Linking “the clouds” to endangered songbird habitat conservation and management

Getting the big picture

Light Detection and Ranging airborne remote sensing technology, widely known as “LiDAR,” is being used more frequently as data collection and computing power for processing it become more affordable. It is often used to create a very detailed model of elevation and topography that can be used in a geographic information system (GIS). A LiDAR instrument sends thousands of infrared laser light pulses toward the ground from an airplane or helicopter and then simply records the x, y and z coordinates marking the return location for each beam of light. When viewed with specialized computer software, the points resemble a cloud, known as a “point cloud” that describes the height of objects. Detailed LiDAR “Bare Earth” models of topography are commonly at a much greater spatial resolution and vertical and horizontal accuracy than those developed through traditional methods such as aerial photography, making them well suited for civil engineering, geology, and hydrology applications.

LiDAR 3D point cloud showing an open area and adjacent trees.

LiDAR 3D point cloud showing an open area and adjacent trees.

Hillshade map of LiDAR bare Earth elevation.

Hillshade map of a LiDAR bare Earth elevation.

Early on, LiDAR points returned from trees, buildings, and other objects above the ground were considered a nuisance to be removed before producing good topographic data. Nevertheless, scientists and natural resource managers quickly understood the value of LiDAR point clouds and potential to create highly detailed information about vegetation structure, habitat conditions, human infrastructure, geomorphology, and other land features that can vary substantially across large landscapes. This potential is now gaining the attention of many private, county, state, and federal entities who are finding LiDAR to be an essential tool for managing natural resources, urban growth, flood control, water management, disaster mitigation, and other purposes, naturally driving down the cost of acquiring LiDAR data.

 Gaining ground for songbird conservation

Currently, LiDAR is opening new doors for characterizing and managing wildlife habitat for the US Fish and Wildlife Service (USFWS) Southwest Region Inventory and Monitoring (I&M) Program, starting with endangered songbirds. A common theme contributing to songbird declines is loss and fragmentation of habitat caused by agricultural development and urbanization. The Golden-cheeked Warbler (Setophaga chrysoparia) and Black-capped Vireo (Vireo atricapilla) were listed by the USFWS as Endangered in 1990 and 1987, respectively. The 25,000 acre Balcones Canyonlands National Wildlife Refuge (BCNWR) was established in 1992 to protect habitat for these two species. Both birds are Neotropical migrants, spending winter months in Mexico and Central America while occupying a narrow breeding range in the southwestern USA during the spring and summer. The warbler prefers older oak (Quercus spp.) and Ashe juniper (Juniperous ashei) woodlands while the vireo prefers semi-open shrublands.


Balcones Canyonlands National Wildlife Refuge is made up of large and small parcels of land purchased from private citizens and resides within the breeding range of the Golden-cheeked Warbler and Black-capped Vireo. Breeding habitat for the vireo (not shown) extends north to Oklahoma and south to northern Mexico.


Typical habitat conditions preferred by the golden-cheeked warbler in oak-juniper woodlands.


Typical habitat conditions preferred by the black-capped vireo in semi-open shrublands.

BCNWR managers and I&M needed a way to determine where the most suitable habitat conditions exist for warblers and vireos on and off Refuge lands. Specifically, we wanted to know how future land acquisitions, habitat restoration, and protection activities can best be prioritized to make the most of resources allocated to warbler and vireo conservation.

Translating point clouds to habitat

In 2012, the first BCNWR-wide bird point count survey was conducted following a protocol developed by I&M Zone Biologist Dr. Jim Mueller. Drawing on modern sampling techniques from published studies, a total of 250 randomly selected locations were surveyed to record presence, distance, and time of detection of the Golden-cheeked Warbler and the Black-capped Vireo, and potential nest predators such as the Brown-headed Cowbird (Molothrus ater), Western Scrub-jay (Aphelocoma californica), and Blue Jay (Cyanocitta cristata), at four separate occasions during the breeding season. Detections for the Northern Bobwhite (Colinus virginianus), a species of conservation concern, were also recorded.

