Archive for the ‘Uncategorized’ Category

Morgan’s Favorite Portal Species

November 1, 2017

As part of our Portal 40th anniversary celebration, some of us will contribute our thoughts on our favorite species at Portal. We’ve already had several posts on the Banner-tailed Kangaroo Rat (a universally beloved species at the site). But, I have a confession, while I love Banner-tails, they are not my favorite species at Portal (cue collective gasp). No, my favorite species is the grasshopper mouse. We have two species of grasshopper mice at Portal, the Northern and the Southern Grasshopper Mouse (Onychomys leucogaster and Onychomys torridus).

They are similar in their biology and morphology. Both are small (usually less than 6 inches or 120-163 mm in length including the tail) and weigh less than 40 grams (or 0.088 lbs). Given their similarities, I like them equally well, so will simply refer to grasshopper mice generically for our purposes today.

Anyone who has interacted with a grasshopper mouse probably remembers the encounter. Grasshopper mice have sharp little teeth and love to use them. Keeping an eye on the front end wouldn’t be that hard if you didn’t also have to also keep a sharp eye on the back end. The teeth are just a distraction from the fact they are trying to coat you  with liquidy, yellowish diarrhea. Oh, and did I mention that grasshopper mice REEK. Yes, I do mean reek. Their oily, acrid scent curdles the nose hairs and lingers after the little rodent is gone (probably because they managed to smear some poo on you in retribution before they headed off).

So right about know, you’re probably wondering why this reeking, vicious little rodent is my favorite species at Portal (or you’re wondering what this says about my personality).  With so many amazing rodents to choose from at Portal, what makes the grasshopper mouse so special? The reason grasshopper mice are notably more aggressive than our other species is that grasshopper mice are predators – yes, predators. They will eat seeds when resources get scarce and cache seeds in their burrows (Ruffer 1965), but they actively hunt insects, small rodents, arthropods, and even reptiles. They even hunt scorpions – see for yourself. The video below shows in sequence an adult, a subadult, and a juvenile attacking a scorpion. The adult knows to chew off the stinger quickly. The younger ones….well, it’s definitely a more difficult experience for them, though they eventually get their meal.

Why can these mice withstand scorpion stings? Without getting into sodium ion channel-level detail , basically they have a special protein that binds to the scorpion’s neurotoxin that changes how it works (Rowe and Rowe 2008)– as a result not only doesn’t the sting hurt, it actually ends up numbing the area of the sting (Rowe et al 2013).

Grasshopper mice also have surprising social relationships. There are a variety of reports that male and female grasshopper mice form strong pair-bonds and that both sexes participate equally in offspring care (McCarty and Southwick, 1977) and make the nest burrows together (Ruffer 1965). Grasshopper mice have a calling behavior using sounds that are almost ultra-sonic (Hafner and Hafner 1979). Though members of a family group have similar calls, every individual has unique call characteristics, which means that Grasshopper mice may be able to use these calls to communicate with family members over long distances (Hafner and Hafner 1979). When they call, they stand on their hind legs and throw their heads back:

Some mammalogists cannot see past the reeking, bitty little animal with the magical stinking poo that seems to get on you no matter how hard you try to avoid it. But when I see a grasshopper mouse, I see a little mouse who thinks it’s a coyote. I see some cool evolution at play that takes a normal mouse and turns it into a scorpion-resistant killing machine. I also see a brave little mouse fearlessly taking on a scary world. There’s something about it that just makes me smile. And then I go get some hand sanitizer.


Scientific Studies Cited in this Post:

Hafner, M.S., and D.J. Hafner. 1979. Vocalizations of Grasshopper Mice (Genus Onychomys). Journal of Mammalogy 60:85-94

McCarty, R., and C. H. Southwick. 1977. Patterns of parental care in two cricetid rodents, Onychomys torridus and Peromyscus leucopus. Animal Behaviour 25:945–948.

Rowe, A. H., and M. P. Rowe. 2008. Physiological resistance of grasshopper mice (Onychomys spp.) to Arizona bark scorpion (Centruroides exilicauda) venom. Toxicon 52:597–605.

Rowe, A. H., Y. Xiao, M. P. Rowe, T. R. Cummins, and H. H. Zakon. 2013. Voltage-Gated Sodium Channel in Grasshopper Mice Defends Against Bark Scorpion Toxin. Science 342:441–446.

Ruffer, D. G. 1965. Burrows and Burrowing Behavior of Onychomys leucogaster. Journal of Mammalogy 46:241–247.




How do people use the Portal Data?

