Wayne National Forest Internship

This summer I had the opportunity to intern at Wayne National Forest, Ohio's only national forest. This internship was focused on wildlife biology, and was part of a larger joint venture between Ohio University and the United States Forest Service out of Wayne National Forest. The main project that I worked on was an environmental impact assessment for a proposed mountain bike trail system.

Beginning in early May, I and another wildlife intern from Ohio University were tasked with surveying the wildlife along an approximate 30 mile section of the proposed trail route. We found many interesting animals and plants over the course of the summer, including discovering two new populations of a state-endangered dragonfly and documenting the first-ever Brown Creeper breeding attempt in the southeastern portion of Ohio.

In addition to assisting with the wildlife portion of the environmental impact assessment, I was given the opportunity to do some guest blogging about my internship experience on the Ohio University College of Arts and Sciences Forum. I wanted to share the four posts that I wrote for the Arts and Sciences Forum on my personal blog for anyone that was interested in reading them. Simply click on the links on the titles of the posts below.

First Post: Working on the Wayne | ‘I Wanted to Get My Boots Dirty’

This first post gives an introduction to the project I worked on, and goes over a few of the initial findings of note.

Second Post: Working on the Wayne | Awesome Arthropods Abound

Arthropods are cool, and I saw many an awesome arthropod this summer. This post explores a few of the stand-out species, including the Camouflaged Looper, Luna Moth, and the rare Northern Metalmark (pictured above).

Third Post: Working on the Wayne | Snazzy Snakes

What's cooler than arthropods? Snakes. This post goes over a few of the common snakes of southeastern Ohio, and attempts to dispel some of the common misconceptions about them.

Fourth Post: Working on the Wayne | An Ending Note

In my final post, I summarize the findings of the wildlife surveys, talk about the potential impacts of the trail, and offer a few musings on the importance of hands-on experiences in the field in addition to a classroom education.

Your blogger in his surveying gear. Yes, I had to wear a hard hat.

This internship was an amazing experience. Not only did I see amazing wildlife and plants, but I also learned a lot (which is really the main goal for any internship). The biggest takeaway for me, however, was that there is always something new to discover if you just take a walk in the woods and keep your eyes open. You never know what you might come across.

As for now, I am in the midst of searching for another job. Wish me luck, and thanks for reading!

To Take a Photo: A Frog's Photoshoot

Today I'm going to do something a bit different from my usual posts. My friend and fellow lab-mate Cassie Thompson is working on a research project involving Wood Frogs and American Toads. This project involved raising hundreds of tadpoles of both the Wood Frog and American Toad. Those tadpoles recently metamorphosed into tiny adults. Cassie wanted some photos of these tiny adults, so she asked me if I was interested in having a little photo shoot with them. I was thrilled to do so, and I went about capturing some high-quality photos that she could use in presentations and outreach. A few of my other friends were interested in how the final product came to be, so I decided to create this blog post to outline my post-processing workflow. This post will follow a single photo from its capture, through its editing, and to its finalized version.

Let's start with the final product. This is a recently-metamorphosed Wood Frog (Lithobates sylvaticus) sitting on a penny. When taking this photo, I knew I wanted a completely clean, white background, and I knew I wanted something in the photo for size reference.

To achieve that look, I created this super simple setup. I used a white piece of computer paper for the backdrop, and I propped this paper up so it would curl upward. For my camera setup, I used a Nikon D5100 DSLR, an 85mm Nikon macro lens, and a Nikon SB-700 external flash. I then mounted my camera and flash on a tripod to allow for easier control. I shoot all of my photos in manual mode, meaning I select what settings the camera will use to expose a photo. I also shoot all of my photos in the RAW format, which I will talk about later. For this photo, I set my aperture to f/20, my shutter speed to 1/200th of a second, my ISO to 125, and my external flash to 1/8th power. In addition, I had Cassie hold up a small reflector on the right side of the backdrop. This reflector allowed some of the flash's light to be reflected back toward the frog from the side, ensuring that the frog's stomach was not underexposed. Finally, and most importantly, I placed the frog on the penny and shot the photo.

This was the RAW photo straight out of the camera. At this point in time, no post-processing had been done. As you can see, the overall temperature is rather cool (meaning there is a blue tint), and the subject is rather small and dull. This is to be expected. As I mentioned earlier, I shoot using the RAW format. Generally speaking, RAW photos tend to be dull and flat.