LiDAR and on-the-ground bird surveys are now beginning to play a role in estimating woodland conditions that are most important to the warbler and vireo, and eventually map locations across the landscape where they are likely to exist or which habitats are likely to be colonized in the future. Of considerable advantage, the state of Texas maintains substantial LiDAR data archives for many of the counties known to maintain warbler and vireo populations. In addition, the US Department of Agriculture National Agricultural Imagery Program (NAIP) acquires high-quality and high spatial-resolution color-infrared (CIR) aerial photography for the entire state of Texas every 2 to 3 years.  Each of these data sources is freely available through the Texas Natural Resource Information System (TNRIS) and important to developing relationships between songbirds and habitat characteristics such as woodland vegetation composition and structure.

Remotely sensed data must first be processed, often using sophisticated computational techniques that require fast computers to translate them into information that is useful for conservation planning and management. However, results can be astonishingly accurate and simple to interpret for making management decisions.  For the warbler, we have developed highly accurate vegetation height, density, and canopy cover data layers from LiDAR that can be mapped and quickly be related to preferred habitat conditions by songbirds.


LiDAR derived vegetation height useful for identifying older oak-juniper woodlands (darker green to blue color) important to the golden-cheeked warbler.


LiDAR derived relative vegetation density for trees between 5 and 10m tall. Height breaks can be used to determine both overstory and understory vegetation density important to songbirds.


Golden-cheeked warbler occurrence data collected in 2012 combined with LiDAR derived vegetation height indicating how late successional oak-juniper woodland structure is important habitat.


Golden-cheeked warbler occurrence data collected in 2012 combined with LiDAR derived canopy cover indicating how relatively closed canopy oak-juniper woodland structure is important habitat.

Synthesizing LiDAR outputs with data collected in the field is not only telling a story about preferred songbird habitat conditions, but also where these conditions exist over large areas. A recent study by Farrell et al. (2013) provides an excellent example of how LiDAR derived vegetation data can be used effectively to identify key habitat for the Golden-cheeked Warbler and Black-capped Vireo on the Fort Hood military installation. We are taking similar steps to develop spatial models of songbird and nest-predator occupancy that will afford important information on where to prioritize conservation and habitat restoration actions both on and off Refuge lands. LiDAR and CIR imagery are also helping to address other questions such as understanding how understory vegetation, heterogeneity in height and canopy structure, successional status, and woodland species composition are related to the presence of warblers and vireos. This information will provide keen insights into how management activities such as hazardous fuels mitigation and other woodland treatments may best enhance habitat conditions and help minimize the negative influence of songbird nest predation. These monitoring and modeling activities are aimed at achieving refuge management goals, consistent with the 2001 Comprehensive Conservation Plan (2001) and Draft Habitat Management Plan (2010).

In the future, larger-scale efforts to characterize habitat conditions throughout the range of these two species may also help to identify locations where conservation credits to private land owners can best meet endangered songbird recovery objectives. Thus, the answer to these and many other questions about wildlife habitat relationships and management might just be in the clouds.


Balcones Canyonlands National Wildlife Refuge Comprehensive Conservation Plan. 2001. U.S. Fish and Wildlife Service, Albuquerque, New Mexico.

Balcones Canyonlands National Wildlife Refuge Habitat Management Plan (Draft). 2010. U.S. Fish and Wildlife Service, Marble Falls, Texas.

Farrell, S. L., B. A. Collier, K. L. Skow, A. M. Long, A. J. Campomizzi, M. L. Morrison, K. B. Hays, and R. N. Wilkins. 2013. Using LiDAR-derived vegetation metrics for high-resolution, species distribution models for conservation planning. Ecosphere 4:1-18.

