The wrong kind of help…and an unexpected friend!

Facilitation is usually considered an ecosystem service — positive interactions between species can increase biodiversity and ecosystem function. But what happens when the beneficiary species is an exotic invader that degrades ecosystems?

This spring, I sampled the annual plant community using a paired shrub-open microsite contrast at six sites situated along an aridity gradient from Mesquite, NV to Panoche Hills, CA.

At each study site, I found that Bromus rubens, an annual grass species native to Eurasia and northern Africa but highly invasive across southwestern North America, associated strongly with native shrubs. Specifically, Bromus abundance, biomass, and fecundity were consistently greater under shrubs than in the open. Interestingly, the strength of facilitation did not depend on the size or species of foundation shrubs, but it did depend on aridity — Bromus-shrub associations were strongest in the most arid environments.

A halo of beefy Bromus rubens plants growing under an Ephedra shrub in the Cuyama Valley, CA. This pattern was typical at all study sites.
Bromus was facilitated in abundance at all sites, but Bromus-shrub associations were strongest in the most arid environments.

These findings suggest that invasive B. rubens can associate with native foundation shrubs across a large portion of the non-native range, and that positive interactions mediated by native shrubs can potentially exacerbate B. rubens invasion by increasing abundance, fitness (i.e., fecundity), and competitive ability (i.e., size). The positive relationship between aridity and facilitation strength suggests that the threat of facilitated invaders may be greatest in the most arid conditions.

Oh, and look what else I found:

An endangered desert tortoise chillin’ under a shrub…amongst the Bromus. Don’t see that every day!

Wildlife of the Granite Mountains

Mammals

Birds

Reptiles

Insects

Will the real cactus flowers please stand up?

All field scientists know that getting out into nature to do your work means problem solving. Usually, you have to do this on the fly and with limited time, internet, communication… limited everything basically. But that’s where the creativity and decision making skills come in handy. Sometimes it’s a simple obstacle like breaking your tape measure or cactus spines lodged in your shoes. But then other times, it’s a seemingly catastrophic event—like flash floods destroying your study species, or political unrest in your study area—that disrupts your plan. Or, if you’re me, cold weather delaying cactus blooming in a cactus flower experiment.

This winter in the Mojave was unusually cold and rainy. The average high in January 2019 was 10.5°F—normally it’s a high of 57°F. Rain is great for flowers, it means there will be much more of them when they bloom. But cold means delayed blooms. And this Spring, it was delayed by about a month. Four weeks was how long I had planned to be in the desert, so after about two weeks of no flowers and a chilly forecast, I knew we needed to come up with some solutions.

The Buckhorn Cholla just wasn’t blooming. But at least it was beautiful.

The most obvious: stay longer. Duh. But this wouldn’t help if the cacti never bloomed, and I had to be back in Toronto to TA eventually. So I planned to hang out in the desert (no complaints here, it’s beautiful out there), but I knew we needed more options. Hire help? Working with birds means access to a large pool of citizen scientists who would give their time to look at birds in a place they otherwise couldn’t go. And I could hire a paid assistant from the area. These two options seemed great, but getting anything done with the public takes several months advanced notice, and there simply wasn’t any interest in my for-hire ad. So help was out. I kept thinking, and waiting, and hoping the flowers would just bloom and I could work extra long days and get it done. But that didn’t happen.

I had one last idea. Perhaps it was my most hair-brained scheme: use fake flowers (more appropriately called mimic flowers). After all, the problem was there were no flowers, and the end goal was to have flowers. A few papers had studied bird (hummingbird, specifically) visits to mimic flowers, and had success. This idea, which we didn’t know would even work, required a lot of experimental design rewiring. Two semester’s worth of planning and design scrapped and reinvented in a hour was terrifying. Whoever I told about my woes all echoed the same reaction, “That’s field ecology for you!” For a worrier and a planner like me, it’s a nerve-wracking line of work.

