Ecological Indicators 146 (2023) 109755

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Ecological Indicators
journal homepage: www.elsevier.com/locate/ecolind

Short Note

Using sUAV imagery to map litter of invasive annual grass in dry

environmental conditions
Tara B.B. Bishop a, c, *, Isabella M. Errigo b
a
USDA Forest Service, Rocky Mountain Research Station, 735 N 500 E, Provo, UT 84606, United States
b
Brigham Young University, Department of Plant and Wildlife Sciences, 4105A LSB, Provo, UT 84604, United States
c
Current address: US Geological Survey Southwest Biological Science Center, 2290 Resource Blvd, Moab, UT 84532, United States

A R T I C L E I N F O A B S T R A C T

Keywords: Invasive annual grasses pose a severe threat to drylands of the United States by increasing habitat degradation
Remote sensing and the occurrence and severity of wildfires, while simultaneously outcompeting native species. Advances in
Bromus technology and accessibility of small uncrewed aerial vehicles (sUAV) provide the opportunity for small preserve
Habitat conservation
managers to map and monitor plant invasions in critical habitats for rare and endemic plant species. Many
Biological invasions
remote sensing techniques rely on the invasive plants’ different phenological signals to distinguish them from
Drones
native plants and habitats. However, invasive annual grasses in the western United States have high variability of
interannual productivity and may not green up each year. Therefore, our objective was to use an sUAV (quad­
copter drone) to map invasive annual grass regardless of phenological stage in critical Mojave Desert habitat. The
study locations were White Dome, a small habitat preserve, and Beehive Dome in Washington County UT, USA.
These areas are critical habitats for several endangered and threatened plant species and are covered with
sensitive biological soil crusts, making on-the-ground measurements destructive. Using imagery collected with
an sUAV we created red, green, blue (RGB) orthomosaics and calculated the Visible Atmospherically Resistant
Index (VARI) across these areas. We successfully mapped the litter of invasive annual grasses at one of the two
sites. At White Dome, we attained 95.2 % and 84.3 % Producer’s and User’s Accuracy in mapping invasive
annual grasses based on the RGB spectral signature of invasive grass litter. At Beehive Dome, the heterogeneous
nature of the edaphic and topographical features made it difficult to accurately map (<20 %) using VARI and
RGB alone. Here, we propose plans to increase accuracy in these dryland systems to be able to map invasive
annual grasses regardless of year or environmental conditions.

1. Introduction selected based on a particular year’s suitability in detecting the invader

Technologies for remotely sensed data collection have made great
strides in detecting biological invasions, down to species level (i.e.,
Müllerová et al. 2013; Vaz et al. 2018), and support rapid response with
earlier invasion detection (Bradley 2014). This allows researchers to
detect the invader based on spectral measurements, such as the
normalized difference vegetation index (NDVI; i.e., Bishop et al. 2019)
and chlorophyll fluorescence (Smith et al. 2018). Such is the case with
invasive annual grasses that can be detected remotely utilizing differ­
ences in phenology in the west and southwestern United States (Bradley
2014; Bishop et al. 2019). Having flexibility for when imagery can be
(Bradley & Mustard 2005) can be sufficient for answering broad land­
scape level ecological questions. However, when working with more
localized, smaller extent, or fine-scale habitats (which is common for
rare, endangered, and threatened native plants) remote sensing using
satellite imagery may not be as useful (Bradley 2014; Vaz et al. 2018;
Müllerová et al. 2017). Here we present an analysis using small
uncrewed aerial vehicles (aka sUAVs, UAVs, or drones) to map and
monitor small areas of critical endemic plant habitat under severe threat
of invasive annual grasses in the southwestern United States. The recent
developments with sUAV have made not only the technology accessible
through commercial sales of drones and user-friendly software, but the

Abbreviations: sUAV, small uncrewed aerial vehicle; VARI, visible atmospherically resistant index; NDVI, normalized difference vegetation index; RGB, red, green,
blue.
* Corresponding author.
E-mail address: tbishop@usgs.gov (T.B.B. Bishop).

