What are the rodents eating?

Last week I talked about our adventures in vouchering the plants of Portal. This week I’ll get a little more in depth about the project that prompted this collection push.

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One of the neatest things about Portal is that we have so many species of rodents coexisting together in the system (up to 21, in fact). Over the years, we’ve speculated on many potential reasons for this. When a fun new technique–DNA metabarcoding–for “easily” analyzing diet from fecal samples popped up on our radar, we started wondering if this was something we could use at our site to ask some neat questions.

For example:

• What are the rodents actually eating?
• Are different species of rodents eating different things? If so, is that possibly one reason so many species are able to coexist at the site?
• Does the presence/absence of a behaviorally dominant species affect the diets of other species?
• How does diet breadth change through time, especially with high seasonal and annual variability in food resources?
• Etc., etc.

Once we started thinking of questions, it was hard to stop. To ask any of these questions, though, we need to know what DNA metabarcoding even meant and whether it could give us the information that we were hoping for. We started looking more into DNA metabarcoding to try to figure out what it actually was, considering none of us have much experience with genetics. We came to understand that, for our intents and purposes, DNA metabarcoding can be best thought of as the simultaneous identification of multiple species from a single sample (fecal samples, in our case). It offers an efficient and effective way to determine diet content without intensive observation or fatal sampling. As it turns out, DNA metabarcoding has actually be around for over a decade, mostly being used in the microbiology world. By the mid-2000s, microbial ecologists had started bringing the technique into ecological circles. Since then, it has been used to enhance biodiversity surveys through environmental DNA, or eDNA, as well as assess the diets of animals. What is just starting to be done with this technique is using it to compare diets between coexisting species.

Figure modified from Valentini et al., 2009

Collecting fecal (and ectoparasite) samples

In order to assess the diets, we needed to create a DNA reference library, with DNA from the plants at Portal. This way, we can compare the sequences that are extracted from the rodents’ fecal samples to the plants found at the site. This is where the plant vouchering came into play! We can also pull in data from huge international genetic databases, such as GenBank, to potentially find any plants we’ve missed.

So far, we’ve done four rounds of fecal collections–usually during plant censuses when we have lots of helping hands! Once the fecal samples have gone through the black box of next generation, or high-throughput, DNA sequencing, what we get back is rows upon rows of data about which plants have been eaten by which rodents. While we’re still working through the results, the preliminary data looks promising! We’re able to identify quite a few of the plants that they are eating, and we might even be picking up some shifts in diet between treatment types. Once we have a better picture of what is happening, I’ll chime back in with an update.

Now we can vouch for the plants!

Early on in my dissertation work, I became interested in using a fairly new technique (DNA metabarcoding) to look at what our rodents are eating and if partitioning their diets might be one way so many species exist in our system. I’ll get into more of the details on that project in a subsequent post; for now, though, I want to tell you about a really fun ancillary project. When you’re interested in what the rodents are eating, it’s pretty important to know what they could be eating! Therefore, over the past few plant censuses, we’ve been collecting vouchers and DNA samples for as many of our plant species as we can find!

Having recorded plants at the site for roughly four decades, we are in a pretty fortunate position—we already have a nearly complete list of plants that could be found at the site. Since most of us know more about rodents than plants, however, we wanted to make sure we were correctly identifying our plant species. This requires collecting voucher specimens for every species we come across, pressing them in a plant press, and then dropping them off at the University of Arizona Herbarium for an official verdict from a botanist who specializes in Arizona plants. Once he has looked over our samples and identified them, the herbarium digitizes the specimens. So far, we’ve vouchered about 85% of the nearly 200 recorded plant species at the site.

Quadrats

Identifying plant species

Putting voucher specimens in the plant press

Delivering our precious plants!

Digitized copy of one of our vouchers

For the most part, we’ve been doing a pretty great job identifying our plant species, considering none of us really identify as botanists. We’ve also had some fun surprises along the way, though! For example, for forty years, we thought we had two species of Acacia at the site: 1) whitethorn acacia, Acacia constrica (now Vachellia constricta), and 2) catclaw acacia, Acacia greggii (now Senegalia greggii). As it turns out, however, we’ve probably never had the catclaw acacia at the site! What we’ve been calling A. greggii is actually a species of mimosa, Mimosa aculeaticarpa.

