Lichens on the Lackawaxen

Over the recent holiday break, I was up in the Pocono Mountains region of Pennsylvania. I was going to spend part of the day looking for river scour sites along the upper Delaware River however, ice-covered roads due to freezing rain prevented that from happening. Instead I ended up at the D & H Canal Park at Lock 31 along the Lackawaxen River, outside of Hawley, which is a local historic site. I went for a brief hike, including some quick peeks at some accessible sites along the river. At one of these sites, I came across this interesting lichen on a small rock along the water's edge. I collected a small sample of it and texted photos to one of my colleagues. We determined that it is likely a species of Dermatocarpon, a genus of lichens in the family Verrucariaceae, also known as the "stippleback lichens". There are two known species in Pennsylvania and both of them are tracked by the Heritage Program. We don't have a full species on it yet, but it compares favorably to D. muhlenbergii.

Back to Basics: Sedge Workshop

A few weeks ago I attended the 3rd bi-annual (biennial???) Pennsylvania Botany Symposium, an event organized by a number of my colleagues. The first day of the event consisted of several workshops for botanists to learn about particular plant groups. I chose to go to the sedge workshop, as I've lost a lot of my sedge knowledge as I've transitioned from a field biologist to having a greater focus on conservation planning (=more inside time!). My friend Dwayne Estes from Austin Peay State University was the instructor for the class and I've heard great things about his sedge class before.

I really can't say enough good things about the class. Dwayne is an excellent teacher and was really able to convey a lot of knowledge.  This is especially true as he normally teaches this material as a five day class in North Carolina. One thing that was emphasized is the drawing of botanical structures to learn the differences between the different sections of Carex--something that is a lost art among modern taxonomists and is something I definately need to practice.

Creating a Topographic Roughness Index for Pennsylvania

In the development of some data layers for a species distribution modeling project, I determined that one of the environmental drivers we might want to use was a measure of Topographic roughness. The topographic ruggedness index (TRI) appears to have been developed by Riley et al. (1999) to express the amount of elevation difference between adjacent cells of a digital elevation grid.

An excellent post by user ‘whuber’ gives a good workflow for creating a TRI:

Compute s = Focal sum (over 3 x 3 square neighborhoods) of [DEM].
Compute DEM2 = [DEM]*[DEM].
Compute t = Focal sum (over 3 x 3 square neighborhoods) of [DEM2].
Compute r2 = [t] + 9*[DEM2] - 2*[DEM]*[s].
Return r = Sqrt([r2]).

Using this as a guide, I created the a TRI layer in ArcGIS using these steps.

So starting with the standard 30-meter USGS DEM (we’ll call this layer “[DEM]”), we calculate the focal sum (over 3 x 3 square neighborhoods) of [DEM] using the Focal Statistics Tool in ArcGIS.

Next we’ll calculate the square of the DEM, naming it “[DEM2]” using the Square Tool in ArcGIS.

Next we calculate “t” which is the focal sum (over 3 x 3 square neighborhoods) of [DEM2].

I was half tempted to stop here as the map appeared to represent what I was going after for this particular species. But we had to complete the analysis, so we used Raster Calculator to compute  r2 which is equal to the  [t] + 9*[DEM2] – 2*[DEM]*[s].   Then we just take the square root of r2 and get this map, which represents topographic roughness for the state:

The darker the color, the more rough the area is.  This appears to be true in the deep valleys section of northcentral PA, as well as the ridge and valley and lots of the Waynesburg Hills in the SW corner.

Although, we have a high resolution LiDAR-derived DEM for the state, this TRI developed from the 30-m dataset should be good enough for our needs, as the error in the DEM should be negligible especially given the modeling environment. Still, it would be fun to run at the finer scale.