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

“Perhaps our most important goal is to provide our students a truly formative and enriching experience that affects the whole person, impacting not only their career goals, but their life trajectory. We provide our students an opportunity to come alongside faculty, and collaborating scientists, and to engage in actual research and to experience a holistic program while on the PCT – the mind, the body, the soul…academics, research, intellectual growth, spiritual growth, physical challenges. There is a spiritual formation component and students are encouraged to draw closer to God while in the wilderness. Our students also become researchers, with their faculty, and contribute to an ongoing study of biodiversity patterns along the Pacific Cordillera.”

– Prof. Michael McGrann

The Paciﬁc Crest Trail is a continuous 2,650-mile long hiking trail that runs from the Mexican border to the Canadian border. The overall goal is to collect data concerning the population trends of hundreds of vertebrate species while hiking the trail.

Courses run in spring semester (beginning in Jan.) through the summer term (end of July). Open to students of all majors who wish to transfer in upper-division science credit to their home institution (approval from your major advisor/home institution required). The instructional coursework, leading into the field expedition, will run in remote/online modality (Jan. to March) with live instruction by faculty or these courses may also be face-to-face (it depends on your home institution and your location).

Students must be physically present at Jessup’s campus by the end of March (likely before your home institution’s spring semester ends) to begin hands-on training, and to begin the expedition on the PCT (beginning of April). Students will be taught the necessary skills to assess vegetation, identify plants and animals, follow scientific protocols, wilderness first aid CPR, and basic mountaineering skills. Jessup is a private Christian liberal arts university: students should expect a spiritual formation component to the curriculum. Students are research assistants and participate in an actual, on-going scientific study alongside faculty and other researchers. The summer hiking expedition occurs over a 15-week period, extensive time will be spent in a wilderness setting with each participant walking over 1000 miles total.

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.

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 not 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

Pruhsmeier, H. N., McGrann, M. C. and J. Graham. In Review. The effects of prolonged drought on habitat suitability for common forest birds of northern California.
McGrann, M.C., Wagner, B., Klauer, M., Kaphan, K., Meyer, E., and B.J. Furnas. 2022. Using an acoustic complexity index to help monitor climate change effects on avian diversity. Ecological Indicators (142):109271. https://doi.org/10.1016/j.ecolind.2022.109271.
Pruhsmeier, H. N., McGrann, M. C.,andJ. Graham. 2021.Combined use of data from avian surveys along the Pacific Crest Trail with biodiversity repositories to model habitat suitability throughout northern California. IdeaFest: Interdisciplinary Journal of Creative Works and Research from Humboldt State University 5(1):3.
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. https://doi.org/10.1650/CONDOR-17-165.1
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. https://esajournals.onlinelibrary.wiley.com/doi/10.1002/ecs2.1419
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. https://doi.org/10.5751/ACE-00695-090208.
McGrann, M. C., and J. H. Thorne. 2014. Elevation Ranges of Birds along California’s Pacific Crest Trail. Western Birds 45(1):18-42. https://www.westernfieldornithologists.org/archive/V45/journal-45-1-p018-p042.php

Collaborators

Principal Investigator: Michael McGrann, Ph.D., Chair of the Institute for Biodiversity and the Environment, and Chair of the Science Honors Program, Jessup University, Rocklin, CA | mmcgrann@jessup.edu | (916) 577-8066
Matthew Klauer (Jessup University)
Dr. Aaron Sullivan (Houghton College)
Bradley Wagner, Ph.D. (Mathematics Professor and Research Faculty member Institute for Biodiversity and the Environment at Jessup University, Rocklin, CA; bwagner@jessup.edu)
Brett Furnas, Ph.D. (Quantitative Ecologist, Wildlife Investigations Laboratory, California Department of Fish and Wildlife, Rancho Cordova, CA; Brett.Furnas@wildlife.ca.gov)
Collaborations with National Park Service ecologists
Undergraduate Research Assistant: Kasia McCann
Graduate Research Assistant: Gregory Lake
Project Coordinator: Amy McGrann (Jessup University)

FAQs

What is it?

Pacific Crest Trail Biodiversity Megatransect (PCTBM) is an undergraduate research and travel studies program hosted by Jessup University. Students take coursework in the spring semester leading up to a 15-week field expedition on the PCT. Students become research assistants alongside faculty as they study the ecology of the Pacific Cordillera.

What is the research?