October 27, 2017

Every so often, someone asks me for a Portal reading list to come up to speed on what we know about the site. This seems like a simple questions, but it is actually pretty difficult. We define a “Portal Paper” as a paper using data collected at the study site (whether or not Portal Project people were involved), or data collected near the study site if that data was collected by the project or with substantive assistance from our project. Over the years, the site has contributed to over 120 papers and book chapters (our current estimate is 123, but we still find older papers that we didn’t know existed).

How the Portal Data is used has been changing in recent years. Historically, most papers were by people affiliated with the group. As we’ve blogged about before, starting in 2009 we have been working on making our data openly available through  number of venues. We post all of our data on the Portal GitHub Repo and we have also published two Data Papers through Ecology’s Ecological Archives. The nice thing about Data Papers is that they are indexed and cited just like regular scholarly papers, which is important because it allows us to 1)  document that the Portal Project is a valuable scientific resource to the community (which theoretically may be helpful on grant applications) and 2) let us here at the Portal Project keep informed of results coming out of the site that we’re not involved in.  So, how are scientists, external to our group, using our openly available data? Google Scholar lists 22 citations between the 2 data papers. (For the non-academics, citing other papers is in our own papers is an important part of scientific publishing. It allows us to give credit to those whose ideas, data, or methods we are working with. It also allows to us provide proof or support that statements we make in our papers are supported by things other people have been finding. Google Scholar is a database that keeps track of these citations). Here’s the breakdown of what Google Scholar says has been citing our Data Papers:

RplotAll the site focused research (papers that use our data as the primary focus of their analysis) was done by  or in collaboration with someone affiliated with the project. If other researchers are using our data, so far they tend to either use it as part of a meta-analysis (i.e. as one of many data points in the analysis) or to make a figure for their statistical or conceptual paper that has an empirical example of what they are talking about. (Three papers cite a Data Paper for reasons that defy classification. After reading their paper I have no idea why they cited us)! This number of citations listed by Google Scholar is probably a little lower than the database’s actual use in papers because data citations for meta-analyses often get shoved off into the supplementary materials and are not indexed by Google Scholar as a result. Our usage in meta-analyses is probably higher, but it is unlikely that we’ve missed a paper focused solely on data from our site.

We are hoping to increase Portal’s usability and we have some things in the works, which we will blog about later, that we hope will make it easier for people to get the data they need to use Portal as part of their analyses. We love seeing the data used but know that the history of the site and all the manipulation changes can make it difficult to figure out how to extract the data you need.


Portal: Then and Now

October 4, 2017

A lot can change in 40 years.  This is perhaps never more apparent than when you find a box of old photographs, and start comparing then to now.  When the Weecology lab immigrated from Utah to Florida in 2015, just such a box surfaced: a glimpse back in time to the beginning of the portal project.  I did my best to re-create some of these photographs—trying to line up horizons and mountains—to show how the site has changed over 40 years.

One thing is immediately apparent: the shrubs have grown up.  The left side of these photographs were taken in 1977 (photographer unknown), and the right side in 2015 (photographer Erica Christensen).  What happened to the rows upon rows of aluminum flashing, indicating the location of the rodent fences?  I assure you the fences are still there, they’re just obscured by the jungle.

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The fact that you used to be able to see clear across the site is shocking to the modern research assistants. These days, part of the training for new RAs taking over work at Portal is receiving a map from the previous RA with routes drawn in for the best paths between plots. Navigation is not trivial.


Erica, circa 2012, demonstrating the problem (photographer Sarah Supp)

Other locations at the site don’t look too different from how they looked in the ‘70s. Grass cover comes and goes depending on the strength and timing of monsoon rains every year, but some plots don’t seem as affected as others by the shrub explosion.

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While shrub encroachment is an annoying obstacle to a human, it is a major ecological shift to a rodent. This was the topic of a 1997 paper by Brown, Valone, and Curtin, where they found a 3-fold increase in shrub cover between 1980 and 1995 by analyzing historical aerial photographs. The authors also noted a concurrent decline in rodent species affiliated with arid grassland (banner-tail kangaroo rat and silky pocket mouse) and an increase in species affiliated with arid shrubland (desert pocket mouse and Bailey’s pocket mouse). It looked like the grassland species were on their way out and the shrubland species were taking over. However banner-tails and silkys continue to be found at the site, despite the fact that shrub cover has increased, if anything, since 1995. They’re now quite rare; these days we pretty much only see them when the rains align just right to give us a “grassy year.”