Among the tiniest of snails…

Bitter Lake National Wildlife Refuge is home to 8 species that are listed as Federally Threatened or Endangered, and to several additional species listed as Threatened or Endangered by the State of New Mexico.  Among the Federally Endangered species is a tiny snail, so small it went unnoticed until 1987.  Pecos assiminea (Assiminea pecos) ranges in size from 1.4 to 2.2 mm.  It occurs near the wetted edges (mud-water interface) of certain sinkholes, springs, and spring-runs (also known as cienega) on the Refuge.  Pecos assiminea was listed as Endangered in 2005.  In addition to Bitter Lake NWR, the snail is found on The Nature Conservancy’s Diamond Y Springs in west Texas.

Sketch of Pecos assiminea, excerpted from Taylor, 1987 (Figure 2):


Due in large part to its tiny size, it is extremely difficult to survey.  Imagine trying to find a small brownish snail that is often less than 2 mm long in a shaded, uneven brown background; this difficulty is compounded because the habitat being searched is also full of small brown seeds, bits and pieces of small brown vegetation, and little mud stained salt crystals.  Search efforts, thus, have traditionally been hindered because they were extremely time-consuming and tedious.  Researchers have to lie on the ground with their face only a few inches above the ground, and several hours might be required to cover only a small area. Additionally, large-scale sampling efforts have been hindered by the lack of a feasible monitoring technique.

Searching for Pecos assiminea along Bitter Creek, Bitter Lake NWR, photo by Patricia Obryon

Searching for Pecos assiminea along Bitter Creek, Bitter Lake NWR, photo by Patricia Obryon.

In 2011, Bitter Lake National Wildlife Refuge decided to pursue a monitoring effort that would help it better understand the species distribution, habitat associations, and density on the refuge.  Field work for this project was largely carried out by Elizabeth (Beth) Roesler, who joined Bitter Lake NWR as an intern working for the Student Conservation Association.  Roesler’s field work involved systematically searching areas of the Refuge where Pecos assiminea is known and suspected to occur.  Roesler searched small quadrats of known size, and the quadrats were regularly spaced in searched habitats.  She also collected habitat information concurrent with each quadrat searched, such as vegetation type, soil texture/saturation, ground temperature, and water quality (from adjacent spring flows).  This information was collected in order to better understand habitat parameters associated with the species, and will eventually be incorporated into models that help predict where the species might occur.  However, even with a scientifically rigorous sampling design, positive finds of Pecos assiminea were few and searches still proved to be a tedious process.

In fall of 2012, Roesler incorporated a second technique into her sampling efforts.  This technique involved using known dimension wood tiles, and was suggested by Brian Lang, invertebrate biologist with New Mexico Department of Game and Fish.  Known dimension clay tiles are often used to sample aquatic snails, but Lang’s prior experience using clay tiles in attempts to sample Pecos assiminea had proved unsuccessful.  However, since Pecos assiminea are sometimes seen attached to small wood fragments, wood tiles seemed like they warranted a try.

Wood tile used to survey Pecos assiminea

Wood tile used to survey Pecos assiminea.

Initially, wood tiles were placed on the ground only along the edges of Sinkhole 31, which is believed to have the highest densities of Pecos assiminea on the Refuge.  Roesler’s use of wood tiles proved almost immediately successful.  Within a few weeks, Pecos assiminea began to attach to the wood tiles, and detection rates with tiles were much higher than detection rates from visually searching quadrats of known area.

As opportunity would have it…

In 2012, Bitter Lake NWR received an “Invasives with Volunteers” grant, which enabled them to initiate an ambitious phragmites (pronounced frag-mit-ies) plant removal program to restore a 1 mile spring run (approximately 7 acres of cienega habitat), known as Bitter Creek, to conditions that existed prior to phragmites invasion.  One of the goals of removing phragmites was to alter habitat in favor of Pecos assiminea and the 5 other federally listed species that occur there.  Pecos assiminea snails rarely occur in phragmites dominated habitats and declined along Bitter Creek after the spread of this invasive plant species.

