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Pacific Crest Trail Biodiversity Megatransect Project

The Pacific Crest Trail Biodiversity Megatransect – A Biodiversity “Barometer”

The avian community is an effective barometer of how climate change is impacting our environment. The Institute for Biodiversity and the Environment (IBE) at William Jessup University has as one of its core research projects the Pacific Crest Trail (PCT) Biodiversity Megatransect, which is an ongoing survey of the montane avian diversity and phenology along the PCT. Central to the research is the novel, noninvasive (not requiring the capture or handling of animals) use of automated recording devices to continuously inventory and monitor biological diversity across the wilderness regions of the entire length of the PCT (from Mexico to Canada, 2,650 miles). While interpreting these recordings can be costly, requiring hundreds of interpreter hours, this approach provides the needed level of replication in the dataset for the use of hierarchical statistical models, such as multi-species occupancy models (MSOMs), to estimate species richness, distributions, population status of individual species (i.e., occupancy), and breeding phenology in response to underlying climatic variables. Alternatively, the PI, Dr. McGrann and his National Park Service and Ca. Dept. of Fish and Wildlife collaborators, recognize tremendous potential value in using bioacoustic indices, calculated from the recordings themselves using a computeralgorithm, as a metric of species richness. Although bioacoustic indices have been shown to positively correlate with species richness, it remains unclear how well acoustic indices perform at large spatiotemporal scales and across heterogeneous landscapes. This study is working to address questions of how well the acoustic complexity index (ACI) correlates with estimated species richness under varying survey conditions. Results have the potential to inform the budding discipline of soundscape ecology and the application of bioacoustic indices in large-scale biodiversity monitoring programs worldwide that employ passive acoustic monitoring devices.

Over the past two decades, ecologists have increasingly recognized the value of passive acoustic recording technologies as a non-invasive approach for acquiring data on large assemblages of vocalizing species, including birds, amphibians, and bats. Due to the promise of this approach in addressing theoretical questions on how biodiversity is responding to global environmental change, vast amounts of acoustic data are being accumulated by researchers world-wide. As a consequence, a new scientific discipline has emerged – soundscape ecology. However, interpreting all this acoustic data by human experts to identify vocalizing species presents logistical challenges and is often cost prohibitive. The purpose of this research is to fill a significant knowledge gap in the field of soundscape ecology.

One of our goals in our research is to describe the relationship at large spatial scales between the widely used bioacoustic index, the acoustic complexity index (ACI), and that of estimated avian richness based on the interpretation of recordings of the singing bird community. Since 2010, IBE’s Pacific Crest Trail Biodiversity Megatransect (PCTBM) – a large-scale and long-term study of passerine climate-diversity relationships along the Pacific Crest National Scenic Trail (PCT) – has employed lightweight, automated bird recorder units (ARUs) that can be packed in on foot and deployed at remote survey sites along the trail. The PCTBM has generated over 4,000 5- and 7-min. recordings of the singing bird community across surveys sites along 1,700 miles of the PCT in California, from Mexico to Oregon. To date, only about 2,000 of these recordings have been interpreted by expert observers who identified all the species vocalizing on each of the recordings. The PCTBM has so far produced 4 peer-reviewed articles on the climatic and environmental drivers of montane avian diversity and breeding phenology.

Although interpreting the recordings in this manner can be labor-intensive, requiring hundreds of interpreter hours, this approach provides the needed level of replication in the dataset to provide detection histories for species and to estimate detection probability for use in multispecies occupancy models (MSOMs). MSOMs can be employed to provide estimates of species richness, population status and distributions of individual species (i.e., the occupancy state), and breeding phenology (i.e., the date of highest singing activity). Furthermore, this approach allows us to track the response of these parameters to climate change and other sources of environmental change over time.

The labor-intensive interpretation of the PCTBM’s recordings highlights the tremendous potential value in using bioacoustic indices as an alternative metric for species richness in large-scale studies. A bioacoustic index employs a computer algorithm that summarizes the acoustic energy produced and estimates the diversity of sounds in the soundscape, including sounds produced by the singing bird community. Although bioacoustic indices have been shown to positively correlate with species richness, it remains unclear how well bioacoustic indices perform at large spatiotemporal scales and across heterogeneous landscapes. In this study, we propose to address questions of how well the ACI correlates with estimated species richness under varying survey conditions (e.g., wind/stream noise, anthropogenic noise) and habitat types. Results from this study have the potential to revolutionize the application of bioacoustic indices in large-scale monitoring programs worldwide that employ passive acoustic monitoring devices.