Nobody tell this adorable silky pocket mouse we’re a shrub habitat now

Those of us who have worked at Portal know that things are always different every time you go down, and yet some things never change. Which is why we keep going, keep collecting data: even after 40 years there is still a lot to learn.

Brown, J.H., Valone, T.J., and Curtin, C.G. (1997). Reorganization of an arid ecosystem in response to recent climate change. Proc. Natl. Acad. Sci. 94, 9729–9733.

Portal Plant Census and Florida Hurricanes

September 18, 2017

Twice each year we head out to the site to do an intensive week of field work. We catch rodents as we do every month, but we also count every plant located in the 384 different plant quadrats, located across the site (for those who want more details: 16 quadrats per plot, locations marked with rebar, each 0.25 m^2 in size). Plants have been counted on these quadrats for nearly 40 years and we have been keeping the tradition alive. These extended trips occur sometime in August/September and March/April to match up with when most plants during that season are flowering or setting seeds (or as best we can given the constraints of the school year). Since the lab moved to Florida, the August/September census has gained an added piece of excitement: hurricanes.


Yes. Hurricanes.

Last year, as the crew was preparing to set out for Arizona, Hurricane Hermine  was lining up to hit Florida. Being the lab’s first hurricane experience (and the first hurricane to hit Florida since 2005), there was a lot of anxiety as the crew packed up to head out. Would they get out ahead of the storm? What would happen while they were gone?

The storm was an exciting experience for those of us who remained in Gainesville (in the ‘uh, wow, look at all those trees down’ way, not the ‘Whoo, let’s do that again’ way). Hurricane Hermine skirted Gainesville, delivering strong winds, rain, and some downed trees.


Image from Wikimedia Commons. Image uses background image from NASA and hurricane tracking data from NOAA. The yellowish color were it hits land indicates it was a Category 1 at landfall. The star is the approximate location of the University of Florida

Though the Portal crew was out in Arizona, they did not escape without their own hurricane experience, though! Hurricane Newton hit Baja California and then came up to the Portal area for a visit.


Image from Wikimedia Commons. Image uses background image from NASA and hurricane tracking data from NOAA. The star is the approximate location of the Portal Project. The blue triangle indicates that Newton was a tropical depression by the time it got close to the site.

Despite my anxiety for the crew, they just got really wet.


Ellen and Joan enjoying a tropical storm in the desert

We laughed about it and then forgot about all this until a couple of weeks ago when Hurricane Irma lined up on Florida as the Portal Plant Crew was preparing to head out to Arizona to count plants.


Hurricane Irma track. Gainesville was luckier than other places that received visits from Irma. It was only a tropical storm when it came by. Image from NASA, track data from NOAA, obtained from Wikimedia Commons

Shawn Taylor, one of Ethan White’s graduate students and regular Portal Plant counter, remarked on his déjà vu feeling in a message to the lab:

“Interestingly this is exactly how leaving for the fall plant census was last year as Hurricane Hermine was bearing down”

Now, any good scientist knows that correlation does not mean causation. Our sample size is also very small, with only two incidences so far. I’ll just say that it’s an interesting coincidence that Florida gets hit with hurricanes when the Portal Plant crew heads to Arizona in September. No one should contact FEMA to have “keep the Portal plant crew in Florida” added to their disaster preparation list. But at the very least, we probably need to add some “in case of hurricane” items to our summer plant census check list for next year!

The Spectabulous Spectabs of Portal

September 1, 2017

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:

Image uploaded from iOS


Image uploaded from iOS (1)


Image uploaded from iOS (2)

“That is definitely not Stephanie…”

Image uploaded from iOS (3)

“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.

How fast can a desert turn green?

August 18, 2017

In the desert, water is life. Without it, the desert is brown and dusty. At our site, the rains come twice a year – once during the ‘winter’ (I put that in quotes for our readers where winter means snow and/or extended periods below freezing) and once during the summer. Water in the summer and water in the winter don’t have the same effect on the desert, though. Plants need both warmth and water to grow. When rain falls in the desert in the winter, growth is slow and typically waits until the warmer temperatures of spring. In the summer, though, the high temperatures and the rain from Arizona’s monsoons make for an explosive combination. How fast can the desert turn green? Here’s a series of photos from our site – one per day for a week that we think conveys this better than words. Enjoy the slide show:

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You might be wondering if that was it. Was that as green as the desert got? Here it is, as of yesterday, 3 and a half weeks after that first brown picture: August 1st was definitely not peak green:


The grasses are greening up nicely and there is no bareground to be seen in the foreground.Water, heat, and sunshine – a very powerful combo indeed!