https://doi.org/10.1016/j.ecolind.2022.109755
Received 30 August 2022; Received in revised form 20 November 2022; Accepted 30 November 2022
Available online 6 December 2022
1470-160X/Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
T.B.B. Bishop and I.M. Errigo
ability for individual managers to tailor their monitoring and subse­
quent response specifically to invasion threats (Vaz et al. 2018; Lou­
haichi et al. 2019). So, while the common limitations of using drones
across large landscapes persist (e.g., short battery life and flight time),
they are well-suited for covering areas on the scale of small preserves or
studies that are at high risk of degradation due to foot traffic and other
disturbances (Cruzan et al. 2016; Räsänen & Virtanen 2019; St. Clair &
Bishop, 2019).
Attempting to monitor invasive annual grass growth using pheno­
logical differences makes the timing of image capture one of the most
critical factors (Bradley 2014; Müllerová et al. 2013; Müllerová et al.
2017). But, in the west and southwest United States, high interannual
variability in precipitation can be linked to boom-and-bust cycles of
invasive annual grass growth (Bradley & Mustard 2005). At White
Dome, a nature preserve located in the northeast corner of the Mojave
Desert (Washington Co., UT, USA), a wet winter led to a highly pro­
ductive growing season for invasive annual grasses (Pilliod et al. 2017)
raising concern for preserve managers. It is habitat for rare, endemic,
endangered, and threatened plant and animal species with specific
habitat parameters, covered in biological soil crusts that are sensitive to
physical disturbance (Belnap 2003). Being able to monitor the preserve
for invasive species remotely is a top priority to help conserve and
protect the habitat that is vulnerable to degradation by invasive grasses
and disturbance (discussed in Germino et al. 2016). But using pheno­
logical differences became impossible when the following winter was
very dry, leading to a poor growing season for invasives. Our objectives
therefore are to assess the accuracy of a map of invasive annual grasses
created based on the spectral signature of the standing litter rather than
active photosynthetic tissue, as is the more common practice (Weisberg
et al. 2021). Our map of litter should accurately delineate invasive
annual grass distribution and provide key information for managers to
identify where invasion has happened and where future invasions are
likely to be based on distribution and viability of the seed bank. Invasive
annual grasses are known to be prolific seed producers and propagule
Fig. 1. Map of two study site locations in Washington Co., UT, USA, one owned and managed by The Nature Conservancy (TNC) and the other by the US Bureau of
Land Management (BLM). These study sites are known habitats for at least two endangered and threatened endemic plant species. UAS Flight Area denotes the small
uncrewed arial vehicle (sUAV) coverage for imagery capture.
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Ecological Indicators 146 (2023) 109755
pressure can push invasion fronts past ecological barriers such as biotic
resistance (St. Clair & Bishop, 2019). Therefore, knowing where litter
(ie., previous years production) has occurred will also show where the
seedbank is most dense and expected to be viable.
2. Methods
2.1. Study site
The study was conducted in Washington County, Utah, USA on
Pueblos and Nuwuvi (Southern Paiute) heritage land (Fig. 1) on what is
now known as White Dome Nature Preserve (37◦ 0′ 50.70′′ N
113◦ 33′ 48.96′′ W) and Beehive Dome (37◦ 0′ 40.94′′ N 113◦ 28′ 0.83′′ W).
Mean annual winter and summer temperatures are 7.2 ◦ C and 32 ◦ C,
respectively. Precipitation mostly falls in winter and spring, with 209.6
mm of mean annual precipitation. Study sites are on the Shnabkaib
member of the Moenkopi formation with soils having 25–50 % by-
weight gypsum content (Nelson & Harper 1991). These sites provide
habitat for rare, endemic, and endangered gypsophile plant species,
including Siler’s pincushion cactus (Pediocactus sileri (Engelm. ex J.M.
Coult.) L.D. Benson), and dwarf bear poppy (Arctemecon humilis Coville).
White Dome Nature Preserve, currently managed by The Nature
Conservancy (TNC), is a 323-hectare preserve that prioritizes the con­
servation of these two endemic plant species with a portion open to
hikers only. The Beehive Dome area along Warner Ridge is currently
managed by the US Bureau of Land Management (BLM) and designated
as an Area of Critical Environmental Concern (ACEC, Warner/Fort
Pearce). The gypsum hills habitat for the endemic plants is open to
hikers and cattle grazing.
2.2. Study design
White Dome imagery was captured in late March 2021 (FAA permit
2021-P107-WSA-06550 including Part 107 certification), but due to
T.B.B. Bishop and I.M. Errigo
sUAV equipment failure, Beehive Dome imagery was not captured until
June 2021 (FAA permit 2021-P107-WSA-14271 including Part 107
certification). Equipment included a DJI Phantom 4 ProV2 sUAV with a
factory camera and using DJI GO4, Drone Harmony and Drone Deploy
applications to control the sUAV and mission planning at 50 m above
ground level (AGL). We produced orthomosaics using RGB imagery and
Pix4D mapper (Pix 4D SA, Switzerland) with known landscape GPS lo­
cations as ground control points. We subdivided each study site into
smaller sections (i.e., tiles) based on flight date and time for easier data
rendering and processing. We calculated across all tiles the Visible
Atmospherically Resistant Index, or VARI, using ArcGIS Pro v 2.8x (ESRI
2021) Band Arithmetic raster function where unique values were
applied to pixels as a 9bit signed rendering. Unique values 0–255 were
explored using supervised classification with cubic convolution and
basic descriptive statistics to identify the unique value range that can
reasonably be identified as containing invasive annual grasses in the
pixel. Invasive annual grasses mainly included Bromus rubens L. and
