Genetics, Aggie Style

Since my last post, I've not spent too much time in the field. Rather, I transitioned from the field into the lab as well as focused on my coursework. I took some pretty awesome classes this past semester: conservation biology and wildlife nutritional ecology. I definitely feel like I've got this grad student thing down, what with the sixteen page exams I've been writing. It's great! And, I'm pretty stoked at the 4.0 I've maintained the first year of grad school.

Whoa! I finished my first year of grad school! Awesomesauce!

I love school so much, I opted to spend my spring break doing even more work. Not that any grad student actually gets to take university breaks, but I was excited nonetheless. Last semester, I contacted Dr. Jan Janecka at Texas A&M University. Dr. Janecka is a research professor in the molecular cytogenetics and genomics laboratory within the veterinary research department. He's done a lot of work in population and conservation genetics, but has a particular interest in wild felids. Dr. Janecka was gracious enough to let me spend two weeks in his laboratory working on bobcat genetics in order to help me learn more about the techniques necessary for my thesis. It was a very rewarding experience. I spent most of my time with a visiting Mongolian PhD student, Narka, who is doing similar genetics research on Eurasian lynx (Lynx lynx) in Mongolia. Together we prepared numerous samples for sequencing, attempted to teach language to one another (my Mongolian is really wretched, but his English so much better), and navigated the famous Aggieland. We also showed our field research photos to one another. Dr. Janecka has done extensive research on snow leopards (Panthera uncia) in Mongolia, and Narka has assisted radio-collaring snow leopards, Pallas cats (Otocolobus manul), and lynx. As a result, I am plotting on how I might end up in Mongolia.

I really enjoyed this externship because of the quick learning curve and high expectations. Dr. Janecka will also sit on my thesis committee to further advise me on the genetic component of my research, as he has an affinity for and a lot of experience with bobcat (Lynx rufus)  research. I was able to assist him on a current research effort as well as learn about tiger, snow leopard, and Mongolian horse genetics. I focused on techniques relevant to my research questions, using exceptional equipment and learning the what and why and how of microsatellite research. I am very fortunate to have been invited to learn in one of the best labs in the country.


Once I created the serum samples of several bobcats' DNA, I created working dilutions of those samples to be used in sequencing.



 Pipetting primers into each sample for the polymerase chain reaction.




Stand back! I'm about to try science!

I didn't catch a photo with my new friend Narka, whom is back in Mongolia and is by now beginning his field research. Like me, he was new to genetics and Dr. Janecka has been most helpful in getting us started. I knew I wanted to work in laboratory research after my internship with the Smithsonian, but I didn't realize I would think genetics equally cool to endocrinology. I gotta say, I'm pretty fascinated with what genetics can teach us. 

At the end of my visit, I attended the Ecological Integration Symposium, a conference focusing on the application of ecology in a changing world. Like any good conference, the beer social was hosted at a professor's home and students and professors alike mingled and discussed hobbies and research. I learned a lot about solifugids (camel spiders), other invertebrates, reptiles in South America, and more. A&M also has some very bright students working in marine biology. The plenary talks and session talks covered several taxa, ecoregions, and interesting questions. This was my third research conference, and I'm looking forward to many more. This time next year, I hope to be presenting!

After my two weeks in Aggieland I see what the hype is all about. Its a pretty cool little town. Great research, great people, and great beer (my advisor, Dr. Matlack, knows I like beer with conservation). 

This summer I will be working with one of my advisors, Dr. Rocky Ward, preparing my samples and testing my newly purchased primers. I will also be live-trapping for bobcats and gray foxes. I recently caught my first bobcat, so look out for that post!

Dr. Janecka contributed to a really beautiful book on snow leopard research called Snow Leopard: Stories from the Roof of the World.  Click the link to check it out!







Field Efforts

A lot has happened in the past month. We have been so busy! Mark and I started our respective field efforts together in the middle of January, and we've been going non-stop through a combination of field trapping and office slaving. The beginning of the season was darkened with the passing of my Granny, a 91 year old southern aristocrat with a sassy attitude and mischievous smile. We will always miss her feisty nature and love of the country.

Mark and I began the season nonetheless excited about what we might encounter, and it's been a little crazy. In a 16-day trapping effort we've caught five foxes, five raccoons, one skunk, and a few narrow misses with those damn bobcats and ringtails... and at least one feral hog. Those damn, invasive hogs!