Portal at the Ecological Society of America Meeting

August 2, 2017

Every year ecologists from across the U.S. descend upon a city to share their most recent findings with each other at the Ecological Society of America’s annual meeting. Normally, the locals are a little befuddled by the sudden influx of people wearing Tevas and Chacos and wearing clothing from various outdoor gear companies, but this year the meeting is being held in Portland, Oregon!

This year there are several presentations featuring data from the Portal Project, ranging from a poster to talks to a workshop. If you are going to be at the meeting and are interested in hearing about the site, learning more about the data, or taking a Data Carpentry that uses a teaching version of our data, check out the events listed below. These are just the things we happen to know about. If your talk uses data from Portal (either focused on the site or as part of a bigger meta-analysis / macroecological study), let us know in the comments and we’ll add you to the list!

Saturday, August 5th

8:00 AM-5:00 PM A105, Oregon Convention Center

Data Carpentry in Ecology Workshop

Organizers: Monica Granados, University of Guelph and Auriel M.V. Fournier, University of Arkansas – Fayetteville

(Paraphrased from the Meeting Program) This workshop uses a tabular ecology dataset from the Portal Project Teaching Database and teaches data cleaning, management, analysis and visualization. We use a single dataset throughout the workshop to model the data management and analysis workflow that a researcher would use.

Monday, August 7th

02:50 PM – 03:10 PM Oregon Convention Center – C120-121:

Novel approach for the analysis of community dynamics: Separating rapid reorganizations from gradual trends by Erica Christensen, S.K. Morgan Ernest and David J. Harris, Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, University of Florida.

03:20 PM – 03:40 PM Oregon Convention Center – C120-121:

Do existing communities slow community reorganization in response to changes in assembly processes? by Erica Christensen and S.K. Morgan Ernest, Wildlife Ecology and Conservation, University of Florida, Gainesville, FL

Thursday, August 10th

04:30 PM – 06:30 PM Oregon Convention Center – Exhibit Hall

DNA metabarcoding of fecal samples provides insight into desert rodent diet partitioning by Ellen K. Bledsoe, Samantha M. Wisely and S.K. Morgan Ernest, Wildlife Ecology and Conservation, University of Florida, Gainesville, FL

Friday, August 11th

8:00 am-08:30 am Oregon Convention Center, Portland Ballroom 257

Advancing biodiversity-ecosystem function research by integrating community assembly: The CAFE approach by Katherine Bannar-Martin, Fisheries and Oceans Canada, Colin T. Kremer, Yale University, S.K. Morgan Ernest, University of Florida, Mathew A. Leibold, University of Texas at Austin, sCAFE working group, iDiv

Hope to see you there!

Walking the beat

October 12, 2016


Last month we highlighted the brains (and a little brawn) of The Portal Project, with a description of the new regime shift research and the requisite hardware-cloth-battle of 2015.  This month we bring out the big brawn guns (and some brains) to show you how the site keeps its youthful glow year after year in the unforgiving desert.  If we could bottle this Portal magic, it would be a best-seller for sure. Here’s our best attempt:


Do you like long walks in the desert?  Do you love cute, cuddly animals?  Do you like to take long walks in the desert with rattlesnakes, scorpions, and tarantulas when it’s 115 degrees out, and do you still love cute, cuddly animals when they bite you and poop on you?  If you answered yes to the last question, you might be Portal Protectors! material. (By the way, Morgan is recruiting another PhD student to work at Portal.  Please see her announcement about that here.) If you answered ‘yes’ to questions one and two but ‘no’ to question three, this blog post, accessed from the comfort of your armchair, is our gift to you.

To be a Portal Protector! is to be a biologist, a naturalist, an outdoor enthusiast/athlete, a team player, and a bit of a masochist. We get up early. We go to bed late. And we spend many of the intervening hours digging trenches, moving large rocks, pounding stakes into the ground, lugging heavy equipment to and fro, crawling around on our hands and knees amidst sharp objects, and catching small critters.  If any of these images below speak to you, then we’re on the same mental page:

Before you assume that these types of activities must only be for blockbusters, game shows, soldiers, or insane people, let us instead convince you how they are necessary and beloved steps in the quest towards scientific truth (I sense a blockbuster there…).  In fact, walking the beat of the Portal Project, including all of the aforementioned digging/crawling jobs, was the start to a successful career in science for a long and distinguished list of people.  Maybe you are one of them!  For that, we salute you.