Subsequent to receiving the “Invasives with Volunteers” grant, Texas Tech University received a Science Support Grant in partnership with U.S. Geological Survey and the Refuge.  The purpose of this grant was to monitor the response of Pecos assiminea to phragmites removal on Bitter Creek.  As Roesler was already experimenting with two monitoring techniques (visual searches of small quadrats and wood tiles) to monitor this species, and had already fully sampled Bitter Creek the prior year using quadrat searches, she was the best choice to make the leap from Student Conservation Association intern to graduate student.  In spring of 2013 she enrolled as a graduate student at Texas Tech University to work on the Science Support Grant funded project.  Two main goals of her graduate project are to monitor the effects of phragmites removal on Pecos assiminea, and to concurrently examine the efficacy of the two monitoring techniques mentioned above.  Unlike most graduate students in the field of conservation science, Roesler actually entered graduate school as one of the leading experts on her study species.  Thanks to her Student Conservation Association internship, perhaps only 1 or 2 people in the world have observed and sampled more Pecos assiminea than Roesler.

Beth Roesler, current graduate student at Texas Tech University surveying Pecos assiminea along Bitter Creek

Beth Roesler, current graduate student at Texas Tech University, surveying Pecos assiminea along Bitter Creek.  Photo by Patricia Obryon.

So what does Bitter Lake NWR gain from this project?  First, the Refuge aims to benefit an endangered species through its management actions/prescriptions, and the monitoring effort will help the Refuge learn how the species responds.  Secondly, the Refuge will get answers concerning the efficacy of two potentially suitable sampling techniques that can each be used to answer questions about Pecos assiminea distribution and density.  Hopefully one of the techniques can be used for “operational” monitoring for the species.  From a general conservation standpoint, the U.S. Fish and Wildlife Service will get estimates of Pecos assiminea density in multiple habitats, which will be among the first abundance estimates for this species!  Upon completion of the work, the Refuge will have enough information to make reasonable predictions about the response of Pecos assiminea to phragmites control if additional removal efforts are pursued, and, lastly, the Refuge should have enough information to start modeling likely occurrence of Pecos assiminea based on its habitat parameters.  This project is adaptive management at its best.

Citation:  Taylor, D.W.  1987.  Fresh-water mullusks from New Mexico and vicinity.  New Mexico Bureau of Mines and Mineral Resources Bulletin 116.

Scientific Leadership Award goes to Southwest Region Chief of Biological Sciences Grant Harris



It’s remarkable to find a great leader who possesses an outstanding scientific mind; in the Southwest Region, the Chief of Biological Sciences, Grant Harris, has the rare qualities of both. Harris took over the Chief role in 2010 when the Biological Services group consisted of two half-time staff. Now, nearly two years later, the group encompasses a scientific team of 12 and growing. Why such growth? When the vision of the Service and the National Wildlife Refuge System was outlined in Conserving the Future, the role of science in the Service was elevated and an Inventory and Monitoring (I&M) program initiated. Harris heard the calls and acted quickly. Under Harris’ leadership, the role of science has grown stronger than it’s ever been in the Southwest Region, which is leading the Service with reinforcing how science informs management decisions, habitat acquisition, and the I&M Initiative. Harris has built a strong foundation for science-based wildlife conservation to grow and flourish in the Southwest.

Harris has developed studies to assess the role of mountain lions in bighorn sheep mortality, led the way for novel techniques to save time and money for monitoring wildlife through camera trapping, assessed habitat fragmentation effects on threatened birds, and helped revamp the survey methodology of wintering whooping crane. His efforts have directed the pioneering of new techniques to estimate the abundance of animals without marks, techniques that can be applied to endangered animals world-wide. Harris’ leadership in addressing a plethora of wildlife management and conservation topics in the Southwest has provided impetus for new partnerships with State wildlife agencies, U.S. Geological Survey, the National Park Service (NPS), NatureServe, NOAA, universities, and NGOs. These include a new I&M collaboration with the NPS in the Chihuahuan and Sonoran desert networks and various applied research projects across the southwest region. In addition to his personal accomplishments, he strongly believes in the importance of increasing science capacity within the Service for the good of conservation. In support of that vision, he has built up a science team that is raising the bar for science on Refuges through the Southwest Region. His “lead by example” attitude motivates those around him to excel, while raising standards such that scientific rigor and defensibility are the norm.

