From Observation to Prediction: Modeling Species Distributions in the Mojave Desert

As I’ve written before, my original internship period, which focused on developing priority species lists for restoration sites in the Mojave and Sonoran deserts, has been extended into the fall in order to work on the next phase of this project. In this extension period, I have dramatically switched gears: from a mode of observation of how species in the low desert of southern Nevada and California operate to one of prediction. What is the scope of distribution for these species? What environmental variables impose limits on the breadth of their occurrence? And how can we make this information as accessible and useful to land managers as possible?


From the list of priority restoration species for the Mojave Desert, my Principal Investigators and I chose 50 species with which to take the next step: creating species distribution models (SDMs) to be incorporated into an adaptive management tool for BLM land managers. This tool would further expedite the restoration process by allowing BLM agents to create “seed menus” for recently disturbed sites. The idea is that land managers would be able to input coordinates for the site in need of restoration into this tool, and up will pop not just one, but a whole suite of plant species suited tailored for the restoration needs of that location, as well as viable seed source locations and information on ecosystem services (specifically for desert tortoise and pollinators) that those plants provide.


My main task in this endeavor has been to gather and vett species occurrence data to use as presence points in our models. My main sources for this information have been unpublished data sets from vegetation surveys taken across the Mojave and herbarium records from public databases such as the California Consortium of Herbaria and the Southwestern Environmental Information Network (SEINet). After a few weeks of gathering a robust number of points and giving them a thorough cleaning, we are ready to actually make some SDMs!

Ephedra nevadensis, one of the species for which we are producing distribution models for our Seed Menus project.


Our process involves three algorithms: 1) a General Additive Model (GAM), a crossbreed between General Linear Models and Additive Models, 2) Random Forest, which is basically a decision tree on steroids, and 3) MaxEnt, the famed maximum entropy algorithm. We first produce an equal number of pseudoabsences (randomly generated points from likely habitat) to go with our presence points. True absence data are rare in vegetation data, so generation of these pseudoabsences is necessary to provide a comparison to presence data. To reduce bias in the data, we thin the presence points to one per grid cell (size of grid cells) and weight ones that are highly isolated from any neighbors. A further bias test we do is cross-validation, in which different models are tested with 75 randomly selected points for a preliminary analysis of goodness-of-fit. After that, we go through each algorithm and formulate response curves of our points to different environmental variables – this helps us determine which variables best explain variance in the data. We then choose a few preliminary models of the best-fitting response curves, and take the mean of these models for each algorithm. After going through all three, we take our top model choices for each algorithm, and take what is known as an ensemble mean. Once this is done, we conduct a last evaluation of performance using the Boyce Index and mask any impervious surfaces in our layers. And voila! We have a robust distribution map for one of our species.

Models of sample data produced with GAM, Random Forest, and MaxEnt algorithms, as well as an ensemble model (the mean of the previous three outputs).

This one-at-a-time approach takes quite a while, but it’s worth it to get sound results for each species. There are alternative modeling methods that are faster (such as Canonical Correspondence Analysis), but the results they produce are not as robust in terms of individual species. Our method aims to produce the most accurate and useful information possible for land managers in the Mojave Desert. With more disturbance happening in the Desert Southwest than ever before, it’s imperative that we have the tools to make sound, on-the-fly decisions. I’m excited to see this tool be put to use in the coming years; to get a better understanding of its strengths and limitations.

Fieldwork (or field trip?) in Red Rock Canyon National Conservation Area

Last week, the Las Vegas BLM, Henderson USGS, and Nevada Conservation Corps  teams from central NV gathered to conduct an experiment on seeding methods for the Burned Areas project. They ended up being short-handed one day, so for the first time in quite a while, I got to go out and do some field work! Outdoor work in the desert during the summer may sound like torture to many, but that day I rediscovered the joys of working outside and being immersed in one’s ecosystem of study.

Sunrise in the Las Vegas Valley.

Besides, desert conservationists are well-versed in the art of beating the heat. In the warm desert, doing fieldwork in the summer means starting at the witching hour and finishing up by noon. We set out for Red Rock Canyon National Conservation Area well before dawn, and set up our supplies under cover of darkness. Our task was to complete a few more plots for the diversionary seed aspect of the Burned Areas project. The lack of palatable vegetation most of the year makes granivory – seed predation – an important diet adaptation. In the Mojave, the chief granivores are harvester ants and rodents, such as pocket mice and kangaroo rats. I understand that seeds are an important part of these animals’ diets, but their caching efforts can throw a huge bone in desert restoration efforts! Previous studies in the Mojave have found that granivores can thieve substantial proportions of propagules from seeded disturbed sites. The diversionary seeding was an effort to distract them from the native seed that we want to keep in place.

Seeds of Joshua tree (Yucca brevifolia), carefully measured for our study plots.

