Data I’ll never publish: Antirrhinum herbivoryEric LoPresti

Cross-posted from Natural Musings. Read more and comment there!

Inspired by this post, I’m going to try to put the results of small (but interesting) experiments up here every once and awhile. In the summer of 2014, I spent a lot of time washing plants. I was – and still am – curious of the function(s) of plant exudates. I primarily did this with Trichostema laxum and Atriplex rosea (in 2013), but I also did it with Mimulus layneae and Antirrhinum cornutum (California snapdragon). The snapdragon gave me interesting results.

(this post should also be regarded as potential project for someone else: I started it in May – there is plenty of time to get up to McLaughlin and do it again this year).

One of the experimental A. cornutum, showing leaf damage.

This snapdragon, while not as heavily glandular as Trichostema or that Mimulus, is fairly glandular-sticky, even entrapping a small number of minute insects (see the table/supplementary material). Under the microscope, you can see the fairly dense short glandular trichomes (the longer trichomes are mostly nonglandular) on the stalk and flower bud.

Stem of A cornutum with an entrapped insect.
Flower bud showing short glandular and long nonglandular trichomes.

Wondering whether the glandular exudate is defensive, I did an experiment where I removed it with water. Most glandular exudates in CA summer annuals seem water soluble, so a spray bottle rainfall takes off much of the exudate (observationally verified in situ with a 20x loupe – plus whatever was in this exudate made suds on the plant!). This manipulation was my first treatment group. Of course, adding water to a plant has an effect of its own, so I also had a water control group, where I added the same amount of water below the plant’s leaves, as to not wash off any exudates. Finally, I had a true control group, which received no water whatsoever. I instituted these treatments on the 30th of May and reapplied them on the 17th of June. Each time, I recorded the number of leaves, flowers, fruit, and plant height, as well as any damage. I also checked the plants, but did not reapply treatments on the 2nd and 19th of July (the last check all were senescent).

During the experiment, plants suffered two main forms of herbivory. The first type, which was most common and most destructive, was that the stems were entirely clipped off. I’m nearly positive this was by jackrabbits (indicated by a single flat cut diagonally across the stem) and it usually killed the plant. The photos below shows what remained.

A killed experimental A. cornutum plant. See it?!? Its the little stem to the bottom left of the flag. Also notice a nice healthy Lessingia in the background. They, too, are extremely glandular and sticky.
A survivor of mammalian herbivory. If the meristem was not completely destroyed, they often came back and branched like this. Like the classic overcompensation “herbivore-plant mutualisms”, the resulting plants were often bigger than the others, with more reproductive structures, but unlike this “mutualism”, it was too late in the season and they had low fitness, as they could not mature these structures.

The mammalian herbivory was not random. Of the 25 plants per treatment, 11 in the control group, 13 in the rainfall simulation (exudate removal) and a whopping 20 in the water control group were eaten by mammals (this is nonlethal, lethally was 10, 12, 18). With a simple chi-squared test, we can demonstrate that this was likely nonrandom (X2 = 7.3688, df =2, p = 0.025) (for lethal, X2 = 5.5714, df=2, p = 0.062). Why were the mammals targetting the water control plants so heavily?

Were they bigger and thus easier to find or just more profitable to eat? They were not significantly different in height, fruit or flower numbers from the other two groups during any check. I don’t have data on plant quality (perhaps the less water-limited plants were more nutritious or something?).

The other type of damage was equally-interesting. Heliothis phloxiphaga is a generalist caterpillar on glandular plants. It was the primary herbivore on my columbines, as well as a common herbivore on Trichostema laxum and other sticky plants. Like most heliothiine noctuids, it feeds primarily (but not exclusively) on reproductive structures. I only observed it once on Antirrhinum (eating a fruit), but all the fruit damage I found was consistent with it (and that’s one more time than I saw a jackrabbit eat it!).

The other type of damage: caterpillar fruit predation.