So why shoot in RAW? The benefit of shooting RAW lies in the flexibility of this file type. The RAW format records a lot of detailed color data, which is what you want. The downside is that the straight-RAW photo is almost always dull and flat; the data is there, but it is "compressed." This means that a RAW photo must be edited to bring out the colors and details that are already present in the file's coding, but just subdued.

We now have the RAW photo, so next we have to begin editing it. For this part, I use Adobe Lightroom. First I remove the chromatic aberration in the photo. Then I crop the photo to get rid of any excess space. Finally, I begin to do whole-photo edits to the exposure. For this part, I first changed the temperature of the photo by making it warmer, as it was initially too cool (i.e. too "blue"). Then I decreased the highlights, brought the shadows up a bit, and then increased the saturation and vibrancy a tad. For my final edit at this stage, I increased the whites a great deal. By increasing the whites, the white paper backdrop began to lose detail. I didn't want the viewer to look at the background and be able to tell it is a piece of paper. I want the focus to be on the frog and the penny, not the background.

Next began the spot editing portion. When shooting amphibians with a flash, their moist skin tends to result in blown out areas. In an attempt to remedy this, I used Lightroom's brush feature to go in and highlight the overexposed or blown out areas of the face, which you can see in the photo above. I then decreased the highlights, shadows, and overall exposure of this highlighted area to recover some of the details that would otherwise be lost.

After this was done, I began using another post-processing program called the Google Nik Collection. Nik is a powerful program that used to cost nearly $200, but Google recently bought it and made it free to use! If you are interested in downloading it, check out this link: Nik Collection. I use it as a plugin for Lightroom. The first Nik plugin I use in my workflow is called Dfine. Dfine is a very useful plugin which "intelligently" smooths out unwanted grain and noise in the photo by automatically analyzing and spot-editing the noise. It's a super useful plugin.

Next I use another Nik plugin called Viveza. This program allows you to do more whole-and-spot editing. Like I said before, I wanted to lose all detail in the background and have it only exist as a white color. To work toward this goal, I added nearly 20 "control points" to the background using Viveza. Viveza has this awesome setting where you can view where your control points are exactly altering the photo. If you look at the photo above, you can see that some areas are super dark, while other areas are super white. Portions that a control point will greatly influence and alter will show up white, while portions that a given control point won't alter will be black. As you can see, the background is white, while the frog is black. That's exactly what I wanted for now. I then turn this informational view off and decrease the "Structure" setting in Viveza. The Structure setting can either bring out or strip away fine details in a photo. By decreasing the structure in the background, I'm washing away any remaining detail of the paper I used.

Then I do the exact opposite with the frog. I want the fine details of the frog to show up crisp and clean. To do this, I add several control points to the frog, using the helpful informational display to ensure that I'm only going to affect the frog and not the background. After making sure the frog is covered adequately, I switch off this informational display and increase the structure of the frog.

I save the photo file from Viveza and then open it back up in Lightroom. By this stage, I'm almost done with post-processing and all that remains are any trouble areas that I missed up to this point. I noticed that my flash reflected oddly in the bottom half of the frog's eye, giving it a gray wash in the bottom half that stood out in an unattractive manner. I used Lightroom's brush feature to try and tackle this problem. I applied a total of 3 separate brush areas to the eye, each with a different set of edits. My goal was to get rid of the gray wash that covered the bottom half of the eye.

Before (left) and after (right).

By using a combination of darkening the shadows, increasing the clarity, decreasing the highlights, and decreasing the brightness of the problem area, I was able to get rid of the gray wash that was a byproduct of my flash. Now the eye looked normal!

And finally, after about 20 minutes of editing, the final product was nearing completion. The only remaining steps were to export the file to a JPEG format, apply some slight sharpening to the entire photo, and add a watermark. And with that, the photo is done.

Taking a photo is only half the battle in photography. Post-processing is an integral step in creating a finalized product that the photographer is happy about. The world of post-processing is complicated, however, with an array of programs available and nearly unlimited stylistic choices and tools to utilize. Hopefully this post gave you a window into my personal workflow. Although the details vary from photo to photo, and case to case, the overall process I explained in this post is how most of my photos are generally post-processed.

The Red-Backed Salamander, Plethodon cinereus

I've been wanting to do a big post on a species of amphibian that is near and dear to my heart for awhile now. With the semester coming to an end, I've finally gotten the chance to write it. This post is all about the Red-Backed Salamander, Plethodon cinereus. My aim is to give a general overview, with some interesting detailed bits, of this incredibly common species. Why is it so special to me? P. cinereus is the first species I've ever had the chance to do real research on. Starting back in the fall of 2014, I began a job as an undergrad research assistant at Ohio University. I work in Dr. Shawn Kuchta's lab under Maggie Hantak, one of Dr. Kuchta's Ph.D students. It's been an incredibly fun, and incredibly educational, experience so far. I'll talk more about her research and what I do at the end of this post.