Senegalia greggii

This is not Acacia

This process has also made us more attentive to the plants surrounding us at the site. It was only at the last census that we noticed a large bush/small tree and realized that it was our first (and maybe only) desert willow tree, Chilopsis linearis, at the site. It was hard to believe we’d never noticed one of the biggest plants at the site as being different, but since it was just outside of a plot, there had never really been a reason to notice.

Example of a desert will tree, Chilopsis linearis

We’re looking forward to more surprises in the future, though we still dread having to figure out how to make these changes in the database!

 

The Spectabulous Spectabs of Portal

Much beloved by those who have worked at the Portal Project, the banner-tailed kangaroo rat (Dipodomys spectabilis) is one of the most charismatic rodents at the site (for us smammal lovers who think rodents can be charismatic, anyway). The fact that they have a nickname—spectabs—attests to this fondness. Look at that mighty tufted tail! Those giant, majestic furred feet! Weighing in at over 100 grams as adults, they are twice the size of our other kangaroo rat species (D. ordii and D. merriami). What’s not to love?

Dipodomys spectabilis

As avid readers of the Portal blog might recall, the site used to be much grassier back in the day. At the start of the project in 1977, spectabs were running the show at Portal; we even had some plots that excluded only D. spectabilis because they were so dominant! For the spectabs, this was a desert paradise, as they tend to prefer grassier habitats. As the site became shrubbier, however, the reign of the spectabs came to a slow end in the 1990’s. Since then, a few individuals have popped up here and there but haven’t stuck around, often heading for greener (grassier?) pastures.

For me, experiencing Portal for the first time in the summer of 2015, D. spectabilis seemed more like a mythical creature than a real species. I resigned myself to the probability that I would never actually get to see this massive kangaroo rat species and would have to be content with its smaller (and equally adorable, mind you) congenerics.

Then Stephanie showed up.

Of course, rodents don’t arrive at the site wearing name tags; names have to be earned. In April of 2016, Erica excitedly reported back from the field that she had caught—you guessed it—a spectab. This young female, weighing only 70 grams, was the first spectab caught at the site since a quick resurgence lasting from 2008-2010.

We assumed she was just passing through. Yet May arrived, and there she was. I finally went out in June, trying desperately not to get my hopes of finally seeing a spectab too high. Over to plot 11 I went, my heart was pounding a little faster than usual. One of the first traps I picked up was very heavy! I’d caught my first spectab! I made my volunteer take a picture of me with Stephanie. You can’t quite tell, but I was teary-eyed with happiness; that might sound a little embarrassing, but I don’t mind admitting it. I was so excited! It felt like I’d completed some type of Portal rite of passage.

Ellen (that’s me!) with Stephanie, who is far less excited about this picture than I am.

I’m not sure when I decided that our new resident spectab needed a name, but I unilaterally decided on Stephanie and, somehow, it stuck. Most of us assumed she’d disappear pretty quickly; since the 90s, most of the spectabs that have been caught have quickly moved on. And especially since she was young, we figured she was just on some rodent version of rumspringa. But month after month, there she was. Same plot, nearly the same stake every time. Spectabs are known for their well-kept, cultivated mounds, and Stephanie’s was shaping up over in the northwestern corner of Plot 11.

A typical spectab mound: raised, multiple holes, and well-manicured.

Soon there was talk of whether Stephanie would get a “boyfriend” or not, which rapidly devolved into thoughts of setting up a twitter account for her or making her a profile on that new-fangled dating app, Granvr: the Dating App for Modern Granivores. Stephanie continued to grow, and we started wondering if she would be the exception to the 21st-century spectab rule and actually stay around. In the end, she stuck around for nearly a year; February was the last time we saw her.

Or was it?

In June, our newest Portal RA, Renata, was in her second month of training. We arrived at Plot 11, and what came out of her trap but a spectab! In shock and excitement, I lurched forward and grabbed the bag with the discombobulated rodent out of her hands without thinking or asking (not my best moment, I admit…). Stephanie was back! Or so we thought. Our volunteer managed to capture a dynamic set of pictures that explains the series of events better than any prose can:

“Stephanie!!!?!”

“Oh…hmmmmm.”

“That is definitely not Stephanie…”

“I shall name him Stephen!”

That’s right. I was holding a very scrotal male…definitely not Stephanie. Stephen hasn’t shown up again, and we assume he’s gone on his way.

Even though we have 40 years of data, the site is still reminding us that we have many unanswered questions. Where are these spectabs coming from? Where are they going? Why now? Will there be more? We sure hope so! And rest assured, we’ll report about them right here.