But I had to do something. I’d finished walking transects to look at birds and needed to start an experiment, any experiment. So I bought a bunch of fake flowers at Michael’s (Michael’s, would you like to sponsor an up-and-coming ecologist??) that looked like the Buckhorn Cholla’s flowers I’d seen on google, and pinned them onto the un-opened buds of my focal cacti. I had four levels of manipulations, set out camera traps, and watched for an hour. I was on the edge of my camping-chair-seat for the first session. There were thirty flowers pinned on this plant, my highest volume of flowers. Would they come? I needed proof of concept, proof that the birds would visit these cacti in some capacity, or else my findings are nothing but “birds don’t visit cacti”. Nothing wrong with this from a scientific perspective, but there’s not much to explore after the fact. A huge part of my Master’s relied on this next hour.

I was lucky. Within seven minutes, a Costa’s Hummingbird visited the cactus and attempted to pollinate the fake flowers. And then 6 more did the same over that hour. Funnily enough, this would be my busiest session for the rest of the field season. But it was peace of mind—the birds came, and no matter what else happened for the rest of the Spring, I had something to compare all my results to. After the 10 day experiment observing these mimic flowers, they finally began to bloom. The flowers really did look similar to the mimics, and I figured next we could see how different concentrations of real flowers on a cactus influenced bird behavior.

The first visitor to the mimic flowers.
The cacti had finally bloomed, now it was time for the second experiment.

The experimental design for the real flowers was exactly the same as the mimic flowers, but this time, there were real flowers on the plants instead of fake ones. So I watched and waited, this time with less anxiety. But the first day passed, and no birds visited the cacti. Strange, but it was a particularly hot day, perhaps they just weren’t out and about. The next day came and went, and still, no birds at the cacti. This stayed true for the rest of the experiment. Birds were still coming to the procedural control (a poll with 30 mimic flowers glued to the top), but not to the real flowers. Not even once in the 10 day experiment. And just like that, the experiment ended. Science waits for no one.

During the second experiment, birds still visited the mimic flowers. Just not the real ones.

Now, I’m back in Toronto. Data analysis is next up on the docket, but one thing is clear even without the statistics: birds will pollinate flowers on a cactus, just not the flowers that a cactus actually produces. It’s not the entire structure of the cactus that deters birds, but something about the flower itself that tells them not to come.

We know that most cacti are primarily pollinated by bees, and now we can say, at least for Buckhorn Cholla, they are absolutely not pollinated by birds. Could the flower have ultraviolet patterns advertising to the birds that this flower is not for them? Or perhaps a chemical signal from the flower deters them? Essentially, what is the mechanism associated with the flower that keeps birds away?

But perhaps even more interesting is this: what is the cactus flower actually saying to different pollinators? Two signal options exists, exclusionary or inclusionary. The flowers may signal that birds should not come here. Or perhaps, the flowers signal that the nectar is explicitly for bees. Imagine a sign outside a young boys treehouse saying, “No girls allowed.” This is an exclusionary signal, telling girls that they cannot come in (but I mean, smash the patriarchy). Now consider a “Man Cave” sign outside a basement. This is an inclusionary signal, suggesting that this space is for men. In the end, these signs have the same outcome: no women are in the space. An observer who cannot read English could observe that no women entered either of these spaces, but would need to be able to interpret the signs to know whether the signal is exclusionary or inclusionary.

This is fascinating, because in our human signage example, the interaction individuals of men, women, and sign-maker all are the same species speaking the same language. But in our bird-bee-cactus scenerio, we have three extremely different taxa (a plant, an insect, and a vertebrate) all possibly “reading” the same language. And they do all this interspecific signalling avoid niche overlap and wasted energy.

Now, we just got to test it. Easier said than done.

All these questions were… not what I was expecting to come home with at the start of my field season. Had the flowers bloomed when I arrived, I would have performed our original experiment manipulating the number of flowers on different sized cacti. And I would’ve gotten a whole lot of nothing. I’m a scientist, so I don’t like to say fate had a hand in this, but it was some good luck that I was so unlucky.

A male Costa’s Hummingbird, possibly a bilingual genius.

Pay to Play: Google API Keys and Mapping in R

In January 2019, Google updated their terms of service and has essentially removed the free access to Google Maps in R. This means that you’ll need to purchase the relevant APIs (compu-speak for Application Programming Interface) from Google in your google account to access these features in R.

So do you need it?

If you’re interested in mapping in R, you basically need it. There are some mapping packages that you can use to get around using any Google products (Leaflet is a great example). But for all the glorious customization and overwhelming ubiquity of the ggmap, this API key is essential for reproducible science in ecology related fields. When I first encountered the problem, troubleshooting was a nightmare–everyone used ggmap, and even those who didn’t still used Google Maps as a source for their base maps. Not. Fun.