Nearly every month, for approximately the last 453 months, one of the Portal Research Assistants has traveled to the site with a brave volunteer to census the rodent community.  Journeying from the original University of New Mexico headquarters, then from Utah State University, and most recently all the way from the University of Florida, they give up their weekends to keep the research going. (Keep the Lights Burning, Abbie…anyone?)  The current Portal RAs, Erica Christensen and Ellen Bledsoe, leave Florida on a Thursday to travel to Tuscon, Arizona, where they then pick up the truck, gather supplies and drive three hours to the site on Friday to set rodent traps on 12 of the 24 quarter-hectare plots before the sun goes down. Early the next morning they process the rodents caught in the traps, recording the species, sex, hind foot length, weight and pit tag number. They then bait and set traps on the other 12 plots to census the next nights’ activity, hauling wooden boxes of metal Sherman traps around a dizzying desert maze — like a Halloween corn maze, but made of spiny acacia bushes and located even more in the middle of nowhere.  After recording details about those rodents the next morning, they download data from the local weather station and make their way back to Florida by Monday night. It all looks something like this:

Many interesting scientific findings about how body size, metabolism, rain, species interactions, and temporal dynamics influence the structure of a rodent community, as well as a unique and impressive long-term community ecology dataset have come out of this workAnd since ecology is all about understanding the ways in which groups of living things interact with each other, additional results have come out of pairing the rodent census data with information collected twice a year about plants.

In both March and September of 2016, the current conglomeration of the Portal Protectors! traveled from Florida to Arizona to chase rodents, crawl around on our hands and knees counting plants, and perform our biannual trench-digging, rock-moving, stake-pounding, equipment-lugging rituals.  The Science Gods demand some weird sacrifices to ensure the everlasting bounty of Portal data.  And we must obey.  For the biannual plant census, we work together to record the sources of greenery around the site. We use meter quadrats (squares made out of PVC pipe, 0.25m on a side), placed at 16 permanent locations evenly spaced across each plot, to count and identify every tiny bud and blade of grass. We then string transect tape in a giant “X” across each plot and measure the width and height of every shrub it crosses. It’s spiny, tedious work. But the show must go on. In blistering heat and unrelenting sun, or through shivers and downpour, the plant census process takes about four long days each season, and looks something like this:

We often return from a plant census bruised, bloody, and burned, ready for a soft bed, a warm shower, a flushing toilet, and a clean shirt.  But we are only out there for a week.  Portal herself must endure the savage sun, devastating aridity, and seasonal deluges year-round.  Four-hundred and fifty-three rodent censuses and thirty-five plant censuses under the daily assault of the desert would take their toll on anyone.  So when the Portal Protectors! make our biannual pilgrimage from the lab to the site, we usually reserve some time, and some brawn, for a little Portal TLC.

Next time on the Portal blog, we’ll unveil both the long-overdue makeover of Plot 24, and our brand new shiny weather station!  This is where all the real trench-digging, rock-moving, stake-pounding, and equipment-lugging comes into play.  We might even include some original pictures of us doing these activities, instead of just George Clooney’s excellent portrayal of our work.  So stay tuned.  And stay safe.  It’s a crazy, dusty, desert world out there. But someone has to keep the lights burning.



August 3, 2016

We return this week from our special, breaking-news post about the recent reappearance of our one-hit-wonder, Twitter-sensation, spectabulous Banner-tailed Kangaroo Rat. This T-Rex of Portal may not be here to stay, but we’re sure excited she stopped by. What is here to stay is that pesky plot switch we mentioned last month. We’re going to continue our series of Portal science updates and tell you all about that now:


The last time we checked in at this blog prior to the 2015 plot switch, Erica was battling monsoon season to record desert rodent dynamics on the twenty-four long-term experimental plots that have been censused almost monthly since the site was established in 1977 by James Brown, James Reichman, and Diane Davidson. That’s thirty-nine years of tracking the occurrence of various species of small mammals. That’s over four hundred visits to Portal, AZ to trap, measure, weigh, and tag rats. And it all started before scientists had thought very much about why fluctuating species abundances in a community might be interesting.

This is cool because now we have decades of data (most of it publicly available) on how these scurrying, hopping, burrowing creatures have been interacting at Portal, just in time to see a surge of researcher interest in community ecology and species dynamics. For example, we were able to document an abundance of the small, pink flower Erodium cicutarium in plots where the competitive seed-foraging Kangaroo rats were excluded (Allington et al, 2013). And, after many years of pondering its absence, we recorded a resurgence of the Northern pygmy mouse, Baiomys taylori, a peculiar trend that would have gone undetected without regular sampling efforts. We’ve seen shrubs increase in both size and abundance, changing the entire look of those plots, not to mention the nature of the local foraging and shade resources. Ecology, in all its complexities, happens over long time scales. To understand it, we must record it over short ones. Few studies exist that have managed to do both, and we are excited about the scientific opportunities the history at Portal affords us and others who use our data.