The bird community serves as a very good “barometer” of the effect of environmental change (climate change, wildfires, drought) on biodiversity in our remote mountain ecosystems. The Institute for Biodiversity and the Environment (IBE) at Jessup University (biodiversity-institute.org) has as one of its core research projects the Pacific Crest Trail Biodiversity Megatransect (PCTBM), which is an ongoing survey of the montane bird diversity patterns and breeding phenology (seasonal timing of breeding behaviors) along the Pacific Cordillera – the mountain chains of California, Oregon, and Washington.

Central to this research is the use of novel, noninvasive methods (survey methods that do not require the capture or handling of animals); this includes the use of automated recording units (ARUs) that record bird song to continuously inventory and monitor bird diversity across the wilderness regions of the entire length of the PCT (from Mexico to Canada, 2,650 miles). The PCTBM combines onsite wildlife surveys by field biologists with the use of lightweight ARUs that can be packed in on foot and deployed at remote survey sites along the trail. Since 2010, PCTBM has generated many thousands of 5- and 7-min. recordings of the singing bird community across 3,578 surveys sites along 1,700 miles of the PCT in California, from Mexico to Oregon.

Interpreting these recordings with human observers that listen to all of the recordings to vocalizing birds can be costly, requiring hundreds of interpreter hours. This approach, however, is needed because it provides the necessary level of replication in the dataset that improves statistical models in the analysis. We employ hierarchical statistical models, such as multi-species occupancy models (MSOMs), to estimate species richness, species distributions, population status of individual species, and the breeding phenology in response to underlying climatic variables.

However, due to this high labor cost of using human observers to interpret hundreds of hours of recordings from the ARUs, we are exploring the use of machine learning and artificial intelligence (AI) to identify vocalizing bird species on the audio files. In addition to AI, we employ other types of computer algorithms that make calculations and that help to summarize and synthesize information on the recordings, such as bioacoustic indices, which can serve as metrics of species richness (the number of species detected at each survey site).

In the past, 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, the PCTBM, thus far, has produced 6 peer-reviewed articles, with 1 more currently in review, on the climatic and environmental drivers of montane avian diversity and breeding phenology.

We feel that the scientific theory, analysis approach, and survey methods has matured to the level that the PCTBM is primed to be implemented 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 addressing climate change and other sources of environmental change. The PCTBM spans multiple administrative units (federal, state, and private lands) and promises to help inform decision-makers across these boundaries on their response climate change, human-land use change, or other sources of environmental change.

How do I apply?

A short one-page essay, application form, and interview process is required. Approval by your major advisor at your home institution may also be required. If you are interested in applying and would like specific instructions, or if you just have general questions and would like more information, please email Professor McGrann at mmcgrann@jessup.edu.

What are the courses?

ESCI 315 Ecology of the Pacific Cordillera (3)

This course examines the interrelationships between organisms and their environments along the Pacific Cordillera (southern California mountains, Sierra Nevada, and Cascade mountain ranges). Topics include a discussion of the abiotic and biotic factors that define the physiographic regions, life zones and patterns in biodiversity along this cordillera. A discussion of the wildlife habitat classification systems is included. More general ecological topics in organismal, population, community, ecosystem, landscape, and conservation ecology are included. A general discussion of evolution, and its mechanisms, are included.

*This course is part of the PCTBM Program: concurrent enrollment in ESCI 316, ESCI 317, ESCI 444, and ESCI 444L is required, followed by ESCI 445L in the summer term.

ESCI 316 Field Ornithology on the Pacific Cordillera (3)

This course examines topics on the biology and conservation of wild birds. Topics include avian ecology, origin and evolution, phylogeny, distribution, migration, behavior, reproduction, anatomy, and physiology. Emphasis is placed on experiential learning in the field and on the birds of the Pacific Cordillera.

*This course is part of the PCTBM Program: concurrent enrollment in ESCI 315, ESCI 317, ESCI 444, and ESCI 444L is required, followed by ESCI 445L in the summer term.

ESCI 317 Field Botany on the Pacific Cordillera (3)

A study of the taxonomy, anatomy, physiology, and ecology of vascular plants. Emphasis is given to exploring plant diversity along the Pacific Cordillera and identification in the field. Methods for surveying and analyzing plant community data are also covered.

*This course is part of the PCTBM Program: concurrent enrollment in ESCI 315, ESCI 316, ESCI 444, and ESCI 444L is required, followed by ESCI 445L in the summer term.

