Monday, July 14, 2014


Today, a bit of a story ...

Kinsman Pond from ledges of North Kinsman

I stood near the edge of the clearing with the two scientists, straining my ears to hear the call of a Bicknell’s Thrush. They played the recording, and we listened. As I recall, it was a relatively cool summer evening, though it was often cool in the evening at Kinsman Pond campsite. It was 2002. I had just finished my third year of college, and I was working as a backcountry campsite caretaker for the Appalachian Mountain Club. I had been dreaming of having this job for at least two years at that point, and a few cold, rainy days aside, I was enjoying every moment of it. It was a stark contrast from the previous summer, when I worked at Brookhaven National Labs as a research assistant for one of my professors. That too was a great experience and important for my development as a scientist. But living in the woods, spending my days doing trail work, sleeping in a canvas tent, dealing with black flies ... that was the life!

On this particular evening, two scientists from the Vermont Institute of Natural Science came to my site, and were planning to spend the night so they could survey for Bicknell's Thrush both that evening and very early the next morning. We chatted for a while, and they told me that they were using known locations of this bird, along with environmental information from those locations, to build a model to predict where it might be observed. I had no knowledge of species distribution modeling, and honestly, probably only a vague notion of what a "species niche" was. What I did know was that I as a physics major, I knew what the word model meant. I knew that any such model would likely be constructed using some computer programming language. I naively thought you would probably code that up in C or C++, because hey, isn't that what most scientists were using? But most importantly, I thought "I could probably learn to do that". 

I've told this story many times over the last 7+ years, in part as a way of explaining to people how I went from physics to ecology. To be honest, the path from physics to ecology was not direct. I finished my degree, spent two more years working as a caretaker, and then spent two years working in a neuroscience research group. But this experience stuck with me, and eventually I got to "build ecological models". I was reflecting on this again recently and I finally went and looked to see if any publications resulted from this field work these scientists had been doing. Here's what I found:

Lambert et al. 2005. A practical model of Bicknell's Thrush distribution in the northeaster United States. The Wilson Bulletin 117(1): 1-12.

And here was the line I was looking for - "during 2000–2002 ... we recorded the presence or presumed absence of Bicknell’s Thrush on 130 mountains first sampled by Atwood et al. (1996) (New York: n = 30, Vermont: n = 56, New Hampshire: n = 26, Maine: n = 18)." I'm assuming that one of the 26 New Hampshire locations was Kinsman Pond.

Perhaps the best part of finding this paper is that since that meeting in 2002, I have acquired the knowledge necessary to understand what these researchers were working on. The species distribution model that they constructed is pretty uncommon compared to today's methods. It appears to be a mixture of quantile regression, which is reminiscent of some of the first distribution models used (e.g., Bioclim), and basic pattern observation. The model options for presence-absence data are quite numerous now, and it would be interesting to see how different the distribution predictions are using more modern techniques. 

It's nice to look back on this story and think "yeah, I did learn how to do that."

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