Erodium cicutarium (left) has been increasing in abundance in plots where Kangaroo rats are excluded.  Baiomys taylori (right), the Northern pygmy mouse, has resurged from apparent rarity.

So now that we have amassed this monstrous dataset and finally understand more about how these rodents have been faring, cohabiting, and influencing the plants of these twenty-four plots in long-term treatment groups over nearly forty years, naturally we decided to turn it all on its head. Yes, after over four hundred samples of the twenty-four plots in their original treatment states, we got a grant from the National Science Foundation to switch them all around. Why? Because we’re scientists, and we like to poke systems to see what happens.

Because we scientists often want to be useful in addition to curious, we also like to simulate real expected ecological change so that we can predict likely outcomes and plan for them. Our world is rapidly changing. We need to understand how ecological communities will respond. When we’re not watching and recording, or sometimes even when we are, seemingly small changes can add up to big shifts. A breeze, a little water vapor, a small temperature change can suddenly turn into a monstrous hurricane, for example, that introduces a whole new set of rules and challenges to human existence.  Similarly, ecological systems can undergo extreme, abrupt changes in state that are very hard to understand and manage unless they have been tracked before, during, and after that transformation.

Questions surrounding the idea of regime shifts, described as dramatic changes in populations, communities, and ecosystems over short periods of time (Hare & Mantua, 2000), represent relatively new challenges in the field of ecology, ones that the Portal project may be uniquely situated to address.  Understanding regime shifts, or how communities of rodents may suddenly shift in their relative species abundances or resource usage, at Portal may help us understand what to expect from other ecosystems undergoing unprecedented levels of environmental change.  We’re not promising X-(woman)-like vanquishing of Hurricanes. We study rats, not wolverines after all. But this is important stuff.


While hurricanes are exceedingly rare in the Arizona desert, there are subtler forces at work which may cause shifts in our Portal rodent community. Knowledge of these forces may help us, and other scientists, understand similar sudden disruptions in unmonitored groups and ecosystems. It’s the scientists’ mutant superpower — studying one thing ‘over here’ can help us predict and manage another thing ‘over there’ which we may have actually never seen…except in our mind’s eye.

The figure below, from Dr. Ernest’s 2014 grant proposal, shows three scenarios in which ecosystems and drivers (e.g. climate, nutrient input, biotic interactions) can be related in ways that might represent system-disrupting regime shifts. Sudden shifts in drivers (e.g. hurricanes) could cause a corresponding shift in ecosystems (e.g. massive urban destruction), which would constitute a regime shift. The same ecosystem pattern, however, could be triggered by simply crossing a threshold along some seemingly innocuous linear increase of a driver (like a slowly rising sea level that causes the sudden collapse of a city when it finally submerges the business district, or the state of water as it’s gradually heated past its boiling point). Regime shifts, like the melting of sea ice caps, can be hard to undo. Sometimes an ecosystem can be brought back down from a boil by turning down the driver dial. But sometimes an ecosystem will fail to revert back to its original state after a driver has increased and then decreased again, taking the ecosystem along a new trajectory. At Portal, where neither massive urban destruction nor hurricanes are a major concern, this might come in the form a plant that fails to return to a location after a particularly dry summer even after rains have resumed, or a Banner-tail Kangaroo rat who once reigned mighty and may never be seen again.


To poke the system and test this at Portal, in March 2015, we reversed some of the long-standing plot treatments. We also, of course, maintained some of the plots in their original treatments to serve as reference plots, against which we can test the existence and magnitude of potential regime shifts caused by introducing a large granivore as a driver. This has rarely been experimentally tested because few systems have the long-term data, ability to simultaneously cause a jump in an ecosystem driver in both directions, and enough plots to maintain replicates with reversed and reference plots.


The Portal project’s twenty-four plots and well-monitored, gated rodent communities is an ideal system to study regime shifts because it does not have these common experimental design limitations. Because we manipulate rodent access to plots via gates of different size, it is also shockingly easy to change the rodent community on a plot – we can make new gates by clipping holes in the fencing, remove gates by applying patches over them, or change the size of gates (and the species that can enter the plot) by either patching or clipping to create new hole sizes. So last spring, Dr. Morgan Ernest led the hardware-cloth-stripping-team in reassigning plots to their new experimental treatment, ending an era, but never the science:

Erica securing the new hardware cloth pieces to close the old gates (left).  This little guy (right) wishes we could strip the hardware cloth off him.  But we are done with that task.