I had hypothesized, that if the exudate were defensive, the washed plants would be most heavily eaten. This hypothesis was supported with the fruit damage. Rainfall plants received far more damage than the other groups. (note: I didn’t actually analyze this with zero-inflated binomial, as it should be. There is a problem, in that only 7/25 of the water control plants had any fruit at all because of the rabbits.)

A crumby excel graph of proportion fruits damaged.

What does this all mean? Obviously, it means that mammalian and insect herbivores are responding to different plant traits. What they are exactly, I’m not sure (especially for mammals). If anyone (nudge, nudge, wink, wink) were to repeat this experiment, with a larger sample size, and maybe some other mechanistic experiments (perhaps cage controls and lots more trait data to see what is different in the water control and rainfall manip groups), I think its a pretty good system that someone could get a paper – if not a few – out of.

GPS My Rattlesnake: A New and Exciting Research Project!

Cross-posted from Strike, Rattle, & Roll. Read more and comment there!

This is a re-post from a site created by Alex Bently (, an aspiring herpetologist who has started an ambitious project that uses GPS technology to track rattlesnakes. He is hoping to secure more funding for his work. Please consider donating. All the information below was written by Alex and can be found on his project website.  

Project Background

The field of Herpetology was revolutionized in the early 1970’s through the use of radio-telemetry (Újvári and Korsós, 2000), which, for the first time, allowed biologists to gather long-term detailed data on animal life histories, including home range size, activity patterns, intraspecific interactions, hibernacula use, and thermoregulatory behavior (Nathan et al., 2008; Ward et al. 2013). Recent advancements in GPS technology, however, have provided biologists with an exciting new window into the lives of animals (Cagnacci et al., 2010; Recio et al., 2011; Tomkiewicz et al., 2010; Urbano et al., 2010; Ward et al., 2013). Due to size issues, GPS tracking has typically been limited to use with large mammals (Recio et al., 2011), but new improvements in miniaturized technology has opened even more doors for novel applications.

Biologist with a radiotelemetry receiver. 

Admittedly, the unique body shape of snakes (e.g. long, cylindrical body and absence of limbs) poses unique challenges in attaching any external unit. Even so, biologists are beginning to experiment with this methodology and are finding some success (Ciofi and Chelazzi, 1991; Madrid-Sotelo and García-Aguayo, 2008; Wolfe unpub., 2016; Wylie et al., 2011). For example, Ernst (2003) used tape and 5-minute epoxy to attach transmitters to the rattles of Prairie Rattlesnakes. Other forms of attachment have been applied to the upper surface of snakes. However, no publications to date report the use of GPS tracking in any snake taxa even though this methodology has great potential to again revolutionize snake field studies, it just needs to be tested.

A beautiful Timber Rattlesnake (Crotalus horridus)

The Timber Rattlesnake, Crotalus horridus, has been a model organism in numerous studies (Clark, 2002). In fact, C. horridus was one of the first snakes species to be studied using radio-telemetry (Brown et al., 1982; Galligan and Dunson, 1979). This large-bodied pitviper snake is native to much of the eastern United States, and can be locally abundant sometimes occurring in great numbers at communal den and gestation sites. Throughout much of its range, individuals emerge from hibernation between the months of March and May, and remain active for five to seven months, with males spending their active season foraging for prey (mainly small mammals) and searching for mates. Females reproduce every three or four years (Martin, 1993) and during reproductive years they gather at gestation sites known as rookeries. These rookery sites, as well as hibernacula, are selected by snakes based on various geographical features such as aspect, slope, proximity to human disturbance, rock formations and more.

Researchers have found a high level of specialization in these snakes. For instance, individuals use chemical cues to track rodent movements and foraging locations (Clark, 2004; 2007). Furthermore, snake foraging positions and locations are specifically selected based on these chemical cues. So while most people think of snakes such as the Timber Rattlesnake as small-brained, “hard-wired” creatures, as we discover more about the complex functions and secretive lives it’s becoming clear that these snakes are highly sophisticated and specialized on many levels.