ESCI 444 Methods in Ecology on the Pacific Cordillera (3)

Introduction to the principles and common techniques employed for surveying wild vertebrates and their habitats. Emphasis is placed on the survey protocols employed on the Pacific Crest Trail Biodiversity Megatransect.

*This course is part of the PCTBM Program: concurrent enrollment in ESCI 315, ESCI 317, ESCI 317, and ESCI 444L is required, followed by ESCI 445 in the summer term.

ESCI 444L Methods in Ecology Lab: Biodiversity Megatransect (2)

While hiking the Pacific Crest Trail, students are provided hands-on training in techniques for surveying biological diversity, with emphasis placed on bird and plant identification of the Pacific Cordillera. This includes learning to identify birds both visually and audibly. Further, wildlife survey techniques, covered in lectures, are applied, including the use of wildlife habitats classification systems and vegetation survey techniques.

*This course is part of the PCTBM Program: concurrent enrollment in ESCI 315, ESCI 317, ESCI 317, and ESCI 444 is required, followed by ESCI 445 in the summer term.

ESCI 445L Applied Field Methods on the Pacific Cordillera (4)

While hiking the Pacific Crest Trail, this intensive field experience engages students in an actual ecological study of the biodiversity of the Pacific Cordillera. Students apply their knowledge of wildlife survey techniques, including plant and animal identification, by following established scientific protocols employed in the study.

*This course is part of the PCTBM Program: ESCI 315, ESCI 317, ESCI 317, and ESCI 444 are prerequisites for this course, or, with approval from the lead faculty of the PCTBM, similar courses from another institution may be substituted.

Is there a prerequisite for this course?

The PCTBM provides a field-based and hands-on experience where students are provided an opportunity to engage in an ongoing scientific study on the ecology and conservation of biodiversity along the Pacific Cordillera. Faculty and other collaborating scientists train and lead teams of student-researchers in the field as they follow scientific protocols and make scientific observations while hiking the Pacific Crest Trail.

Due to conditions in the field (e.g. snow conditions) and the seasonal timing of the breeding biology of the organisms being studied, this program requires field work to be conducted from beginning April to the end of July. Therefore, instructional courses will run January through the end of March, to be followed by field work beginning in April.

This program is open to all who are interested. Prior knowledge of the diversity of life and ecological and evolutionary principles (covered in BIOL 102/102L: Principles of Biology II w/ Lab) is recommended, but not required.

The application process includes a short essay of interest/intent and an interview with the program lead faculty.

Open to students of all majors who are motivated, interested, and excited about learning the ecology along the Pacific Crest Trail and who are detailed-oriented and able to follow scientific protocols.

What is the course summary?

The application process includes a short essay of interest/intent and an interview with the program lead faculty.

How is student performance measured?

Each course will have a separate syllabus describing expectations, but generally speaking, student performance will be assessed based on the following: 1) maintaining a professional, positive, and team-player attitude throughout the field season while working in strenuous wilderness conditions, 2) comprehension of the protocols, 3) natural history knowledge and skills (such as plant and animal identification), 4) and lastly, completion of a literature review paper.

What fieldwork is involved?

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 2 to 4 students. Students will conduct biological surveys while hiking the PCT for a total of 15 weeks with 1 or 4 days off for every 7 to 10 days on the trail. 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 bird-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 10 days in the field consecutively and hiking 10 to 20 miles/day (usually 12 to 15 miles/day). One to 4 days off, between stints on the trail, will be provided at the resupply points, at basecamp, throughout the field season. We usually rent houses in various small towns at strategic locations dotted along the PCT.

What equipment is needed/provided?

We will provide all the euipement needed, include personal backpacking equipment. For example, e will fit you to your own backpack and hiking shoes. For long-distance backpacking, it is very important to have the right equipment that fits you properly. Your personal backpacking gear, that we cannot reuse, such as your backpack, you may keep at the end of the trip. We will also purchase sleeping bags for you. Clothing, however, you are responsible for purchasing. You will be instructed on what clothing to use for the expedition. We will provide all scientific equipment.

How much does it cost?

Your financial aid, depending on your home institution, may be transferable to the program for the spring courses. Your financial aid may apply toward the cost of the tuition for the PCTBM courses in the spring. For the 14 units in the spring semester…the cost is your normal tuition plus a $1,500 course fee. This course fee is non-refundable. For the summer 4 units, for the Applied Field Methods course, their is a flat rate of $500 for the course, plus an additional $800 course fee. So the total cost for the entire program, outside your normal tuition, is $2,800. If you have enough financial aid remaining in the spring, you may be able to apply some this toward the $1,500 course fee. The $1,500 fee is due when you register for course in the spring semester, in January, while the remaining $1,300 for the summer course is due when you register for the summer course, in April.