Luckily, it’s relatively cheap at $2/month for the first 100,000 static maps in each month (dynamic maps, street maps, embed advance, and dynamic street maps cost more, but we aren’t likely using these tools in our work). Even luckier, there’s a $200 credit/month for the first year of use!

But how?

It’s a bit confusing to navigate the Google Cloud Console if you’re trying to figure it out solo (and scary considering you’re paying for something), but the actual steps are easy and quick. There are two main steps to the process: 1)Get an API key and 2) Show R your API key. There’s just a few ministeps in between.

Get an API key:

  1. Go to this website.
  2. Pick your product (Maps).
  3. Select a Project. If you don’t have one, create one. It won’t matter later.
  4. Enter your billing information.
  5. Copy your API key. Consider pasting it into a .txt file on your machine for safe keeping.

Show R your API key:

  1. In your R console, enter this code:
    • register_google(key = “YOUR_API_KEY”)
  2. Run this code for every new session you need to map in, and you’re ready to go!

a daRk tuRn

Open science is good for everyone!

R is popular among scientists (especially ecology/conservation scientists) because of its power. But it’s basically essential for scientists because it’s free. In a field where funding is scarce and costs are high, R has been a blessing for open science and has seriously moved the discipline forward. But the same reason R is powerful is because it’s not entirely autonomous; it (in large part) relies on monolithic companies like Google to up the ante. It may not be a very expensive fee, but it is yet another barrier for researchers and open science. Hopefully someday we can return to a free, open access Google Maps. After all, open science benefits scientists, the general public, and corporations–even Google.

Experiential Education Symposium at York University

I had a great time last week representing the Lortie lab and discussing work from my research practicum with president and vice chancellor of York university Rhonda Lenton. Aside from gaining wonderful feedback from her, which will definitely assist me in my future endeavours, I was thrilled to present the importance and impact of biology research with her as well as the many other influential attendees. I am excited and eager to experience the opportunities that lie ahead.

RuPaul’s Cactus Race: a baseline cactus size survey

What are the cacti?

For the bird-cactus double mutualism project, we had planned on observing two study species: Cylindropuntia anthrocarpa (Buckhorn Cholla) and Opuntia basilaris var. basilaris (Beavertail Cactus). We also needed 3 class sizes (small, medium, and large) in which to bin the cacti. This would impact our sample size and equipment list. That being said, the best laid plans of mice and men (and grad students) often go awry. I’d only briefly visited our study site the summer before I’d officially started at York, so we knew we would need to revisit Sunset Cove to do some preliminary exploration before getting into the trenches and collecting end-game data. Getting to the site, it was immediately apparent that we would need to examine our plants more closely; there was nearly no beavertail in sight. So we altered the protocol, then added Cylindropuntia enchinocarpa (Silver Cholla) into the mix. The goal? Determine the location, size, size-variability, and health. We want a tall-ish species (so pollinators and frugivores would be interested) with plenty of variability in size, enough of them to manipulate conditions, and healthy enough so we can expect some flowers and fruit later on. And, for fun, we took a quick look at shrubs to see if they’re associated with cacti in any respect (I don’t go into that here, but the data is available on Github).

Sunset Cove: a desert haven nestled in the Granite Mountains, and also our study site.

Where are the cacti?

Let’s make a quick map and take a look at the cacti individuals sampled. For C. anthrocarpa, we were easily able to sample at every 5 meters along 5 transects that were spaced 5 meters a part (n=105). C. enchinocarpa, however, was more sparsely distributed. So, after doing our first two transects 5 meters apart, we realized we needed to increase the distance between transects to 10 meters. We also weren’t able to get a cactus sample at every 5 meters, so we sampled 9 transects in total (n=98). The least common species, however, was Opuntia basilaris, which was so rare that transects were ineffective, so we instead unsystematically searched the entire site only to find a paltry number of individuals (n=26).