Moreover, C. horridus is a key stone species where it is found, playing a critical role in the ecological function of various habitats. Complex relationships have been noted between the presence of gypsy moths, cycles in oak mast production, variation in rodent populations, and Timber Rattlesnakes (McGowan and Martin, 2004). Crotalus horridus is an apex predator responsible for maintaining ecological equilibrium. A number of factors, including their ecological importance, physiological specialization, and relative wide spread abundance make the Timber Rattlesnake an appropriate organism for a wide range of ecological and biological studies. Furthermore, Crotalus horridus, should be an organism apt for testing the viability of GPS tracking in snakes.

What More Info Can GPS Tracking Offer?

Radio tracking still produces valuable data, however advances in technology have provided other tools for wildlife tracking that have the potential to resolve some limitations of telemtry. Among these, the use of GPS has emerged as a viable option for wildlife tracking. (Cognacci et al. 2010; Tomkiewicz et al. 2010; Ward et al. 2013). GPS tracking has several advantages over radiotelemetry. One such advantage is continuous data transmission through a number of mediums (cellular, bluetooth, and wi-fi). Moreover, the ability to obtain position time series data representing movement paths affords biologists more data and greater insights into the spatial ecology of organisms (Nathan et al. 2008). Position time data can now be obtained from a distance without disturbing the animals being tracked. Some GPS units, such as those that I will be using, have a “smart GPS” function, which logs position time data only when the animal moves a specified distance! The possibilities for field based applications are endless with this type of technology.

Custom designed GPS transmitters will be attached to snakes’
rattles using epoxy, tape, and light-weight zip ties. We hope
they stand up to field conditions!

Automated receiving units (ARU) have been used as an alternative to radiotelemetry in several snake studies, but have, in some cases, reported estimated accuracy of positions to 42 meters (Ward et al. 2013). Furthermore ARU is extremely expensive and can produces unreliable data as a result of “postural” changes in snakes and more.

Currently, GPS has been miniaturized to the point of telemetry, and thus is an option for  tracking much smaller animals. This method has  been applied to various mammals and birds (Tomkiewicz et al., 2010), however very little GPS tracking has been done with reptiles. Ashleigh Wolfe, a Ph.D. student at Curtin University, recently tested GPS tracking on Dugite snakes and experienced relative success in obtaining data (Wolfe personal correspondence, 2016). Wolfe implemented an attachment technique following that described by Ciofi and colleagues (1991), who also successfully gathered data from snakes with externally attached tracking units (radiotelemeters in this case). Ernst (2003, 2004) attached radio transmitters to the rattles of Prairie Rattlesnakes, Crotalus viridis. Rattle attachment is not a novel technique, but it’s never been done with GPS transmitters! GPS has the potential to once again revolutionize the field of wildlife biology. Now that the technology exists, the next step in snake tracking is to incorporate GPS.
A Timber Rattlesnake coiled in a mixed-hardword forest.
Such forests are often dominated by oak tree species. 

Alex’s project has three goals: 

  1. Test the application of GPS snake tracking by successfully tracking a population of Timber Rattlesnakes
  2. Determine if small scale population migrations made by rodents influence foraging patterns in Timber Rattlesnakes 
  3. Investigate whether oak-mast fluctuations influence rattlesnake populations through their effects on rodent populations (rattlesnake’s prey).
To learn even more about the project, watch the YouTube video below or visit to project website. With your help, we can learn even more about these mysterious and ecologically important creatures!

To support the project visit:

Please feel free to contact Alex with questions or concerns!

In the Black & Green at Stebbins ReserveAllie Weill

Cross-posted from What We Talk About When We Talk About Fire. Read more and comment there!

Note to local readers: Stebbins is presently still CLOSED to the public and is expected to reopen in early May. Please respect the closure and allow the ecosystem some time to recover. In the interim you can visit via a guided walk or as trail crew–see here for more information.