It's been an awesome skills test for both of us to recall our experiences with blood drawing. Of course, we both visited the veterinarian who sits on our IACUC committee (the committee that approves our animal-use tactics and ensure we are complying with animal welfare regulations, etc) for a refresher prior to going out in the field. Here is the general breakdown of how things have been going in Palo Duro Canyon State Park:

This was Day 1 when we were setting traps. This little gem is the first of my bobcat traps (photo taken before the masterpiece was actually complete/covered). This was when I was still hopeful that catching those silly cats was going to be [relatively, maybe, oh god hopefully] easy. 

First trap night! This little Gray Fox (Urocyon cinereoargenteus) was a feisty little lady. She was relatively young, likely in her first year, and easily drawn into our trap with the tasty sardines we use as bait. Gray foxes are really cool little critters, being well adapted to a variety of environments but preferring dense cover to avoid predators (particularly bobcats and coyotes). Gray foxes are omnivores and eat a variety of small rodents, opportunistic meals like roadkill or cached kills from other predators, as well as a lot of plant material and berries. The majority of gray fox scat I have found in this area is primarily composed of cactus berry remains. These little guys don't really live too long in the wild, between 2-4 years, and are adept at climbing trees and dashing about on the cliffs of the canyon. This was my first fox encounter! Mark was super helpful in walking me through the anesthetization process, as it had been a while since I'd last processed wildlife. I love this picture because the fox is kind of 'looking into the future' because of the anesthetic. This photo was snapped after taking morphological measurements and obtaining genetic material. All captures are monitored closely for changes in temperature, heart rate, and respiratory rate. Most procedures take 25 minutes. Animals are not harmed from data collection. Participants even get a free meal! In winter, the extra fat and protein from the sardines can be particularly helpful for these little guys

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And when you purchase your Gray Fox package with just three easy payments of $64.95, you also get this really nice watch.

Pretty little fox face!

Mark is pulling out delicious sardine fillets to bait a trap for ringtails (we only caught foxes at this one trap, however). You can somewhat reference the cliff we are on based on the background.

Another day, another fox. This day we caught two! The traps were right near one another, and we had both a male and a female in each trap, so we suspect that these two were a mated pair (they were of a similar age). Gray foxes, like a lot of their canid cousins, are monogamous for life. Here, Mark is pictured with the healthy male. We ear tag all processed animals to eliminate re-processing of individuals. 

Our good friend and lab mate Lena is doing her thesis work on bobcat anthropogenic structure use. We had a lot of fun doing this work-up together and getting a few good pics with this little guy. We don't always photograph animals because each individual responds to the anesthetic differently. In this photo, the fox appears to be awake, but is in fact sedated. We use eye drops to minimize drying, and we never interact with animals in a way that compromises our safety or their well being. 

I traveled to North Carolina for a few days in January to attend a family event, and while I was gone Mark caught a skunk! Here, he shows just how gorgeous (anesthetized) skunks are! He did smell a little funny when I came home, however...

We're really lucky to have volunteer interest in our projects. We're able to have undergraduate students join us in the field for both educational and enjoyable experiences, and everyone is able to learn and share. Clay Rushton is a freshman at West Texas A&M... awesome that he's starting to get in the field early! This little fox was caught in a trap meant for bobcats.

We document all sorts of morphological measurements as well as any new or old injuries. This little gal had an old scratch under her eye, but it didn't make her any less gorgeous!

We monitor temperature, heart rate, and respiratory rate as an assessment of how the animal is responding to the anesthetic. Anesthesia makes temperature regulation a little harder, and in harsh conditions, this can be a problem. It was really cold this day and our little fox needed some assistance in staying warm while under the anesthesia. While this is in no way an emergency, we take it very seriously. The anesthetic we use rarely has serious complications in the species we are studying, but nevertheless Clay got to sit with our fox a bit longer while she was still sedated to help warm her back up (she's in his lap). 

Cue the "awwwwww." How adorable is this guy? This was my very first raccoon !He was enormous, I mean absolutely huge. He was twice the size of my house cats and weighed 20 lbs. To give that some perspective, my foxes weight 8-9 lbs. I have always marveled at the dexterity of their 'hands,' and I am so fascinated at what these animals survive out there in the harsh wild. This old guy had a dental infection, unrelated to being trapped, but was still in good health. Another freshman volunteer was also able to experience his first raccoon as we assisted Mark on the work-up of his study animal. 