A quick map of the Cacti at Sunset Cove
Green = Buckhorn Cholla, Blue = Silver Cholla, Pink = Beavertail, Orange= Sunset Cove (Mapped in R using Leaflet)

Based on the proposed protocol, we need 150 individuals of each study species to replicate each combination of variables 10 times. Ideally, the individuals manipulated between flowering and fruiting season will not be resampled in the the fruiting season, as our manipulation of the flowers in April may impact the number of fruits in August. This means that C. anthrocarpa is a solid study species option. C. enchinocarpa is certainly possible, but not as dominant as its cousin, and O. basilaris is out of the question.

How big are the cacti?

We’ve seen the distribution of cacti, but size of the cacti is what’s really important for this study. We need to know if the sizes are variable enough to split into 3 class sizes (small, medium, and large). We also need a general idea of their height to consider if pollinating and frugivorous birds will engage with the flower and fruits of the cacti at all. The three species did indeed have significantly different mean heights (Kruskall Wallis Test, p > 0.0001, df = 52, x^2 = 151.52), with means of 1.04, 0.55, and 0.17 for Cylindropuntia anthrocarpa, Cylindropuntia echinocarpa, and Opuntia basilaris, respectively.

Cylindropuntia anthrocarpa is the tallest of the three, followed by Cylindropuntia enchinocarpa, with Opuntia basilaris being the smallest (p>0.0001)

How should we bin the cacti?

One important variable of our project is size classes within a species: small, medium, and large. Because height is what may influence pollination and frugivory, we will use the “z-axis” that we measured as the factor for size. Each size class must contain enough individuals for replication. We need to decide how to bin the size classes; either we can use natural breaks present in the data, or we can create equally-sized bins for the study species. Let’s examine each species’ size distribution, and make decisions about size class breaks on that.

None of the species have distributions with natural breaks (see density plots), and, especially for our two Cylindropuntia species, we can see that there are even distances between quartiles (see boxplots). For these reasons, I propose an equal-size binning method to determine size class.

Size-classes of cacti

But what exactly are the equal size classes for each species?

SpeciesSmallMediumLarge
Cylindropuntia anthrocarpa<85cm86cm – 152cm>153cm
Cylindropuntia 
enchinocarpa
<45cm46cm – 72cm>73cm
Opuntia basilaris<15cm16cm – 22cm>23cm

We can see that Buckhorn Cholla (C. anthrocarpa) has the largest class sizes, followed by Silver Cholla, and then Beavertail. Having large classes may translate more clearly to birds, and therefore be a suitable metric to see if bird visitation is influenced by cactus size.

Health of cacti

Another important factor to consider when exploring potential study species is their overall health. After all, are these individuals even capable of flowering and fruiting? To measure health, we created a health index based on the Wind Wolves Bakersfield Cactus Report, which classifies each individual’s health on a discrete scale of 1-5 (1 being the least healthy, and 5 being the healthiest). We considered overall paddle/branch death, as well as scarification and rot.

Buckhorn and Silver Cholla both have a strong representation of 4 and 5 level health individuals, whereas Beavertail is equally distributed among all the health classes.

We can see that the Cylindropuntia species are healthier than their Opuntia counterparts. The question is, will an unhealthy population still flower/fruit as much as a healthy population? Perhaps, but this is not the question of my project.

Who is America’s Next Cactus Superstar?

Considering its abundance, size, and health, Opuntia basilaris is not a realistic contender as a study species. It is likely to be overlooked by birds, not bloom/fruit due to poor health, and is in small supply. Therefore I must remove it from the running. Both of Cylindropuntias are healthy. Silver Cholla, however, is still less dominant than Buckhorn Cholla, is smaller overall, and doesn’t have the width of size classes that Buckhorn Cholla does. While these traits do not mean the Silver Cholla could not be a viable study species, I propose that focusing more on Buckhorn Cholla by deepening the methods of observation (i.e., joy sampling: stationary versus mobile count data, and increased hours of focal observation) will be more beneficial to answering my study questions than a comparative study between cacti species would.

Buckhorn Cholla, Shantay you stay.

A workflow for pollen identification.


The reproductive ecology of cactus is not well-studied. A small, side project of mine is to determine the pollinator guild of buckhorn cholla at Sunset Cove, Mojave Desert, and with which plant species, if any, it shares pollinators. The genera Opuntia and Cylindropuntia are known to be insect-pollinated, but I am curious which of the more than 659 species of bees in the Mojave Desert desert are pollinators.