In addition to the above climate-diversity and soundscape ecology research questions. The PCTBM has also piloted the use of environmental DNA (eDNA) techniques to survey aquatic vertebrates. Where the PCT intersects waterbodies, including streams and lakes, water is run through a portable filtering apparatus to collect samples of organic matter. The eDNA, collected onthese filters, is then analyzed in lab polymerase chain reaction to determine rare/secretive aquatic vertebrates presence in aquatic systems simply based on the DNA (from sloughed-off cells) leftbehind in the water. Although eDNA, over the past 10 years, are increasingly applied in wildlife studies, they have never before been applied at such a large geographic scales and in remote settings. This work promises to provide an important baseline on the distributions of rare species in these remote montane ecosystems. 

In previous years, on seven separate field seasons, we have implemented surveys along the PCT across 3,578 survey sites, including the entire length of California (1,700 mi) in 2006 and several sections (hundreds of miles long) in California in subsequent years (2010, 2015, 2016, 2017, and 2019 as of the date of this writing).

With the scientific theory supporting the research fully-matured, the methodology peer-reviewed, and the logistics well thought-out and previously executed, the PCTBM is primed to be implement at a larger spatial-temporal scales across the entire length of the PCT from Mexico to Canada (2,650 mi). The overarching goal of the PCTBM is to become established as a regular monitoring program that informs the decision-making response of government agencies addressing climate change and other sources of global environmental change. Further, the PCTBM spans multiple administrative units (Federal, State, and Private lands) and promises help inform decision-makers across these boundaries on their climate change response.

We are currently seeking funding to support the future implementation of the program across the entire length of the PCT. Further, this program allows undergraduates at WJU’s Science Honors Program, as well as other collaborating universities, to come alongside research faculty and other collaborating scientists.

Research Goals

To track the response of biodiversity, namely songbird diversity but also other taxa, to climate change and other sources of global environmental change. Specifically, we are examining how birds are adjusting their populations, distributions and the timing of their breeding behaviors to climate change across the Pacific Cordillera.

To study the patterns of biodiversity on the Pacific Cordillera by tracking population trends and the distributions of wildlife species, and the habitat factors that drive these patterns along the Pacific Crest Trail (PCT).

To inform conservation efforts and decision-making responding to climate change throughout the Pacific Cordillera.

To study the use of bioacoustic indices, which our derived from computer algorithms applied to recordings of the singing bird community, as a measure of bird species richness. Specifically, we are exploring the application of these computer algorithms for thousands of 5- and 7-minute recordings collected by our field crews across thousands of survey sites along the PCT.

Establish the PCTBM as a regularly occurring biodiversity monitoring and research program where surveys are performed across the entire length of the PCT from Mexico to Canada.

Watch Jessup students on the PCT

Participant Testimonials

Important Findings From Our Work to Date

  • Our results suggest that Neotropical migrants (long distance migrants) may be less able to adapt to warming trends in the future (McGrann and Furnas 2016, Furnas and McGrann 2018).
  • We have provided baseline distributional data on bird species distributions on  for the entire length of the PCT in California (McGrann and Thorne 2014).
  • We found that species vary  in their response to underlying environmental variables across different ecoregions, suggesting that a “one-size-fits-all” conservation response to climate change may be appropriate, and that decisions should be based on region-specific information (McGrann et al. 2014)
  • We found that migratory guilds (neotropical migrants, altitudinal migrants, and birds resident in California year-round)  differ in their response to climate variables (McGrann and Furnas 2016).
  • We found that we can detect the date of peak vocal activity in songbirds, a key indicator of the timing of the breeding cycle of songbirds, as they respond to climate change and other sources of environmental change (Furnas 2018 and McGrann 2016). Specifically, e found that repeating our level of survey effort on an annual basis would allow detection of an advancement of average peak vocal activity by as small as 2.2 days over 10 yr in the songbird community (McGrann and Furnas 2018). 

Research Papers associated with the PCTBM

  • Furnas, B. J., and M. C. McGrann. 2018. Using occupancy modeling to monitor dates of peak vocal activity for passerines in California. The Condor 120(1):188-200.
  • McGrann, M. C. and B. J. Furnas. 2016. Divergent species richness and vocal behavior in avian migratory guilds along an elevational gradient. Ecosphere 7(8):e01419.
  • McGrann, M. C., M. W. Tingley, J. H. Thorne, D. L. Elliott-Fisk, and A. M. McGrann. 2014. Heterogeneity in Avian Richness-Environment Relationships Along the Pacific Crest Trail. Avian Conservation and Ecology 9(2):8.


Principal Investigator: Michael McGrann, Ph.D., Chair of the Institute for Biodiversity and the Environment, and Chair of the Science Honors Program, William Jessup University, Rocklin, CA | | (916) 577-8066

Matthew Klauer (William Jessup University)

Dr. Aaron Sullivan (Houghton College)

Bradley Wagner, Ph.D. (Mathematics Professor and Research Faculty member Institute for Biodiversity and the Environment at William Jessup University, Rocklin, CA;

Brett Furnas, Ph.D. (Quantitative Ecologist, Wildlife Investigations Laboratory, California Department of Fish and Wildlife, Rancho Cordova, CA;

Erik W. Meyer (Ecologist, Sequoia and Kings Canyon National Park, Three Rivers, CA)

Megan F. McKenna, Ph.D. (Bio-acoustic Biologist, Natural Sounds and Night Skies Division, National Park Service)

Undergraduate Research Assistant: Kasia McCann

Graduate Research Assistant: Gregory Lake

Project Coordinator: Amy McGrann (William Jessup University)


PCT Megatransect undergraduate research and Biodiversity Study Program at William Jessup University.