That aside, let's move on to some basics! Be warned, this is going to be a really long post.

The Red-Backed Salamander, Plethodon cinereus, is a terrestrial species of Plethodontid salamander. As with all other salamanders in the family Plethodontidae, the Red-Backed is lungless. Since they lack lungs, respiration instead occurs across the skin and the lining of the mouth. For these salamanders to breathe correctly, they must remain moist so gas can be exchanged freely across the cells in the skin. As a result, desiccation (drying out) is a constant threat to this salamander. In order to remain moist, they must inhabit areas that meet a certain threshold for moisture. These salamanders can be found in deciduous forests, mainly under rocks and logs where moisture is retained. When it is wet enough, they will travel throughout the leaf litter on the forest floor in search of food. During the summer months, when the heat dries out the top layers of the forest floor, P. cinereus will move into the ground, using old worm burrows or possibly making burrows itself.

P. cinereus is an incredibly abundant species in the forests of the Northeast part of the US, and it can be found in nearly every county here in Ohio. In fact, P. cinereus is thought to be the most abundant vertebrate species in the Northeast quarter of the US. They can reach densities of 2.8 individuals per square meter in good habitats, making this species more abundant than birds and mammals combined. In addition, there is some compelling evidence that the 2.8 individuals per square meter number is actually an underestimate; it might be double that number (See Semlitsch et al., 2014)! It is important to note that the bulk of a given population of Red-Backed Salamanders lives below the surface, so trying to accurately estimate a population is difficult when you can only find those individuals who are on the surface (See Taub 1961). When Maggie and I travel to a good location in Northern Ohio, we can normally find at least one individual under every rock or log you flip. It's amazing to think that all those individuals we readily find under cover objects represent only a fraction of the individuals actually living in that location.

The two common morphs of the Red-Backed Salamander, with the red-stripe morph on the right, and the lead morph on the left.

One of the really interesting characteristics about this salamander is its color polymorphism. Polymorphism is where there are two or more clearly different phenotypes (an individual's set of physical traits) in a species. Generally speaking, P. cinereus exhibits three color morphs. First is the red-stripe morph (pictured above on the right). This is by far the most common morph. The second most common morph is the lead (or lead-backed) morph (pictured above on the left). The third morph is the erythristic morph, which is very rare. The erythristic morph is essentially all red with a creamy white stomach. In addition to these three morphs, there are several other rare color anomalies: iridistic, albino, leucistic, amelanistic, and melanistic. You can read more about the different color phenotypes in J.D. Moore's paper here.

As stated previously, the red-stripe morph is by far the most common, especially in Ohio. There are, however, many polymorphic populations. Northern Ohio has a relatively high density of polymorphic populations, where one can find both the lead and red-stripe morph (and occasionally the erythristic morph) all living together in the same location. The ratios between the morphs vary according to each site. Interestingly, there are a few all-lead populations in Ohio, such as the population on South Bass Island. This is not a common occurrence by any means.

There is an extreme amount of color variation not only between color morphs, but also within the morphs and anomalies. At some locations we visit, the red-stripe morphs have a very bright and well defined red stripe. At other locations, the red stripe is very mottled and dull with high amounts of black across the body. On the other side of the coin, the leads at some locations are a very dull and subdued black, while other locations have very iridescent and beautiful leads, like the one pictured above.

Unlike many salamander species, P. cinereus does not have an aquatic larval stage. The entire life cycle is terrestrial, and that means we run into many juvenile individuals when in the field. And the juveniles are cute. Extremely cute. Pictured above is a small (yes, small) adult red-stripe individual next to a juvenile lead individual. Many of the juveniles we find could easily fit on a penny.

Most, but not all, salamanders lay eggs, and this includes the Red-Backed Salamander. When we measure the salamanders, we are able to see the eggs of any pregnant females. These eggs can be very pronounced, as the photo above shows. If you count carefully, you can see a total of 8 eggs (the white blobby things in the abdomen) in the individual above. As mentioned earlier, while many salamanders have an aquatic larval stage, the Red-Backed is completely terrestrial. The eggs are laid in a protected area, mainly in rotten logs. There is a larval stage, but this stage happens completely in the egg. Upon hatching, the juveniles are fully developed and essentially a smaller version of the adult.