As visitation does not necessarily lead to pollination, I removed the pollen loads from 22 bee visitors I caught during insitu observation periods. I also removed stigma from the cholla to quantify heterospecific pollen deposition i.e. evidence of pollinator sharing. Pollen ID is not easy task and so I have developed a workflow to make it more streamlined.


Prep a reference collection:

  1. Create a reference collection by removing pollen from the anthers of several flowers of every species blooming in the area. Store in ethanol.
  2. Mount and stain the pollen with fushcin jelly.
  3. Image each species of pollen grain at 3 magnifications. Measure the length and width of about 10 grains per species. I calibrated Lumenera’s Infinity Analyze software using a stage micrometer to make this really quick.
  4. Make a reference document to consult. I use a word doc where every page is a species. Add in the photos at several magnifications, the mean size and any notes.
Sample reference page for Echinocereus engelmanni (Hedgehog cactus)


To go through the stigma or bee pollen load samples, I use my Canon EOS 60D dslr with a 60mm macro lens pointed confocally into a light microsite at 100x. I used the remote shooting utility from Canon to control the camera with my computer and display the view onto a second monitor.

Home example of confocal setup
  1. I designate each coverslip on the slide as a zone and do 8 transects through each, counting the grains. Each line in my spreadsheet is a transect, each column is a species. I use 5 columns for buckhorn so I never have to count very high.
  2. I don’t count damaged grains, or grains in air bubbles.
  3. Each slide gets its own folder. I take photos of each heterospecific grain with the file name as the zone + transect + species, which is simple using the photo utility. Knowing where the grain is on the slide and what its surroundings are will be helpful if you need to find it again.
  4. The species can be tentative for now so don’t get too bogged down.
  5. Take photos of unknowns when first encountered and assign them morphospecies ID. I put these in a separate folder as a reference.
  6. Some species are easy to ID. Quite a few are not. The more grains you see the easier it is to spot the differences.
  7. To help ID, we can take a page from entomologists. Sort the photos by their tentative IDs, putting each species in a folder so they are visible all at once (do a bulk rename to append the folder name first). It is difficult to compare grains unless they are side by side, which isn’t realistic with one microscope.
  8. Sort until each folder contains identical grains, then assign them a species from the reference collection. Or assign them to a species group for species that are virtually identical (likely Asteraceae!). Assign any remaining to morphospecies. Update the datasheet with the corrections.  
Buckhorn cholla (larger) and silver cholla (smaller). Thankfully the most abundant grains are simple to differentiate.

Commencement of Native vs. Exotic Competition

After a 2 month growing and censusing period, followed by a harvesting, drying, and biomass census I have concluded my 200 pot competition series.
During this period, I had obtained a photometer to measure light levels and did two light census for both the overall pot as well as below canopy. I am hoping that these light measures will provide quantifiable insight on the effect light has on growth. I hypothesize that plants receiving ambient light will yield greater mean biomass per species, while those in shade conditions (to mimic shrub presence) will have a greater mean height due to leggy growth.
I wanted to quantify the growth of my plants through several metrics, and therefore chose to obtain both height and leaf measurements for each species from each pot. In order to acquire these measurements, I implemented a new censusing technique for my second and final census. In this census I counted the number of individuals of each separate species there were per pot. Following this, I took the tallest individual of each species, and recorded its height along with the number of leaves. This way, following the harvest and mechanical oven drying period I would be able to compare the biomass of the plant with its height and leaf count. This would allow me to evaluate plant growth using two separate dimensions; plant height along and number of leaves vs. plant biomass.

After using a mechanical drying oven set to 62 degrees Fahrenheit for 48 hours, I used a precision scale to obtain the biomass of each plant.

The experiment planning, seed counting, pot filling, plant censusing, harvesting, and biomass analysis processing were extensive processes. I am extraordinarily grateful to Dr. Christopher Lortie, Dr. Jacob Lucero, Masters graduate Jenna Braun, research practicum student Anuja, and Economics and Finance student Denis Karasik for their time, efforts, and immense assistance with running this experiment.

Statistical analyses for all of the results are still in work, and I am eager to see the conclusion my experiment comes to.

Hours of biomass censusing in one photo

All the plants before the harvest

A flower from the beautiful Phacelia tanacetifolia
Plantago insularis also grew flowers