Bromus tectorum L. The resulting invasive annual grass map (hereafter
brome map) contained pixels categorized into three classes; 2 = high
likelihood of invasive annual grass presence, 1 = mixed pixel/invasive
annual grass likely present, and 0 = invasive annual grass absent. To fall
into a 2 (high likelihood category) a pixel would have more than seven
nearest neighbors that were also identified as having invasive grass
present. We validated the brome maps 500 random points and
Fig. 2. Selection from RGB orthomosaics of a) White Dome and b) Beehive Dome. This comparison highlights the difference in color and pattern of habitat. The
zoomed-in subselection (bottom) shows outlined invasive annual grass. It is more easily seen at White Dome (bottom left) than at Beehive Dome (bottom right) likely
due to edaphic and topographic heterogeneity.
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Ecological Indicators 146 (2023) 109755
conducted an accuracy assessment by calculating producer’s and user’s
accuracy along with the Kappa coefficient at each location.
2.3. Seed bank collection
We collected seed bank samples along six different transects in the
southwest portion of TNC property. These transects started at the bottom
of a hill with a north-facing aspect and would continue up and over the
hill to end at the bottom of the south-facing aspect. Close to twelve
samples were collected for each transect, every 2 m in the top 4 cm of
soil, with a total of 115 samples. Seeds were sifted out and identified to
species (Bromus rubens L. or Bromus tectorum L.) and relative age (cur­
rent/<1 yr old or > 1 yr old) based on appearance (color, shape, and
length) in under a stereoscope. Seeds were germinated at 20 ◦ C on blue
blotter paper in petri dishes that were bagged for sixty days. Water was
added as needed. Number of seeds germinated was counted as a percent
of the total seed collected.
3. Results
3.1. White Dome brome maps
At White Dome, we captured imagery across 215 ha of the TNC
preserve (~67 %) and an additional 26 ha outside of TNC property for a
T.B.B. Bishop and I.M. Errigo
total of 241 ha of habitat. The resulting RGB orthomosaics we produced
using Pix4D at centimeter-level resolution. There were areas surveyed
that had redder or orange-hued soils with high false positives, where the
maps indicated brome litter was present but it was not (error of com­
mission). These areas were the hiking trails maintained by TNC and a
small portion of the southwest and eastern corner of the survey area and
were subsequently excluded from further classification (~2 ha).
Otherwise, the color of the habitat was fairly evenly patterned and toned
(Fig. 2). Further classification (Figs. 3 & 4) had > 95 % Producer’s and
User’s accuracy in identifying pixels that contained invasive annual
grass litter (Table 1) with an 0.88 Kappa coefficient.
3.2. Beehive Dome brome maps
At Beehive Dome, we captured imagery across 62 ha of habitat and
used it to create RGB orthomosaics between 1.5 and 1.7 cm resolution.
The surveyed area had a much more heterogeneous background/basal
color, including more red, orange, and brown hues in the soil as
compared to White Dome (Fig. 2). This heterogeneous soil created more
confusion with the VARI brome map with very low accuracy (Fig. 5). Of
the correctly sampled validation points, only 5 % of brome pixels were
classified correctly. The Producer’s and User’s accuracy varied between
10 % and 66 % where classification was most accurate for no brome
litter pixels but classification was not accurate for brome litter (Kappa =
0.08, Table 1). Brome litter cover was noticeably less at Beehive Dome
(personal observation).
3.3. Seed bank viability
Overall seed bank viability was high regardless of the age of the seed.
Fig. 3. Overall brome map of the White Dome habitat area, owned and managed by The Nature Conservancy (TNC). Black pixels indicate no invasive annual grass
detected (0), whereas yellow (1) and green (2) pixels (difficult to differentiate at this scale) indicate the increasing presence of invasive annual grasses.
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Ecological Indicators 146 (2023) 109755
Bromus rubens had 90 % ± 1.8 % viability, and Bromus tectorum had
slightly lower viability at 83 % ± 4.8 % (Fig. 6). Current season Bromus
rubens seeds had higher percent viability (92 % ± 1.5) than seeds
identified as > 1 yr old (85 % ± 5 %). Similar trends could be seen with
Bromus tectorum, where the current season Bromus tectorum seed had
higher percent viability (85 % ± 5 %) compared to seed older than 1 yr
(80.7 % ± 9 %).
4. Discussion
In the Mojave desert, non-native annual grass invasion has become a
major problem in just the last few decades (Germino et al. 2016). In fact,
when the dwarf bear poppy was first listed as endangered, there were no
mentions of invasive species as being potential threats towards extinc­
tion in the subsequent recovery plan (USFWS, 1979). It was not until the
first 5-year review, published in 2016, that invasive annual plants were
mentioned as threats to the dwarf bear poppy (USFWS, 2016). In more
recent monitoring of Siler’s pincushion cactus and dwarf bear poppy
where invasive grasses were suggested as possible threats (Abella 2014;
Abella personal communication). However, it is not understood how
these endemic plants interact with invasive annual grasses in their
habitat. The novelty of our findings, by mapping invasive annuals based
on litter rather than just photosynthetic tissue, therefore, indicates the
possibility and opportunity to expand mapping of invasive annual grass
species in a variety of environments (St. Clair & Bishop, 2019) and years.
This can broaden the application and usefulness of utilizing sUAVs to
monitor invasions in critical habitats.
Mapping brome litter across dryland habitats using just RGB ortho­
mosaics and VARI proved successful at White Dome but came with
challenges at Beehive Dome. To make the technology the most user-
T.B.B. Bishop and I.M. Errigo Ecological Indicators 146 (2023) 109755

