Finally, a one-stop shop for locating California’s fishes

Source: UC Davis Center for Watershed Sciences

Introducing PISCES 2.0, an open-source software and data storage platform that uses primary source data, modeling and expert analysis to generate current and historical locations of California’s freshwater fishes. “Fish richness” is the number of different fish species in an area. Source: UC Davis Center for Watershed Sciences

By Nick Santos


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 in tools to systematically collect, store and map data on where California’s freshwater fishes are located.

A reliable and comprehensive compilation of standardized species data is especially important for tracking California’s 133 native fishes 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 UC 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 fishes.

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 overall distribution of fishes, patterns of biodiversity and areas where biological data are lacking.

Sample range map for hardhead generated by PISCES 2.0. Source: UC Davis Center for Watershed Sciences

A sample range map generated by PISCES 2.0. Hardhead, a native California fish, are widely distributed in streams at low- to mid-elevations of the Sacramento, San Joaquin and Russian river watersheds. HUC12 or 12-digit Hydrologic Unit Code delineates sub-watersheds. Source: UC Davis Center for Watershed Sciences

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 fishes. They needed to know with good precision the current and former ranges of imperiled species in relation to dams. This information in turn can be used to determine which dams would provide the most benefit to native fishes 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 flows. 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 UC Davis professor emeritus of fish biology, PISCES is the culmination of several efforts to aggregate and digitize scientists’ scattered field notes and databases on locations of California fishes.

Moyle made his first attempt in the mid-1980s, to inform state fish and game wardens of the fishes 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.

Species range maps can be combined to show patterns.

Species range maps can be combined to show patterns, such as “species richness”  — the number of different species in an area. Source: UC Davis Center for Watershed Sciences.

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

The turning point came in 2011. The U.S. Forest Service issued a solicitation 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 like 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 are a generalized system for tracking and analyzing ranges. It 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 ones 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 my foggy recollections and penciled field notes,” he said. “You’ll have the database.”

Nick Santos creates geospatial applications for the UC Davis Center for Watershed Sciences and developed the PISCES software.

PISCES is the product of several current and former researchers at the UC Davis Center for Watershed Sciences, including Andy Bell, Jacob Katz, Cathryn Lawrence, Peter Moyle, Megan Nguyen, Alyssa Obester, Ryan Peek, Rebecca Quiñones, Nick Santos, Joshua Viers, Dave Waetjen and Terence Wu.

The platform was developed in partnership with the U.S. Forest Service (Region 5), California Department of Fish and Wildlife, Center for Information Technology Research in the Interest of Society (CITRIS) at UC Merced, the Nature Conservancy, California Trout and Trout Unlimited.

To learn how the software works, see the documentation or the 2014 journal article on the system.

 Further reading

Santos NR, et al. 2014. “A programmable information system for management and analysis of aquatic species range data in California.” Environmental Modelling & Software.

Grantham TE and Moyle PB. 2014. “Assessing flows for fish below dams: a systematic approach to evaluate compliance of California’s dams with Fish and Game Code Section 5937.” UC Davis Center for Watershed Sciences Technical Reports (CWS-2014-01) :1-136

Grantham TE, Viers JH, Moyle PB. 2014. “Systematic screening of dams for environmental flow assessment and implementation.” BioScience. biu159

Moyle PB and Randall PJ. 1998. California Native Fish Distributions. Environment.

Quiñones RM, et al. 2015. “Dam removal and anadromous salmonid (Oncorhynchus spp.) conservation in California.” Reviews in Fish Biology and Fisheries

Howard JK, et al. 2015. “Patterns of Freshwater Species Richness, Endemism, and Vulnerability in California.” PLoS ONE

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7 Responses to Finally, a one-stop shop for locating California’s fishes

  1. peter wotruba says:

    There is actually no such word as “fishes” in formal English. The plural of fish is fish.


    • nickrsan says:

      Hi Peter, you’re correct in most uses. We make a distinction between “fish” and “fishes” for scientific use where “fish” refers to many fish, like a school of fish, while “fishes” refers to many distinct species of fish. I can’t say whether it’s truly grammatically correct, but it’s at least in common use in the scientific circles we work in to use “fish” and “fishes” in this way so that you can understand which quantity is being specified (someone here may be able to better refine what I’m saying though).


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