Other incidents not photographed include a feral hog messing with one of my traps (those darn hogs are so destructive), seeing my first feral hog (I ate one in Missouri and got close to some but never actually saw one), and chasing a rooster through a field with Mark. We released a few animals because of the weather a couple of days... the Panhandle is so windy! Some days were just too brutal to try and process an animal that we just let them go. Mark has captured one little raccoon three times already, and I've recaptured one of my foxes. So far we have not trapped bobcats or ringtails, but a grad student saw a bobcat the day after I closed my traps! I'm trying to catch one in particular who hangs around a campground in the park, and naturally she shows up when my traps are closed! Such are the joys of wildlife research.

I'm really excited to broaden my sampling area with the assistance of Texas Parks and Wildlife biologists, and I'm testing out a DNA amplification protocol in the lab. I am planning to get back out in the field at the end of the month. Next week I'll be traveling to Houston with some of my fellow students to attend the annual meeting for the Texas chapter of The Wildlife Society. It's going to be so much fun! Lots of students at West Texas A&M will be presenting their research and I can't wait to learn about the research going on in this state. 

I'm also stoked to announce that I'll be spending two weeks in March at a genetics lab at Texas A&M focusing on microsatellite research. The professor I'll be working under has done a lot of amazing research on felids, both nationally and internationally,  as well as helped develop the first conservation genetics lab in Bhutan. More updates soon!

Field Day Prep

ZOMG! Tomorrow is my first field day as a graduate student! I'm so excited. Mark and I will be setting some wildlife traps in hopes of catching a variety of species. It's currently 19F outside and dropping, and with 2" of snow yesterday, it promises to be rather chilly! Now if only I can find my thickest baselayer pants.... no seriously, I've torn the house apart and I can't find them...

New Year, New Adventure

It's been an intense few months, and they have passed far more quickly than I realized. My first semester of graduate school came and went in a whirlwind, and I've been busy with fun classes, new friends, and a few adventures.

Primarily, I've been working on the experimental design for my thesis. Ultimately, I've learned what NOT to do in science in terms of creating and implementing an experiment, and it's been super duper cool to sort it all out. In a nutshell, I'll be examining the effects of the landscape on the gene flow of bobcats, gray foxes, and coyotes in the Panhandle of Texas. Specifically, I'll get to look at the escarpment, which is the region of the landscape that separates the High Plains from the Rolling Plains in Texas and is part of the second largest canyon system in the United States. Basically, I'll be sniffing around a mini-Grand Canyon looking for mesocarnivores. I start my field efforts in two weeks, and I can't wait to collect samples for laboratory analysis! I am most excited about seeing wildlife again... I've been in the classroom most of the semester, with the exception of a few test scat transect runs with undergrads. It's going to be a seriously intense field effort because I'll be taking classes at the same time, but Mark and I will be helping one another out.

Mark will be looking at the genetic structure and ecology of ringtails, as well as investigating similar aspects of gene flow in raccoons and skunks. I've only seen a ringtail once, and I have zero problem being his field assistant if that means I get to handle one of those little guys! Mark has a lot more trapping experience than I do, so I'm looking forward to brushing up on my injection skills from undergrad and hopefully becoming super efficient at catching every living animal out there!

Although I've primarily been in the classroom and office this semester, I did manage to sneak in a few more adventures:

 
Lena Thurmond is another graduate student in my lab, and she's looking at the use of anthropogenic structure in a bobcat population. She let me help out on one of her captures... it's been over a year since I've seen a bobcat, and I was so elated!

 
A few graduate students and undergrad volunteers with our advisor, Dr. Matlack, and one of Lena's cats. This big male was radio collared for Lena's research. For me, it was really cool to see firsthand the wide-open habitat these cats are navigating- it's a far cry from the montane forests of the northwest US!

 
I was mildly concerned one morning when an undergrad threw herself out of my moving vehicle, but it was to grab this 4.5 ft long bull snake out of the road. I don't have a lot of experience with snakes, so I was pretty stoked to handle her and not get bitten.


 This landscape is just awesome. I'm sitting on top of some huge rocks within Palo Duro Canyon State Park on a morning I took an undergrad out to search for scat. So far, my searches have yielded primarily coyote scat, but here I'm collecting a gray fox sample. Since coyotes are difficult to live-trap, I'll be using scat to extract DNA for that species.


