Western Division Project Spotlight: Mobile PIT Tag Technology Provides New Insights into Endangered Fish Ecology in the San Juan River
By Adam Barkalow, San Juan River Native Fish Biologist with the New Mexico Department of Game and Fish
Understanding the spawning behavior, population size, and movement of endangered fishes is often critical to ensuring their recovery. Recent advances in mobile Passive Integrated Transponder (PIT) tag technology offer new insights into the ecology and recovery of two federally endangered fishes—Colorado Pikeminnow Ptychocheilus lucius and Razorback Sucker Xyrauchen texanus—in the San Juan River Basin. Endemic to the Colorado River Basin, these two species have declined due to anthropogenic and climate-related alterations to flow regimes and connectivity. Since the late 1990s, the San Juan River Basin Recovery and Implementation Program (SJRBRIP) and its signatories have worked collaboratively to repatriate these endangered species to the San Juan River through hatchery augmentation. Both species currently have established adult populations that spawn annually, but wild recruitment remains limited.
Colorado Pikeminnow Ptychocheilus lucius and Razorback Sucker Xyrauchen texanus on the San Juan River, New Mexico.
The SJRBRIP recently funded two studies, conducted by the American Southwest Ichthyological Researchers (ASIR) and the New Mexico Department of Game and Fish (NMDGF), that utilize the fact that nearly all the Colorado Pikeminnow and Razorback Sucker in the San Juan River are hatchery-origin and PIT tagged before release. This ambitious research employs Biomark PIT Portable Antenna SystemS (PITPASS) and stationary antennas to identify spawning sites, track individual movements, assess barrier passage, and estimate population sizes.
The first study focused on identifying Razorback Sucker spawning sites using PITPASS technology across a 15-mile reach in the upper San Juan River near Farmington, NM. During six passes in each spawning season in 2022 and 2023, researchers detected 2,002 and 1,170 unique Razorback Sucker respectively. Spawning sites were verified by embryo collection at selected high-density detection sites, and post-hoc spatial analyses confirmed these areas as significant hot spots. The study also revealed evidence of spawning site fidelity, with 23% of recaptured fish returning to the same location across consecutive years.
Passive Integrated Transponder Portable Antenna SystemS (PITPASS) used to survey for endangered fishes in the San Juan River, NM.
Building on the success of the spawning study, ASIR and NMDGF expanded the spatial and ecological scope of this research. The 2024–2026 study spans 50 river miles within the San Juan and the lower Animas Rivers, near Farmington, NM, focusing on movement ecology, population demographics, and interactions with three major instream barriers.
Results from 2024 uncovered stark differences in movement and barrier interactions between species. Colorado Pikeminnow demonstrated extensive mobility; the longest recorded movement exceeded 400 river miles within a year, which is more than double the designated critical habitat in the San Juan River. While some Razorback Sucker exhibited movements greater than 100 river miles, most moved less than two river miles. Barrier passage assessments also differed between species. Colorado Pikeminnow exhibited relatively high passage rates across all barriers, especially regarding upstream movements, while Razorback Sucker showed limited upstream movement between reaches fragmented by diversions. Cumulative barrier effects were evident for both species, with declining passage rates as fish encountered multiple structures.
Map of the San Juan River in northwest New Mexico. The PITPASS study area (highlighted in blue) spans 60 river miles and includes the Animas and San Juan Rivers. The red square in the inset map indicates the extent.
To quantify population sizes and inform recovery efforts, researchers are using mark-recapture methods to estimate population size and survival of both species. Initial population modeling produced an estimate of 6,467 Razorback Suckers in the San Juan River upstream of Shiprock, NM—nearly double the most recent population estimate for Razorback Sucker downstream. Over 90% of these individuals were not detected in recent downstream SJRBRIP demographic monitoring, indicating a large and previously unaccounted for population of Razorback Sucker. These findings underscore the value of mobile detection technologies to improve our understanding of abundance and distribution of imperiled desert fish species, especially for resident individuals not detected by traditional electrofishing or stationary antenna methods.
Collectively, these studies demonstrate the power of combining mobile and passive PIT tag monitoring to illuminate fish behavior at ecologically relevant scales. PITPASS technology enables fine-scale detection of spawning events, migration patterns, and barrier interactions providing a reproducible approach to identify habitat bottlenecks and evaluate passage infrastructure. Notably, the observed fidelity of Razorback Sucker spawning sites suggests that habitat enhancements or nursery developments near verified spawning bars could increase larval retention and potentially improve recruitment. Meanwhile, the extensive movements of Colorado Pikeminnow—especially during presumed spawning periods—indicate a need to reassess passage structures to better support their life history.
These timely and actionable findings provide the SJRBRIP with novel tools and critical data to support adaptive management, habitat restoration, and recovery planning.