The deadline to apply is April 2020. Submitting your application as early as possible is very much appreciated as space is limited! Follow the instructions on the application form carefully.

Field Course Description: ESCI 442 Field Studies in Ecology (5-units).

This course is open to non-science majors with an aptitude, interest, or appreciation for science, particularly ecology and conservation science. A general biology course for science majors is beneficial but not required. For example, see Biol 101 or Biol 102 Principles of Biology I or II in the WJU Catalog. A general ecology course may also be beneficial, but not required.

This is a 6-week upper-division course in the Environmental Science Department at William Jessup University. This course provides students with hands-on training in the field while participating in an actual ecological study and biodiversity monitoring program– the Pacific Crest Trail (PCT) Biodiversity Megatransect. The course will also provide rigorous study of the natural history and ecology of the Pacific cordillera. Students will learn wildlife survey techniques under the close mentorship and guidance of collaborating faculty and professional field biologists. The research is a collaborative project with WJU and 4 other Universities.

Student performance in the course will be assessed based on the following: 1) maintaining a professional, positive, and team-player attitude throughout the field season, 2) comprehension of the protocols (there will be an exam), 3) basic natural history skills of the PCT (basic plant and animal identification), 4) and lastly, completion of a review paper. The review paper will be submitted to Dr. McGrann after completion of the field season.

Students (i.e., undergraduate researchers) will be assigned to teams, each team consisting of a team leader (who may be a faculty member or biologist) and 1 to 4 students. Students will conduct biological surveys while hiking the PCT for a total of 5 to 6 weeks with 1 or 3 days offer every week. Biodiversity data is collected at regular intervals along the trail. Depending on which team a student is assigned, students may shadow a professional biologist or faculty member who is performing avian-habitat surveys (using point count methods and automated recorder technologies), herptile surveys, aquatic vertebrate surveys (using eDNA techniques), or a combination of the above. Students are not expected to have knowledge of these methods. We will provide training on the protocols before fieldwork begins. The fieldwork is strenuous and students will spend extended periods of time in the wilderness living and working with others. Students will be expected to carry their own backpack and equipment plus scientific equipment needed for data collection. Students may spend up to 8 days in the field consecutively and hiking 10 to 15 miles/day (usually 12 miles/day). One or more days off will be provided at the resupply points throughout the field season.

Students are responsible for providing their own backpack and appropriate clothing, sleeping bag, sleeping mat, etc. However, certain backing supplies will be provided by the program, including, tent, water filter, cooking stove, trekking poles, scientific supplies, etc. Students will be informed as to which supplies that they need to provide on their own.

The summer tuition rate at WJU is a flat rate of $2,500 for this 5-unit course. This includes tuition, housing on campus for the training seminar, while on campus or on the trail.

Spending cash is recommended for eating out while traveling (Important: food expenses will not be provided by the BSP while on the road to the PCT or while students sightsee or travel on their own time).

  1. Complete the attached Biodiversity Study Program Application and follow the instructions carefully. A deposit is required.
  2. For off-campus students (non-WJU students): complete and submit the “Non-Matriculated Student Application” to the WJU registrar. Complete this form here.


Note: Start and end date are tentative. These dates will be firmed up as we get closer to the field season.

  • Start of megatransect: Highway 58, Tehachapi Pass, End of megatransect: Hwy 120, Tuolumne Meadows, Yosemite.
  • Length of megatransect: approximately 375 mi total (teams of students will “leap-frog” each, so no one student will hike this entire length, each student may hike between 150 to 200 miles total).
  • Daily miles hiked: approximately 12 mi per day (at least 16 days total hiking on the trail, not including days off).
  • Start date: June 15th (tentative, may be pushed back, depending on weather, snow pack).
  • Total length of field season on the PCT: 5 – 6 weeks, or about 35 days, including days off and setbacks due to weather or other mishaps.
  • Training period at start of field season: 3-6 days, we will spend at least 3 days training in the field on the protocols before starting the actual transect and we will spend 2-3 in classroom lecture on WJU campus.
  • Break after training: 2 to 5 days off.
  • Halfway break: 2-4 days off, recovery, process data, resupply, rest and recovery.
  • End date: July 31st (tentative). The end date depends on if you are lead team placing automated recorders or on team retrieving automated recorders or on eDNA team.
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