 
Like I said, this landscape is just amazing! No trees, deep fingers of canyon digging into the earth, crazy dirt formations shooting into the sky, and plentiful wildlife. This was my first "field day" as a grad student on my own project, and these two undergrads were crazy enough to go out with me! They helped me run a road scat transect (because wildlife often travel on roads) and learned about scat and track identification of carnivores. 

We'll be tightening up our schedule for trapping effort next week, and I'll be coming back to civilization most nights, meaning very soon that I will be once again posting cool photos and recounting tales of my glorious mishaps!

I'm currently sitting at my grandmother's kitchen table in North Carolina. Being a tough biologist and all, I opted to not get the flu shot, so I naturally came down with easily the worst flu virus I've ever had. I rang in the new year with NyQuil and saltines (ok, and a little bubbly), but it's gonna be a good one! I really am proud to say that I accomplished my goal to enter graduate school in 2012, and I'm lucky to have been able to design my own project from the ground up based on my own idea. I've already done good things this semester, and I have amazing prospects for spring and summer. As I sit here watching cardinals, the state bird of North Carolina, dance about on the front porch, I'm rejuvenated by and excited for the wildlife I'm sure to encounter this year. And, I got my rabies vaccination, so no one has to worry!

Happy New Year friends!

Amarillo News Channel 10!

This morning I visited the local Amarillo news station with my advisor, Dr. Ray Matlack, to watch him film his weekly educational segment,  "West Texas Wild." I got a behind-the-scenes look at the blue screen, the cameras (all taller than me), and I met a few of the news anchors. We hung out all morning comparing wildlife stories and discussing tornadoes with the storm-chasing meteorologist (he is braver than me!). Afterward Ray and I scoped out some waterfowl on a flooded lake; it's been raining all week and numerous species are very pleased with the churned sediment and elevated water levels. Be sure to tune in every Friday morning to learn a little more about wildlife in the Panhandle of Texas, and be on the lookout for more videography and educational films, because Ray and I have plans, and soon I'll be coming to a television near you!


Sequoia National Forest, Week 1

The end of a run is almost as busy as the beginning of a run. For us, a "run" is classified as a four week period in which Primary Sampling Units, or PSU's (defined in our training book, by the way, as "a unit which is primarily sampled"...), are set and checked once every seven days. Each PSU consists of three stations, and each station has one each of a camera trap, bait, and hair snags, as well as a track plate box to collect the tracks (and hopefully hair) of whomever or whatever decides to enter (or, more commonly, destroy) the box.

The end of Run 1 saw everyone arriving on that Friday sweaty, dirty, and smelly... well, that's not particularly any different from field days all over the world, but the end of a run involves pulling all field sampling material and organizing (organizing?!) data by the end of business, so we were all rushing about. Luckily, we had a week of office work between runs.

The office week included sorting photos ("is that a cow?"), washing track plates, organizing all written data for each PSU, and re-sooting track plates. Our track plates are metal sheets burned with an acetylene torch, the result being a black ash that gets on the paws of an animal and is then pressed onto sticky paper as it walks through the track plate box. I was really excited to learn how to use the torch, as it was highschool the last time I touched one. In learning how to use the torch, I was reminded of our oxyacetylene lesson in highschool in which  one of my fellow classmates caught his pants on fire and didn't realize it until the flames were licking up to his thighs. No one was hurt too badly, so I can laugh in hindsight, but the acetylene torch is no joke and a lot of caution goes into sooting track plates.

With trucks cleaned, blisters healed, and new partners, we embarked south into Sequoia National Forest!

 For this first week I was assigned SCA volunteer Katy, a really awesome chick with zero fear and an intense love for soccer. We were stationed near an area known as "The Needles." The name comes from the intensity of the granite peaks that cap the landscape. Additionally,  the lines on the topographic map are so close together that it looks like needles drew it!