Fig. 4. Zoomed in comparisons of the a) RGB orthomosaic, b) brome map, and c) digital surface model (DSM) at a location in White Dome Nature Preserve. Brome
invasion showed spatial patterns that are part of further analysis into spatial signatures in relation to the threatened native plants.

which is a leading reason for degradation in this habitat (USFWS 1979;

Table 1
USFWS, 2016). At White Dome, the consistency of the spectral patterns
Accuracy Assessment matrix including Producer’s Accuracy (PA) and User’s
across the habitat with high contrast to the spectral range of brome litter
Accuracy (UA) and Kappa coefficient for each study location. Used in assessing
made this process straightforward. We aim to utilize these brome maps
accuracy of classification of presence or absence pixel counts of invasive annual
grass litter between whether invasive annual grasses were present in the red to model measurements such as percent cover of brome (He et al. 2015)
green blue orthomosaic (reference data) as compared to the classified brome to help in assessing whether invasive annual grasses are an immediate
map. threat to the cactus and poppy or even the risk of wildfire (Chambers
et al. 2016). In 2016, the US Fish and Wildlife estimated that invasive
Reference Data
White Brome No brome Total PA UA species comprised < 2 % of cover in dwarf bear poppy habitat (USFWS,
dome litter litter 2016). Our measurements estimate cover of Bromus spp. to be as high as
Classified Brome 59 3 62 95.2 84.3 20 % (Bishop, unpublished data). The benefit of having the sUAV im­
Data litter % % agery now is the ability to spatially analyze where invasive annual
No brome 11 427 438 97.5 99.3 grasses are so that management can target native plant conservation. An
litter % % additional benefit is that we have an estimate of where they might
Total 70 430 500
spread based on seedbank presence and viability signaled by litter
Kappa coef. 0.88
Beehive Brome No brome Total PA UA presence (Figs. 4–6). Knowing that seed has high viability regardless of
dome litter litter age offers information to decision makers that where litter is dense
Brome 21 182 203 10.3 67.7 enough to be mapped, they can infer that seed bank will be high and
litter % %
viable. From our preliminary analysis, while invasive annual grasses are
No brome 10 287 297 96.6 61.2
litter % % at White Dome, they are not abundant on the native plant microhabitat
Total 31 469 500 of barren gypsum shale within the area. But as invasive brome grasses
Kappa coef. 0.08 are prolific seed producers and seed viability is high (Fig. 6), propagule
pressure may eventually overcome any environmental barrier (St. Clair
& Bishop, 2019).
friendly, keeping the data and data analysis simple was important for
The challenges at Beehive Dome came from the heterogeneous na­
future accessibility. We concur with others that collecting imagery with
ture of that habitat color in addition to the color being much more
low-cost sUAVs and analyzing RGB orthomosaics was easier, safer, and
similar to that of the brome litter (Figs. 2 & 5), indicating that spectral
more cost-effective than on-the-ground data collection and/or crewed
signature alone is not enough for acceptable accuracy (Table 1).
aerial vehicles (Müllerová et al. 2017; Kattenborn et al. 2019). In
Heterogenous habitats, such as Beehive Dome, may need additional
addition, this method provided us with a balance between acquiring
measures, such as spatial information, and/or additional spectral in­
data needed for restoration versus creating on-the-ground disturbance,
formation, such as near-infrared to delineate between soil and litter