Seeds of Joshua trees, white bursage, and creosote bush, all mixed up with millet and ready for broadcasting!


We mixed small portions of Yucca brevifolia, Ambrosia dumosa, and Larrea tridentata with several ounces of millet seed. The millet seed is more nutritious, and thus more attractive, for granivores. Millet is also not adapted to the Mojave’s hot, dry climate, eliminating the danger of germination of thousands of non-native seedlings. The idea is that any would-be rodent seed thieves would fill up on millet, and then be too stuffed to bother with the native seed. In conjunction with the diversionary seeding efforts, USGS wildlife biologists, along with several volunteers, conducted trapping surveys to gain an understanding of what rodent species were active in the project area.


After weighing out pounds of millet and mixing in carefully calculated quantities of the native seed, my crewmate and I trekked out to our sites. As the sun crested the ridge to the east, it burnished the conservation area’s namesake mountains into a deep crimson. The blue yucca made a lovely contrast with the rocks. Slowly, the air warmed, but a light breeze kept the morning air pleasant as we flagged and hand-seeded our plots.

Sunrise at Red Rocks Canyon NCA.

A pin flag amidst Bromus madritensis and Schismus arabicus, two invasive annual grasses that are major problems in the southwest. These grasses artificially increase the fuel load and create continuity between shrubs in an otherwise sparsely vegetated landscape.


The scenery would have been perfect if not for the haunting reminders of the fires of a decade ago. The difference in plant communities between burned and unburned areas was incredibly stark, with far fewer perennial shrubs – mainly burroweed (Gutierrezia), brittlebush (Encelia) and desert globemallow (Sphaeralcea ambigua) – growing in the disturbed areas. Bromus and Schismus carpeted our sites, and twisted stumps of dead Mojave yucca, some still blackened, dotted the landscape like desecrated statues.

Mojave yucca (Yucca schidigera) that has re-sprouted after fire. It took 12 years…but it is re-sprouting nonetheless!




At the base of many, however, emerged the new green spikes of a re-sprouting individual. The sight of these little green spears reminded me that despite the vulnerability of this ecosystem to fire, tolerance to harsh conditions has always been the name of the game here, and that many desert plants are more resilient than one might think.

Due to my office schedule and the blazing summer heat, I hadn’t had much opportunity to venture out into the Mojave over the last few months. Admittedly, since the annuals died back and the shrubs went to seed, there wasn’t as much draw for me to go outdoors as there was in the spring! However, while out in the field I was pleased to see the desert marigold (Baileya multiradiata) still going strong in the anthesis department. And to be fair, just because a plant is past flower certainly doesn’t mean that it is of no interest! Several species were still loaded down with seeds. We found plenty of desert wishbone-bushes that were bursting with cured achenes, and many creosote bushes were still covered with their iconic downey schizocarps. While I’ve learned more information that I ever thought I could about desert plants, from their phenology to palatability to seed dormancy, even the most well-written scientific paper is no substitute for getting out in the field and learning about these species hands-on.

Larrea tridentata, the iconic creosote bush, chock-full of ripe seeds.

Baileya multiradiata, a year-round bloomer in the Mojave Desert.

Monsoon season is in full swing here in the Desert Southwest. For the last week, the morning sun has been blocked from delivering his usual greeting at dawn by thick, blue-grey thunderclouds. On such mornings, the mountains are dyed a deep indigo, and the smell of creosote is thick in the air. Every Vegas Local’s commute is focused on the same goal: to make it to the office, or home, or wherever, before the rain comes down and the flash floods ensue. I for one am grateful for the reprieve from blistering heat and endless sunshine, and even more so for the promise the rain brings – that there is a second bloom happening further south! I hope that I will be able to see the spiderling, devil’s claw, and agave bloom in the Sonoran before the second dry spell of autumn comes along.


SERCal 2017: A week-long lesson in restoration history, practices, and future directions

As a veteran CLM intern who isn’t doing SOS work this season, I was given the option to do a training alternative to the week-long workshop at Chicago Botanic Garden. After a couple weeks of hunting for desert botanical classes at Zyzx and the Jepson Herbarium, I stumbled on the jackpot: the California chapter of the Society for Ecological Restoration (SERCal) was holding its annual conference in mid-May at the University of California – Davis!

Private contractors, university professors, students, and nonprofit conservationists  converged on the UC-Davis campus, many of them restoration professionals who have been in the field (literally) for decades. Their collective experience fit well into the conference theme: ‘Looking back…Leaping forward’. Much of the research presented at the conference examined the success or lack thereof of restoration projects that were 30+ years old. In this field, it’s rare to keep up with monitoring for that long, and some of the findings were not what I would have expected.

