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

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) 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.

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.

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.

Reserach 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 are 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.
• Explore the use of artificial intelligence (AI) (such as BirdNet) in the interpretation of the thousands of 5- and 7-minute recordings that we have collected 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.

• Using our protocols and modeling approach, we can track the future response of bird diversity to climate change and other sources of environmental change (McGrann et al. 2022).
• 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, we 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 years in the songbird community (McGrann and Furnas 2018).

• 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
• 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.

• Principal Investigator: Michael McGrann, Ph.D., CEO of the Institute for Biodiversity and the Environment, and Director of Peak Eco-Challenge
• 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; [email protected])
• Brett Furnas, Ph.D. (Quantitative Ecologist, Wildlife Investigations Laboratory, California Department of Fish and Wildlife, Rancho Cordova, CA; [email protected])
• Collaborations with National Park Service ecologists
• Undergraduate Research Assistant: Kasia McCann
• Graduate Research Assistant: Gregory Lake
• Project Coordinator: Amy McGrann