I have written a couple of times now about last summer’s fire at Stebbins Cold Canyon Reserve. It’s not a fire that you would have heard about on national news. It wasn’t very big, and it didn’t cause a lot of infrastructure damage. But I’ve been very interested in this particular fire, because it’s local. I can drive to the burn site from my house in about 30 minutes. In fact, I can take a quick turn off the street where I live and can then drive all the way to Stebbins on the same road. When the fire was burning, I watched the smoke sit heavy on the horizon from my front yard, and I watched ash fall from the sky like summertime snowflakes. Stebbins is a place where I and my fellow residents of Davis go hiking on weekends; it’s where I took a visiting prospective student to give her a taste of California ecosystems; it’s where my colleagues and I built a new citizen science program over the last few years. Stebbins has become one of “my places,” along with the reservation behind my family’s house in New Jersey, my island scout camp in the Adirondacks, Lake Michigan, and others.

In environmental education and related fields, we talk about one’s “sense of place.” Your sense of place includes your knowledge of a landscape, ecological or otherwise, how you fit into it, and your experiences there. I am interested in the fire at Stebbins because it is a major change in a landscape for which myself and many people around me have a sense of place. Not only has the color and composition of this landscape changed since the fire, but so has the way we interact with and experience this place.

I have visited Stebbins now three times since the fire: August 2015, November 2015, and February 2016, each time with a different group of people. Here is what I’ve observed so far:


Visit 1: August 2015 (just 2 fire ecologists)

My first visit was about a month after the fire. I stopped by with a friend who has worked on the CPP-Stebbins citizen science project on the way to do some fieldwork for my dissertation research, just up the road. We were two fire ecologists, and we were excited to be there. The most striking thing was how the landscape had opened. I could suddenly see hillsides stretching up high to both sides, and out beyond the trail. Before, trees and dense shrubs blocked that view. Most trees still stood as they always had, but many shrubs were skeletons. We saw crisp blackened leaves still hanging on the trees and ash covering the ground. The bulletin board near the entrance had become a window, and fiberglass posts marking phenology trail plants had exploded–proving that they were, indeed, made of fibers. And amidst the brown and black and grey, even in the dry heat of California summer only a month post-fire–during a drought no less–was green. Green sprouts on a hillside of black soil, green sprouts at the base of trees, and green sprouts from the branches of a California buckeye! The buckeye wasn’t supposed to have any leaves at all in the summertime! We poked at resprouts and talked fire ecology until we reached a point where the trail was covered in debris, and we headed home.

Visit 2: November 2015 (citizen scientists)

In November, I put together a visit for the volunteers for our citizen science project, the California Phenology Project at Stebbins. These volunteers had been taking data on the timing of leafing out, flowering, and fruiting for a year before the fire, and they were eager to visit. We had a group of about 15. Our mission was to see how the reserve had changed, to take an informal inventory of the plants that they had monitored, and brainstorm how we might begin to do citizen science again post-fire. Though we’d had rain at this point, the landscape didn’t look too different than it had in August. The green sprouts were taller. Ladybugs had taken up residence in the remains of a shrub.

But this time, I got to watch a bunch of people who had developed a very strong sense of place in this landscape see how the place had changed. I had adopted Stebbins as my own over the past couple of years, but I didn’t really visit all that often. Our volunteers were out there every month, or every couple of weeks. They had a routine. They observed their plants closely. They knew them well. I had been concerned that we’d need to use GPS data to find the plants that they’d monitored, but I needn’t have worried. I watched with amazement as the volunteers identified the location of nearly every plant–chatting amongst themselves, “No, that toyon was definitely by this rock here” or “This is where one of the monkeyflowers was, I’m sure of it.” In the end, we located all of the plants except a few monkeyflowers, which would have had the least protection of any of the plants during a fire. For the volunteers, they not only saw the broad landscape change, but they could pick out changes to individual plants.

