I have been studying the ecology and conservation of freshwater and estuarine fishes in California for over 54 years, with a major landmark being Inland Fishes of California, Revised and Expanded (2002). Working with a shifting team of graduate students, postdocs, and colleagues, I have documented the status, ecology, and life histories of the 130 or so native freshwater fish species in California, with special interest in salmon, smelt, and other anadromous fishes. The interactions among native and non-native species in environments with varying degrees of disturbance have provided a major basis for my ecological studies and have led to management actions to improve conservation of native fishes. In the years immediately before I switched to Emeritus status (2015), my group developed large data sets on the status, distribution, and ecology of native and non-native fishes of California, and quantified potential impacts of climate change on each species. The team also created data bases on California dams and their impacts on fishes, especially through altered flows. These data sets have been a major source of publications.

Another past research focus is the ecology and conservation of fishes of the San Francisco Estuary, research that includes 43+ years of monthly fish and macroinvertebrate sampling at multiple locations in Suisun Marsh. Additional work has been done on fish assemblages in other parts of the estuary, including development of techniques to combine data from diverse fish sampling programs, by Dylan Stompe to better understand trends in fish populations. This research and monitoring program is now the charge of Dr. John Durand, research scientist with CWS. 

I often discuss research results in the context of novel ecosystems and reconciliation ecology. A good example of this is the studies on the Yolo Bypass and other floodplain systems. Here management for desirable species is imbedded in understanding how highly altered ecosystems function, when they contain many non-native species and often seemingly conflicting land and water uses.

A major emeritus project has been to look for and describe cryptic or new species among California's endemic fishes, using genomic techniques. I have been fortunate to be able to cooperate with a group of fish geneticists who use genomic techniques to define populations of native fishes. Together we have used genomics to identify members of species complexes’ that deserve species recognition. Thus the Riffle Sculpin complex of three species was found to contain 1 new species and 4 new subspecies. The California Roach complex started as a single species but was found to consist 5 species and 4 subspecies. Only one of these roach taxa was new to science. The rest were resurrected taxa that had been described by early workers but dismissed by later workers because the species had no strong distinguishing characteristics. Genomics validated past field work of good observers. Likewise the Speckled Dace was found to consist of 3 species with 6 subspecies, 5 of them new. This work has added 11 taxa to the fish fauna of California, 15 if you count resurrected taxa.

Otherwise, I contribute to the California WaterBlog and co-author papers based on past research in which I was involved. I do keep track of native fishes through various means, including maintaining a list of all freshwater and estuarine fishes in California and their status. Then, for the third time in about 30 years, Rob Leidy and I have written an essay on the status of the world’s freshwater fishes, which is not a pretty picture.