In recognition of these outstanding contributions, Grant Harris is hereby awarded the 2012 Scientific Leadership Award.

Ozark big-eared bat monitoring at Ozark Plateau National Wildlife Refuge

OBEB from video

Population counts of Ozark big-eared bat (Corynorhinus townsendii ingens) maternity colonies have been performed annually for several decades. The process consists of lighting the cave entrance with infrared lights and using night vision goggles to determine how many Ozark big-eared bats fly out. Bats are extremely good fliers and can exit out of the cave very fast. It takes several years to develop the skills to be an accurate counter. In the summer of 2006, Richard Stark of the Oklahoma Ecological Services Field Office began utilizing infrared video and acoustic detectors to supplement the traditional count method. The infrared video and acoustic method consisted of deploying a single Anabat near the cave entrance and filming the bat emergence with the use of a Sony Handycam with nightshot and infrared lights. The video footage was then later reviewed in slow motion on a large television screen to obtain a count of Ozark big-eared bats exiting the cave. Ozark big-eared bats could be distinguished from other species by their large ears which are over 1 inch long. When a bat suspected to be an zark big-eared bat on film could not be confirmed by the video footage alone, the Anabat data were reviewed to determine if a bat call was recorded at the same time the suspect bat emerged from the cave for possible confirmation. The method proved successful and showed great promise. Colony size estimates from the infrared video method were compared to estimates by the traditional count method, and results were very similar. The infrared video and acoustic method also detected use of two caves in Cherokee County, Oklahoma by Ozark big-eared bats that was not detected by the traditional method conducted simultaneously. These caves subsequently have been added to the annual monitoring efforts and are now known to be used by a colony of Ozark big-eared bats at various times of the year. Although the new infrared video and acoustic detector method proved very valuable, due to time and resource limitations, the method was utilized at only a few caves per year between 2006 and 2008.

The initial success of the method warranted expanded use and fine-tuning of the technique. Ozark Plateau National Wildlife Refuge in conjunction with the Service’s Inventory and Monitoring Program expanded use of the method in 2009. The method currently being utilized consists of filming the bat emergence with two or more cameras from multiple angles and deploying multiple acoustic detectors (both Anabat and Pettersson units). A black backdrop also is now utilized which enhances the counter’s ability to identify Ozark big-eared bats. The number of caves at which this technique is utilized also has been expanded to about 25 per summer and includes the essential maternity caves and numerous limited-use sites.

Video monitoring has several advantage over the traditional method. First, it doesn’t take several years to become an accurate counter. Second, video playback allows counter to slow down playback and use individual frames to identify Ozark big-eared bats. The video is time stamped to provide a log of the time of each bat’s emergence. Since the video has a time stamp and the acoustic monitors can be time synced, we can get a total bat species population count for each cave. With the threat of white nose syndrome it is important that we get population data on all cave dwelling bat species. White nose syndrome is non selective and can affect all cave dwelling species.

Click here for a short video on Ozark big-eared bat monitoring at Ozark Plateau National Wildlife Refuge

Feral Burros Gather to Improve Habitat for Native Species on Imperial and Cibola NWR