 
The Needles

 Sequoia is lower elevation that Sierra, and as a result it was HOT. Our first day of sampling was in an area similar to rolling plains in that it was entirely open and the majority of the vegetation was a wheat-like grass (sorry, I don't know the species!). However, it isn't prairie land, so the hills were steep and there were actually a few trees. Because the hike was so long, however, we only got two of the three stations set. On the hike out, Katy saw her first rattlesnake! I tried so hard to get a decent photo, but he was almost five feet long and as thick around as my forearm, so my trekking poles weren't actually long enough for me to be very safe. I did get a decent audio piece, so I will post it later (I have a difficult time with video on this blog domain).
Katy on the hike out from our open site

 You can hardly see him, but this picture is a great example of why those rattlers are a good warning. He was HUGE!

I also found a little scorpion

We stayed at a remote little campsite at the center of our PSU's. Unfortunately, every week we returned, someone had left a bunch of garbage in the non-bear-safe containers and some critters had strewn the trash throughout the site. The first two nights of this week, Katy and I shared the site with two other crew members, Brad and Ben. We had an interesting time starting a fire with random kindling (I brought marshmallows) and chasing some curious cows away from our campsite. When Brad and Ben left, however, Katy and I were happy to have the cows as company, because the trash issue meant there was one very curious black bear who circled our campsite every night. We never saw him/her, but the animal made enough noise to convince us that it wasn't a raccoon.

The rest of our week involved my introduction to some pretty intense hikes (because of the way SCA's rotate, Katy was only with me for the install week). While I've always enjoyed a challenge, I don't think I've ever really had a hiking experience that I disliked in any way... until now. Katy and I had one hike that was 1500 m in to the first station, and it took us four hours to get down (yes, very, very down) because the landscape was literally a slide pf pine needles and rock drop-offs. Using the topo map wasn't very helpful because every time we thought we'd hiked up to a ridgeline, it dropped off again. Katy and I get along famously so the days were full of laughs and exploring and enjoying our surroundings as we completed our tasks, but this site was brutal. It could be the yellow jacket nest I stepped on first thing in the morning, or it could be that the hike out- scratch that- up, was one of the most intense I've ever done while working. Before you assume that it's either A) the worst thing in the entire world and that we are just that badass, or B) that is wasn't actually that hard and I'm just whining, remember that we were carrying fifty pounds on our backs! Despite the site being old growth forest and therefore shady, we both went through four liters of water each and were still dehydrated. However, the site was really beautiful... I just never got any pictures of it the entire run because it was so intense.

 The third day involved road drops... meaning that the hikes weren't very far from roads and we didn't have to suit up for all three at once. The drive out to our first site was easily one of the most beautiful I've ever seen! We were really in the heart of the Needles on this day. On the early morning drive, we saw several critters, including squirrels, tons of adorable cottontails, and one grey fox.

One cottontail was brave enough to let me lean out of the truck window and snap a few.

Katy and I thought our second hike would be as easy as the first one and that we would probably complete the day an hour earlier than usual. The hike in question was only 317 m from the truck! It was pretty much straight up, but the directions from the crew who did this hike five years ago said to stick to the ridgeline and avoid the brush.

Well.... it wasn't exactly that easy. The brush was everywhere! It was impenetrable. Manzanita is a real pain in the ass- it's similar to the northwest plant called Alder in it's rigidity, satanic nature, and desire to suck you into the earth (I'm only slightly kidding). The "manz" was uphill, sidehill, downhill. It was indeed a slippery slope. Looking at the topo map and comparing it with the written directions and drawings, we decided it would be best to scale some rocks and approach our site from behind. We climbed for about half an hour and dropped into a pretty little stream full of wildflowers:


 It took us THREE HOURS to hike 300m! THREE! We were not impressed with ourselves, and even less impressed with how overgrown the site was and how difficult it was to swim through the vegetation. But, it is wonderful wildlife habitat, and it if were easy everyone would be doing it!

Day four, by comparison, wasn't that hard at all. We had some longer hikes and a little confusion with abandoned service roads, but since it was a drive out day (that alone takes four hours), the sites had to be a little easier. Because the vegetation changed in the five years since it had last been serviced, however, we were unable to get to one of the locations in time because an old road was so overgrown.

I think this is a juvenile male western tanager. I tried so hard to photograph an adult tanager, but alas!

We had an awesome install week. It was really hard physically, but Sequoia National Forest is SO beautiful. We even saw a few Sequoias (we camped right by the famous Trail of a Hundred Giants). Here are a few landscape photos:

 View of the Little Kern River 

 Nature is so large and we are so small. It's beautiful.

 Searching for lizards!

We get paid to work here!


I'm definitely having a "top of the world" moment.