Visit 3: February 2016 (fire ecology students)

My most recent visit was less than two weeks ago, a little more than 6 months post-fire. I tagged along on the class field trip for UC Davis’s fire ecology course. It was obvious from the moment we got there that there had been big changes: there was lots of green. The shrub skeletons remained, but grass and moss had filled in between them on many hillsides. California poppies colored some slopes yellow-green. We paused every hundred feet or so to get the name of another wildflower. I saw tiny, half-inch seedlings of the Ceanothus species that I am germinating (with fake fire!) in the lab. Not all was green–some areas are still pretty black and brown. But other places are brighter green than I’ve ever seen them. One hillside was covered in moss so colorful and soft that a student and I agreed that we should like to take a nap right there, on the new green carpet that had sprouted under the burned out chamise. It was so cool that I went home and googled “fire moss regeneration,” but I didn’t find much–just papers about fires in peat.

Over the course of three visits, I’ve built on my sense of place at Stebbins, watchning how it has grown and changed so far. I’ve seen changes to the landscape view–the macro scale–and to branches of individual trees–the micro scale. And I’ve watched other people build their sense of place, too.

I’ve been in several post-fire landscapes before–including several on a much larger, more newsworthy scale. I remember seeing the effects of the Yellowstone Fires in about 1998 with my family, ten years after those huge fires shaped national perceptions of wildfire on the landscape. More recently, I had the opportunity to explore high-severity areas of the Rim Fire in Yosemite. I learned a lot in those landscapes. But there is something truly special about watching a fire change a landscape that you know well, that you can visit by driving down the street for half an hour. That’s what a sense of place is all about.


Books on parasitesKelly Weinersmith

Cross-posted from Weinersmith. Read more and comment there!

I’m often asked by students to suggest books they can read about parasites. Below is a list of books that I’ve read and enjoyed. The list will be updated over time. Please feel free to suggest books that I should add to the list in the comments.

Textbooks or textbook-like books



Host Manipulation by Parasites edited by David Hughes, Jacques Brodeur, and Frédéric Thomas


Foundations of Parasitology (textbook) by Larry Roberts and John Janovy Jr.


Evolutionary Parasitology by Paul Schmid-Hempel




Parasitism and Ecosystems edited by Frédéric Thomas, François Renaud, and Jean-François Guégan (thanks to Alex Ley for reminding me to include this great book)


More pop sci-esque parasite books



This book played a huge role in my decision to become a parasitologist. Highly recommend.



Stories about how we become connected to our parasites through our long co-evolutionary history.


People, Parasites, and Plowshares by Dickson Despommier


This book is about one of my favorite topics: What have parasites “learned” through the process of natural selection about how human physiology works? How can we take the lessons these parasites have learned and use them to treat human disease?



Amazing stories of past and present parasites that jumped from wild hosts to human hosts. Also lots of stories about scientists being badasses.



Robert Desowitz talks about his experiences working with parasites (particularly neglected tropical diseases), and the people infected with these parasites.  He is an amazing story-teller, and really connects the reader with the human-suffering caused by these diseases.



More stories from Robert Desowitz.



The mind-blowing story about how D.A. Henderson led the battle against smallpox, and all of the hurdles he had to jump through in order to eradicate this disease.



An extremely well-researched overview of the Hygiene Hypothesis.  Moises Velasquez-Manoff provides a balanced view of the evidence for and against this hypothesis, and walks the reader through his experience with helminth therapy to treat his autoimmune diseases.

First edition of The aGGiE Brickyard is published!Michael Koontz

Welcome to the first edition of The aGGiE Brickyard!

From the editors (John Mola, Matt Williamson, Ryan Peek, & Madeline Gottlieb):

“Not so long ago, the students of the Ecology Graduate Group put together a quarterly newsletter known as The Egg. The Egg showcased the scientific, artistic, comedic, and general brilliance of the students and faculty of the Ecology Graduate Group. Beyond just a reflection of the community of ecologists at UC Davis, The Egg provided a forum for student and faculty interaction that helped to strengthen our community. In that spirit, we decided to revive the student publication and bring you The Aggie Brickyard. We hope that this publication can serve an important role in the beautiful, large, (at times) amorphous, force of ecological research and social revelry that is the Graduate Group in Ecology at UC Davis.”

Without further ado… The aGGiE Brickyard — Volume 001 — Winter 2016