For instance, one presentation by the long-time native propagator and restorationist Ed Kleiner (Comstock Seed, Inc.) revealed an interesting trend in restoration sites across the Great Basin and Mojave Deserts. Initially, restored sites would be overtaken by invasive species like Halogeten glomeratus. However, after ten years of low-level maintenance that did not involve targeted herbicide spraying, Kleiner’s team found that the native shrubs they planted eventually outcompeted the Halogeten, and after 15-20 years, the site had matured into a thriving sagebrush community. I was pretty surprised at the success of this hands-off method, particularly in a region of the country that’s drowning in cheatgrass (Bromus). I guess only more time will tell if these restored ecosystems are as resilient as they look.

This year was also the first time that SERCal devoted an entire session to that ever-looming threat to ecological work: climate change. The talks in this session focused not so much on discrete studies as they did on frameworks for approaching climate-smart restoration and management. One presentation, by Tom Giraldi of Point Blue Conservation Science, highlighted the need for vulnerability assessments in restoration planning, and the use of past projects in predicting challenges. Another talk that focused on policy challenges advocated for “boldness in the face of uncertainty” – a not-so-subtle reminder that we are running out of time in which to act. Overall, researchers stressed the practice of asking smarter, more structured questions before and during the restoration process.

My favorite session (and that which was most applicable to my internship) was the one on native plant and seed source management. Presentations included germination work with rare species, the use of large-scale and sustainable agricultural practices for propagating native species, and the finer points of designing seed mixes for disturbed sites. Most touched upon the National Seed Strategy (NSS) and its importance in guiding long-term, interdisciplinary restoration projects, speaking of it as though it were a battle plan that could lead them through the uncertain mire of the future. As a CLM intern and a former SOS worker, I felt privileged to be part of a grand design of such importance.

Perhaps the most exciting take-away of mine from SERCal 2017 are the networks I built with the conservation professionals I met. One of them, Professor Neville Slade of Victor Valley College (VCC), located in the western Mojave Desert, is interested in helping his students plug into the NSS as CLM interns. In June, I’ll be visiting VCC to talk to these students about my experiences as a SOS/CLM intern. It’s my hope that I’ll be able to plant some seeds in these students’ heads that will grow into commitment to conservation and sustainable, long-lasting repair of the damage that we humans so easily wreak on this precious planet of ours.


Fire, invasion, and forgotten pollinators – Determining restoration species for disturbance in southwestern deserts.

Last fall, when I rolled down the leeward side of the Sierra Nevada and landed in the Mojave Desert, I finally understood why the word “enchanted” is so often used to describe the southwestern landscape. To someone born and raised east of the Mississippi, the desert looks impossible, a landscape too strange to exist. Bare ground dotted here and there with lonely shrubs; enormous, rounded boulders piled haphazardly together like toys; the eerie sight of Joshua trees, arms outstretched, waiting for some unknown sign that may never come. I was only able to stay for a few days, but I had a feeling that I would be back sooner rather than later. Lo and behold, here I am, beginning my 24th year as a Las Vegas local, and an intern of the US Geological Survey.

The Mojave Desert, just south of the Hoover Dam.

Compared to the cold desert of the Intermountain West, the warm southwestern deserts of North America have a remarkable history of escaping postcolonial mass disturbance. The Mojave and Sonoran regions are too hot and dry to support large-scale livestock operations, and are not as rich in fossil fuels as their northern counterpart. In short, the landscape didn’t have much to offer, so there was little reason to tear it up. However, in the last several decades rising incidence of severe wildfires and the development of renewable resource infrastructure in the southwest has made ecological restoration a priority, particularly in regards to desert tortoise critical habitat. The Mojave Desert and Sonoran Basin and Range Native Plant Programs were created to begin developing native seed sources for restoration needs in accordance with the national Native Plant Materials Development program. This is a massive, long-term undertaking involving seed collection, genetic and ecological experimentation, and collaboration with an assortment of interest groups, from public land managers to private business owners.


Before any of these steps can be taken, however, land managers must first determine which species to use for landscape-scale restoration. In desert ecosystems, where succession takes place on a scale of decades to centuries, it is particularly important to carefully select pioneer, mid-, and late-seral assemblages that can transition smoothly from one to the next. This is where I come in. My job is to develop lists of priority restoration species for both the Mojave Desert and the Sonoran Basin and Range ecoregions. Both of these programs are in their infancy, so while this internship project is a hefty responsibility, I also have considerable room for creativity.


The first item on my plate is to enhance the Mojave Desert list. For the first few weeks of my internship, I educated myself on the ecology of North America’s smallest warm desert, particularly in regards to succession of disturbed communities and the impact of invasive annual grasses such as Bromus madritensis. Once I felt I had a good working knowledge of the ecosystem, I set to work. Researchers at my field office had already developed a species list regarding the diet and cover plant needs of desert tortoise, but other important taxa, namely pollinators, had been neglected. Using this original list and other literature on diet and cover plants used by G. agassizii as my baseline, I compiled a list of candidates. I then researched each species individually to assess its potential use in restoration projects; this involved researching traits like successional stage, ease of collection, propagation, and seed storage, and whether or not each plant hosted native pollinators.  

