Katie Fisch accepts position at The Scripps Research Institute

July 17, 2013
Media Contact— / ccoomber@ucsd.edu / 858-534-0580

Katie Fisch, a 2011 Delta Science Fellowship recipient, has accepted a research associate position studying human health at The Scripps Research Institute in La Jolla.

Her new research project, funded in part by the National Institutes of Health, examines genomic factors that may predispose people to – or protect people from – osteoarthritis and breast cancer.

As a Delta Science Fellow, she has explored strategies for protecting the wild gene pools of endangered, native fishes in the San Francisco Bay-Delta and Central Valley.

The focus of her ongoing Delta Science project is to figure out whether breeding strategies used by zoos for species such as the giant panda, California condor and black-footed ferret could be applied at fish conservation hatcheries.

“My project is looking at whether minimal kinship selection that is used at zoos can be implemented at fish conservation hatcheries and if it and other hatchery management techniques can successfully preserve the evolutionary potential of fish species in captivity,” Fisch said.  “At the very least, we want to make sure that hatcheries don’t do more harm than good.”

Below is a technical summary of her project to date, which California Sea Grant communications will update and distribute for the State of the San Francisco Estuary Conference this fall.

Saving San Francisco Bay-Delta native fishes: hatchery management and reintroduction strategies

Katie Fisch, Delta Science Fellow, 2011-2013


Several native fish species in the San Francisco Bay-Delta and Central Valley have experienced dramatic population declines and could realistically go extinct in the wild. As a conservation measure, scientists have proposed establishing refugial populations – modern Noah’s Arks – that could help rebuild or re-establish populations should their numbers continue to slide. The longfin smelt, Sacramento splittail, Sacramento perch, green sturgeon, delta smelt, Chinook salmon and steelhead trout are among the region’s imperiled species that could potentially benefit from zoo population management techniques.

The overarching purpose of this project is to identify hatchery management strategies for minimizing the genetic impacts of artificial propagation on wild fish.
To this end, the fellow has been surveying and reviewing management practices currently in use at salmon and trout hatcheries along the West Coast and Idaho. She has been documenting:
  1. The different options for managing the genetics of fish at conservation hatcheries
  2. The approaches currently in use, and
  3. The different goals of individual hatcheries

She is also developing a computer simulation model that estimates the effects of different hatchery management plans on the genetics of hatchery and wild, supplemented fish. This model can be “tuned” to the life history characteristics of any species of interest and in this way is adaptable to all species of management concern in the Bay-Delta and Central Valley.

Progress to date

Based on survey responses from 36 hatchery programs, the currently available options for managing the genetics of fish include:
  1. Factorial mating  – a female is mated to several males; and a male is mated to several females, basically at random.
  2. Equalizing family size – the number of offspring from each pair of breeding fish is equalized.
  3. Reconstructing pedigrees – a multi-generational family tree is constructed for each fish, and only unrelated individuals are mated.
  4. Estimating molecular relatedness – in the absence of information on who was mated with whom, researchers look at the genetics of each fish to estimate relatedness among individuals (e.g., are two fish siblings or cousins) and then avoid mating closely related pairs.
  5. Selecting minimal or mean kinship – pedigrees are used to identify relatedness among individuals and only the least related individuals, with the most desired genes, are mated. This is the strategy employed often at zoos for species such as the giant panda.

Most of the hatcheries that responded to the fellow’s questionnaire use random factorial mating to breed fish, which basically means that fish are spawned at random, the fellow explained. A few hatcheries use molecular relatedness estimation, and one uses a modified version of mean kinship selection.

Even though the majority of hatcheries are not incorporating molecular data into their spawning and release programs, hatchery managers widely recognize the value of conserving wild genetics, she said. The reasons for random mating are mostly logistical, somewhat cultural, and somewhat knowledge-based.

The computer model, mentioned previously, when finalized, will be “run” to simulate a hatchery population managed in each of the five ways listed above for a given species.  The simulation output will provide estimates of the effects of each breeding strategy, at the end of each generation, on genetic diversity, levels of inbreeding and effective population size for hatchery fish and wild fish supplemented with hatchery releases. These results will then be analyzed to determine, for example, the value of minimal kinship selection breeding methods versus less intensive management programs. The analysis will ultimately be compiled into a guide for hatchery managers that will let them weigh different options for conserving wild fish genetics.

Peer-reviewed publications

3Fisch, K., Ivy, J., Burton, R. & B. May.  2013.  Evaluating the performance of captive breeding techniques for conservation hatcheries: A case study of the delta smelt captive breeding program. Journal of Heredity 104(1): 92–104.

3Lindberg, J., Tigan, G., Ellison, L., Rettinghouse, T., & K. Fisch. 2013. Aquaculture methods for a genetically managed population of endangered delta smelt. North American Journal of Aquaculture 75(2): 186-196.

2Fisch, K., Henderson, J., Burton, R. & B. May. 2011.  Population genetics and conservation implications for the endangered delta smelt in the San Francisco Bay-Delta. Conservation Genetics 12(6): 1421-1434.

2Israel, J., Fisch, K., Turner, T., & R. Waples. 2011.  Conservation of native Bay-Delta fishes: past experience and future considerations for artificial propagation of Chinook salmon, delta smelt, and green sturgeon.  San Francisco Estuary & Watershed Science 9(1): 1-20.

2Fisch, K., Petersen, J., Pedroia, J., Baerwald, M. & B. May. 2009. Characterization of 24 microsatellite loci in delta smelt, Hypomesus transpacificus, and their cross-species amplification in two other smelt species of the Osmeridae family. Molecular Ecology Resources 9(1): 405-408.

Manuscripts in review

2Fisch, K., Mahardja, B., Burton, R. & B. May. In Review. Identification of hybridization between delta smelt and two other species within the family Osmeridae in the San Francisco Bay-Delta. Submitted to Conservation Genetics in May 2013.

1Fisch, K., Kozfkay, C., Ivy, J., Ryder, O., & R. Waples. In Review. Fish hatchery genetic management techniques: Lessons from zoo population management. Submitted to Journal of Heredity in July 2013.

Technical reports

3Nagel, M., Finger, A., Ellison, L., Tigan, G., Lindberg, J., May, B. & K. Fisch. 2013. Delta smelt captive refuge population update. Interagency Ecological Program Newsletter 26(1): 53-55.

 2,3Fisch, K., Mahardja, B., Rettinghouse, T., Ellison, L, Tigan, G., Lindberg, J. & B. May. 2012. Delta smelt captive refugial population–2011 Season Summary. Interagency Ecological Program Newsletter 25(1): 9-10.

 2,3Fisch, K., Mahardja, B., Rettinghouse, T., Ellison, L., Tigan, G., Lindberg, J. & B. May. 2010. Captive Breeding Plan for the Endangered Delta Smelt Refugial Population: Genetic Management and Fish Rearing Modifications for 2010. Interagency Ecological Program Newsletter 23(3): 13-20.

 2,3Fisch, K., Rettinghouse, T., Ellison, L., Tigan, G., Lindberg, J. & B. May. 2009. Delta smelt refugial population development and genetic management—2009 season summary.  Interagency Ecological Program Newsletter 22(3): 3-9.

Funding Agencies

1California Sea Grant/Delta Science Program

2United States Fish & Wildlife Service

3United States Bureau of Reclamation

About California Sea Grant

NOAA’s California Sea Grant College Program funds marine research, education and outreach throughout California. Our headquarters is at Scripps Institution of Oceanography, University of California, San Diego; we are one of 33 Sea Grant programs in the National Oceanic and Atmospheric Administration (NOAA), U.S. Department of Commerce.