burros-FU2-9-17-09Zaun (2)
In June 2012, the Bureau of Land Management (BLM), Yuma, Arizona office, gathered 350 feral burros on private, state, military, BLM and National Wildlife Refuge lands along the lower Colorado River in the southwestern corner Arizona.  The gather was funded by the U.S. Army Garrison – Yuma due to an overabundance of burros and safety concerns.
The Cibola-Trigo Herd Management Area, encompassing ~832,000 acres, located in southwestern Arizona and extreme southeastern California, supports populations of wild horses and burros that use lands administered by the U.S. Army Garrison, Yuma Proving Ground, U.S. Fish and Wildlife Service (Imperial and Cibola National Wildlife Refuges), and the BLM. BLM is responsible for managing the herd according to the Wild and Free-Roaming Horse and Burro Act of 1971. The BLM Cibola-Trigo Herd Management Area Plan, approved in September of 1980, determined that the Appropriate Management Level for burros is approximately 165, based on “a grazing capacity calculated to restore the vegetative communities within the critical area to approximate original conditions”. The feral burro population within the HMA is, conservatively, over five times the AML and increasing.
Burros consistently tear down/damage fences, feed in refuge restoration project areas and farm fields, make trails through the desert, increase erosion, prohibit natural regeneration of native riparian vegetation, and cause an extreme safety hazard on roads (human injuries and fatalities from collisions with burros). Studies have also found that that feral horses and burros also compete with native wildlife at water sources. The Arizona Invasive Species Strike Team, I&M Program and Imperial and Cibola NWRs assist BLM with annual vegetation monitoring to assess the degree of burro utilization and damage to native plant species in selected areas throughout the Herd Management Area. The Arizona Invasive Species Strike Team coordinator recently entered into an Inter-agency agreement with the Arizona Game and Fish Department to conduct a thorough survey of burros in the Herd Management Area. Better management of feral burros on the landscape will minimize degradation and prolonged long-term impacts to native wildlife and plants and assist managers in improving ecological health, biological integrity and diversity and natural processes and conditions on the refuges.

Who Ate the Corn? Using Monitoring to Feed Management Decisions

Bosque del Apache National Wildlife Refuge cultivates corn to redistribute sandhill crane (Grus canadensis) and waterfowl populations off of private agricultural fields throughout the Middle Rio Grande Valley in New Mexico.  Corn production on the Refuge also helps the birds maintain their body condition as they migrate and overwinter on and around the Refuge.  The current goal of the Refuge is to produce 1.5 million pounds of corn.  Unfortunately, corn production on the Refuge was low during the summer of 2011, raising concerns about meeting the energetic needs of sandhill cranes and increased crop depredation by waterfowl on neighboring farms.  These concerns have prompted Refuge biologists to investigate causes of crop failure.

Many reasons for poor corn production have been proposed.  It could be crop depredation and damage by elk (Cervus elaphus), mule deer (Odocoileus hemionus), and trespass cattle, as well as ineffective farming practices.  Further, the current drought has put additional stress on the farming program.

A wire exclosure used to exclude elk, mule deer, and trespass cattle allowing Refuge biologists to determine potential corn growth and yield without ungulate depredation and damage.

With Region 2 I&M staff, Refuge biologists are leading a monitoring strategy to quantify three things 1) crop depredation and damage from ungulates, 2) identification of species responsible for crop damage, and 3) determining the stages of plant development in which corn is most vulnerable to depredation and damage.  The approach consists of repeated monitoring of corn depredation and damage in exclosures and treatment plots throughout the summer.  These plots are located across a sample of the Refuge’s corn fields.

The Refuge will tolerate some ungulate depredation and damage to the corn crop.  However, aversion techniques, which are methods designed to prevent and control depredation and damage of crops by wildlife, might need to be deployed if depredation and damage is excessive.  Continued crop monitoring will allow Refuge staff to follow plant development and damage of the crop throughout the summer.  If predetermined thresholds of depredation and damage are exceeded, Refuge personnel will implement aversion techniques on affected farm fields.

SCEP Student, Reggie Perkins, monitors corn growth at Bosque del Apache NWR.

Knowledge gained this summer will inform the Refuge as to how much depredation and damage is occurring, which species is responsible, and which developmental stage of corn is most vulnerable.  These kernels of knowledge will inform an adaptive management strategy as the Refuge builds a better understanding of the scale of the depredation issue, and therefore, can design more informed management actions to mitigate corn damage caused by ungulates.  Crop monitoring will continue over subsequent years, allowing further refinement of management strategies.