A limited amount of competitive scholarships may be available (please inquire with program lead faculty, Prof. McGrann)

Are there additional expenses?

Spending money is recommended for buying souvenirs and eating out or for travel on off days to other locations. However, the PCTBM will provide for your food on the trail and at basecamp for your lodging at bacecamp and for travel to and from basecamp.

How should I schedule my travel plans, airline reservations, etc.?

Although the instructional portion of the courses will be offered remotely January through March, and you will remain at your home institution for that time, you will need to be physically present at Jessup beginning the last week of March or first week of April. Hand-on training in the field and the actual expedition on the PCT will begin in April. Surveys will continue on the PCT to approximately the first week of August. It is difficult to provide firm end dates because it depends on conditions on the ground (snow conditions on the PCT, etc.). That said, we will try to firm up dates as soon as possible so that students traveling greater distances can make airline ticket reservations or other travel plans. We will arrange for pick-ups and drop-offs from the airport. As we approach the start of the program in January, we will communicate with everyone and we will firm up dates for when students need to arrive at Jessup’s campus and the dates for when we will finish field work as we approach the start of the program in January.

Watch Jessup students on the PCT

Participant Testimonials

“There were many challenging components that made this experience difficult and allowed me. to push myself physically, mentally, emotionally, and spiritually, but having completed this program, I feel stronger in those areas. It has also given me a hands-on taste of fieldwork and clarified for me that this is something. I hope to be doing in the future.”

EMILIA G.

“I cherished my time in the field as I learned more about myself and my teammates. i think that the connections I have built and the friendships I have made on the trail this year will be life long ones.”

hannah m.

“This trip has taught me the true meaning of perseverance and being able to buckle down when going gets tough. I no longer see mountains as cell bars , but challenges I can overcome and work through, both in a literal and figurative sense.”

Merrick B.

“I developed invaluable skills in teamwork, followership, teamwork, humility, patience, and servitude. I wanted to come out of this experience well-armed to face job opportunities when I come home, and I definitely feel these soft skills are just as important to potential employers as the hard skills I learned through conducting the science.”

courtney g.

“Rather than feeling like I have conquer something to do with any of those aspects, my greatest takeaway is instead to develop a closer spiritual connection based on respect to overcoming these very difficult challenges that were faced. I now have a new respect for the way that these types of obstacles are handled and look forward to tackling life’s new challenges with the same sense of going over a mountain pass or hauling water through the desert.”

Gregory L.

“The unique combination of practical field work and natural setting not only sharpened my observational skills and ignited my intellectual appetite but also created an environment that stimulated my growth as a person, spiritually, and emotionally. Having hiked my fair share of miles, entering into a wilderness setting is no novelty, but the addition of field work allowed for a level of closeness with a natural world that I have not experienced before. The experience of taking time to observe my surrounding at regular intervals has given me an invaluable perspective that has potential to be applied to so many other areas of life that just this trip.”

Ramon g.

“Waking up at 5am every day, sometimes in just above freezing temperatures, to start the research was definitely a challenge. however, watching the sun creep up over the seeming endless mountains, trying to absorb its vivid and diverse colors, and feelings its warmth made me nothing but grateful to be alive in those places at those times. Hiking aloms 200 miles gave me a lot of time to be in the presence of God, to pray for people in my life and to the thank the Lord of His provision, faithfulness, and magnificent natural wonders. I found an internal alignment being surrounded by wilderness, nothing man made, having to rely on the environment for sustenance, especially when founding and pumping water out of streams and springs.”

erica b.

“There is truly no other way to accurately describe the experiences on the PCT this summer other than “life changing.” I can say with absolute confidence that because of this project, I’ve grown physically stronger, mentally resilient, and spiritually consistent in my walk with Christ. It’s not easy—being forced to do difficult work in stressful situations with people you may not know very well going into the project, pushing your body to its limit, carrying everything with you need and more equipment on top of it all—but there’s no way to quantify what you gain from the experience… Through this project, I’ve gained a sense of quiet humility backed by a foundation of confidence not only in myself, but also in God and His faithful provision for us. The Pacific Crest Trail Biodiversity Megatransect is a project that will significantly benefit anybody who takes part in it.”

tice d.

Pacific Crest Trail Biodiversity Megatransect Project