1999 Progress Report: Genetic Diversity in California Native Fish Exposed to Pesticides

EPA Grant Number: R826603
Title: Genetic Diversity in California Native Fish Exposed to Pesticides
Investigators: Anderson, Susan L. , Hinton, David E. , Kuivila, Katherine , May, Bernard
Current Investigators: Anderson, Susan L. , Kuivila, Katherine , May, Bernard , Wilson, Barry W.
Institution: University of California - Davis , Bodega Marine Laboratory
Current Institution: University of California - Davis
EPA Project Officer: Packard, Benjamin H
Project Period: August 1, 1998 through January 31, 2003
Project Period Covered by this Report: August 1, 1998 through January 31, 1999
Project Amount: $649,003
RFA: Ecological Indicators (1998) RFA Text |  Recipients Lists
Research Category: Ecological Indicators/Assessment/Restoration , Ecosystems


The overarching goal of this project is to determine the effect pesticide exposure may have on genetic variation in a California native fish. The first objective was to examine populations of Sacramento sucker (Catostomus occidentalis) exposed to landscape-scale pesticide releases to determine whether changes in genetic diversity were associated with indicators of pesticide exposure or natural genetic variation. Molecular techniques used included Amplified Fragment Length Polymorphisms (AFLP) and variation in microsatellite loci. The second objective was to compare the AFLP technique with the Randomly Amplified Polymorphic DNA (RAPD) technique to determine which produces the most informative and reproducible DNA fingerprints. The RAPD technique is significant because it is used in ongoing U.S. EPA Environmental Monitoring and Assessment Program (EMAP) studies; yet, the newly available AFLP technique allows examination of more of the genome per unit effort and is reputed to be more reproducible. The third objective was to evaluate potential linkages between any observed changes in genetic variation and fitness parameters in individuals and populations. This study was unique because genetic variation associated with contaminant exposure has not been evaluated in fish populations on a large geographic scale.

Progress Summary:

For the first objective mentioned above, pesticide exposure patterns are being characterized as one step in separating natural genetic variation from pesticide-related variation. Dr. Kuivila (U.S. Geological Survey, Sacramento) is quantifying both historical patterns of exposure, using an existing pesticide-use database in combination with geographic information system (GIS) applications. Dr. Kuivila also is analyzing for pesticide concentrations in rivers and creeks using gas chromatography/mass spectrometry with ion-trap detection. Analytes include atrazine, azinphos-methyl, captan, carbaryl, carbofuran, chlorpyrifos, cyanazine, diazinon, dicofol, dimethoate, eptam, hexazinone, malathion, methidathion, and simazine.

Using data on pesticide exposure and information regarding fish availability, a definitive study design was devised and 700 fin-clip samples of Sacramento sucker from multiple watersheds were archived. Seven watersheds, three in northern California (Sacramento River tributaries) and four in central California (San Joaquin River tributaries) are being sampled. The Sacramento and San Joaquin drainages receive runoff from approximately 40 percent of the entire State of California and are vital to the health of numerous California ecosystems and economies. At this time, field sampling for AFLP analyses is approximately 75 percent complete. Biomarkers indicating genetic damage and enzyme inhibition in fish exposed to pesticides were being examined at reference and exposed sites as an additional method of discriminating pesticide-exposed populations from reference populations. The DNA strand break assay (Single Cell Gel Electrophoresis, SCGE assay) was tested and developed this year by Dr. Anderson's group at the Bodega Marine Laboratory using a model species (fathead minnow). Additionally, the acetylcholinesterase enzyme inhibition assay is being optimized with an examination of variation in response among tissues, variation in time course of response, and characterization of different isoforms of the enzyme. Laboratory exposure studies using Sacramento sucker exposed to diazinon at field-relevant doses are being conducted to characterize strand break and acetylcholinesterase response.

For the second objective, an assessment of the informativeness and reliability of RAPD and AFLP fingerprinting methodologies for population genetic analyses using fish with a well-established pedigree was completed. The number of segregating bands was found to be higher using RAPD than AFLP, but the reproducibility of RAPD bands was far lower. The reproducibility of AFLP bands was found to be a function of band intensity. Thus, a criterion was adopted where only bands that represented greater than 1 percent of total band intensity should be scored. Using this approach, only 1 percent of the AFLP bands were judged to be irreproducible. In contrast, using the same 1 percent band intensity criterion, 16.1 percent of the RAPD bands were irreproducible. It is unreasonable to believe that any developed criterion will increase the reliability of RAPD methodology to a level that is comparable to AFLP analysis.

Future Activities:

Activities for the year 2000 are directed entirely at making progress on Objective 1. Three major tasks will be undertaken. The first task is completion of approximately one-half of the AFLP analyses. The second task is development of a suite of microsatellite loci specific to suckers and analysis of approximately 50 percent of the field samples using these markers. The third task is evaluation of DNA strand breaks and acetylcholinesterase enzyme inhibition in laboratory exposures to diazinon as well as in field caging studies.

Journal Articles on this Report : 1 Displayed | Download in RIS Format

Other project views: All 32 publications 5 publications in selected types All 4 journal articles
Type Citation Project Document Sources
Journal Article Belfiore NM, Anderson SL. Effects of contaminants on genetic patterns in aquatic organisms: a review. Mutation Research-Reviews in Mutation Research 2001;489(2-3):97-122. R826603 (1999)
R826603 (2000)
R826603 (2001)
R826603 (Final)
  • Abstract from PubMed
  • Abstract: Science Direct Abstract
  • Other: Science Direct PDF
  • Supplemental Keywords:

    watersheds, estuary, precipitation, mutagen, ecological effects, population, enzymes, genetic polymorphisms, toxics, ecosystem indicators, aquatic, integrated assessment, environmental chemistry, ecology, genetics, zoology, EMAP, monitoring, western, EPA Region 9, agriculture., RFA, Scientific Discipline, Toxics, Geographic Area, Water, Ecosystem Protection/Environmental Exposure & Risk, Hydrology, Ecology, Water & Watershed, exploratory research environmental biology, Genetics, Environmental Chemistry, Ecosystem/Assessment/Indicators, Ecosystem Protection, Chemistry, pesticides, State, Ecological Effects - Environmental Exposure & Risk, EPA Region, Watersheds, Ecological Indicators, anthropogenic stresses, genotype, pesticide exposure, risk assessment, Region 9, ecological exposure, agricultural watershed, biomonitoring, AFLP, aquatic ecosystems, DNA, pesticide runoff, water quality, fish , California (CA), agriculture ecosystems

    Relevant Websites:

    http://genome-lab.ucdavis.edu Exit
    http://www-bml.ucdavis.edu Exit

    Progress and Final Reports:

    Original Abstract
  • 2000 Progress Report
  • 2001 Progress Report
  • 2002
  • Final Report