In a gesture of inclusiveness and diversity characteristic of the Weecology lab group ideology, we broke down barriers between different rodent communities by enlarging or creating gates in some of the plots that had previously excluded the granivorous, large-skulled (and adorable) Kangaroo rats:


A Kangaroo rat, Dipodomys merriami.  What plot wouldn’t want these cuties?

But because this is science and not social revolution after all, we are also testing the influence of these large-skulled favorites as ecosystem drivers by excluding Kangaroo rats from some of their previous home plots by patching up or narrowing gates in plot fences that had previously allowed them to pass into these areas.

Example of a gate in a Control plot, open (left) and closed (right), which provides free, open access for all knowledge-(or seed)-seeking rodents!
Example of a gate in a Kangaroo rat exclosure plot, open (left) and closed (right), which is very oppressive of Krats, but great for controlling their influence in plots as a driver.


In case you have ever doubted the dedication of field biologists, thinking perhaps that we enjoy a life of sipping Coronas in a scenic field station after a day of wandering through the hills sniffing at plants, we would like to explain to you the unnatural nature of hardware cloth. Hardware cloth is not cloth. It is, however, hard. It is also pointy and sharp and vexingly narrow. To enact the plot treatments switch described above, the valiant hardware-cloth-team-of-2015 used pliers to strip countless thin layers of wire off of small metal squares of fencing, creating exposed, pointy wire ends along the hardware cloth, which must then be woven through the tiny squares in the existing plot fence to close off or narrow old treatment gates. They then cut or adjusted new treatment gates in the existing fence hardware cloth to create new access for the Kangaroo rat ‘drivers.’ Science is not all high-tech gadgets and sophisticated computer algorithms. Sometimes real science is stabbing yourself with hardware cloth one thousand times and squatting on the ground in the blazing hot desert to sew patches over gates in metal fences because you want to see what the rats will do. We happen to actually love this type of self-brutality in the name of science, and how it makes our evening Coronas, enjoyed together around the campfire at our beautiful field station, taste that much better.


The field crew taking a break at the Ramada, our two-sided field station.

And that is the story of how the plot switch, and the finger-massacre, of 2015 was recorded in Portal history. We won’t show you the blood, but we will show you the final plot map result, and a much cleaner schematic of plot treatment shifts:




Next time on the Portal blog we will fast-forward to a year after this historic plot switch when, wiser, hardier, and with more Band-Aids and guacamole in tow (though there is never, ever enough guacamole), the Weecology field crew hit the road again, in our new University of Florida vehicle, to undertake the 447th sampling of desert rodents, and the twelfth under a possible new regime.

The Banner-tailed Kangaroo Rat: The Once – but probably not future – King

July 27, 2016

In 1977 when Jim Brown, Diane Davidson, and Jim Reichman started the Portal Project, the site looked like this:


Photo of Portal Project from around 1977 (we think).


This desert heaven was home to a variety of small mammals. One of the most abundant of these was the Banner-tailed Kangaroo Rat. While I feel that most small mammals are adorable (*cough* *cough* Packrat), the Banner-tail is the one that is universally beloved by generations of Portal researchers.


summer 110

Banner-tailed Kangaroo Rat (Dipodomys spectabilis). How can we tell? Note its size relative to the hand and the white tuft at the end of the tail.

Kangaroo rats in general are lovely creatures. As their name suggests, these nocturnal rodents hop around like kangaroos on enlarged backlegs. As least one scientist has seen a kangaroo rat use those strong back legs to leap 5 feet horizontally (with a two foot ground clearance)1. They have a long tail which may play a role in locomotion1 and fur-lined cheek pouches that they use like a bag to carry around seeds they gather from the environment. Most kangaroo rats eat primarily seeds. A study in Nevada found that Merriam’s Kangaroo Rat (a species we have at Portal) has a diet of  approximately 70-100% seeds (it varies over the year) and they eat a small number of insects as well.2 Anyway, you get the idea, kangaroo rats in general are cool. Most kangaroo rats – like Merriam’s – are about 40-70 grams (that’s about 0.09-0.15 pounds). But there are a few kangaroo rats that are notably larger. The Banner-tailed Kangaroo Rat is one of these, being closer to ¼ of a pound.


So, in 1977 three kangaroo rats, alike in dignity in fair Portal where we lay our scene, coexisted without evidence of ancient grudge or new mutiny4: Banner-tails (Dipodomys spectabilis), Merriam’s (Dipodomys merriami) and Ord’s (Dipodomys ordii).

