Sampling Yaqui Fish in Streams

Yaqui Chub

San Bernardino and Leslie Canyon National Wildlife Refuges recently developed a protocol to formalize their approach to monitoring Yaqui topminnow and Yaqui chub

Counting fish is just like counting trees – except that they are invisible and keep moving,” John Sheperd, University of South Hampton

In southern Arizona, the Yaqui topminnow and Yaqui chub are endemic to the Río Yaqui watershed and remain at and around San Bernardino and Leslie Canyon National Wildlife Refuges. Both species are federally listed as endangered. These fish are relegated to spring-fed ponds and streams, and monitored annually to inform recovery. This is not an easy task.

Imagine trying to count something that you cannot see. Now imagine trying to do this in a stream or river, where conditions like high flows and stream width can vary significantly. Counting fish in these environments is difficult but needed. The collection and evaluation of abundance data is often used to define if the species are doing well or poor. It also allows biologists to check for changes through time, quantify the impacts of management activities and environmental variability in terms of sustainability, and is used by to help make management decisions. It is important that it be collected and even more important that it is accurate.

The methods for counting invisible fish in streams are catch per unit effort, capture mark recapture analysis (tagging and retagging fish to estimate population size), and survey techniques that can estimate population size without having to tag and retag fish. Catch per unit effort is exactly what it sounds like: the amount of fish captured during sampling per the amount of time spent sampling. Historically, fishery biologists would use catch per unit effort to determine local abundance. It is now widely known that this is an unreliable method to count invisible fish. Streams with fast flow or those that are exceptionally wide make it difficult to capture species, and as a result one might conclude that they are not abundant. However, the opposite could just as likely be true. How can this be? Catch per unit effort does not account for how the environment influences a biologist’s ability to capture an invisible fish. Mark recapture analysis (the second technique mentioned above) which provides reliable abundance estimates requires a significant resource investment, meaning higher cost and more time spent sampling and is therefore just not feasible for the Refuge. Other methods exist that do not require handling individual (once invisible) fish like the mark recapture method. These use specific sampling methods, total counts of invisible fish, and complex models to measure how the environment influences capture efficiency to produce a reliable abundance estimate that is reflective of the abundance of the species at each stream section at a fraction of the time and effort of mark recapture methods. The former is the method that we sought to evaluate.

San Bernardino and Leslie Canyon National Wildlife Refuges recently developed a method to track abundance of Yaqui chub and Yaqui topminnow in streams and have formalized this approach in a protocol entitled: “Site-specific protocol for monitoring abundance of Río Yaqui fishes in streams”. This protocol was developed in cooperation with the National Wildlife Refuge System’s Inventory and Monitoring. Although the Refuge has long surveyed invisible fish with reliable methods, the purpose is to standardize the collection of information to insure the data remains reliable and informs recovery. It standardizes the timing of the survey, how to collect samples of indivisible fish and how to measure their habitat, data sheets, data storage, and reporting of their findings. This protocol leaves nothing for interpretation, and thus bias created by an individual and their beliefs and experience is removed, data storage prevents data from being lost, and insures continuity of the Refuges biological program through time.

This protocol doesn’t simply focus on the Yaqui chub and Yaqui topminnow populations on the Refuge. It also covers the populations of each species found on conservation easements and any future populations that may be established offsite. This is important to consider as the recovery criteria for each species requires many independent populations, and more than what can be established solely on Refuge property. Thus we tested the surveys ability to estimate abundance of these species at stream sites on the Refuge and off. The results from this pilot work are included in the protocol. It was also peer-reviewed by experts in the field and published in the journal Fisheries Research ( This is important, we sought to also increase the reliability and credibility of our protocol and how it can be used to index abundance of these species in southeastern Arizona by allowing experts to comment on our method.

The Río Yaqui fish stream monitoring protocol is available for public download at the following URL: For more information, please contact the Refuge Biologist at 520-364-2104.