5
T.B.B. Bishop and I.M. Errigo
Fig. 5. Zoomed in comparisons of the a) RGB orthomosaic, b) brome map, and c) digital surface model (DSM) at a location at Beehive Dome. Soil heterogeneity and
sparse brome coverage made mapping inaccurate.
Fig. 6. Viability results from germinating seed bank samples at White Dome
Nature Preserve. Seeds were identified to species: Bromus rubens (BRRU) or B.
tectorum (BRTE), and age: current (within one calendar year) or more than one
year old. Means ± standard error presented.
6
Ecological Indicators 146 (2023) 109755
(Räsänen & Virtanen 2019). It was personally observed that the cover of
invasive annual grasses was lower at Beehive Dome compared to White
Dome, which also could interfere with the ability to pull out brome
pixels in the sUAV imagery. As we continue this research, we note
several suggestions to increase our accuracy for a heterogeneous, spec­
trally similar area in mapping invasive annual grasses using low-cost
sUAVs. 1) Collect imagery first in the springtime (Beehive Dome
flights were in summer) when even a little bit of photosynthetic growth
could help differentiate pixels. 2) Collect imagery at two times: once in
spring, and once in summer, so that we can calculate the difference in
VARI. This is similar to the methods used by Bishop et al. (2019) using
difference NDVI (dNDVI) to map invasive annual grasses with Landsat
imagery (Kokaly 2010). 3) Adding a multispectral sensor to capture
more bands of spectral information. And lastly, 4) use object-based
image analysis techniques where texture and other spatially explicit
characteristics can be used to differentiate objects (St. Clair & Bishop,
2019). We believe one or more of these steps would alleviate the chal­
lenges and provide an accurate map of the heterogenous areas, like
Beehive Dome. In conclusion, we have found the initial use of low-cost
sUAV/drones and RGB orthomosaics to map (Louhaichi et al. 2019) and
monitor litter of plant invasions across critical habitats to be effective in
providing high-resolution information to aid preserve managers with
real-time decision-making in the context of plant invasions with mini­
mal disturbance to the landscape (Cruzan et al. 2016).
CRediT authorship contribution statement
Tara B.B. Bishop: Conceptualization, Data curation, Formal anal­
ysis, Project administration, Methodology, Validation, Visualization,
Software, Writing – original draft. Isabella M. Errigo: Methodology,
Data curation, Supervision, Visualization, Writing – review & editing.
T.B.B. Bishop and I.M. Errigo
Declaration of Competing Interest
The authors declare that they have no known competing financial
interests or personal relationships that could have appeared to influence
the work reported in this paper.
Data availability
Data will be made available on request.
Acknowledgements
This study was funded by The Nature Conservancy and its citizen
partners, and the USDA Forest Service Rocky Mountain Research Sta­
tion. We also thank Suzette Clements and Dr. Susan Meyer for identi­
fying and germinating the seed, Aly DeNittis and Eli Hartung for their
help in collecting the seed bank samples, and Sydney McGovern for
sUAV organization. The findings and conclusions in this publication are
those of the authors and should not be construed to represent any official
USDA or U.S. Government determination or policy.
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