FRC Wild Trout Monitoring Program Reveals Two Genetically Distinct Rainbow Trout Populations

Round 4 of PIT Tagging and Genetic Analysis: 1000 Wild Trout Tagged to Date

Before the start of the 2014 fishing season began, the Fall River Conservancy and its partners California Trout, the UC Davis Center for Watershed Sciences and the California Department of Fish and Wildlife successfully completed round 4 of tagging wild trout for the Fall River Wild Trout PIT Tagging Program. Using an innovative Memorandum of Understanding with UC Davis, California Trout played a key leadership role in this unique partnership. Collaboratively the team of researchers, scientists, and conservationists tagged over 500 Wild Trout with passive integrated responders, or P.I.T. tags, that help researcher’s track the movement of fish throughout the river. This will help identify key spawning and rearing habitat for future restoration projects.

For each fish, fork length was measured, a photograph was taken, a uniquely identifiable PIT Tag was inserted and a small fin clip was taken for genetic analysis.  The most recent round of Wild Trout PIT Tagging, has brought the total number of wild trout tagged to over 1000. With only two recaptures to date, there is a sense of how expansive (and elusive) the Fall River’s wild trout population is. The fish are then released unharmed at the same location they were captured.

Read on to learn about early findings from UC Davis regarding the movement of trout in the system and genetic sequencing analysis.

_DSC3368CalDFW Boat Electro-fishing

PIT Tag Antenna Arrays Track Trout Movement

Two PIT tag antenna arrays were installed in early spring 2014 (think FasTrak bridge toll plaza) at two strategic locations to track the movement of rainbow trout in the system: one was installed just below the Thousands Springs spawning area and the second at the mouth of Bear Creek.

Although the antenna arrays were installed relatively late in the spawning season, we still recorded dozens of fish moving into the spawning areas and then back out into the main system. Early findings of fish movement so far:

  • Approximately 2/3 of the fish we recorded moved though the Thousands Springs array and
  • 1/3 fish moved into Bear Creek.
  • Each movement record has a precise date and time. The PIT tags that were inserted into the fish remain functional for years so many thousand movements will be recorded during the next several years.

These data will allow us to answer many interesting and important questions such as:

  1. Do the same fish return the same spawning location year after year?
  2. What is the distribution of spawning times throughout the year?
  3. Does an individual fish tend to spawn at similar dates year after year or can the same fish spawn at very different dates in different years?
  4. To what extent can one fish spawn multiple times in the same season?

_DSC3384CalTrout Mt. Shasta Conservation Director Andrew Braugh with CalDFW

 Genetically distinct Fall River Wild Trout: Cutting Edge DNA Sequencing

A key objective of this project is to determine if there are two genetically distinct populations of wild rainbow trout  in the Fall River.  So far we have generated genetic data from approximately 200 of the sampled fish.  For each fish, UC Davis researchers isolated DNA from its fin clip and then used cutting-edge DNA sequencing technology to decode its genetic information. We use computer algorithms to sort through the millions of bases of DNA sequence from each fish to identify positions in the DNA sequence that are variable i.e. different fish have different DNA variants at the same genomic location. Both demographic and adaptive events leave traces on patterns of genetic variation so examining this variation can reveal much about historic and recent events that have influenced Fall River rainbow trout.

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Initial Genetic Analysis Findings:

The most obvious and striking result from our initial genetic analysis is that the Fall River contains two very genetically distinct populations of rainbow trout.

  • These races essentially behave as independent populations with very little genetic exchange.
  • By cross referencing the genetics with  movement and collection location data, we determined that one population corresponds to fish that reproduce in Bear Creek and the other is fish that spawn within the spring-fed system.

 Another interesting result is that these two populations are not only genetically differentiated, but the genetic patterns demonstrate they are also adaptively differentiated with distinct growth rates:

  • Fish from the Bear Creek population contain gene variants that will make them grow faster than the spring-fed population. This is likely necessary to compensate for the colder water temperatures experienced by Bear Creek fish early in their life.

   These results are only the tip of the iceberg as far as what will be unveiled as our genetic data collection and analysis are expended. Stay tuned for future FRC updates to stay abreast as this ground-breaking research project unfolds.

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