How do you tell the sex of a Red-Backed Salamander? There are a few differences between the two sexes, but the easiest way is to look at their heads. Females have a very round snout. Males, on the other hand, have a very broad, square-like snout, which you can see above. Another feature to look for is the presence of cirri. Cirri (singular cirrus) are a fleshy downward extension of the upper lip. Cirri function as chemoreceptors, and the males use these for a multitude of reasons, most commonly to sense out a potential mate's pheromones. You can see the cirri on the male above; they are the two tiny, mustache-like extensions hanging down on either side of the snout. As always, you can click on a photo to view a larger version of it.

One of the incredibly interesting characteristics of salamanders is their ability to regenerate whole limbs and parts of major organs. It's a tough world out there, and salamanders can lose parts of their body due to predators, but also due to fights with larger salamanders. Red-Backed Salamanders are known for being fiercely territorial, and they will defend their territories against many different intruders like the Northern Ravine Salamander, Spotted Salamanders, or centipedes, occasionally resulting in the loss of limbs. The tail is the part that is most often lost, like in the individual above. When it comes to tails, salamanders are like lizards. When in a situation with a predator, the Red-Backed Salamander will wave its tail in an attempt to get the predator to go after that part instead of elsewhere. As soon as the predator latches onto the tail, the tail pops off giving the salamander time to escape. The tail wiggles violently for a short bit to confuse the predator even further in order to hopefully allow a safe escape for the salamander. Salamanders can regrow legs in only 7-10 weeks, but tails take a little long due to their size and how much actually comes off. The individual above (who was found in the Fall) probably has a fully regrown tail by now.

While the Red-Backed Salamander is a prey item for many other animals, it is still a ferocious predator itself. I'm currently in the middle of a dietary study that aims to find out if there is a difference in the type of food the red-stripe and lead morphs eat. The Red-Backed Salamander eats a large variety of arthropods, although I did find a weird one who ate a mushroom. The photos above give you an idea of some of their usual prey items. On the far right is their favorite type of food, mites. There's an incredible diversity of mite species on the forest flood, and the salamanders will eat many of them. In the center are Springtails, another favorite. On the far left is a pseudoscorpion, one of the more awesome-looking arthropods they eat. In addition, they also consume ants, beetles, assorted tiny wasps, spiders, and more.

One of more interesting individuals we've come across so far this Spring is the one pictured above. We had traveled to a location where around 15% of the population was erythristic (an unusual reddish or orange coloration). While we didn't find any completely erythristic individuals, Maggie did find the one above which exhibits partial erythrism. Note how most of the body is a red-orange, while the stomach is a creamy white. There's too much black on the individual for it to be considered completely erythristic, but you can tell it is definitely not a normal red-stripe individual. If you're interested in learning more, partial erythrism and erythrism in general is covered in the J.D. Moore paper that I linked to earlier in the post.

Several weeks after I wrote this initial post, we came across another interesting individual, pictured above. This is what has been called the "Silver-Striped" or "Silver-Backed" variant of the Red-Backed Salamander. As you can see, the stripe running down the back in this individual is a silvery-grey color instead of the normal red color. Sadly there's not much information I can find on this color abnormality other than assorted photos of similar individuals. Vincent Farallo, an Ohio University graduate student, did tell me that he has seen a lot of individuals like this at Strouds Run State Park in Athens County.

Maggie Hantak measuring a Red-Backed Salamander using a method termed "Mander-Mashing." Seriously. (No salamanders are harmed in this process.)

As I mentioned earlier, I currently have a job as an undergrad research assistant. My job is essentially to help Maggie Hantak, a Ph.D student at Ohio University, collect data at her field sites in Northern Ohio, as well as working independently on a dietary study for her. In a nutshell, Maggie is exploring multiple facets of the evolutionary ecology of the Red-Backed Salamander with regard to the differences between the red-stripe and lead morphs. She's been a wonderful mentor to me and has helped me get involved in real research. I'll be spending the first half of this summer in Northern Ohio as her field assistant, with the last half spent down in Athens to try and finish the dietary study. I'll also hopefully have the opportunity to begin my own research on Plethodon electromorphus, the Northern Ravine Salamander, this summer.  As of October, 2016, I am beginning my own independent project on the Northern Ravine Salamander. Stay tuned for more information in the upcoming months!

I've got several more salamander posts in the works that I'll hopefully be finishing up sometime during Summer, so if you're a herpetology person, stay tuned! Otherwise, I'll be covering the usual interesting things I come across this summer, including flowers, birds, insects, parks and more. Thanks for reading!