Desert Globemallow (Sphaeralcea ambigua) with some insect visitors.

Unfortunately, I quickly learned that there is a great dearth of information on pollinators of the Mojave Desert. Aside from a few highly impressive natural history papers from the 1950’s – 70’s, very little research has been conducted on native insects and their relationships with desert plants. Considering that the desert southwest is a hotspot for bee diversity, I found this surprising, not to mention frustrating! A 2006 USDA study found that in Carbon County, NV alone, there are nearly 600 species of native bees, over 30 of which are endemic (for more information, look up the Pollination Ecology Final Report for the Clark Co., NV 2003 Biennium). Environmental heterogeneity in desert regions promotes evolutionary divergence, and speciose taxa range from pupfish to insects to cacti. Combined with a high incidence of monolecty (ecological relationships in which a host species is visited by only one pollinator species), this makes the Mojave Desert a difficult but imperative environment in which to conduct pollinator research.


Much of what pollinator research has been done in the Mojave focuses on Larrea tridentata, the iconic creosote bush. As a ubiquitous, dominant presence throughout the Mojave, Larrea is visited by over one hundred species of bee, twenty of which are specialists. With such a massive guild and widespread distribution, one wonders if creosote facilitates pollination of other desert plants, acting as a pollen “pit stop” of sorts. While L. tridentata already performs many services to its community, if this idea is correct, creosote bush may turn out be even more important to warm desert ecosystems than we realize!

The iconic creosote bush (Larrea tridentata) at the Eureka Dunes in Death Valley National Park.

After several weeks of work, my principal investigators and I are in the revision stages of the Mojave Desert priority species list. Our ultimate goal is to craft a tool that land managers can use in conjunction with seed transfer zones, a novel and instrumental tool to help land managers effectively source native seed for use in revegetation and restoration projects, to make the best choice of a species suite for use in restoration projects. Such tools would expedite the process of restoring public lands with seeds that are best suited to each project restoration site.


In addition to reading papers and writing species profiles, I have had the opportunity to assist with ecotype research at the USGS greenhouse and a few of the common gardens that are established in the Mojave Desert. This spring, we have been growing Chylismia brevipes and Plantago ovata in the greenhouse. Chylismia will be outplanted in a garden south of Las Vegas as part of a study of native plant transplantation methods. The Plantago seeds will be harvested and used in other restoration experiments. Much of the greenhouse work involved daily hand-pollinating sessions for the Chylismia (as we cannot allow it to cross-pollinated between populations and genetically muddy our research specimens) and bagging the P. ovata to ensure that we don’t lose any seed to natural dispersal. In the gardens, I have assisted with monthly plant assessments, conducting morpho- and phenological measurements of Ambrosia dumosa, L. tridentata, Sphaeralcea ambigua, and Achnatherum hymenoides. These assessments are part of a long-term ecological research project on the limitations of seed source in restoration sites across the Mojave Desert. The results from this research further contribute to the development of seed transfer zones.

A suncup blossom (Chylismia brevipes), ready to be hand-pollinated!

A tray of desert plantain (Plantago ovata), some of which has been sacked in order to prevent seed escape!

And, since 40 hours a week of researching and working with native plants isn’t enough, I have also spent quite a few evenings and weekends botanizing in the amazing natural areas that surround Las Vegas. Lake Mead National Recreation Area, Red Rocks National Recreation Area, Death Valley National Park, and Ash Meadows National Wildlife Refuge are just a few of the places I have ventured into, armed with my hand lens and a borrowed copy of the Jepson Desert Manual. As I am not spending a substantial amount of time out in the field during my internship, this is a way for me to both enjoy desert natural areas and begin to learn the flora of the Mojave. A few of my favorite spring-flowering desert plants have been sand blazing star (Mentzelia involucrata), turpentine-broom (Thamnosma montanus), Mojave hedgehog cactus (Echinicereus triglochidiatus), ground cherry (Physalis crassifolia), and desert sandmat (Euphorbia albomarginata).  

Ground cherry (Physalis crassifolia), a member of Solanaceae.

Sand blazingstar (Mentzelia involucrata), a member of Loaceae, a family that I’d never encountered before coming to the Mojave!

Whitemargin sandmat (Euphorbia albomarginata), a member of Euphorbiaceae and possibly my favorite desert wildflower.

To my knowledge, this is the first CLM internship of its kind. It’s been very exciting to be part of such groundbreaking work. After my work on the Mojave Desert is finished, I’ll be working on a similar document for the Sonoran Basin and Range – an ecosystem which, with its biannual blooms and distinct subdivisions, may prove to be even more challenging to understand than its northern counterpart.