day. To overcome sample size issues, I also looked at patterns over time, the whole four-month periods. Both of these analyses showed the same patterns. I was looking for genetic structure across geographic distance. I found in both the shorter and longer time frames, that genetic and geographic distances were autocorrelated within distances of five kilometers. Therefore, despite the large genetic diversity in this area, kin maintain a close proximity to one another.
When I started reading about forest elephants, I could not believe how little information is known about them and how understudied they are. Now, I have some understanding on the reasons behind this. My research contributes to the much-needed knowledge base of this endangered species, and hopefully, encourage others to build future research to build upon it.