The plot below shows the population dynamics of the three kangaroo rats. The plot goes from 1977 to 20145 and shows the population size in energy use6. I like energy use – especially when I’m dealing with Banner-tails – because large animals need more food than small animals. So one large banner-tail needs the equivalent amount of energy as 2¾ Merriam’s (based on their metabolic rates). By converting the population numbers to energy use, it helps correct for this difference in food consumption. So, the graph shows that early on in the study, Banner-tails were energetically more dominant than Merriam’s or Ord’s.


This is data from our long-term site. Photo credits: Merriam’s by Sarah Supp, Ord’s by Andy Teucher via, Banner-tail by an unknown Portal researcher (i.e. we forgot to document who)

This all changes, though in the mid 1980s. Why? Blame Tropical Storm Octave which dumped nearly half of the annual rainfall in less than a week7. While the other kangaroo rats barely noticed this event, the Banner-tails hated it. Many individuals disappeared over the following months. The population tried to stage a comeback in the late 80s and early 90s, but like a one-hit wonder band, it fizzled. By the late 90s, the era of the Banner-tail was over. The last Banner-tail disappeared and there was much sadness among the researchers.

But you’ll notice some blips. Like a heart that beats irregularly, every few years a few little lost souls, wandering across the desert, find our site. Hopes and dreams of a new era of banner-tails spring anew only to be crushed by disappointment when once again they disappear.

Why did the Banner-tails disappear after Tropical Storm Octave and why can’t they seem to make it at our site now? It’s not entirely clear, but we think it has to do with shrubs. Banner-tails love grasslands. They don’t mind a scattered shrub here or there, but they don’t like too many shrubs 8. Sadly, since 1977, the site has become steadily shrubbier. Below are paired photos taken from approximately the same location at the site. On the left is Jim Brown on plot 4 in the late 1970s. On the right is 19959. Notice any differences? The Banner-tails definitely do!


All of this is ancient history. So why blog about it now? Because we are happy to report the return of the Banner-tail! Well, kind of. I mean, we currently have one lonely female – probably fairly young given her weight and state of her fur when she showed up. We’ve caught her 3 months in a row now on plot 11. The students have joked about setting up a twitter feed for her. Tweets suggested include:

“4 months since I left home. The food here is great and all the other mice are small and easy to fight off. I’m gaining lots of weight”

“Returning to my favorite bed and breakfast this weekend. Predator-free and good but monotonous breakfast. Four out of five stars”

“Young professional female spectab [shortened form of the species name of Bannertails] seeking like-minded male. Looking for something casual and fun, no relationship. Interested suitors should arrive at Plot 11”

Needless to say, we’ve been excited by the Banner-tail. Every month we’ve been wondering “Is she still here?” One day, probably soon, the answer will be no because our site is too shrubby for a Banner-tail to be happy there, but for now we dream of fields of Banner-tails.




  1. George Bartholomew and Herbert H Caswell. 1951. Locomotion in Kangaroo Rats and its Adaptive Significance. Journal of Mammalogy. Vol 32. Pages 155-169.
  2. Glen Bradley and Roger A. Mauer. 1971. Reproduction and Food Habits of Merriam’s Kangaroo Rat, Dipodomys merriami. Vol 52 Pages 497-507.
  3. Ana Davidson and DC Lightfoot. 2008. Burrowing rodents increase landscape heterogeneity in a desert grassland. Journal of Arid Environments. Vol 72 pages 1133-1145.
  4. How Shakespeare should have written the opening to Romeo and Juliet. (Sorry, Shakespeare).
  5. I had this data on hand and was too lazy to update with the newest data
  6. How do we figure out energy use? We estimate it from metabolic rate. There is a well known relationship between the size of an individual and its metabolic rate – larger individuals have higher metabolic rates (i.e. they require more food per unit time than smaller organisms). We used an equation for the relationship between metabolic rate and weight that was calculated for wild rodents to figure out the metabolic rate for each individual and then summed across all individuals of the species.
  7. Thomas J. Valone, James H. Brown, Carrie L. Jacobi. 1995. Catastrophic decline of a desert rodent, Dipodomys spectabilis: insights from a long-term study. Journal of Mammalogy, vol 76, pages 428-436.
  8. Peter M. Waser and James M. Ayers. 2003. Microhabitat use and population decline in Banner-tailed Kangaroo Rats. Journal of Mammalogy vol 84. Pages 1031-1043.
  9. I keep meaning to take a recent version of this, but haven’t remembered to do this when I’m at the site.