Dear Deeply Readers,

Welcome to the archives of Water Deeply. While we paused regular publication of the site on November 1, 2018, we are happy to serve as an ongoing public resource on water resilience. We hope you’ll enjoy the reporting and analysis that was produced by our dedicated community of editors and contributors.

We continue to produce events and special projects while we explore where the on-site journalism goes next. If you’d like to reach us with feedback or ideas for collaboration you can do so at [email protected].

Where Are the Fish? Finally, Answers for Water Managers

When it comes to managing scarce water supplies in California, it’s important to know where the fish are to avoid killing them during pumping and transfer operations. Up to now, this has been difficult, but new open-source software may provide the solution.

Written by Nick Santos Published on Read time Approx. 4 minutes


The question is foundational to conservation biology and policy. To take a conservation action, you need to know where to act. And, yet, for decades, stewards and researchers of aquatic fauna have been sorely lacking the tools to systematically collect, store and map data on where California’s freshwater fish are located.

A reliable and comprehensive compilation of standardized species data is especially important for tracking California’s 133 native fish because 100 of them are officially designated as being in trouble – “endangered” or “threatened” with extinction – or otherwise of “special concern.”

This need led the U.C. Davis Center for Watershed Sciences to develop “PISCES,” an open-source suite of data and software providing the most comprehensive and accurate information on current and historic ranges of California’s fish.

The center has just released PISCES to the public; the software and data can be downloaded for free from its website. The data also can be viewed from interactive maps on the website showing species ranges or species richness.

More than a data aggregator, PISCES converts different forms of data to a standard format and provides easily updatable, high-resolution maps outlining species’ ranges with the best and latest location information available. The program also produces summary California maps showing the overall distribution of fish, patterns of biodiversity and areas where biological data are lacking.

Watershed Sciences researchers have already deployed PISCES on several projects, including:

A 2014 center study by Ted Grantham and co-researchers Joshua Viers and Peter Moyle is a good example of how PISCES can be used.

The scientists found PISCES invaluable for quantifying the impacts of individual dams on California’s native fish. They needed precise information on the current and former ranges of imperiled species in relation to dams. This data can in turn be used to determine which dams would provide the most benefit to native fish with improved flow releases.

PISCES enabled the researchers to flag dams in drainages known to support salmon, lamprey, splittail and other species sensitive to unnatural changes in flow. Using this filter and several others, they evaluated 753 dams on relatively large streams and rivers and identified 181 of them – 25 percent – as high-priority candidates for enforcement, under a law requiring dam owners to release enough flow “at all times” to keep fish “in good condition.”

For Moyle, a U.C. Davis professor emeritus of fish biology, PISCES is the culmination of several efforts to aggregate and digitize scientists’ scattered field notes and databases on the locations of California’s fish.

Moyle made his first attempt in the mid-1980s in order to inform state fish and game wardens of the fish likely to be affected by proposed stream alterations. He and then-graduate student Paul Randall conducted a more sophisticated cataloguing and mapping of native fish ranges in the mid-1990s as part of the Sierra Nevada Ecosystem Project, a sweeping scientific study benchmarking the ecological health of the 400-mile-long mountain range.

However, none of these efforts gained traction beyond the specific projects.

The turning point came in 2011. The U.S. Forest Service issued an appeal for accurate maps of fish species locations on California’s national forests, which cover one-fifth of the state. Moyle, Viers and graduate student Jacob Katz saw an opportunity to develop a comprehensive database.

A team of center scientists and computer programmers embarked on an extensive literature search for empirical and inferred observations of fish locations. In many cases, though, the information was stored in the unwritten memories of veteran biologists such as Moyle. Researchers spent countless hours interviewing experts and poring over maps. By 2014, the group had collected 274,555 records documenting the range of California fish species.

As open-source software, PISCES allows users to enhance the tools and software and propose updates and corrections on the data. The data are available in many standard spatial and relational forms accessible from ArcGIS, QGIS, Google Earth, Microsoft Access and other software.

Although PISCES is focused on California fish, the software and database form a generalized system for tracking and analyzing ranges. The system can be quickly adapted to track fauna anywhere. Scientists can install and use the software to tweak their own species ranges, export data into other formats, generate custom range maps or create versions for whole new areas or species.

Moyle said he can live easier knowing that his four decades of memories on species locations in California can be easily downloaded from a website.

“The future won’t have to rely on my foggy recollections and penciled field notes,” he said. “You’ll have the database.”

Top image: A threatened delta smelt shown at the U.C. Davis Fish Conservation and Culture Laboratory. A new online mapping database developed by U.C. Davis makes it easier to locate known populations of California fish such as smelt. (California Department of Water Resources)

Suggest your story or issue.


Share Your Story.

Have a story idea? Interested in adding your voice to our growing community?

Learn more
× Dismiss
We have updated our Privacy Policy with a few important changes specific to General Data Protection Regulations (GDPR) and our use of cookies. If you continue to use this site, you consent to our use of cookies. Read our full Privacy Policy here.